23-Sep-2005 23-Sep-2005 OREGEC00000 OREGES00000 OREGET00000 obig 4312 MMP1 NCBI 7 POSITIVE OUTCOME 9850057 0 search_space EMPTY 0 false 0 search_space EMPTY 0 false 0 search_space EMPTY 0 false Homo sapiens OREG0000006 UNKNOWN-ETS UNKNOWN-ETS USER DEFINED REGULATORY POLYMORPHISM 23-Sep-2005 0 reference_sequence aattgtagttaaataattagaaaGGatatgacttatctcaaatcaat 0 false rs17886084 dbSNP GERMLINE 0 variant_sequence aattgtagttaaataattagaaaGatatgacttatctcaaatcaat 0 false 23-Sep-2005 G) showed 2-fold increase in luciferase activity]]> 23-Sep-2005 OREGEC00001 OREGES00004 OREGET00002 obig 8531 CSDA NCBI 8 POSITIVE OUTCOME 12239625 0 search_space EMPTY 0 false 0 search_space EMPTY 0 false 0 search_space EMPTY 0 false Homo sapiens OREG0000014 SRE/E2F SRE/E2F USER DEFINED REGULATORY POLYMORPHISM 23-Sep-2005 0 reference_sequence agaaaaacttgtgcggggccatttttggggcagtaagatcgagcgaggagc 0 false GERMLINE 0 variant_sequence agaaaaacttgtgcggggccattttGggggcagtaagatcgagcgaggagc 0 false 23-Sep-2005 After stimulation with LPS or IL-1, expression from the -174C construct did not significantly change after 24 h, whereas expression from the -174G construct increased by 2.35+/-0.10- and 3.60+/-0.26-fold, respectively, compared with the unstimulated level. 23-Sep-2005 OREGEC00001 OREGES00004 OREGET00002 obig 3569 IL6 NCBI 9 POSITIVE OUTCOME 9769329 0 search_space EMPTY 0 false 0 search_space EMPTY 0 false 0 search_space EMPTY 0 false Homo sapiens OREG0000015 UNKNOWN UNKNOWN USER DEFINED REGULATORY POLYMORPHISM 23-Sep-2005 0 reference_sequence ttgtgtcttgccatgctaaaggacgtcacattgca 0 false rs1800795 dbSNP GERMLINE 0 variant_sequence ttgtgtcttgcGatgctaaaggacgtcacattgca 0 false 26-Sep-2005 Detected significantly higher constitutive transcriptional activity of the -401A construct (versus -401G) in both HMC-1 and Jurkat cell lines. 26-Sep-2005 OREGEC00001 OREGES00004 OREGET00002 obig EMSAs showed clear cut differences in binding of nuclear proteins extracted from both HMC-1 and Jurkat cells to probes containing the sequence between base pairs -409 and -392 of the wild-type and the mutant RANTES promoter. Using HMC-1 extracts, treatment of the complexes with Abs directed against GATA-1 or -2 resulted in supershifts of two DNA-protein complexes, formed exclusively with the mutant (-401A) probe, whereas anti-GATA 3 had no effect on the pattern of complex formation (Fig. 3). Using Jurkat extracts, supershifts were observed when complexes (-401A probe) were treated with anti-GATA-3, whereas anti-GATA -1 and -2 had no effect on the pattern of complex formation (Fig. 4). Taken together, these findings are consistent with published GATA binding protein expression patterns in T lymphoid cells and mast cells. 26-Sep-2005 OREGEC00002 OREGES00002 OREGET00001 obig 26-Sep-2005 OREGEC00001 OREGES00011 OREGET00006 obig 6352 CCL5 NCBI 10 POSITIVE OUTCOME 10640782 0 search_space EMPTY 0 false 0 sequence AGATAA 0 false 0 search_space EMPTY 0 false Homo sapiens OREG0000007 GATA transcription factor family GATA transcription factor family USER DEFINED REGULATORY POLYMORPHISM 26-Sep-2005 0 reference_sequence ttccatggatgagggaaaggaggtaagatctgtaatgaataagcag 0 false rs2107538 dbSNP GERMLINE 0 variant_sequence ttccatggatgagggaaaggagAtaagatctgtaatgaataagcag 0 false 28-Sep-2005 Mutation of ATTTA to GTTTA did not affect transcript stability. 28-Sep-2005 OREGEC00000 OREGES00016 OREGET00007 obig ENSG00000113580 NR3C1 ENSEMBL homo_sapiens_core_33_35f 13 NEGATIVE OUTCOME 11996936 0 search_space EMPTY 0 false 0 sequence ATTTA 0 false 0 sequence_with_flank ttaattatgtttaattgtggATTTAagtgctatatggtggtgctg 0 false Homo sapiens OREG0000011 UNKNOWN UNKNOWN USER DEFINED TRANSCRIPTION FACTOR BINDING SITE 28-Sep-2005 Mutation of ATTTA to GTTTA resulted in significantly higher transcript stability levels. 28-Sep-2005 OREGEC00000 OREGES00016 OREGET00007 obig Mutation of ATTTA to GTTTA resulted in significantly higher protein levels. 28-Sep-2005 OREGEC00000 OREGES00008 OREGET00005 obig ENSG00000113580 NR3C1 ENSEMBL homo_sapiens_core_33_35f 16 POSITIVE OUTCOME 11996936 0 search_space EMPTY 0 false 0 sequence ATTTA 0 false 0 sequence_with_flank ggtggtgctgtttgaaagcagATTTAtttcctatgtatgtgttatc 0 false Homo sapiens OREG0000016 UNKNOWN UNKNOWN USER DEFINED TRANSCRIPTION FACTOR BINDING SITE This naturally occuring motif was shown to be associated with rheumatoid arthritis in a previous study. 28-Sep-2005 obig 28-Sep-2005 Mutation of ATTTA to GTTTA resulted in significantly higher protein levels 28-Sep-2005 OREGEC00000 OREGES00008 OREGET00005 obig Mutation of ATTTA to GTTTA resulted in significantly higher transcript stability levels 28-Sep-2005 OREGEC00000 OREGES00016 OREGET00007 obig ENSG00000113580 NR3C1 ENSEMBL homo_sapiens_core_33_35f 17 POSITIVE OUTCOME 11996936 0 search_space EMPTY 0 false 0 sequence ATTTA 0 false 0 search_space EMPTY 0 false Homo sapiens OREG0000017 UNKNOWN UNKNOWN USER DEFINED REGULATORY POLYMORPHISM 28-Sep-2005 0 reference_sequence tgtttaacttttattttttcatttaaatttgctgttctggtatta 0 false rs6198 dbSNP GERMLINE 0 variant_sequence tgtttaacttttattttttcGtttaaatttgctgttctggtatta 0 false 28-Sep-2005 Mutation of ATTTA to GTTTA resulted in significantly higher protein levels 28-Sep-2005 OREGEC00000 OREGES00008 OREGET00005 obig Mutation of ATTTA to GTTTA resulted in significantly higher transcript stability levels 28-Sep-2005 OREGEC00000 OREGES00016 OREGET00007 obig ENSG00000113580 NR3C1 ENSEMBL homo_sapiens_core_33_35f 18 POSITIVE OUTCOME 11996936 0 search_space EMPTY 0 false 0 sequence ATTTA 0 false 0 sequence_with_flank attggcagtaaatgttagccATTTAcagcaatgccaaatatggag 0 false Homo sapiens OREG0000018 UNKNOWN UNKNOWN USER DEFINED TRANSCRIPTION FACTOR BINDING SITE 28-Sep-2005 28-Sep-2005 OREGEC00000 OREGES00016 OREGET00007 obig Showed that the 1484insG variation, in two different populations, is associated with several features of insulin resistance: among male individuals, higher values of the insulin resistance HOMA(IR) index (P=.006), serum triglycerides (P=.0002), and total/HDL cholesterol ratio (P=.025) and, among female individuals, higher blood pressure (P=.01). 28-Sep-2005 OREGEC00000 OREGES00017 OREGET00006 obig 28-Sep-2005 OREGEC00000 OREGES00018 OREGET00004 obig ENSG00000196396 PTPN1 ENSEMBL homo_sapiens_core_33_35f 21 POSITIVE OUTCOME 11833006 0 search_space EMPTY 0 false 0 search_space EMPTY 0 false 0 search_space EMPTY 0 false Homo sapiens OREG0000021 UNKNOWN UNKNOWN USER DEFINED REGULATORY POLYMORPHISM 28-Sep-2005 0 reference_sequence gccgcggtaggtaagggccgccggaccgcgtagagagccgggccccggacggacgttggt 0 false rs16989673 dbSNP GERMLINE 0 variant_sequence gccgcggtaggtaagggccgccggaccgcgGtagagagccgggccccggacggacgttggt 0 false 16-Aug-2005 16-Aug-2005 OREGEC00000 OREGES00000 OREGET00000 obig ENSG00000133315 LRP16 ENSEMBL homo_sapiens_core_28_35a 24 POSITIVE OUTCOME 15691879 0 search_space EMPTY 0 false 0 sequence ACTGG 0 false 0 sequence_with_flank ggcggggctccatccgcgacACTGGgagcccgggcgggcgcgcac 0 false Homo sapiens OREG0000010 ENSG00000091831 Er-alpha ENSEMBL homo_sapiens_core_28_35a TRANSCRIPTION FACTOR BINDING SITE 16-Aug-2005 16-Aug-2005 OREGEC00000 OREGES00000 OREGET00000 obig ENSG00000133315 LRP16 ENSEMBL homo_sapiens_core_28_35a 25 POSITIVE OUTCOME 15691879 0 search_space EMPTY 0 false 0 sequence CGGGCGGGCG 0 false 0 sequence_with_flank catccgcgacactgggagccCGGGCGGGCGcgcacgtgtgtatacgagtg 0 false Homo sapiens OREG0000024 ENSG00000185591 Sp1 ENSEMBL homo_sapiens_core_28_35a TRANSCRIPTION FACTOR BINDING SITE 16-Aug-2005 16-Aug-2005 OREGEC00000 OREGES00000 OREGET00000 obig ENSG00000107984 DKK1 ENSEMBL homo_sapiens_core_28_35a 26 POSITIVE OUTCOME 15592430 0 search_space EMPTY 0 false 0 sequence CTTTGTT 0 false 0 sequence_with_flank gctttgaaatcccatcccggCTTTGTTgtctccctcccaaggggccg 0 false Homo sapiens OREG0000025 Beta-catenin/TCF Beta-catenin/TCF USER DEFINED homo_sapiens_core_28_35a TRANSCRIPTION FACTOR BINDING SITE 16-Aug-2005 16-Aug-2005 OREGEC00000 OREGES00000 OREGET00000 obig ENSG00000107984 DKK1 ENSEMBL homo_sapiens_core_28_35a 27 POSITIVE OUTCOME 15592430 0 search_space EMPTY 0 false 0 sequence CTTTGAA 0 false 0 sequence_with_flank cctcccagcccctcccagcgCTTTGAAatcccatcccggctttgttg 0 false Homo sapiens OREG0000026 Beta-catenin/TCF Beta-catenin/TCF USER DEFINED homo_sapiens_core_28_35a TRANSCRIPTION FACTOR BINDING SITE 16-Aug-2005 16-Aug-2005 OREGEC00000 OREGES00000 OREGET00000 obig ENSG00000078579 FGF20 ENSEMBL homo_sapiens_core_28_35a 28 POSITIVE OUTCOME 15592430 0 search_space EMPTY 0 false 0 sequence ATCAAAG 0 false 0 sequence_with_flank tttatcactgcaaagctcacATCAAAGacggttgcacggccgcagct 0 false Homo sapiens OREG0000027 Beta-catenin/TCF Beta-catenin/TCF USER DEFINED homo_sapiens_core_28_35a TRANSCRIPTION FACTOR BINDING SITE 16-Aug-2005 16-Aug-2005 OREGEC00000 OREGES00000 OREGET00000 obig ENSG00000078579 FGF20 ENSEMBL homo_sapiens_core_28_35a 29 POSITIVE OUTCOME 15592430 0 search_space EMPTY 0 false 0 sequence CTTTGAT 0 false 0 sequence_with_flank agtgagttaaactgtcaaagCTTTGATttttctttcatgtgtgtctg 0 false Homo sapiens OREG0000028 Beta-catenin/TCF Beta-catenin/TCF USER DEFINED homo_sapiens_core_28_35a TRANSCRIPTION FACTOR BINDING SITE 16-Aug-2005 16-Aug-2005 OREGEC00000 OREGES00000 OREGET00000 obig ENSG00000089685 BIRC5 ENSEMBL homo_sapiens_core_28_35a 30 POSITIVE OUTCOME 15383173 0 search_space EMPTY 0 false 0 sequence CCGCC 0 false 0 sequence_with_flank gccccgcggcgcgccattaaCCGCCagatttgaatcgcgggaccc 0 false Homo sapiens OREG0000029 UNKNOWN UNKNOWN USER DEFINED homo_sapiens_core_28_35a TRANSCRIPTION FACTOR BINDING SITE 16-Aug-2005 16-Aug-2005 OREGEC00000 OREGES00000 OREGET00000 obig ENSG00000089685 BIRC5 ENSEMBL homo_sapiens_core_28_35a 31 POSITIVE OUTCOME 15383173 0 search_space EMPTY 0 false 0 sequence ATTTGAATC 0 false 0 sequence_with_flank ggcgcgccattaaccgccagATTTGAATCgcgggacccgttggcagagg 0 false Homo sapiens OREG0000030 UNKNOWN UNKNOWN USER DEFINED homo_sapiens_core_28_35a TRANSCRIPTION FACTOR BINDING SITE 16-Aug-2005 16-Aug-2005 OREGEC00000 OREGES00000 OREGET00000 obig ENSG00000089685 BIRC5 ENSEMBL homo_sapiens_core_28_35a 32 POSITIVE OUTCOME 15383173 0 search_space EMPTY 0 false 0 sequence GCGGG 0 false 0 sequence_with_flank ttaaccgccagatttgaatcGCGGGacccgttggcagaggtggcg 0 false Homo sapiens OREG0000031 UNKNOWN UNKNOWN USER DEFINED homo_sapiens_core_28_35a TRANSCRIPTION FACTOR BINDING SITE 16-Aug-2005 16-Aug-2005 OREGEC00000 OREGES00000 OREGET00000 obig ENSG00000089685 BIRC5 ENSEMBL homo_sapiens_core_28_35a 33 POSITIVE OUTCOME 15383173 0 search_space EMPTY 0 false 0 sequence GGCGGCGGCGG 0 false 0 sequence_with_flank cgggacccgttggcagaggtGGCGGCGGCGGcatgggtgccccgacgttgc 0 false Homo sapiens OREG0000032 UNKNOWN UNKNOWN USER DEFINED homo_sapiens_core_28_35a TRANSCRIPTION FACTOR BINDING SITE 16-Aug-2005 Transfection and Luciferase Assays with 2 single bp mutations in element and ectopic expression of CEBPB 16-Aug-2005 OREGEC00001 OREGES00004 OREGET00002 obig ENSG00000082196 AMACR ENSEMBL homo_sapiens_core_29_35b 34 POSITIVE OUTCOME 15755877 0 search_space EMPTY 0 false 0 sequence GTGCGCAGA 0 false 0 sequence_with_flank cgggggtggggaagcgcccaGTGCGCAGActccgcgggcttgcgcaggc 0 false Homo sapiens OREG0000033 ENSG00000172216 CCAAT enhancer binding protein B ENSEMBL homo_sapiens_core_29_35b TRANSCRIPTION FACTOR BINDING SITE Not an E2F binding element 16-Aug-2005 obig 16-Aug-2005 16-Aug-2005 OREGEC00001 OREGES00013 OREGET00001 obig 16-Aug-2005 OREGEC00001 OREGES00004 OREGET00002 obig ENSG00000117632 STMN1 ENSEMBL homo_sapiens_core_29_35b 35 POSITIVE OUTCOME 15474303 0 search_space EMPTY 0 false 0 sequence TTTCCCG 0 false 0 sequence_with_flank caaattccagagccccacgcTTTCCCGcacaggtccctggtcaccgg 0 false Homo sapiens OREG0000034 UNKNOWN UNKNOWN USER DEFINED homo_sapiens_core_29_35b TRANSCRIPTION FACTOR BINDING SITE Appears to be bound by a member of the E2F family of transcription factors. May also bind NF1 as part of a larger overlapping binding site gcggaggtcacgtgcctctgTTTGGCGctTTTGTGCGCgcccgggtctgttggtgctc (site 2 and 3 as indicated in PMID: 15474303) 16-Aug-2005 obig 16-Aug-2005 16-Aug-2005 OREGEC00001 OREGES00013 OREGET00001 obig 16-Aug-2005 OREGEC00001 OREGES00004 OREGET00002 obig 16-Aug-2005 OREGEC00001 OREGES00005 OREGET00003 obig ENSG00000117632 STMN1 ENSEMBL homo_sapiens_core_29_35b 36 POSITIVE OUTCOME 15474303 0 search_space EMPTY 0 false 0 sequence TTTGGCG 0 false 0 sequence_with_flank gcggaggtcacgtgcctctgTTTGGCGcttttgtgcgcgcccgggtc 0 false Homo sapiens OREG0000035 UNKNOWN UNKNOWN USER DEFINED homo_sapiens_core_29_35b TRANSCRIPTION FACTOR BINDING SITE May bind NF1 as part of a larger overlapping binding site gcggaggtcacgtgcctctgTTTGGCGctTTTGTGCGCgcccgggtctgttggtgctc (site 2 and 3 as indicated in PMID: 15474303) 16-Aug-2005 obig 16-Aug-2005 16-Aug-2005 OREGEC00001 OREGES00013 OREGET00001 obig 16-Aug-2005 OREGEC00001 OREGES00004 OREGET00002 obig ENSG00000117632 STMN1 ENSEMBL homo_sapiens_core_29_35b 37 POSITIVE OUTCOME 15474303 0 search_space EMPTY 0 false 0 sequence TTTGTGCGC 0 false 0 sequence_with_flank acgtgcctctgtttggcgctTTTGTGCGCgcccgggtctgttggtgctc 0 false Homo sapiens OREG0000036 UNKNOWN UNKNOWN USER DEFINED homo_sapiens_core_29_35b TRANSCRIPTION FACTOR BINDING SITE Appears to be bound by a member of the E2F family of transcription factors 16-Aug-2005 obig 16-Aug-2005 16-Aug-2005 OREGEC00001 OREGES00013 OREGET00001 obig 16-Aug-2005 OREGEC00001 OREGES00004 OREGET00002 obig 16-Aug-2005 OREGEC00001 OREGES00005 OREGET00003 obig ENSG00000117632 STMN1 ENSEMBL homo_sapiens_core_29_35b 38 POSITIVE OUTCOME 15474303 0 search_space EMPTY 0 false 0 sequence TTTGGCG 0 false 0 sequence_with_flank ggcggcggcctggaggtgttTTTGGCGggagttggggggggcgtccg 0 false Homo sapiens OREG0000037 UNKNOWN UNKNOWN USER DEFINED homo_sapiens_core_29_35b TRANSCRIPTION FACTOR BINDING SITE Most evidence is for sequence site function. The actual binding protein (MAZ) has less evidence. 16-Aug-2005 obig 16-Aug-2005 16-Aug-2005 OREGEC00001 OREGES00013 OREGET00001 obig Transient transfection and luciferase reporter assay with wt and mutant constructs and also cotransfected with MAZ (the putative TF) expression vector 16-Aug-2005 OREGEC00001 OREGES00004 OREGET00002 obig Rnase protection assay was used to measure changes in P2 specific expression in response to dsDNA competition (of TFBS). 16-Aug-2005 OREGEC00001 OREGES00006 OREGET00004 obig ENSG00000160801 PTHR1 ENSEMBL homo_sapiens_core_29_35b 39 POSITIVE OUTCOME 14765995 0 search_space EMPTY 0 false 0 sequence GGGAGGG 0 false 0 sequence_with_flank agaggcccgggagggcgcggGGGAGGGaagaggcgcccggccgggga 0 false Homo sapiens OREG0000038 ENSG00000103495 MAZ ENSEMBL homo_sapiens_core_29_35b TRANSCRIPTION FACTOR BINDING SITE 16-Aug-2005 16-Aug-2005 OREGEC00001 OREGES00002 OREGET00001 obig 16-Aug-2005 OREGEC00001 OREGES00004 OREGET00002 obig 16-Aug-2005 OREGEC00001 OREGES00005 OREGET00003 obig ENSG00000146674 IGFBP3 ENSEMBL homo_sapiens_core_29_35b 40 POSITIVE OUTCOME 14963110 0 search_space EMPTY 0 false 0 sequence GGTTCAccgGGTGCA 0 false 0 sequence_with_flank gacagcagagaaaacagagaGGTTCAccgGGTGCAtttataaccctgctggaggg 0 false Homo sapiens OREG0000039 ENSG00000111424 VDR ENSEMBL homo_sapiens_core_29_35b TRANSCRIPTION FACTOR BINDING SITE 16-Aug-2005 16-Aug-2005 OREGEC00001 OREGES00003 OREGET00001 obig 16-Aug-2005 OREGEC00001 OREGES00004 OREGET00002 obig ENSG00000143627 PKLR ENSEMBL homo_sapiens_core_29_35b 41 POSITIVE OUTCOME 12393511 0 search_space EMPTY 0 false 0 sequence CTGTC 0 false 0 sequence_with_flank gtgtgccccttttctcttctCTGTCtcccttagataagaccagca 0 false Homo sapiens OREG0000040 UNKNOWN UNKNOWN USER DEFINED homo_sapiens_core_29_35b TRANSCRIPTION FACTOR BINDING SITE 16-Aug-2005 16-Aug-2005 OREGEC00001 OREGES00003 OREGET00001 obig ENSG00000143627 PKLR ENSEMBL homo_sapiens_core_29_35b 42 POSITIVE OUTCOME 15727904 0 search_space EMPTY 0 false 0 sequence CTGTC 0 false 0 sequence_with_flank gtgtgccccttttctcttctCTGTCtcccttagataagaccagca 0 false Homo sapiens OREG0000041 UNKNOWN UNKNOWN USER DEFINED homo_sapiens_core_29_35b TRANSCRIPTION FACTOR BINDING SITE 16-Aug-2005 16-Aug-2005 OREGEC00001 OREGES00003 OREGET00001 obig 16-Aug-2005 OREGEC00001 OREGES00004 OREGET00002 obig ENSG00000156515 HK1 ENSEMBL homo_sapiens_core_29_35b 43 POSITIVE OUTCOME 15727904 0 search_space EMPTY 0 false 0 sequence CTGTC 0 false 0 sequence_with_flank tgggccctggcctcaggaagCTGTCtgattggggcagataggacc 0 false Homo sapiens OREG0000042 UNKNOWN UNKNOWN USER DEFINED homo_sapiens_core_29_35b TRANSCRIPTION FACTOR BINDING SITE Both STAT1 and STAT3 were shown to bind the site. Normally STAT family members function as homo- or hetero-dimers. It could not be determined whether STAT1 or STAT3 homodimers or STAT1-STAT3 heterodimers bind to the characterized element because these two factors are not distinguishable by their size and thus can't de discriminated by EMSA. 16-Aug-2005 obig 16-Aug-2005 16-Aug-2005 OREGEC00001 OREGES00013 OREGET00001 obig 16-Aug-2005 OREGEC00001 OREGES00004 OREGET00002 obig ENSG00000112038 OPRM1 ENSEMBL homo_sapiens_core_29_35b 44 POSITIVE OUTCOME 15448191 0 search_space EMPTY 0 false 0 sequence TTCAtGGAA 0 false 0 sequence_with_flank taagagaattgttacattagTTCAtGGAAgaatatgttttaaggtattt 0 false Homo sapiens OREG0000043 STAT1/STAT3 STAT1/STAT3 USER DEFINED homo_sapiens_core_29_35b TRANSCRIPTION FACTOR BINDING SITE ARE sequence in paper is actualy reverse complement of sequence shown here. 16-Aug-2005 obig 16-Aug-2005 Mutation assay of some kind. 16-Aug-2005 OREGEC00000 OREGES00000 OREGET00000 obig ENSG00000197956 S100A6 ENSEMBL homo_sapiens_core_31_35d 45 POSITIVE OUTCOME 15878395 0 search_space EMPTY 0 false 0 sequence GCCGAGTCAC 0 false 0 sequence_with_flank gccgcagtcctcctcctgctccccttGCCGAGTCACgtgtcacgaagagcaaactgagcaaactga 0 false Homo sapiens OREG0000044 UNKNOWN UNKNOWN USER DEFINED homo_sapiens_core_31_35d TRANSCRIPTION FACTOR BINDING SITE A and -480C->T substitutions show high allelic association and are correlated with decreased hepatic lipase activity and increased high-density lipoprotein cholesterol levels]]> 30-Sep-2005 obig 30-Sep-2005 T substitution]]> 30-Sep-2005 OREGEC00001 OREGES00003 OREGET00001 obig LIPC (-650/+48) constructs with both -216A and -480T exhibited significantly lower promoter activity (-45%) than the wild-type form 30-Sep-2005 OREGEC00001 OREGES00019 OREGET00002 obig 3990 LIPC NCBI 75 POSITIVE OUTCOME 11257263 0 search_space EMPTY 0 false 0 search_space EMPTY 0 false 0 search_space EMPTY 0 false Homo sapiens OREG0000074 REGULATORY HAPLOTYPE 30-Sep-2005 0 reference_sequence ttcgtcagctccttttgacaCgggggtgaagggttttctgc 0 false rs1800588 dbSNP GERMLINE 0 variant_sequence ttcgtcagctccttttgacaTgggggtgaagggttttctgc 0 false 30-Sep-2005 0 reference_sequence acacaacacagtagctttaaGttgattaatttggaactctg 0 false rs2070895 dbSNP GERMLINE 0 variant_sequence acacaacacagtagctttaaAttgattaatttggaactctg 0 false See PMID:11916005 for a good source of information on this and other SNPs in the non-coding regions of ADH4 6-Oct-2005 obig 6-Oct-2005 The -75A allele had promoter activity more than twice that of the -75C allele 6-Oct-2005 OREGEC00001 OREGES00004 OREGET00002 obig 127 ADH4 NCBI 362 POSITIVE OUTCOME 10208639 0 search_space EMPTY 0 false 0 search_space EMPTY 0 false 0 search_space EMPTY 0 false Homo sapiens OREG0000364 UNKNOWN UNKNOWN USER DEFINED REGULATORY POLYMORPHISM 6-Oct-2005 0 reference_sequence cagcaacaaaggagaaaaggAagtgattggagaattaagca 0 false rs1800759 dbSNP GERMLINE 0 variant_sequence cagcaacaaaggagaaaaggCagtgattggagaattaagca 0 false There are two separate records for this publication: This one for the YY1 site and another for the USF1 site 7-Oct-2005 obig 7-Oct-2005 A point mutation at the YY1 core-binding site, which permits only USF1 binding, showed a 13% reduction in the promoter activity, whereas a point mutation at the USF1 core-binding site, which permits only YY1 binding, reduced the promoter activity by 28%. The double mutation at YY1- and USF1-binding sites reduced the luciferase gene expression by 60% 7-Oct-2005 OREGEC00001 OREGES00004 OREGET00002 obig preincubation with the anti-YY1 antibody reduced the level of complex B, but had no effect on the complex A (Fig. 6B, lane 3). Note that complex B' was also supershifted by the anti-YY1 antibody. Conversely, preincubation with the anti-USF1 antibody selectively inhibited the formation of complex A and generated a supershifted complex but did not affect the formation of complexes B and B' 7-Oct-2005 OREGEC00002 OREGES00002 OREGET00001 obig M1 oligonucleotide contained mutated sequences in the YY1 core-binding element (CCAT), and M2 oligonucleotide was mutated in the E box (CACATG) as shown in Fig. 5B. The complex A selectively decreased in the presence of the excess M1 oligonucleotide, and this inhibition was dose-dependent with respect to the amount of the M1 oligonucleotide used in the assay, but the complexes B and B' were not affected by the M1 oligonucleotide (Fig. 5C, lanes 3-6). Conversely, preincubation with the excess M2 oligonucleotide selectively eliminated complexes B and B' but did not affect complex A (lanes 7-10). 7-Oct-2005 OREGEC00001 OREGES00003 OREGET00001 obig 7156 TOP3A NCBI 374 POSITIVE OUTCOME 9748294 0 search_space EMPTY 0 false 0 sequence CCAT 0 false 0 sequence_with_flank cacaacccggatcctgctaccgcggcgccgCCATcttgacatcacatgactcctggtgtccgcg 0 false Homo sapiens OREG0000374 7528 YY1 NCBI TRANSCRIPTION FACTOR BINDING SITE This publication has two records in oreganno. This one for USF1 and another one for YY1. 7-Oct-2005 obig 7-Oct-2005 A point mutation at the YY1 core-binding site, which permits only USF1 binding, showed a 13% reduction in the promoter activity, whereas a point mutation at the USF1 core-binding site, which permits only YY1 binding, reduced the promoter activity by 28%. The double mutation at YY1- and USF1-binding sites reduced the luciferase gene expression by 60% 7-Oct-2005 OREGEC00001 OREGES00004 OREGET00002 obig M1 oligonucleotide contained mutated sequences in the YY1 core-binding element (CCAT), and M2 oligonucleotide was mutated in the E box (CACATG) as shown in Fig. 5B. The complex A selectively decreased in the presence of the excess M1 oligonucleotide, and this inhibition was dose-dependent with respect to the amount of the M1 oligonucleotide used in the assay, but the complexes B and B' were not affected by the M1 oligonucleotide (Fig. 5C, lanes 3-6). Conversely, preincubation with the excess M2 oligonucleotide selectively eliminated complexes B and B' but did not affect complex A (lanes 7-10). 7-Oct-2005 OREGEC00001 OREGES00001 OREGET00001 obig preincubation with the anti-YY1 antibody reduced the level of complex B, but had no effect on the complex A (Fig. 6B, lane 3). Note that complex B' was also supershifted by the anti-YY1 antibody. Conversely, preincubation with the anti-USF1 antibody selectively inhibited the formation of complex A and generated a supershifted complex but did not affect the formation of complexes B and B' 7-Oct-2005 OREGEC00002 OREGES00002 OREGET00001 obig 7156 TOP3A NCBI 376 POSITIVE OUTCOME 9748294 0 search_space EMPTY 0 false 0 sequence CACATG 0 false 0 sequence_with_flank cctgctaccgcggcgccgccatcttgacatCACATGactcctggtgtccgcgccgcgtgacccgga 0 false Homo sapiens OREG0000386 7391 USF1 NCBI TRANSCRIPTION FACTOR BINDING SITE 2-Nov-2005 Human-zebrafish conserved sequences (within 100kb of a gene with known function) were tested for regulatory function by GFP. Conserved non-coding sequences were amplified by PCR and inserted into constructs with the Zebrafish cardiac myosin light chain 2 (cMLC2) promoter and green fluorescent protein (GFP). cMLC2 is cardiomyocyte specific with essentially no extra-cardiac expression in either stable or transient transgenesis. Transgenic embyros were examined for extra-cardiac GFP expression indicating cis-acting transcriptional regulation of the conserved sequence. 2-Nov-2005 OREGEC00001 OREGES00021 OREGET00002 obig Human-zebrafish conserved sequences (within 100kb of a gene with known function) were tested for regulatory function by Dual luciferase reporter gene assay. Conserved non-coding sequences were amplified by PCR and inserted into constructs with the Zebrafish cardiac myosin light chain 2 (cMLC2) promoter and the firefly luciferase sequence in pGL2 plasmids. Control plasmids (pRL) were created with the cMLC2 promoter and renilla luciferase but no test sequence. Luciferase ratio was determined and compared to that observed for negative controls (where test sequence was non-conserved sequences). Ratios that exceeded the mean of the negative control ratios by at least 2 standard deviations were considered positive. 2-Nov-2005 OREGEC00001 OREGES00026 OREGET00002 obig UNKNOWN UNKNOWN USER DEFINED 2743 POSITIVE OUTCOME 16179648 0 search_space EMPTY 0 false 0 sequence tccaggcaataatgagaaaggtatgttctgtaaaatgtctcctcccctaaaaaacaaaacacataaacattacataaattaagctcaagagaaaaaacaattcttaggattcagtgtgtttgaacagtggagctcttaataagtttttaaaatttttttatttttaaaaccttaactatcttctaagatgggacacttcagttttacagttttatatactttttgaatttaaaagcaaattttaacattgcaggatttttgaagcgcagagagatttgaaaaataagcctccaaaataaaagacagacaagtgacagggcatgatgtcttgcctaagtttttatggacgttacaaaagttttcttttaaaaattacaataacatgctttttcgtcaagtacaaaataagataggagggaaaaaaaatgaagaaaaagtctccctctcactctctcccaccaaaagaccccaaacaacaacaaaacaaaataaaaagaaacccaaatcctaaaccccataaatggagccccttaccatgttgggaaagtttctgtgcaaactgaactgtttctgtgggtcctgccaagctcctggctggtcaactttttaaacacggcaggcaatggttagactgaggtgagcagcctggcagcctagagaaggaggcagactagagctcagctccagagacctaccacttagagggaaagttgggacagcaactgttgagagttaacctctcctttccaaaggaggtttgcagaggcaggacagtgagagctgataccaccaattttattcttttctcaggcatttctaacttttatgatttcccccctccttcctttactatctgtctttgtgcctccagggccagtgaaagagcagggcagattctagattgctttcagagtttgccttctctgatgatggattaccatgtcaatttaaacagcataggattaatttgtttcaatgatttctctttaggctgaatgccagccgtttttctatctttctctttgctcttcagaacaacaacaacaaccaaaaaaaaaaaaaaaagccttctttccatattctaagttaagagacaataatagaaatagacaagttaggtgtaatgttgcaacacagttataggtctgagtgttttttatctctgcctaagaggctgaaacatacagtcagtcacattaaaatgaaattggactcaacatttattcaataaatacttgtcttgtagataatccagtgccgagtgcttttgacatataagaacttaatttgtcttggataacaagttattaatatggcacatttaaacttgccacctacaataaggttactgagctctacaacaaactcaaatgatcattgtgaaaaacagtttgtgggaagaagggagacattttttgagaatgcttatattattatatgtaagtatattcacatacaaaccagtaacacataggggcacacatgcatgtgtacacactctccccaacatatgtgtgtgtgtgtatatatatatatacatatatattcagatcacatatgacaaaaatgttcagtgaagttaaaaaaaagtccatccattatacagatgtatctaacctttcctgaataagaatgtgtcagagaattttctcttttgaaagatttctaaagtgcacttgaaaaatgctgttcaaatccaatttttttgcaagaccaaacccattatgaggttgaaaatgtcacagaaaaagcacttaggtgcaatccaaaatcaaacaacccctccacattttttacctagtctgagcttgcagccagccagagcatgttgctggtagaataaagccaatttaagtgaaataatctattgctaaagtgattatttaatttcccgctctaacaggaggtcctccaatggatgcaaaaggacaggagagacatttcatcctatgcactgaatatattgggcaaacatatttcgaattacgggcttcttttccaccaccctcttctaattgtctctccttttcccagcattc 0 false 0 search_space EMPTY 0 false Homo sapiens OREG0004179 REGULATORY REGION 2-Nov-2005 Human-zebrafish conserved sequences (within 100kb of a gene with known function) were tested for regulatory function by GFP. Conserved non-coding sequences were amplified by PCR and inserted into constructs with the Zebrafish cardiac myosin light chain 2 (cMLC2) promoter and green fluorescent protein (GFP). cMLC2 is cardiomyocyte specific with essentially no extra-cardiac expression in either stable or transient transgenesis. Transgenic embyros were examined for extra-cardiac GFP expression indicating cis-acting transcriptional regulation of the conserved sequence. 2-Nov-2005 OREGEC00001 OREGES00021 OREGET00002 obig Human-zebrafish conserved sequences (within 100kb of a gene with known function) were tested for regulatory function by Dual luciferase reporter gene assay. Conserved non-coding sequences were amplified by PCR and inserted into constructs with the Zebrafish cardiac myosin light chain 2 (cMLC2) promoter and the firefly luciferase sequence in pGL2 plasmids. Control plasmids (pRL) were created with the cMLC2 promoter and renilla luciferase but no test sequence. Luciferase ratio was determined and compared to that observed for negative controls (where test sequence was non-conserved sequences). Ratios that exceeded the mean of the negative control ratios by at least 2 standard deviations were considered positive. 2-Nov-2005 OREGEC00001 OREGES00026 OREGET00002 obig UNKNOWN UNKNOWN USER DEFINED 2744 POSITIVE OUTCOME 16179648 0 search_space EMPTY 0 false 0 sequence ttgtgccatcagagtcttgcctatagaagttttgcaataaagcaaacccaaataagacctttcaggtaaaatatccatctatttcagtagaaccaaatgctatgctaattacttagtagacatttatgaacagtctttaactcgacagcaaagaaattttattgatggagccttctttagatatttttattcattttttatttaaaaaatgaagacatgtgagttttaaatgctttttcttttcccctcctcctcccccatctctctcattctccccccttctgaagaccctctctttcctctccagctctttttgattaatagatccatgtggctaacggcctgacatatggtgtgcgaagcagcttgagatagtaccttaggcatcccctacggccattaacatattaggggcttatgtgcagtcagacagtcagacctcatcgagagccagcattttcagaaaggctgaaccccagagctgtttgatagagagtttcaataatgcaccactcttcaattttaagggagttgcttctggtgctgaaacactgggacagaaccagaataaagtttagcaataagactcagttacattcaacagcaacagtaaaaaatgcgcttacatctgtttgtatatggatatgcacgtggaggcacagcttcaagctcacaaacatacaccagctcctgagtattatcagtaaacaggcaatgtcagctgcctggattt 0 false 0 search_space EMPTY 0 false Homo sapiens OREG0004180 REGULATORY REGION 2-Nov-2005 Human-zebrafish conserved sequences (within 100kb of a gene with known function) were tested for regulatory function by GFP. Conserved non-coding sequences were amplified by PCR and inserted into constructs with the Zebrafish cardiac myosin light chain 2 (cMLC2) promoter and green fluorescent protein (GFP). cMLC2 is cardiomyocyte specific with essentially no extra-cardiac expression in either stable or transient transgenesis. Transgenic embyros were examined for extra-cardiac GFP expression indicating cis-acting transcriptional regulation of the conserved sequence. 2-Nov-2005 OREGEC00001 OREGES00021 OREGET00002 obig UNKNOWN UNKNOWN USER DEFINED 2745 POSITIVE OUTCOME 16179648 0 search_space EMPTY 0 false 0 sequence tacgatgggattgtgtctgcgcttttgttggtaattaaataaattatttatacatttaacacaatcttgaattaccaggtgatcatcttaggcactcaaaagcataagagcccttgaaagcaatatctaagcatagatattccatagcacgtcttacaatctaaatattgcttttagtgtaatcgaagcagcaagagtagtcacagcagttgatggactatttttcaaattgatttcaaaaatgtatttaaggggatgatcttctagtctagattacctattgatttttaatatgaaaagctcattatgtaagcagtaaccgcatataaaaacctagcaaacctttgcataaatcctttaattgaatttccagagcctgtggttctactttttttttaattaaatctatttctttttttaagtgttactgtgtaatttgcatgctgtgaagaggccctgtcccagataaagtgccattgatccttattaaacctcacctctgggcttgcttaaaactaactggaaaaattaaagtgttcatgccgcaatgcacttatagcttgtgtgataggattatggaaaaaataataaaactaatttccaggggagaatttctaatgtgagattttattttttttcaatttgataattaatagtgaaatcatatcatatatataaatcatattttagcctataaactgaaatggcaattaggaaagataatatatacttgatgtaaaaccatgttacgtgcggataatcttttagcactttaattttttaattgtagaaggagagaattatgaattcaagtcaaacacattaaatggtgggtttcatccaaaaaatctgattcttttactatgtactgtattagtggatttataatattagtgggaggaagtataaaagatatggaaaaagatattctggttatgttcgtgctaaaatgtgtgtattagaattaccaggggaaagaaaaatataaaagctgcaataggtttttctattttttaatacctaacatttgttattttaaaagcaataaaatcccctaaagaaatattcgtaatcaataagaacacaaaatatggaatatattaactgagttataaaaatgtttgtagtatagcacagaatgaaaaacacagcaaggtatgtacggtttaaagtgtaatcaattttgaggttgtatacaaggatataaatgataaatacaagtagtagcatttttagtaaaggctgttacaaaatactgtatttatggcctattccattctttttatagctcattaatgtagaaaacaaacacagtgtatccatcttctcagacggtttaaaattcccttaaatgatgtttttaaatgtaaataactgagctcatttgatctggttcttccttaagccaatgttagcatgaatggccatatttaccaccccggggttccttttcagactccggaaagaaaaagcgatgataatgacgtatttccctcccttccacaaaacagggccaggtgtaacacactaagaacaaatggcttggcagcctactctcctctctcgaagctccatgcccaccttgctgttgcaccccccaccccaaggaaagccttcccacctttggaagctgcattaattattccaggccacaagggtgccgttgagttactggttcactgcactggctggcaggaaagagttttaatgcaggctccaaaggtgcttaatttcctgtggtccttatgaatatgcatacagtatgtgctcagcaatctagcagttcaaactagacagctggttctggtggtgagggttttttaaatttattttttatttatttattttttctctcccctttccttggacaagccctttctgaataagctg 0 false 0 search_space EMPTY 0 false Homo sapiens OREG0004181 REGULATORY REGION 2-Nov-2005 Human-zebrafish conserved sequences (within 100kb of a gene with known function) were tested for regulatory function by GFP. Conserved non-coding sequences were amplified by PCR and inserted into constructs with the Zebrafish cardiac myosin light chain 2 (cMLC2) promoter and green fluorescent protein (GFP). cMLC2 is cardiomyocyte specific with essentially no extra-cardiac expression in either stable or transient transgenesis. Transgenic embyros were examined for extra-cardiac GFP expression indicating cis-acting transcriptional regulation of the conserved sequence. 2-Nov-2005 OREGEC00001 OREGES00021 OREGET00002 obig Human-zebrafish conserved sequences (within 100kb of a gene with known function) were tested for regulatory function by Dual luciferase reporter gene assay. Conserved non-coding sequences were amplified by PCR and inserted into constructs with the Zebrafish cardiac myosin light chain 2 (cMLC2) promoter and the firefly luciferase sequence in pGL2 plasmids. Control plasmids (pRL) were created with the cMLC2 promoter and renilla luciferase but no test sequence. Luciferase ratio was determined and compared to that observed for negative controls (where test sequence was non-conserved sequences). Ratios that exceeded the mean of the negative control ratios by at least 2 standard deviations were considered positive. 2-Nov-2005 OREGEC00001 OREGES00026 OREGET00002 obig UNKNOWN UNKNOWN USER DEFINED 2746 POSITIVE OUTCOME 16179648 0 search_space EMPTY 0 false 0 sequence tcctccttgtgttcatttcttgcatttagtttaatttcttacttgcttgttcgttgtaaaaatcatttgtgtttacagtaaattcatttttttattaaatctgtttggctaattgagacattattaacctatgaccaaatagccagtgagaaaatcagctctgggttaaaggttaccatgatttatgctatgactcttttggaaactttaccttaacttgtggtgctcctgtttggctggaaaaagccatatggccaatgaaaatgtgcagaagttgcctgaaaccaatccacagagagctggtaaactataactttaggctgtgatgaccacatgctgcctttcatcagccaagaaaacaaaaatagccaagctttttataatgctttctaaaaaaattgtaaatccatgattgtatcttctatcagaaagtcttagtggtaatacaggtatcctaggtatgggcctcattgatcctctaaaaaaaatgtaccactagggaattctacttcaccaacattttcttgacaatagttgaatcaatcatgtaaatcagtcttaggatttagctgattctgcagcatggtggttttctttgaaaagaagaaatgtcttgatcctgaagacattcaccgtcatctaaatgtcttccccttgattcagtttcttacattatagactactttagtgaagatatccttttcttgcaacagttattcacttaaaaagacttcaaaatattatccagtcactgaagcttctttgaagaaaaatatgactgctcgtgtaaacaattaatggttgttaagcatggcagtgtatattatgacaaacaacacatgctacattatgccagctggtgtaatgatgtgataatgtctgactcattaactctggcacacagtttacgatgcccttctatgacaggattaattgattcacacatacattaaaacaaaaataactaaactgaaatttagctggaagcctggctcctcatttgtcataaaccctgctgttggtgatagctgacaaagaccctaatgccgaacggggttgaggttcccttcctgacctcacctttctttctgaatggaaacaagagccttggaaacaaaccagaatgctttaaggtaaagtctcccctagagaataattcatgctggaatatatatatatgcacatacagttttcacagtgaaattgctcaaaatacttttttaaaagcaagtagctacaaaccaaccattactaaagggtgtctggtctaccagaaatacagtttagatgactttttgaaatacttggatgtttaaagataactcatcaaatacttgtcagagaactttttgtaactgtaactaatccagaatgatgttaagcagaataataaacagaaggctaacaggagtgctaacttttactcttggtctcatctacaatttcatctattcattgaagtgtgagggttgacaatgcttaaaatctgagcctagggaactcttcttcacctaaaacatgaaaaatgcaataacagttctattaaattgaaaggctcacttattccaatacaaaatccgtatttggcattctatgacactttcaattaagaactaaattatttctttattaagtgttcattgtttcacttgagatgatattgtatttaacaatttctagttgttttattaagtcaaaactgaattgtataatatgatttttatttcacaagtgcttctatacactggatttattaatattattgttactattgttgttactagcaattttggcccaaatgttggaggatatagaaaacccaaaagtttacctgagtgtattttattcaacatactgaaagacaaaatgtaagggggaaaaagtgaaaa 0 false 0 search_space EMPTY 0 false Homo sapiens OREG0004182 REGULATORY REGION 2-Nov-2005 Human-zebrafish conserved sequences (within 100kb of a gene with known function) were tested for regulatory function by GFP. Conserved non-coding sequences were amplified by PCR and inserted into constructs with the Zebrafish cardiac myosin light chain 2 (cMLC2) promoter and green fluorescent protein (GFP). cMLC2 is cardiomyocyte specific with essentially no extra-cardiac expression in either stable or transient transgenesis. Transgenic embyros were examined for extra-cardiac GFP expression indicating cis-acting transcriptional regulation of the conserved sequence. 2-Nov-2005 OREGEC00001 OREGES00021 OREGET00002 obig Human-zebrafish conserved sequences (within 100kb of a gene with known function) were tested for regulatory function by Dual luciferase reporter gene assay. Conserved non-coding sequences were amplified by PCR and inserted into constructs with the Zebrafish cardiac myosin light chain 2 (cMLC2) promoter and the firefly luciferase sequence in pGL2 plasmids. Control plasmids (pRL) were created with the cMLC2 promoter and renilla luciferase but no test sequence. Luciferase ratio was determined and compared to that observed for negative controls (where test sequence was non-conserved sequences). Ratios that exceeded the mean of the negative control ratios by at least 2 standard deviations were considered positive. 2-Nov-2005 OREGEC00001 OREGES00026 OREGET00002 obig UNKNOWN UNKNOWN USER DEFINED 2747 POSITIVE OUTCOME 16179648 0 search_space EMPTY 0 false 0 sequence ttttgttccttcggcgttagggtaaaagacaaaagaaacaaaaatgccaattattggacttaattaaccattaaatgagatgtgtatcctcttctctctaactcaaaaatggagggaagttgatgaggttaggtgtggggtggggtctaggagcaccctcccacccttgtgatctaattagaggaaacctatgcatattccgccagtgttaacagacaaagccaggatatatatatacatatatatataacacacacacacacacacacacacacacacacacacatgcatacttttataaaaaagagcaataaacatggagaggaaccaggaattgattttttttttcttgtttacttggaatggggctggagtgggcagcagttagggtgggagctgttgggggggcgagctctggtgaggagagagaacatctcagaaaaattaacattattggtatctttctatataaagatgcaaatggcattttattttaacttggccctgtgctttagtcagtgtttatgattaattatctcctttttcataaaaataaatcatgttaaaaattaggatctccacgctggggagaaactaagcactagtttcaggtcgatcttgttaatttcagcctgaaattgacacactaattaaagagcagcgtggtaaagcacgagcaggcaagattatactcagctttttttttttttttttatcagatctaccttatattttcccaattaaaaactgcgaaaagcagtttcattgccccaggataaaaaataagggcccccttttcacaacatgggccatcactttctaccatcagattcattgtgatgtattagatgcaataaattatcccatgtaacaaaacattgggagctgaaaggcagataatctggaaagcagagataaggattcattattccaaatcattatgaatccaacgttgcctctgacttctttcttaatcagctcctctgatcctggatatgtgagcagcacagataaggaaagagtcgtttataattctccacctcgtctaatattttaaaataaagtcagaggcaagaaaacgccataaaacactggtgagcaggcaagcgccgaatgaaaaatcacttccatgttattatatccacagtaagatttaattaaaattctccacgtccacgtgctttattttcagataggattttttcccatcacgtaataattgataggaatttgcaaacggggctatttatttagggcgcctgggtggaataggtctgatttttttttttaattttcagtcattgcttttgaaactttcatttgcgatatccatagtttcagaccacctaggcccccatcacccacccgccccacccgggctacagttcttggtcccggaaatgtagtcgtagtcatggtcctgaaagggagtttaacaaaaatgttcttttataagaagaaacagaaaactgggttgttcccatgtgatacctcttttatgccctctcaattcctacccccacgcatatttataataaaataaatctcaatgagtggagttggaagattagaactttcaaacccggtggtgtgtgttgttgtgtggaggagtgcactttaaggaactaaaccaatctgagtatttgtaggaaggtagaacaattgaaaagggagggtgacgctgaacactgatgggcagaaagaaaaatattatctgttttagggaaaagaaacaagttgttggaaacctggatgaataaatatgttggttctgcagctctacacagagctactctatgtggccacacgttcttaggaagattggagattctgccactgattacctcttcctacaggatctctttttctttatccaacaggtgaacttcatatctatgtggccatcgtggagatctggacac 0 false 0 search_space EMPTY 0 false Homo sapiens OREG0004183 REGULATORY REGION 2-Nov-2005 Human-zebrafish conserved sequences (within 100kb of a gene with known function) were tested for regulatory function by GFP. Conserved non-coding sequences were amplified by PCR and inserted into constructs with the Zebrafish cardiac myosin light chain 2 (cMLC2) promoter and green fluorescent protein (GFP). cMLC2 is cardiomyocyte specific with essentially no extra-cardiac expression in either stable or transient transgenesis. Transgenic embyros were examined for extra-cardiac GFP expression indicating cis-acting transcriptional regulation of the conserved sequence. 2-Nov-2005 OREGEC00001 OREGES00021 OREGET00002 obig Human-zebrafish conserved sequences (within 100kb of a gene with known function) were tested for regulatory function by Dual luciferase reporter gene assay. Conserved non-coding sequences were amplified by PCR and inserted into constructs with the Zebrafish cardiac myosin light chain 2 (cMLC2) promoter and the firefly luciferase sequence in pGL2 plasmids. Control plasmids (pRL) were created with the cMLC2 promoter and renilla luciferase but no test sequence. Luciferase ratio was determined and compared to that observed for negative controls (where test sequence was non-conserved sequences). Ratios that exceeded the mean of the negative control ratios by at least 2 standard deviations were considered positive. 2-Nov-2005 OREGEC00001 OREGES00026 OREGET00002 obig UNKNOWN UNKNOWN USER DEFINED 2748 POSITIVE OUTCOME 16179648 0 search_space EMPTY 0 false 0 sequence gtcactctttgggctggatgtcagtcactgtagtttttgaggatacagaaatgtctgcattctgaagtgtaaacaaaggagtaaataaatttattttttacatggcttgatgtaatagtatagaatctagacatggataatagatgcaactcagtcaacatggataaccaaagttcttaaaactacgctttcaatgaacacatatcctttgagcaagactaataatgaggaatgggagccagctcctgtgatatttatgcaactactaaattctcactgaagtcaatgggagtttgcttacgtaagggctgcaaactttagcctccagagattaaaggggaaaaaaatccttaaactctttcaacattaatattgcctgtaaggaatccagccatgacctaagccatggagctttctgaacctagcaagtagaagggtaaacagtaaacaccagttattttaagcacaatctaatcagagttcaatgagaagcaatattatatttgatctctaaggtattaatacttgtatatcactattagacatctttatgtagtccattatccaaacaatggcttaagtctgtggtatttaataaatcaagtttccatggccgtgagactgagtgggagtggggatgaagccttttttcttcatttttttttcctcaggtgcaattctgtgttaatataagagaagtgtggccttccttctcatagcactaaaagtgagataatccctgtgtaagaaatcagtaagtacggtctgcttaatctagtcccagtgtgaaactgttgacatttgttcttttttctatcattatgtgactgggcctgttttgtgctggattaggcacaaatctcctatgcagcacatttggcatgttactagtagtttaacttcattaataatgtatgaagaaaatgtaatccatgacaaggaagcaaagaaaagtatttttttttttttttgcttctcccaaatcctttggaatgagtaattattcaacattttatgtttgatgttatattttacaattcaacttccatagtgatatttaaaaaagaaactttggcaaatgcttgcaaaaaacacaccttttacaattttaaatgtgatttactgatggccagaacttgttaaacatagtaggaaattaaatatttattcatcttatttcattttcagggccgtaaacgctccttctgagtcattcccaataacaagaatttctaccagtaaagctattaacaggcatcaaaataggggagtgctaaattaagatgagattgtaaaagcaaataagaacatacgcagactcgcataggagtgcaaatgatcgtttctgattgaaatgtttatagctaaatgagtttggctgaattaaacacaaatgttccaaaagataagccgtagctggtgcttcttttttctgttttttaagctgctttacagacgaaaatggaactatatttggaacaatgctttctgtttttccatactattgatatttgtggaaagtcacaaaatggcctaaggaagctaagctcgccccaagcagtggtcacttacaagtacttttgtactctgtactcctgtcacatttgggcgatcagagcaacagctggggagactttttcaacaaagatgagtgtcagataatcctgatgagattccacatccaacatcttttgtaattatgtcacattcagctgtaatggaataattcaagctgaaagaacaagctttgatcctttcttaaacctttccctgtggactggctatctaaaagatttaaagatatttctgttacaagatctagtgtttcctcagagaagtcatgcttctgaagcatcgtgatctacaagaacaatatcaagtttgccaaacacatttctgaaagcatcgtg 0 false 0 search_space EMPTY 0 false Homo sapiens OREG0004184 REGULATORY REGION 3-Nov-2005 Human-zebrafish conserved sequences (within 100kb of a gene with known function) were tested for regulatory function by Dual luciferase reporter gene assay. Conserved non-coding sequences were amplified by PCR and inserted into constructs with the Zebrafish cardiac myosin light chain 2 (cMLC2) promoter and the firefly luciferase sequence in pGL2 plasmids. Control plasmids (pRL) were created with the cMLC2 promoter and renilla luciferase but no test sequence. Luciferase ratio was determined and compared to that observed for negative controls (where test sequence was non-conserved sequences). Ratios that exceeded the mean of the negative control ratios by at least 2 standard deviations were considered positive. 3-Nov-2005 OREGEC00001 OREGES00026 OREGET00002 obig UNKNOWN UNKNOWN USER DEFINED 2749 POSITIVE OUTCOME 16179648 0 search_space EMPTY 0 false 0 sequence gctacctcacttcacgctttctcacgttaaataaactagttttatttccaaaatgctgactttctacatttgcctccttgttcctacatttccctcataaaaaaatcagttttaatttattgggactgaccaagaaagataatgaagtcctttcaaaaactctttatgtgtgaaaccctggaggaaaaccctagagccttcttacttctagcaaccaattactacatacaaaaaaaactttccccaattatgaagtccactaatgcattctgcacagactcaatttcacgaactctgttgcggaggcacccctcacataattaacagcaagacactgcatgtggtcagaccttctgctaattgattaaatgagtctattcctaaatcagattctaatcacactagctagcatggctatggaacacagcgtgtataacagaatttccagaaatccaaactgtggacccgcaaaaaatttaaattactcattgggggagctgcttcagaactgaacctaagaaaaaaattaaaaggccaccttgctctcttgaaatgccactctccctgggtgtctttctttagtattcccacttctgtttgatccgtgtccttttgtgattcatcatccacacctaaacgatataaagcatgtcatactgtggccctgtctttatgattattttagttaacaagtgctggatagtttgcctgcagtttcctagtataacacaaaacctcccatctgcttgtcagtttttcttttttctttttcttttcgtctttaaaaaaaaaaaaaaaatgaaggctgtggtgttccctaagggttgtgagagaagttcatcccattgaactggtcagcaagatatcattagctcgttgtgtacatgaaatccaggggttagagcaccaagcgtcacaagccagtttctttacctccttgagctgatcagaggatcagagtatcaaggaaggattagcactgacttgggatttgtgtgattggttaatttattgcggcaatggcaggcctttcatctatggcaacatttaatcagcacagccatggaggctattaccggttagctcctttctcaagtcagccagggctgcaccatcagccctatcacaactcccctgaaatttccaaattatctggaacaggctttagcctcacagtaataaaaattagaagagattcctgatagcactggtggaaaaggctttcacttgcacagggcaaattataaatagtatgaatgtgcactttaaaaaaaaaattctccacctcttaagagatgtgcaggacttatcacccctgctctgatccaaatcctcatggttgaaaatttatattagattttatcagagaggcctaagtctagaaaaatcaatgaaggttatcttttatgttgcaggaacttgtggaaatattgattttcattttatagtgaatttggagcatgagttggtaatcactgctgagccgaccacaatgtttgcctactgtatcttttactgagttttgctcaagtatttaagatagtattcctgttgattttagtctacagtgtgaagacagatgttcctaaaacacaaagttgtacttgggaaaaaatacacccgaaagctccctatttacaataatgagatcagtattttgagactatattttgactattaatgatggatttgggaataaaatatactctgaaatgtttgtaagatttcttttttgcttctgtcaagtttataaaccaagagaaagattatttttgagtaaggaaaactgcatatgtataaaaaaatacatcattgaaacattgaagtcctactaagaaaagagggatttctttttttcaattaattattgtctttgtatctgacaaatattaatcaaaagtttcccttctgttgtatttttaaggtttttgtttcatgaatttgctaacttatttttatttcattctttctcttaaaatttaataaatgctatagttaatgcaagttaaaaagcattagggaa 0 false 0 search_space EMPTY 0 false Homo sapiens OREG0004185 REGULATORY REGION 3-Nov-2005 Human-zebrafish conserved sequences (within 100kb of a gene with known function) were tested for regulatory function by GFP. Conserved non-coding sequences were amplified by PCR and inserted into constructs with the Zebrafish cardiac myosin light chain 2 (cMLC2) promoter and green fluorescent protein (GFP). cMLC2 is cardiomyocyte specific with essentially no extra-cardiac expression in either stable or transient transgenesis. Transgenic embyros were examined for extra-cardiac GFP expression indicating cis-acting transcriptional regulation of the conserved sequence. 3-Nov-2005 OREGEC00001 OREGES00021 OREGET00002 obig Human-zebrafish conserved sequences (within 100kb of a gene with known function) were tested for regulatory function by Dual luciferase reporter gene assay. Conserved non-coding sequences were amplified by PCR and inserted into constructs with the Zebrafish cardiac myosin light chain 2 (cMLC2) promoter and the firefly luciferase sequence in pGL2 plasmids. Control plasmids (pRL) were created with the cMLC2 promoter and renilla luciferase but no test sequence. Luciferase ratio was determined and compared to that observed for negative controls (where test sequence was non-conserved sequences). Ratios that exceeded the mean of the negative control ratios by at least 2 standard deviations were considered positive. 3-Nov-2005 OREGEC00001 OREGES00026 OREGET00002 obig UNKNOWN UNKNOWN USER DEFINED 2750 POSITIVE OUTCOME 16179648 0 search_space EMPTY 0 false 0 sequence ttggctaggggtagcagttgactgttcatggtagcggtttctctagccatggcagaggtttgggcctcagagagtagttgagtaaaaaagaaatagcattagcagtgaagtaaaatctctgtggacatatatagattatattaaaattacgtcatagaggcaaatcctactttgccccttggtaggccccttgggaagaccttacggagaagagaacactgcatgctttaaaaaaaaccattacagcctttaattttatatatttaaagatattggaccttgatgcaaggaaaccaacttttaattcatcctgcttatttatttattttgagacagagtctcactctatcgcccaggctggagtacagtggcatgatctctgctcactgcaacctccaccttccaggttcaagcgattctcctgcctcagcctcccgagtagctgggattacaggcacgcaccaccacgccaggttaatttttgtatttgtagtagagatggggtttcaccatgttggccaagctggtctcgaactcttgactttgggtgatccgcccaccttggcctcccaaagtgctcagattacaggcatgagccaccgtgcccggcccccagttttatttttactgagcacctactatgtgccatgcactgggttaagccctggcaggttcagagatgtccaagggatggccctcagctctaaagagcatctcaaggccagggcccttagggagccctccctagggagagccaggggcagaagggcatgctcaggggctcgctctgcccagtgtggctctgtccgctctcattccgggtgggtgggagggtcagcttcctgcaagagatcagtctggggcgtctctctttctcctgtctctccctcaccttccacactccaccccctcctctggctgattgaaaaggtgcaagggggaatctgagagattctgtgctgtttgttttgggttcaatggaatctcatttacacgtgttaattgcaactaattggcactaattggatgaacaggaaacctctgggagcactcatacctttaatttatagtaaatatcattaattaacatatgctaattagagccaattaacattgattaagggttgccagctacttggaaagtacaactctgtgtcctcctcccttgattgtctgaagtcagcacaaaatatgatacatgaagtctgaggggaggagaagatggcacatggaatcgggtggcatctcccagcggagggcatcacggctccagcagccctcaccgaagctgggcacttagaggatggcaccaccctcaccttccccagggaaaaggggtctgcaggggaagggccctgcgagattagcacttctcagggagtgggaaggagcagatggtgggaggttctgggtgctgagatgttctcccttttgcctggcccccagatggcagacccagccagggtgggttgaaacaggactggaggtcagctggtggagagactggggccactgagagcaaggaatgtttgggactcctcctccagagatgagtggtggtgagctacccactgcccattgacccagtaccatctggcatggggcgtatgtgtgtggccaattggagtgaccctttctggatcccagtaacatctctcatcatccagaaaggccacacagatgaaggagggcatgccaggaggagtcagaggggcgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgcgcgcgcgcgcgcgtgcgcacaaagcctcctccatctgacatggatgtatgaatggggatatatctcctccatctgacacgaggtgcatagatgataggaccacctctgtcagacatctcctttgagagttttgagatattttttactgaagactaggatgctattcaaacttcccaggggcggtgtcagttaaaaaaaaaaatcatttgcccaggagccagaatgcttttagtttccactttcagttctgttactaactagttatgggacccttgggatt 0 false 0 search_space EMPTY 0 false Homo sapiens OREG0004186 REGULATORY REGION The putative regulatory region tested for this record maps with 100% identity to multiple places in the genome (possibly the result of a large gene duplication event). Therefore, it is impossible to map to a single genome location. 24-Apr-2007 bcb 3-Nov-2005 Human-zebrafish conserved sequences (within 100kb of a gene with known function) were tested for regulatory function by GFP. Conserved non-coding sequences were amplified by PCR and inserted into constructs with the Zebrafish cardiac myosin light chain 2 (cMLC2) promoter and green fluorescent protein (GFP). cMLC2 is cardiomyocyte specific with essentially no extra-cardiac expression in either stable or transient transgenesis. Transgenic embyros were examined for extra-cardiac GFP expression indicating cis-acting transcriptional regulation of the conserved sequence. 3-Nov-2005 OREGEC00001 OREGES00021 OREGET00002 obig Human-zebrafish conserved sequences (within 100kb of a gene with known function) were tested for regulatory function by Dual luciferase reporter gene assay. Conserved non-coding sequences were amplified by PCR and inserted into constructs with the Zebrafish cardiac myosin light chain 2 (cMLC2) promoter and the firefly luciferase sequence in pGL2 plasmids. Control plasmids (pRL) were created with the cMLC2 promoter and renilla luciferase but no test sequence. Luciferase ratio was determined and compared to that observed for negative controls (where test sequence was non-conserved sequences). Ratios that exceeded the mean of the negative control ratios by at least 2 standard deviations were considered positive. 3-Nov-2005 OREGEC00001 OREGES00026 OREGET00002 obig UNKNOWN UNKNOWN USER DEFINED 2751 POSITIVE OUTCOME 16179648 0 search_space EMPTY 0 false 0 sequence caagcactgagcgtattccatgtatagagatactaaaagctaatgtttatgttaaatcgtcttttacaagaatgtaaataattttgtgtttgtgttaagtttgctacaattttaacacaaagtatacttccaagaagtatgtaattgtcaatattttgtcaataaagttttatcaatatgttgctcagaataaaaaaaaaaaacagcctttttgttctaccaaaaggggccaaaatgaaacttttgccatgtagaggtaatggtttgtattgcattctattatgtctgtttttagaaatcaattataatatgggtatgggttgcaatgacagttgtctttagatgcggtccattgtttcattgtccttcaaatgacaagcagacaacaagcgaggtatcgtcattttatcaatggaattttccactagctgcctaattaatttgagcacatgtaacggggaaattgactggttaaattgcaacacacatagaaatgctagcaacggtcttgagctcggtttttccagagcaaagtgcttgtttttttcttgcctcatttgccgctcagtctgatagactggcattaaccagttttatttccattggtagaagagcagcgtctggtctgttcaagctacaaagagtcctgcgagcttttgtgaaagtgcaaatcagtttaggcaattatcatacgagtaatatgtgggggaaaggggatgcattgcccagtggtccactttaatctgttaatccgtggatccaagggggcctggttggacataatttagtacaatctgactacctctcacaacgcgataagagaaggtttgcaatgtgccgcaaaataggagctttgtttaaaatcttgtctgcagcaacggctgggctctatttgcatttgttgtcagttcctgtattttattatataaaataacagaacgtgaaatttatatttgtatttgagcacatgtaaatacatccagagactgtattttgcatccatttaaaaagtatcctaaaatagtcaacgatttcaaaacaaaattgcattaaatatcattattgatcaaatgttacgaaacccacaacaaactatggttaagcgtttttcgtgttgtcccaaaaacttttaatcatagtttgataaatgttggagatttcagacggctatacatacacatgctatataaagggatttttgaacggtctgtggactataacggtaataaaaaaatctgcagagaatactattagctttgaaaaacccctaaaagctttattacaaacccagctttgaaatagagggattagaaggctgaaagggtcccacaatagttagaagaaaaggtttcatgctaatgaggttaatgccctttgtatctccggactccacaacttcattactcctatctcgggcaacaccgagcggctcagagcccacaatccactcgagctgttccctaccctgcctaaagaaggatttgatagcagccctgttcaaactagataattatatcttttcaagttggaattaagataaagaaagtgcagtgaaggcggtgagccttgatccgctgcaaacaaatttggcgcactttctccctccgttgtgcctcaaaagacaggacaccccctcgttaccgctcggctcccctttattaattttgcattgccggtttaaatgcgcctggtgttttgcatttaaaggtggacaattagctgaatttaaaggaggggatttatatttcagttttagaaagtttgtattatttgttaacgttgagaacattaaattaattaattttagaggcccagatagcttgcaaaattaagattaaaaggcttcaattgtgtggc 0 false 0 search_space EMPTY 0 false Danio rerio OREG0004187 REGULATORY REGION 3-Nov-2005 Human-zebrafish conserved sequences (within 100kb of a gene with known function) were tested for regulatory function by GFP. Conserved non-coding sequences were amplified by PCR and inserted into constructs with the Zebrafish cardiac myosin light chain 2 (cMLC2) promoter and green fluorescent protein (GFP). cMLC2 is cardiomyocyte specific with essentially no extra-cardiac expression in either stable or transient transgenesis. Transgenic embyros were examined for extra-cardiac GFP expression indicating cis-acting transcriptional regulation of the conserved sequence. 3-Nov-2005 OREGEC00001 OREGES00021 OREGET00002 obig Human-zebrafish conserved sequences (within 100kb of a gene with known function) were tested for regulatory function by Dual luciferase reporter gene assay. Conserved non-coding sequences were amplified by PCR and inserted into constructs with the Zebrafish cardiac myosin light chain 2 (cMLC2) promoter and the firefly luciferase sequence in pGL2 plasmids. Control plasmids (pRL) were created with the cMLC2 promoter and renilla luciferase but no test sequence. Luciferase ratio was determined and compared to that observed for negative controls (where test sequence was non-conserved sequences). Ratios that exceeded the mean of the negative control ratios by at least 2 standard deviations were considered positive. 3-Nov-2005 OREGEC00001 OREGES00026 OREGET00002 obig UNKNOWN UNKNOWN USER DEFINED 2752 POSITIVE OUTCOME 16179648 0 search_space EMPTY 0 false 0 sequence tcaattgttgccgtagtccattggtgaaagatcttatagaggtatagcatatacaactttgactcttttctgtgcttttcttaattcttaaattctggtaataatatcagagcacaactagactgaaagcatattcatatgacctgctatagttctggagtagagaatcaacaaattttataactgtagtataatggaactatacagttgaagtcagaattattagccaccctgaattattagacagctcgtttatttttcccccaatttctgtttaacagagagcagatttgtttagcacatttctaatagttttaataacacatcgctaataactgatttcttttatctttaccatgatgactgtaaataatatttactagatagttttcaatacacttttatttagcttaaattaacatttaaaggcttaactaggttagttatgtaaactaggcaggttagggtaattaggcaagttattgtataacagtgttttgttctgtagattatcgagaaaaaatatagctaaaaggggctaaaaattttgtccctaaaatggtgtttataaaattaaaaactccttttattctcgccaaaatacaacaaaaaatactttttccagaagaaaaaatattatcaaacatactgtaaacattttcttgctctgttaaacattatttggaaaatatttaaaatagaagaaaaaaattcaaagggggctaataattttgacttcaactgtacataacagaactcaagtgttatccttcagctaaatacacttatggtgcaaataaataaacaaatcaattaaaaaactaagttttgctgtcattaatctgatgtaatgcaaccacagtatgtgatttgagattatgctaattgtttgccatatgcagccaatctttaacagcagcatctaattatgaaaagattttgaagtgattattgctatttgtcgttgtatgcacgtatggctatgtgacgttaacccaaacattagttaagatgagagttaattgcaatattttctagtttgttctatgcttataagcttaatctttttatcatctggtacatatatataagagtgcctttacaacttataaaatattaaaatgaaggcattgatgaaagagtcagatttagagggggtgctgtaatatatttaattttgataaaaagaataaaaactataaaagtttaaacctgatcaattgaaaacaaaaataattagtgacgattaaatgattatatatttatgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtctttgtgtgattgattcattcaattggtgcaggttaccctcttcctgtttatttctgtttgccctaagggccaatctaaagagccagcagattcatgatagatcacagggttcgattctccaatgatggattacagagccaatttaaaaagcaaaagcttaatttgtttcaataatctcctctttgaatgccaaacctcattttaccttcacatcaaagtaaaataatactaataataaatattaataatacatgaacttgcatttctatatttacaagcatgatgtttgtgttaataatttggcgtcatctaatattggtgcctttgactgtcatgtgcttacatcagaaagttaattgctaagtatagtgttcttaattttttcaagttctgttgcaaaaacaggataactttatattagtgtctttcctacacatctcatgtacttactgtaataacaatatattatcagaacattacatgcaactaaccatcatcctaaccctaacaacaatatttattattgctcagtactcagatataatgttagacaataacaataacactataaaattaccacaaatgcctaataacctaatacactctagttgaagacaagctaggaaacagttaagcttaagccgaggtttaggggttactttgggtaaaagggctagattaagggctaacattataattatagatgcgtttacagaaattattacatgcagttttttttaaatattacacaatgcaaagagatgtatctagacagaataactgcattgtatcaaacaatagtttaaatgtcagtgcatagtaatttaaagcattcatttattgttttacagttgatcactgttggcaaactttaaaaaaagttcctttgtatataccatacatcaaaccaaataaagcataacagaaaaaaaattgccttaatgctaagattttcagtgaaatacagagcaaataatagattataataatatggttgctaccaacaacctaaactatgatcaattgttcataactttaggtataatcggcggtctggctggcagactaccattgcattgtgtcggagctctctgcaggactctgaagactggagaatgctgagtgctgacatcaacacctaatgcatgacgg 0 false 0 search_space EMPTY 0 false Danio rerio OREG0004188 REGULATORY REGION This polymorphism was reported in the same publication that identified OREG0000031 in which this polymorphism resides. 17-Nov-2005 obig 17-Nov-2005 G transversion was found in 15 of 22 cancer cell lines tested versus and in none of the normal cell lines tested.]]> 17-Nov-2005 OREGEC00001 OREGES00010 OREGET00006 obig G transversion was found to significantly increase luciferase expression]]> 17-Nov-2005 OREGEC00001 OREGES00004 OREGET00002 obig G transversion was found to significantly increase mRNA expression levels in all cell lines including colon cancer, prostate cancer, breast cancer, and normals.]]> 17-Nov-2005 OREGEC00001 OREGES00007 OREGET00004 obig G transversion was found to significantly increase protein expression levels in all cell lines including colon cancer, prostate cancer, breast cancer, and normals.]]> 17-Nov-2005 OREGEC00001 OREGES00008 OREGET00005 obig ENSG00000089685 BIRC5 ENSEMBL homo_sapiens_core_33_35f 2869 POSITIVE OUTCOME 15383173 0 search_space EMPTY 0 false 0 search_space EMPTY 0 false 0 search_space EMPTY 0 false Homo sapiens OREG0001800 UNKNOWN UNKNOWN USER DEFINED REGULATORY POLYMORPHISM 17-Nov-2005 0 reference_sequence gccccgcggcgcgccattaaccgccagatttgaatcgcGggacccgttggcagaggtggcggcggcggcatgggtgcccc 0 false rs9904341 dbSNP GERMLINE 0 variant_sequence gccccgcggcgcgccattaaccgccagatttgaatcgcCggacccgttggcagaggtggcggcggcggcatgggtgcccc 0 false A locus is centered in a sequence that is nearly identical to the consensus binding site for the PLAG1 transcription factor. XRCC1 IVS10+141G>A is an intronic polymorphism that is associated with XRCC1 expression, apoptosis and familial breast cancer. It may occur within an intronic regulatory sequence.]]> 18-Apr-2006 obig 18-Apr-2006 A genotype. The mean XRCC1/GAPDH mRNA ratio was 0.34 for homozygous wild type breast cancer cell lines as compared to 0.43 for heterozygous lines (P = 0.02, Fig. 1a).]]> 18-Apr-2006 OREGEC00001 OREGES00007 OREGET00004 obig A variant allele showed increased XRCC1 protein expression (0.64 vs. 1.20, P = 0.03).]]> 18-Apr-2006 OREGEC00001 OREGES00008 OREGET00005 obig A was associated with an increased breast cancer risk (O.R. = 1.7, 95% C.I. 1.016–2.827, P = 0.04) as was homozygous XRCC1 IVS10+141G>A (O.R. = 4.7, 95% C.I. 1.028–21.444, P = 0.03)]]> 18-Apr-2006 OREGEC00001 OREGES00010 OREGET00006 obig 7515 XRCC1 NCBI 2955 POSITIVE OUTCOME 16596326 0 search_space EMPTY 0 false 0 search_space EMPTY 0 false 0 search_space EMPTY 0 false Homo sapiens OREG0001895 UNKNOWN UNKNOWN USER DEFINED REGULATORY HAPLOTYPE 18-Apr-2006 0 reference_sequence gaacacaggtggtcccagcccagagccagcagactactgagaggagcgggGcaggggctggggtactccagatgagggaaggaggacctgcctgggaggtc 0 false rs2139720 dbSNP GERMLINE 0 variant_sequence gaacacaggtggtcccagcccagagccagcagactactgagaggagcgggAcaggggctggggtactccagatgagggaaggaggacctgcctgggaggtc 0 false This polymorphism is one bp off rs11911934. This could be an annotation mistake at some level (in the paper? dbSNP?). 18-Apr-2006 obig 18-Apr-2006 Showed variant specific DNA-protein interactions in a number of cell lines (NB, Hela, MB) 18-Apr-2006 OREGEC00001 OREGES00001 OREGET00001 obig 18-Apr-2006 OREGEC00001 OREGES00003 OREGET00001 obig "...the majority allele -3829C drove expression that was significantly greater than that of unmodified SV40 promoter in the pCAT3-P vector, while -3829T actually reduced expression below that of the unmodified vector (Fig. 5A). In comparison to the majority allele, the -3829T variant reduced expression by 66% (Fig. 5B)" 18-Apr-2006 OREGEC00001 OREGES00019 OREGET00002 obig 351 APP NCBI 2958 POSITIVE OUTCOME 16243604 0 search_space EMPTY 0 false 0 search_space EMPTY 0 false 0 search_space EMPTY 0 false Homo sapiens OREG0001904 UNKNOWN UNKNOWN USER DEFINED REGULATORY POLYMORPHISM 18-Apr-2006 0 reference_sequence acaggattatagaataagtcttagctgttctaaagaaggacatattatgtacccCcacccccaaattcatatgttgaagtcctaacccgacagtgtctcaaaatgtgacc 0 false NOT SPECIFIED 0 variant_sequence acaggattatagaataagtcttagctgttctaaagaaggacatattatgtacccTcacccccaaattcatatgttgaagtcctaacccgacagtgtctcaaaatgtgacc 0 false 18-Apr-2006 Showed variant specific DNA-protein interactions in a number of cell lines (NB, Hela, MB) 18-Apr-2006 OREGEC00001 OREGES00001 OREGET00001 obig "...gain of DNA–protein binding for this region is specific to the naturally occurring -1023C variant" 18-Apr-2006 OREGEC00001 OREGES00003 OREGET00001 obig "The expression profile of -1023T and -1023C was nearly the opposite in that the majority allele -1023T did not increase CAT expression above the unmodified SV40 promoter, but -1023C increased reporter gene expression to levels comparable to that of -3829C (Fig. 5A). In comparison to the majority allele, the -1023C variant increased CAT levels by 41% (Fig. 5B)." 18-Apr-2006 OREGEC00001 OREGES00019 OREGET00002 obig 351 APP NCBI 2959 POSITIVE OUTCOME 16243604 0 search_space EMPTY 0 false 0 search_space EMPTY 0 false 0 search_space EMPTY 0 false Homo sapiens OREG0001905 UNKNOWN UNKNOWN USER DEFINED REGULATORY POLYMORPHISM 18-Apr-2006 0 reference_sequence gggctgtggcttggtaactaaatgctacttcaggtcaagagcaggggataTatctgggcagttctagagcattctaaactatctggacactaactggacag 0 false rs466448 dbSNP NOT SPECIFIED 0 variant_sequence gggctgtggcttggtaactaaatgctacttcaggtcaagagcaggggataCatctgggcagttctagagcattctaaactatctggacactaactggacag 0 false From the abstract: "In this report, a single nucleotide polymorphism (SNP309) is found in the MDM2 promoter and is shown to increase the affinity of the transcriptional activator Sp1, resulting in higher levels of MDM2 RNA and protein and the subsequent attenuation of the p53 pathway. In humans, SNP309 is shown to associate with accelerated tumor formation in both hereditary and sporadic cancers. A model is proposed whereby SNP309 serves as a rate-limiting event in carcinogenesis." 19-Apr-2006 obig 19-Apr-2006 EMSAs were carried out with purified recombinant human Sp1 protein and labeled double-stranded oligonucleotides containing either the wild-type sequence (T/T) or the SNP309 sequence (G/G). The binding affinity of oligonucleotides containing SNP309 to a range of concentrations (150 ng-450 ng) of purified Sp1 is much higher (2-4-fold) than that of the wild-type sequence (Figure 1C, lanes 2-5 versus lanes 7-10). The same assays were carried out using HeLa cell nuclear extracts as a source of protein instead of purified Sp1, and similar results were obtained (data not shown) 19-Apr-2006 OREGEC00001 OREGES00001 OREGET00001 obig To verify the presence of Sp1 on the MDM2 promoter in vivo, a chromatin immunoprecipitation (ChIP) was performed. Lysates were prepared from growing Manca cells, homozygous for SNP309 (G/G), and immunoprecipitations were carried out using antibodies against either Sp1 or lamin A. The MDM2 promoter was detected in the ChIP using the Sp1 antibody but not using the lamin A antibody. These data suggest that Sp1 binds this region of the MDM2 promoter in vivo. 19-Apr-2006 OREGEC00002 OREGES00005 OREGET00003 obig SL2 cells were transiently transfected with an Sp1 expression vector (pPac-Sp1) and a luciferase reporter plasmid driven by the MDM2 promoter either wild-type (T/T) or homozygous (G/G) for SNP309. Cotransfection of Sp1 strongly stimulated luciferase expression of the reporter plasmid driven by the MDM2 promoter, as measured by luciferase activity, suggesting that Sp1 can bind to this region of the MDM2 promoter and activate transcription. The presence of SNP309 in the reporter plasmid consistently showed higher Sp1-induced luciferase expression (~50%) over the presence of wild-type sequence in the reporter plasmid. Similar results were obtained when both reporter plasmids were transfected into the mammalian HeLa cell line which has an abundance of Sp1. The reporter plasmid containing SNP309 (G) yielded significantly higher luciferase levels (60%) than the plasmid containing the wild-type sequence (T) (data not shown). 19-Apr-2006 OREGEC00001 OREGES00004 OREGET00002 obig MDM2 RNA levels were measured by real-time PCR (TaqMan). The presence of SNP309 correlated with high expression of the MDM2 transcript (on average 8-fold) when compared to the levels seen in cells wild-type for SNP309 (T/T). 19-Apr-2006 OREGEC00001 OREGES00007 OREGET00004 obig MDM2 protein levels were found to be significantly higher (on average 4-fold) in cell lines homozygous for SNP309 (G/G), as seen in the Western blot analysis of total cell lysates. Two methods of Sp1 inhibition were shown to preferentially reduce the heightened levels of MDM2 protein in cells homozygous for SNP309, thereby supporting the hypothesis that the Sp1 transcription factor is indeed responsible for the heightened levels of MDM2 in cells homozygous for SNP309. 19-Apr-2006 OREGEC00001 OREGES00008 OREGET00005 obig 4193 MDM2 NCBI 2962 POSITIVE OUTCOME 15550242 0 search_space EMPTY 0 false 0 sequence GCGGCGCGGGAGG 0 false 0 search_space EMPTY 0 false Homo sapiens OREG0001909 6667 SP1 NCBI REGULATORY POLYMORPHISM 19-Apr-2006 0 reference_sequence cgcgggagttcagggtaaaggtcacgggggccgggggctgcggggccgctTcggcgcgggaggtccggatgatcgcaggtgcctgtcgggtcactagtgtg 0 false rs2279744 dbSNP GERMLINE 0 variant_sequence cgcgggagttcagggtaaaggtcacgggggccgggggctgcggggccgctGcggcgcgggaggtccggatgatcgcaggtgcctgtcgggtcactagtgtg 0 false From the abstract: "Transient transfections of S2 cells showed that both individually and together, Sp1 and Sp3 were able to trans-activate a wild type CT-box-driven luciferase reporter construct in a dose-dependent manner. Transfection of the wild type but not mutant CT-box oligonucleotide was able to decrease endogenous N-myc expression in neuroblastoma cells. Together these results suggest that the CT-box element serves a critically functional role, and in the basal state, allows for N-myc trans-activation by Sp1 and Sp3. Moreover when mutated, the CT-box may still function as a binding motif for alternate transcription factors such as NF-1 that can allow persistent N-myc expression." 20-Apr-2006 obig 20-Apr-2006 Mutations 2G and 5G within the central CT-box motif of the RARR resulted in a decrease of promoter activity, whereas mutations either upstream or downstream of the CT-box (-7G, +5A, and +7C) did not diminish promoter activity. 20-Apr-2006 OREGEC00001 OREGES00004 OREGET00002 obig Gel shift analysis performed using nuclear extracts and RARR oligonucleotide probes containing the same mutations within or outside of core CT-box indicated that the CT-box motif was involved in basal DNA–protein complexes that formed at the N-myc RARR. Mutations either upstream or downstream of the CT-box did not alter DNA–protein complexes A, B, or C. Conversely, mutations within the CT-box resulted in novel DNA–protein complexes D and E. 20-Apr-2006 OREGEC00001 OREGES00001 OREGET00001 obig To confirm the involvement of Sp1 in complexes A, B, and C, gel shift analysis was performed in the presence of non-labeled competitor oligonucleotides. Fig. 3 shows that the addition of an unlabeled canonical Sp1-binding GC-box competitor was able to successfully diminish the intensity of bands A, B, and C formed by RARR probe. Addition of an unrelated competitor did not alter these complexes. 20-Apr-2006 OREGEC00002 OREGES00003 OREGET00001 obig The addition of Sp1- and Sp3-specific antibodies resulted in the super-shifting of the protein complexes that interacted with the wt RARR probe (Fig. 4A). Anti-Sp1 appeared to primarily super-shift complexes A and B, while anti-Sp3 antibody affected bands B and C. However, antibodies targeting Sp2 and Sp4 had no effect on the DNA–protein complexes. 20-Apr-2006 OREGEC00002 OREGES00002 OREGET00001 obig 4613 MYCN NCBI 2963 POSITIVE OUTCOME 14567977 0 search_space EMPTY 0 false 0 sequence CCTCCC 0 false 0 sequence_with_flank cttctctctgcaaagaaaagcaagtggcttttggcgcgaaagccttggcgCCTCCCctgatttttatggaaatcaggagggcggggtaaagccgctttcctctcct 0 false Homo sapiens OREG0001910 SP1 and SP3 SP1 and SP3 USER DEFINED TRANSCRIPTION FACTOR BINDING SITE From the abstract: "Our findings suggest that G-33A mutation reduces the thrombomodulin promoter activity and is associated with carotid atherosclerosis in younger subjects." 28-Apr-2006 obig 28-Apr-2006 28-Apr-2006 OREGEC00001 OREGES00011 OREGET00006 obig EV:0200028 28-Apr-2006 OREGEC00001 OREGES00004 OREGET00002 obig 7056 THBD NCBI 3015 POSITIVE OUTCOME 11257274 0 search_space EMPTY 0 false 0 search_space EMPTY 0 false 0 search_space EMPTY 0 false Homo sapiens OREG0001959 UNKNOWN UNKNOWN USER DEFINED REGULATORY POLYMORPHISM 28-Apr-2006 0 reference_sequence gaggcagcctctgacatgcggatcggccagggctcgagtttataagtgccCggccctccctccctggacgttcgggaaaaggaaggaagtgcctggtggga 0 false rs13306848 dbSNP GERMLINE 0 variant_sequence gaggcagcctctgacatgcggatcggccagggctcgagtttataagtgccTggccctccctccctggacgttcgggaaaaggaaggaagtgcctggtggga 0 false From Results: "Although it is possible that the candidate REs are not specifically responsible for the observed expression changes, the transfection assays establish that the sites are strongly functional. Given the functional spacing of the REs relative to the genes (as compared with established p53 targets), their demonstrated activity, and the p53 responsiveness of the candidate genes, it is likely that the candidate polymorphic REs are involved directly in p53 transactivation." 28-Jun-2006 obig 28-Jun-2006 28-Jun-2006 OREG0002192 obig Cell type: Yeast. Observed strong differences in p53 induced expression between p53 response element SNPs (strong/weak: G/A) (see figure 1). 28-Jun-2006 OREGEC00001 OREGES00026 OREGET00002 obig Cell type: Human SaOS-2 osteosarcoma cell line. Observed strong differences in p53 induced expression between p53 response element SNPs (strong/weak: G/A) (see figure 1). 28-Jun-2006 OREGEC00001 OREGES00026 OREGET00002 obig Cell type: Human RKO colon carcinoma cell line. Observed strong differences in p53 induced expression between p53 response element SNPs (strong/weak: G/A) (see figure 1). 28-Jun-2006 OREGEC00001 OREGES00026 OREGET00002 obig Cell type: Human RKO colon carcinoma cell line. The authors state (in results): "Of the genes examined, six exhibited increased expression after p53 induction in at least one cell type." However, it is difficult to determine how many or which of the cell lines (SaOS-2 osteosarcoma, RKO colon carcinoma, HT1080 fibrosarcoma and lymphoblastoid cells) showed a significant difference for any particular gene. I have reported as evidence only those that appeared significant by comparing the error bars (see figure 2). 28-Jun-2006 OREGEC00001 OREGES00007 OREGET00004 obig Cell type: Human HT1080 fibrosarcoma. The authors state (in results): "Of the genes examined, six exhibited increased expression after p53 induction in at least one cell type." However, it is difficult to determine how many or which of the cell lines (SaOS-2 osteosarcoma, RKO colon carcinoma, HT1080 fibrosarcoma and lymphoblastoid cells) showed a significant difference for any particular gene. I have reported as evidence only those that appeared significant by comparing the error bars (see figure 2). 28-Jun-2006 OREGEC00001 OREGES00007 OREGET00004 obig Cell type: Human SaOS-2 osteosarcoma cell line. The authors state (in results): "Of the genes examined, six exhibited increased expression after p53 induction in at least one cell type." However, it is difficult to determine how many or which of the cell lines (SaOS-2 osteosarcoma, RKO colon carcinoma, HT1080 fibrosarcoma and lymphoblastoid cells) showed a significant difference for any particular gene. I have reported as evidence only those that appeared significant by comparing the error bars (see figure 2). 28-Jun-2006 OREGEC00001 OREGES00007 OREGET00004 obig 104 ADARB1 NCBI 3237 POSITIVE OUTCOME 15843459 0 search_space EMPTY 0 false 0 sequence GGACAAGTTGAAACTTGCAC 0 false 0 search_space EMPTY 0 false Homo sapiens OREG0002189 7157 TP53 NCBI REGULATORY POLYMORPHISM 28-Jun-2006 0 reference_sequence gtcccggccttgggcgccatccgctctctgctgctctggagggagaaaaaggacaagttgaaacttGcacaagcagcctccattctggggagttcccttgtattccccacaccaacccgc 0 false rs2838769 dbSNP GERMLINE 0 variant_sequence gtcccggccttgggcgccatccgctctctgctgctctggagggagaaaaaggacaagttgaaacttAcacaagcagcctccattctggggagttcccttgtattccccacaccaacccgc 0 false From Results: "Although it is possible that the candidate REs are not specifically responsible for the observed expression changes, the transfection assays establish that the sites are strongly functional. Given the functional spacing of the REs relative to the genes (as compared with established p53 targets), their demonstrated activity, and the p53 responsiveness of the candidate genes, it is likely that the candidate polymorphic REs are involved directly in p53 transactivation." Also, note that the variation type was not specified as germline because because it was found to be very rare (only one in 365 individuals tested). 28-Jun-2006 obig 28-Jun-2006 28-Jun-2006 OREG0002193 obig Cell type: Human SaOS-2 osteosarcoma cell line. Observed strong differences in p53 induced expression between p53 response element SNPs (strong/weak: G/A) (see figure 1). 28-Jun-2006 OREGEC00001 OREGES00026 OREGET00002 obig Cell type: Human RKO colon carcinoma cell line. Observed strong differences in p53 induced expression between p53 response element SNPs (strong/weak: G/A) (see figure 1). 28-Jun-2006 OREGEC00001 OREGES00026 OREGET00002 obig Cell type: Human HT1080 fibrosarcoma. The authors state (in results): "Of the genes examined, six exhibited increased expression after p53 induction in at least one cell type." However, it is difficult to determine how many or which of the cell lines (SaOS-2 osteosarcoma, RKO colon carcinoma, HT1080 fibrosarcoma and lymphoblastoid cells) showed a significant difference for any particular gene. I have reported as evidence only those that appeared significant by comparing the error bars (see figure 2). 28-Jun-2006 OREGEC00002 OREGES00007 OREGET00004 obig Cell type: Human SaOS-2 osteosarcoma cell line. The authors state (in results): "Of the genes examined, six exhibited increased expression after p53 induction in at least one cell type." However, it is difficult to determine how many or which of the cell lines (SaOS-2 osteosarcoma, RKO colon carcinoma, HT1080 fibrosarcoma and lymphoblastoid cells) showed a significant difference for any particular gene. I have reported as evidence only those that appeared significant by comparing the error bars (see figure 2). 28-Jun-2006 OREGEC00002 OREGES00007 OREGET00004 obig 8874 ARHGEF7 NCBI 3238 POSITIVE OUTCOME 15843459 0 search_space EMPTY 0 false 0 sequence AAACATGTCAGCACTTGCTT 0 false 0 search_space EMPTY 0 false Homo sapiens OREG0002191 7157 TP53 NCBI REGULATORY POLYMORPHISM 28-Jun-2006 0 reference_sequence aagcagctttgcttttgccattccactgaaaaaatgtacagtttcgatggaaacatgtcaGcacttgcttgaaggaatttttcaactatagaaagaaaaaagcttcatttcatccctttt 0 false rs1658728 dbSNP NOT SPECIFIED 0 variant_sequence aagcagctttgcttttgccattccactgaaaaaatgtacagtttcgatggaaacatgtcaTcacttgcttgaaggaatttttcaactatagaaagaaaaaagcttcatttcatccctttt 0 false This record was updated to fix an error in the evidence code classification. 28-Jun-2006 obig From Results: "Although it is possible that the candidate REs are not specifically responsible for the observed expression changes, the transfection assays establish that the sites are strongly functional. Given the functional spacing of the REs relative to the genes (as compared with established p53 targets), their demonstrated activity, and the p53 responsiveness of the candidate genes, it is likely that the candidate polymorphic REs are involved directly in p53 transactivation." 28-Jun-2006 obig 28-Jun-2006 Cell type: Yeast. Observed strong differences in p53 induced expression between p53 response element SNPs (strong/weak: G/A) (see figure 1). 28-Jun-2006 OREGEC00001 OREGES00026 OREGET00002 obig Cell type: Human SaOS-2 osteosarcoma cell line. Observed strong differences in p53 induced expression between p53 response element SNPs (strong/weak: G/A) (see figure 1). 28-Jun-2006 OREGEC00001 OREGES00026 OREGET00002 obig Cell type: Human RKO colon carcinoma cell line. Observed strong differences in p53 induced expression between p53 response element SNPs (strong/weak: G/A) (see figure 1). 28-Jun-2006 OREGEC00001 OREGES00026 OREGET00002 obig Cell type: Human RKO colon carcinoma cell line. The authors state (in results): "Of the genes examined, six exhibited increased expression after p53 induction in at least one cell type." However, it is difficult to determine how many or which of the cell lines (SaOS-2 osteosarcoma, RKO colon carcinoma, HT1080 fibrosarcoma and lymphoblastoid cells) showed a significant difference for any particular gene. I have reported as evidence only those that appeared significant by comparing the error bars (see figure 2). 28-Jun-2006 OREGEC00002 OREGES00007 OREGET00004 obig Cell type: Human HT1080 fibrosarcoma. The authors state (in results): "Of the genes examined, six exhibited increased expression after p53 induction in at least one cell type." However, it is difficult to determine how many or which of the cell lines (SaOS-2 osteosarcoma, RKO colon carcinoma, HT1080 fibrosarcoma and lymphoblastoid cells) showed a significant difference for any particular gene. I have reported as evidence only those that appeared significant by comparing the error bars (see figure 2). 28-Jun-2006 OREGEC00002 OREGES00007 OREGET00004 obig Cell type: Human SaOS-2 osteosarcoma cell line. The authors state (in results): "Of the genes examined, six exhibited increased expression after p53 induction in at least one cell type." However, it is difficult to determine how many or which of the cell lines (SaOS-2 osteosarcoma, RKO colon carcinoma, HT1080 fibrosarcoma and lymphoblastoid cells) showed a significant difference for any particular gene. I have reported as evidence only those that appeared significant by comparing the error bars (see figure 2). 28-Jun-2006 OREGEC00002 OREGES00007 OREGET00004 obig 104 ADARB1 NCBI 3239 POSITIVE OUTCOME 15843459 0 search_space EMPTY 0 false 0 sequence GGACAAGTTGAAACTTGCAC 0 false 0 search_space EMPTY 0 false Homo sapiens OREG0002192 7157 TP53 NCBI REGULATORY POLYMORPHISM 28-Jun-2006 0 reference_sequence gtcccggccttgggcgccatccgctctctgctgctctggagggagaaaaaggacaagttgaaacttGcacaagcagcctccattctggggagttcccttgtattccccacaccaacccgc 0 false rs2838769 dbSNP GERMLINE 0 variant_sequence gtcccggccttgggcgccatccgctctctgctgctctggagggagaaaaaggacaagttgaaacttAcacaagcagcctccattctggggagttcccttgtattccccacaccaacccgc 0 false From Results: "Although it is possible that the candidate REs are not specifically responsible for the observed expression changes, the transfection assays establish that the sites are strongly functional. Given the functional spacing of the REs relative to the genes (as compared with established p53 targets), their demonstrated activity, and the p53 responsiveness of the candidate genes, it is likely that the candidate polymorphic REs are involved directly in p53 transactivation." Also, note that the variation type was not specified as germline because because it was found to be very rare (only one in 365 individuals tested). 28-Jun-2006 obig 28-Jun-2006 Cell type: Human SaOS-2 osteosarcoma cell line. Observed strong differences in p53 induced expression between p53 response element SNPs (strong/weak: G/T) (see figure 1). 28-Jun-2006 OREGEC00001 OREGES00026 OREGET00002 obig Cell type: Human RKO colon carcinoma cell line. Observed strong differences in p53 induced expression between p53 response element SNPs (strong/weak: G/T) (see figure 1). 28-Jun-2006 OREGEC00001 OREGES00026 OREGET00002 obig Cell type: Human HT1080 fibrosarcoma. The authors state (in results): "Of the genes examined, six exhibited increased expression after p53 induction in at least one cell type." However, it is difficult to determine how many or which of the cell lines (SaOS-2 osteosarcoma, RKO colon carcinoma, HT1080 fibrosarcoma and lymphoblastoid cells) showed a significant difference for any particular gene. I have reported as evidence only those that appeared significant by comparing the error bars (see figure 2). 28-Jun-2006 OREGEC00002 OREGES00007 OREGET00004 obig Cell type: Human SaOS-2 osteosarcoma cell line. The authors state (in results): "Of the genes examined, six exhibited increased expression after p53 induction in at least one cell type." However, it is difficult to determine how many or which of the cell lines (SaOS-2 osteosarcoma, RKO colon carcinoma, HT1080 fibrosarcoma and lymphoblastoid cells) showed a significant difference for any particular gene. I have reported as evidence only those that appeared significant by comparing the error bars (see figure 2). 28-Jun-2006 OREGEC00002 OREGES00007 OREGET00004 obig 8874 ARHGEF7 NCBI 3241 POSITIVE OUTCOME 15843459 0 search_space EMPTY 0 false 0 sequence AAACATGTCAGCACTTGCTT 0 false 0 search_space EMPTY 0 false Homo sapiens OREG0002193 7157 TP53 NCBI REGULATORY POLYMORPHISM 28-Jun-2006 0 reference_sequence aagcagctttgcttttgccattccactgaaaaaatgtacagtttcgatggaaacatgtcaGcacttgcttgaaggaatttttcaactatagaaagaaaaaagcttcatttcatccctttt 0 false rs1658728 dbSNP NOT SPECIFIED 0 variant_sequence aagcagctttgcttttgccattccactgaaaaaatgtacagtttcgatggaaacatgtcaTcacttgcttgaaggaatttttcaactatagaaagaaaaaagcttcatttcatccctttt 0 false From Results: "Although it is possible that the candidate REs are not specifically responsible for the observed expression changes, the transfection assays establish that the sites are strongly functional. Given the functional spacing of the REs relative to the genes (as compared with established p53 targets), their demonstrated activity, and the p53 responsiveness of the candidate genes, it is likely that the candidate polymorphic REs are involved directly in p53 transactivation." 28-Jun-2006 obig 28-Jun-2006 Cell type: Yeast. Observed strong differences in p53 induced expression between p53 response element SNPs (strong/weak: G/C) (see figure 1). 28-Jun-2006 OREGEC00001 OREGES00026 OREGET00002 obig Cell type: Human SaOS-2 osteosarcoma cell line. Observed strong differences in p53 induced expression between p53 response element SNPs (strong/weak: G/C) (see figure 1). 28-Jun-2006 OREGEC00001 OREGES00026 OREGET00002 obig Cell type: Human RKO colon carcinoma cell line. The authors state (in results): "Of the genes examined, six exhibited increased expression after p53 induction in at least one cell type." However, it is difficult to determine how many or which of the cell lines (SaOS-2 osteosarcoma, RKO colon carcinoma, HT1080 fibrosarcoma and lymphoblastoid cells) showed a significant difference for any particular gene. I have reported as evidence only those that appeared significant by comparing the error bars (see figure 2). 28-Jun-2006 OREGEC00002 OREGES00007 OREGET00004 obig Cell type: Human SaOS-2 osteosarcoma cell line. The authors state (in results): "Of the genes examined, six exhibited increased expression after p53 induction in at least one cell type." However, it is difficult to determine how many or which of the cell lines (SaOS-2 osteosarcoma, RKO colon carcinoma, HT1080 fibrosarcoma and lymphoblastoid cells) showed a significant difference for any particular gene. I have reported as evidence only those that appeared significant by comparing the error bars (see figure 2). 28-Jun-2006 OREGEC00002 OREGES00007 OREGET00004 obig 1630 DCC NCBI 3242 POSITIVE OUTCOME 15843459 0 search_space EMPTY 0 false 0 sequence CAGCATGTTCACACAAGCCA 0 false 0 search_space EMPTY 0 false Homo sapiens OREG0002194 7157 TP53 NCBI REGULATORY POLYMORPHISM 28-Jun-2006 0 reference_sequence aactcaccttatacatttactgaaagctaaagattcccttcccagttaaaCagcatgttcacacaagccaatcacttttcataaaatttcaggatattcacaaacttcctgaattttgtt 0 false rs934345 dbSNP GERMLINE 0 variant_sequence aactcaccttatacatttactgaaagctaaagattcccttcccagttaaaGagcatgttcacacaagccaatcacttttcataaaatttcaggatattcacaaacttcctgaattttgtt 0 false From Results: "Although it is possible that the candidate REs are not specifically responsible for the observed expression changes, the transfection assays establish that the sites are strongly functional. Given the functional spacing of the REs relative to the genes (as compared with established p53 targets), their demonstrated activity, and the p53 responsiveness of the candidate genes, it is likely that the candidate polymorphic REs are involved directly in p53 transactivation." 28-Jun-2006 obig 28-Jun-2006 Cell type: Yeast. Observed strong differences in p53 induced expression between p53 response element SNPs (strong/weak: T/C) (see figure 1). 28-Jun-2006 OREGEC00001 OREGES00026 OREGET00002 obig Cell type: Human RKO colon carcinoma cell line. The authors state (in results): "Of the genes examined, six exhibited increased expression after p53 induction in at least one cell type." However, it is difficult to determine how many or which of the cell lines (SaOS-2 osteosarcoma, RKO colon carcinoma, HT1080 fibrosarcoma and lymphoblastoid cells) showed a significant difference for any particular gene. I have reported as evidence only those that appeared significant by comparing the error bars (see figure 2). 28-Jun-2006 OREGEC00002 OREGES00007 OREGET00004 obig Cell type: Human GM15223 (PDR004) lymphoblastoid cells. The authors state (in results): "Of the genes examined, six exhibited increased expression after p53 induction in at least one cell type." However, it is difficult to determine how many or which of the cell lines (SaOS-2 osteosarcoma, RKO colon carcinoma, HT1080 fibrosarcoma and lymphoblastoid cells) showed a significant difference for any particular gene. I have reported as evidence only those that appeared significant by comparing the error bars (see figure 2). 28-Jun-2006 OREGEC00002 OREGES00007 OREGET00004 obig Cell type: Human SaOS-2 osteosarcoma cell line. The authors state (in results): "Of the genes examined, six exhibited increased expression after p53 induction in at least one cell type." However, it is difficult to determine how many or which of the cell lines (SaOS-2 osteosarcoma, RKO colon carcinoma, HT1080 fibrosarcoma and lymphoblastoid cells) showed a significant difference for any particular gene. I have reported as evidence only those that appeared significant by comparing the error bars (see figure 2). 28-Jun-2006 OREGEC00002 OREGES00007 OREGET00004 obig 8320 EOMES NCBI 3243 POSITIVE OUTCOME 15843459 0 search_space EMPTY 0 false 0 sequence GGGCCTGTCTCCAACTTGCCC 0 false 0 search_space EMPTY 0 false Homo sapiens OREG0002195 7157 TP53 NCBI REGULATORY POLYMORPHISM 28-Jun-2006 0 reference_sequence agttacagcttccgacgaggaaagagacttccttgggcctgtctccaactTgccccagtttccccagcctccgggacgggcgcttccctgcaagctatcag 0 false rs3806624 dbSNP GERMLINE 0 variant_sequence agttacagcttccgacgaggaaagagacttccttgggcctgtctccaactCgccccagtttccccagcctccgggacgggcgcttccctgcaagctatcag 0 false From Results: "Although it is possible that the candidate REs are not specifically responsible for the observed expression changes, the transfection assays establish that the sites are strongly functional. Given the functional spacing of the REs relative to the genes (as compared with established p53 targets), their demonstrated activity, and the p53 responsiveness of the candidate genes, it is likely that the candidate polymorphic REs are involved directly in p53 transactivation." RRM1 was not induced by p53 in any cell type tested by Rt-PCR. Therefore the evidence for P53 as its TF is less convincing. However, there was evidence for induction by P53 by luciferase and there does appear to be differential expression depending on which SNP variant is present (more convincing in Yeast than the cell line). 28-Jun-2006 obig 28-Jun-2006 Cell type: Yeast. Observed strong differences in p53 induced expression between p53 response element SNPs (strong/weak: C/T) (see figure 1). 28-Jun-2006 OREGEC00001 OREGES00026 OREGET00002 obig Cell type: Human SaOS-2 osteosarcoma cell line. Observed strong differences in p53 induced expression between p53 response element SNPs (strong/weak: C/T) (see figure 1). 28-Jun-2006 OREGEC00001 OREGES00026 OREGET00002 obig 6240 RRM1 NCBI 3244 POSITIVE OUTCOME 15843459 0 search_space EMPTY 0 false 0 sequence GGGCATGTGCATTCAAGTTT 0 false 0 search_space EMPTY 0 false Homo sapiens OREG0002196 7157 TP53 NCBI REGULATORY POLYMORPHISM 28-Jun-2006 0 reference_sequence tttaactggtcatcctgcatttatctggtaaccctgcccacagagcttctgggCatgtgcattcaagtttcattttccctgggcaaaggaaagattgtct 0 false rs1465952 dbSNP GERMLINE 0 variant_sequence tttaactggtcatcctgcatttatctggtaaccctgcccacagagcttctgggTatgtgcattcaagtttcattttccctgggcaaaggaaagattgtct 0 false From Results: "Although it is possible that the candidate REs are not specifically responsible for the observed expression changes, the transfection assays establish that the sites are strongly functional. Given the functional spacing of the REs relative to the genes (as compared with established p53 targets), their demonstrated activity, and the p53 responsiveness of the candidate genes, it is likely that the candidate polymorphic REs are involved directly in p53 transactivation." Also, note that the variation type was not specified as germline because it was found to be very rare (only one in 365 individuals tested). 28-Jun-2006 obig 28-Jun-2006 Cell type: Yeast. Observed strong differences in p53 induced expression between p53 response element SNPs (strong/weak: G/A) (see figure 1). 28-Jun-2006 OREGEC00001 OREGES00026 OREGET00002 obig Cell type: Human SaOS-2 osteosarcoma cell line. Observed strong differences in p53 induced expression between p53 response element SNPs (strong/weak: G/A) (see figure 1). 28-Jun-2006 OREGEC00001 OREGES00026 OREGET00002 obig Cell type: Human RKO colon carcinoma cell line. Observed strong differences in p53 induced expression between p53 response element SNPs (strong/weak: G/A) (see figure 1). 28-Jun-2006 OREGEC00001 OREGES00026 OREGET00002 obig Cell type: Human RKO colon carcinoma cell line. The authors state (in results): "Of the genes examined, six exhibited increased expression after p53 induction in at least one cell type." However, it is difficult to determine how many or which of the cell lines (SaOS-2 osteosarcoma, RKO colon carcinoma, HT1080 fibrosarcoma and lymphoblastoid cells) showed a significant difference for any particular gene. I have reported as evidence only those that appeared significant by comparing the error bars (see figure 2). 28-Jun-2006 OREGEC00002 OREGES00007 OREGET00004 obig Cell type: Human GM15223 (PDR004) lymphoblastoid cells. The authors state (in results): "Of the genes examined, six exhibited increased expression after p53 induction in at least one cell type." However, it is difficult to determine how many or which of the cell lines (SaOS-2 osteosarcoma, RKO colon carcinoma, HT1080 fibrosarcoma and lymphoblastoid cells) showed a significant difference for any particular gene. I have reported as evidence only those that appeared significant by comparing the error bars (see figure 2). 28-Jun-2006 OREGEC00002 OREGES00007 OREGET00004 obig Cell type: Human HT1080 fibrosarcoma. The authors state (in results): "Of the genes examined, six exhibited increased expression after p53 induction in at least one cell type." However, it is difficult to determine how many or which of the cell lines (SaOS-2 osteosarcoma, RKO colon carcinoma, HT1080 fibrosarcoma and lymphoblastoid cells) showed a significant difference for any particular gene. I have reported as evidence only those that appeared significant by comparing the error bars (see figure 2). 28-Jun-2006 OREGEC00002 OREGES00007 OREGET00004 obig 10647 SCGB1D2 NCBI 3245 POSITIVE OUTCOME 15843459 0 search_space EMPTY 0 false 0 sequence GGTCTTGTTTAGACTTGCTC 0 false 0 search_space EMPTY 0 false Homo sapiens OREG0002197 7157 TP53 NCBI REGULATORY POLYMORPHISM 28-Jun-2006 0 reference_sequence aggtacctatgcagtgaacatggtggtgatgggaggggctgaggggaataggtcttgtttagacttGctcaatgtgcaactgaaacaagcctactggttgtcagacatgcagggggatca 0 false rs2232945 dbSNP NOT SPECIFIED 0 variant_sequence aggtacctatgcagtgaacatggtggtgatgggaggggctgaggggaataggtcttgtttagacttActcaatgtgcaactgaaacaagcctactggttgtcagacatgcagggggatca 0 false From Results: "Although it is possible that the candidate REs are not specifically responsible for the observed expression changes, the transfection assays establish that the sites are strongly functional. Given the functional spacing of the REs relative to the genes (as compared with established p53 targets), their demonstrated activity, and the p53 responsiveness of the candidate genes, it is likely that the candidate polymorphic REs are involved directly in p53 transactivation." 28-Jun-2006 obig Note: the SNP ID provided in the paper (rs14716) does not seem to be correct or has been replaced by rs268682. The SNP for rs268682 is located upstream of the correct gene, with the correct flanking sequence, and correct variant sequences. 28-Jun-2006 obig 28-Jun-2006 Cell type: Human RKO colon carcinoma cell line. Observed strong differences in p53 induced expression between p53 response element SNPs (strong/weak: G/C) (see figure 1). 28-Jun-2006 OREGEC00001 OREGES00026 OREGET00002 obig Cell type: Human RKO colon carcinoma cell line. The authors state (in results): "Of the genes examined, six exhibited increased expression after p53 induction in at least one cell type." However, it is difficult to determine how many or which of the cell lines (SaOS-2 osteosarcoma, RKO colon carcinoma, HT1080 fibrosarcoma and lymphoblastoid cells) showed a significant difference for any particular gene. I have reported as evidence only those that appeared significant by comparing the error bars (see figure 2). 28-Jun-2006 OREGEC00002 OREGES00007 OREGET00004 obig Cell type: Human GM15223 (PDR004) lymphoblastoid cells. The authors state (in results): "Of the genes examined, six exhibited increased expression after p53 induction in at least one cell type." However, it is difficult to determine how many or which of the cell lines (SaOS-2 osteosarcoma, RKO colon carcinoma, HT1080 fibrosarcoma and lymphoblastoid cells) showed a significant difference for any particular gene. I have reported as evidence only those that appeared significant by comparing the error bars (see figure 2). 28-Jun-2006 OREGEC00002 OREGES00007 OREGET00004 obig Cell type: Human HT1080 fibrosarcoma. The authors state (in results): "Of the genes examined, six exhibited increased expression after p53 induction in at least one cell type." However, it is difficult to determine how many or which of the cell lines (SaOS-2 osteosarcoma, RKO colon carcinoma, HT1080 fibrosarcoma and lymphoblastoid cells) showed a significant difference for any particular gene. I have reported as evidence only those that appeared significant by comparing the error bars (see figure 2). 28-Jun-2006 OREGEC00002 OREGES00007 OREGET00004 obig Cell type: Human SaOS-2 osteosarcoma cell line. The authors state (in results): "Of the genes examined, six exhibited increased expression after p53 induction in at least one cell type." However, it is difficult to determine how many or which of the cell lines (SaOS-2 osteosarcoma, RKO colon carcinoma, HT1080 fibrosarcoma and lymphoblastoid cells) showed a significant difference for any particular gene. I have reported as evidence only those that appeared significant by comparing the error bars (see figure 2). 28-Jun-2006 OREGEC00002 OREGES00007 OREGET00004 obig 29950 SERTAD1 NCBI 3247 POSITIVE OUTCOME 15843459 0 search_space EMPTY 0 false 0 sequence GGGCTTCAGGGCGCATGCCC 0 false 0 search_space EMPTY 0 false Homo sapiens OREG0002199 7157 TP53 NCBI REGULATORY POLYMORPHISM 28-Jun-2006 0 reference_sequence ggccctgcatggtgatgggcggagcttgtagggggcggattctgaaggaggggcttCagggcgcatgcccgggcagctgcgcgagtgaggggtggaaagaggtggctttttactccgggg 0 false rs268682 dbSNP GERMLINE 0 variant_sequence ggccctgcatggtgatgggcggagcttgtagggggcggattctgaaggaggggcttGagggcgcatgcccgggcagctgcgcgagtgaggggtggaaagaggtggctttttactccgggg 0 false From Results: "Although it is possible that the candidate REs are not specifically responsible for the observed expression changes, the transfection assays establish that the sites are strongly functional. Given the functional spacing of the REs relative to the genes (as compared with established p53 targets), their demonstrated activity, and the p53 responsiveness of the candidate genes, it is likely that the candidate polymorphic REs are involved directly in p53 transactivation." TLR8 mRNA was not detectable in any cell type tested by Rt-PCR after p53 induction. Therefore the evidence for P53 as its TF is less convincing. However, there was evidence for induction by P53 by luciferase assay and there does appear to be differential expression depending on which SNP variant is present. 28-Jun-2006 obig 28-Jun-2006 Cell type: Yeast. Observed strong differences in p53 induced expression between p53 response element SNPs (strong/weak: G/A) (see figure 1). 28-Jun-2006 OREGEC00001 OREGES00026 OREGET00002 obig Cell type: Human SaOS-2 osteosarcoma cell line. Observed strong differences in p53 induced expression between p53 response element SNPs (strong/weak: G/A) (see figure 1). 28-Jun-2006 OREGEC00001 OREGES00026 OREGET00002 obig Cell type: Human RKO colon carcinoma cell line. Observed strong differences in p53 induced expression between p53 response element SNPs (strong/weak: G/A) (see figure 1). 28-Jun-2006 OREGEC00001 OREGES00026 OREGET00002 obig 51311 TLR8 NCBI 3248 POSITIVE OUTCOME 15843459 0 search_space EMPTY 0 false 0 sequence AGGCAAGATGAAACATATCA 0 false 0 search_space EMPTY 0 false Homo sapiens OREG0002200 7157 TP53 NCBI REGULATORY POLYMORPHISM 28-Jun-2006 0 reference_sequence tctctgcccaccctgctgccaatttggttttctcccactcctggggtgtaaggcaagatgaaacatAtcacatcccgttctaaactttattcttgtggccaggggtcagcaaactttttc 0 false rs3761624 dbSNP GERMLINE 0 variant_sequence tctctgcccaccctgctgccaatttggttttctcccactcctggggtgtaaggcaagatgaaacatGtcacatcccgttctaaactttattcttgtggccaggggtcagcaaactttttc 0 false From Results: "Although it is possible that the candidate REs are not specifically responsible for the observed expression changes, the transfection assays establish that the sites are strongly functional. Given the functional spacing of the REs relative to the genes (as compared with established p53 targets), their demonstrated activity, and the p53 responsiveness of the candidate genes, it is likely that the candidate polymorphic REs are involved directly in p53 transactivation." 28-Jun-2006 obig 28-Jun-2006 Cell type: Yeast. Observed strong differences in p53 induced expression between p53 response element SNPs (strong/weak: G/A) (see figure 1). 28-Jun-2006 OREGEC00001 OREGES00026 OREGET00002 obig Cell type: Human SaOS-2 osteosarcoma cell line. Observed strong differences in p53 induced expression between p53 response element SNPs (strong/weak: G/A) (see figure 1). 28-Jun-2006 OREGEC00001 OREGES00026 OREGET00002 obig Cell type: Human RKO colon carcinoma cell line. Observed strong differences in p53 induced expression between p53 response element SNPs (strong/weak: G/A) (see figure 1). 28-Jun-2006 OREGEC00001 OREGES00026 OREGET00002 obig Cell type: Human RKO colon carcinoma cell line. The authors state (in results): "Of the genes examined, six exhibited increased expression after p53 induction in at least one cell type." However, it is difficult to determine how many or which of the cell lines (SaOS-2 osteosarcoma, RKO colon carcinoma, HT1080 fibrosarcoma and lymphoblastoid cells) showed a significant difference for any particular gene. I have reported as evidence only those that appeared significant by comparing the error bars (see figure 2). 28-Jun-2006 OREGEC00002 OREGES00007 OREGET00004 obig Cell type: Human HT1080 fibrosarcoma. The authors state (in results): "Of the genes examined, six exhibited increased expression after p53 induction in at least one cell type." However, it is difficult to determine how many or which of the cell lines (SaOS-2 osteosarcoma, RKO colon carcinoma, HT1080 fibrosarcoma and lymphoblastoid cells) showed a significant difference for any particular gene. I have reported as evidence only those that appeared significant by comparing the error bars (see figure 2). 28-Jun-2006 OREGEC00002 OREGES00007 OREGET00004 obig Cell type: Human SaOS-2 osteosarcoma cell line. The authors state (in results): "Of the genes examined, six exhibited increased expression after p53 induction in at least one cell type." However, it is difficult to determine how many or which of the cell lines (SaOS-2 osteosarcoma, RKO colon carcinoma, HT1080 fibrosarcoma and lymphoblastoid cells) showed a significant difference for any particular gene. I have reported as evidence only those that appeared significant by comparing the error bars (see figure 2). 28-Jun-2006 OREGEC00002 OREGES00007 OREGET00004 obig 104 ADARB1 NCBI 3249 POSITIVE OUTCOME 15843459 0 search_space EMPTY 0 false 0 sequence GGACAAGTTGAAACTTGCAC 0 false 0 sequence_with_flank gtcccggccttgggcgccatccgctctctgctgctctggagggagaaaaaGGACAAGTTGAAACTTGCACaagcagcctccattctggggagttcccttgtattccccacaccaacccgc 0 false Homo sapiens OREG0002201 7157 TP53 NCBI TRANSCRIPTION FACTOR BINDING SITE From Results: "Although it is possible that the candidate REs are not specifically responsible for the observed expression changes, the transfection assays establish that the sites are strongly functional. Given the functional spacing of the REs relative to the genes (as compared with established p53 targets), their demonstrated activity, and the p53 responsiveness of the candidate genes, it is likely that the candidate polymorphic REs are involved directly in p53 transactivation." 28-Jun-2006 obig 28-Jun-2006 Cell type: Human SaOS-2 osteosarcoma cell line. Observed strong differences in p53 induced expression between p53 response element SNPs (strong/weak: G/T) (see figure 1). 28-Jun-2006 OREGEC00001 OREGES00026 OREGET00002 obig Cell type: Human RKO colon carcinoma cell line. Observed strong differences in p53 induced expression between p53 response element SNPs (strong/weak: G/T) (see figure 1). 28-Jun-2006 OREGEC00001 OREGES00026 OREGET00002 obig Cell type: Human HT1080 fibrosarcoma. The authors state (in results): "Of the genes examined, six exhibited increased expression after p53 induction in at least one cell type." However, it is difficult to determine how many or which of the cell lines (SaOS-2 osteosarcoma, RKO colon carcinoma, HT1080 fibrosarcoma and lymphoblastoid cells) showed a significant difference for any particular gene. I have reported as evidence only those that appeared significant by comparing the error bars (see figure 2). 28-Jun-2006 OREGEC00002 OREGES00007 OREGET00004 obig Cell type: Human SaOS-2 osteosarcoma cell line. The authors state (in results): "Of the genes examined, six exhibited increased expression after p53 induction in at least one cell type." However, it is difficult to determine how many or which of the cell lines (SaOS-2 osteosarcoma, RKO colon carcinoma, HT1080 fibrosarcoma and lymphoblastoid cells) showed a significant difference for any particular gene. I have reported as evidence only those that appeared significant by comparing the error bars (see figure 2). 28-Jun-2006 OREGEC00002 OREGES00007 OREGET00004 obig 8874 ARHGEF7 NCBI 3250 POSITIVE OUTCOME 15843459 0 search_space EMPTY 0 false 0 sequence AAACATGTCAGCACTTGCTT 0 false 0 sequence_with_flank aagcagctttgcttttgccattccactgaaaaaatgtacagtttcgatggAAACATGTCAGCACTTGCTTgaaggaatttttcaactatagaaagaaaaaagcttcatttcatccctttt 0 false Homo sapiens OREG0002202 7157 TP53 NCBI TRANSCRIPTION FACTOR BINDING SITE From Results: "Although it is possible that the candidate REs are not specifically responsible for the observed expression changes, the transfection assays establish that the sites are strongly functional. Given the functional spacing of the REs relative to the genes (as compared with established p53 targets), their demonstrated activity, and the p53 responsiveness of the candidate genes, it is likely that the candidate polymorphic REs are involved directly in p53 transactivation." 28-Jun-2006 obig 28-Jun-2006 Cell type: Yeast. Observed strong differences in p53 induced expression between p53 response element SNPs (strong/weak: G/C) (see figure 1). 28-Jun-2006 OREGEC00001 OREGES00026 OREGET00002 obig Cell type: Human SaOS-2 osteosarcoma cell line. Observed strong differences in p53 induced expression between p53 response element SNPs (strong/weak: G/C) (see figure 1). 28-Jun-2006 OREGEC00001 OREGES00026 OREGET00002 obig Cell type: Human RKO colon carcinoma cell line. The authors state (in results): "Of the genes examined, six exhibited increased expression after p53 induction in at least one cell type." However, it is difficult to determine how many or which of the cell lines (SaOS-2 osteosarcoma, RKO colon carcinoma, HT1080 fibrosarcoma and lymphoblastoid cells) showed a significant difference for any particular gene. I have reported as evidence only those that appeared significant by comparing the error bars (see figure 2). 28-Jun-2006 OREGEC00002 OREGES00007 OREGET00004 obig Cell type: Human SaOS-2 osteosarcoma cell line. The authors state (in results): "Of the genes examined, six exhibited increased expression after p53 induction in at least one cell type." However, it is difficult to determine how many or which of the cell lines (SaOS-2 osteosarcoma, RKO colon carcinoma, HT1080 fibrosarcoma and lymphoblastoid cells) showed a significant difference for any particular gene. I have reported as evidence only those that appeared significant by comparing the error bars (see figure 2). 28-Jun-2006 OREGEC00002 OREGES00007 OREGET00004 obig 1630 DCC NCBI 3251 POSITIVE OUTCOME 15843459 0 search_space EMPTY 0 false 0 sequence CAGCATGTTCACACAAGCCA 0 false 0 sequence_with_flank aactcaccttatacatttactgaaagctaaagattcccttcccagttaaaCAGCATGTTCACACAAGCCAatcacttttcataaaatttcaggatattcacaaacttcctgaattttgtt 0 false Homo sapiens OREG0002203 7157 TP53 NCBI TRANSCRIPTION FACTOR BINDING SITE From Results: "Although it is possible that the candidate REs are not specifically responsible for the observed expression changes, the transfection assays establish that the sites are strongly functional. Given the functional spacing of the REs relative to the genes (as compared with established p53 targets), their demonstrated activity, and the p53 responsiveness of the candidate genes, it is likely that the candidate polymorphic REs are involved directly in p53 transactivation." 28-Jun-2006 obig 28-Jun-2006 Cell type: Yeast. Observed strong differences in p53 induced expression between p53 response element SNPs (strong/weak: T/C) (see figure 1). 28-Jun-2006 OREGEC00001 OREGES00026 OREGET00002 obig Cell type: Human RKO colon carcinoma cell line. The authors state (in results): "Of the genes examined, six exhibited increased expression after p53 induction in at least one cell type." However, it is difficult to determine how many or which of the cell lines (SaOS-2 osteosarcoma, RKO colon carcinoma, HT1080 fibrosarcoma and lymphoblastoid cells) showed a significant difference for any particular gene. I have reported as evidence only those that appeared significant by comparing the error bars (see figure 2). 28-Jun-2006 OREGEC00002 OREGES00007 OREGET00004 obig Cell type: Human GM15223 (PDR004) lymphoblastoid cells. The authors state (in results): "Of the genes examined, six exhibited increased expression after p53 induction in at least one cell type." However, it is difficult to determine how many or which of the cell lines (SaOS-2 osteosarcoma, RKO colon carcinoma, HT1080 fibrosarcoma and lymphoblastoid cells) showed a significant difference for any particular gene. I have reported as evidence only those that appeared significant by comparing the error bars (see figure 2). 28-Jun-2006 OREGEC00002 OREGES00007 OREGET00004 obig Cell type: Human SaOS-2 osteosarcoma cell line. The authors state (in results): "Of the genes examined, six exhibited increased expression after p53 induction in at least one cell type." However, it is difficult to determine how many or which of the cell lines (SaOS-2 osteosarcoma, RKO colon carcinoma, HT1080 fibrosarcoma and lymphoblastoid cells) showed a significant difference for any particular gene. I have reported as evidence only those that appeared significant by comparing the error bars (see figure 2). 28-Jun-2006 OREGEC00002 OREGES00007 OREGET00004 obig 8320 EOMES NCBI 3252 POSITIVE OUTCOME 15843459 0 search_space EMPTY 0 false 0 sequence GGGCCTGTCTCCAACTTGCCC 0 false 0 sequence_with_flank agttacagcttccgacgaggaaagagacttccttGGGCCTGTCTCCAACTTGCCCcagtttccccagcctccgggacgggcgcttccctgcaagctatcag 0 false Homo sapiens OREG0002204 7157 TP53 NCBI TRANSCRIPTION FACTOR BINDING SITE From Results: "Although it is possible that the candidate REs are not specifically responsible for the observed expression changes, the transfection assays establish that the sites are strongly functional. Given the functional spacing of the REs relative to the genes (as compared with established p53 targets), their demonstrated activity, and the p53 responsiveness of the candidate genes, it is likely that the candidate polymorphic REs are involved directly in p53 transactivation." RRM1 was not induced by p53 in any cell type tested by Rt-PCR. Therefore the evidence for P53 as its TF is less convincing. However, there was evidence for induction by P53 by luciferase and there does appear to be differential expression depending on which SNP variant is present (more convincing in Yeast than the cell line). 28-Jun-2006 obig 28-Jun-2006 Cell type: Yeast. Observed strong differences in p53 induced expression between p53 response element SNPs (strong/weak: C/T) (see figure 1). 28-Jun-2006 OREGEC00001 OREGES00026 OREGET00002 obig Cell type: Human SaOS-2 osteosarcoma cell line. Observed strong differences in p53 induced expression between p53 response element SNPs (strong/weak: C/T) (see figure 1). 28-Jun-2006 OREGEC00001 OREGES00026 OREGET00002 obig 6240 RRM1 NCBI 3253 POSITIVE OUTCOME 15843459 0 search_space EMPTY 0 false 0 sequence GGGCATGTGCATTCAAGTTT 0 false 0 sequence_with_flank tttaactggtcatcctgcatttatctggtaaccctgcccacagagcttctGGGCATGTGCATTCAAGTTTcattttccctgggcaaaggaaagattgtct 0 false Homo sapiens OREG0002205 7157 TP53 NCBI TRANSCRIPTION FACTOR BINDING SITE From Results: "Although it is possible that the candidate REs are not specifically responsible for the observed expression changes, the transfection assays establish that the sites are strongly functional. Given the functional spacing of the REs relative to the genes (as compared with established p53 targets), their demonstrated activity, and the p53 responsiveness of the candidate genes, it is likely that the candidate polymorphic REs are involved directly in p53 transactivation." 28-Jun-2006 obig 28-Jun-2006 Cell type: Yeast. Observed strong differences in p53 induced expression between p53 response element SNPs (strong/weak: G/A) (see figure 1). 28-Jun-2006 OREGEC00001 OREGES00026 OREGET00002 obig Cell type: Human SaOS-2 osteosarcoma cell line. Observed strong differences in p53 induced expression between p53 response element SNPs (strong/weak: G/A) (see figure 1). 28-Jun-2006 OREGEC00001 OREGES00026 OREGET00002 obig Cell type: Human RKO colon carcinoma cell line. Observed strong differences in p53 induced expression between p53 response element SNPs (strong/weak: G/A) (see figure 1). 28-Jun-2006 OREGEC00001 OREGES00026 OREGET00002 obig Cell type: Human RKO colon carcinoma cell line. The authors state (in results): "Of the genes examined, six exhibited increased expression after p53 induction in at least one cell type." However, it is difficult to determine how many or which of the cell lines (SaOS-2 osteosarcoma, RKO colon carcinoma, HT1080 fibrosarcoma and lymphoblastoid cells) showed a significant difference for any particular gene. I have reported as evidence only those that appeared significant by comparing the error bars (see figure 2). 28-Jun-2006 OREGEC00002 OREGES00007 OREGET00004 obig Cell type: Human GM15223 (PDR004) lymphoblastoid cells. The authors state (in results): "Of the genes examined, six exhibited increased expression after p53 induction in at least one cell type." However, it is difficult to determine how many or which of the cell lines (SaOS-2 osteosarcoma, RKO colon carcinoma, HT1080 fibrosarcoma and lymphoblastoid cells) showed a significant difference for any particular gene. I have reported as evidence only those that appeared significant by comparing the error bars (see figure 2). 28-Jun-2006 OREGEC00002 OREGES00007 OREGET00004 obig Cell type: Human HT1080 fibrosarcoma. The authors state (in results): "Of the genes examined, six exhibited increased expression after p53 induction in at least one cell type." However, it is difficult to determine how many or which of the cell lines (SaOS-2 osteosarcoma, RKO colon carcinoma, HT1080 fibrosarcoma and lymphoblastoid cells) showed a significant difference for any particular gene. I have reported as evidence only those that appeared significant by comparing the error bars (see figure 2). 28-Jun-2006 OREGEC00002 OREGES00007 OREGET00004 obig 10647 SCGB1D2 NCBI 3254 POSITIVE OUTCOME 15843459 0 search_space EMPTY 0 false 0 sequence GGTCTTGTTTAGACTTGCTC 0 false 0 sequence_with_flank aggtacctatgcagtgaacatggtggtgatgggaggggctgaggggaataGGTCTTGTTTAGACTTGCTCaatgtgcaactgaaacaagcctactggttgtcagacatgcagggggatca 0 false Homo sapiens OREG0002206 7157 TP53 NCBI TRANSCRIPTION FACTOR BINDING SITE From Results: "Although it is possible that the candidate REs are not specifically responsible for the observed expression changes, the transfection assays establish that the sites are strongly functional. Given the functional spacing of the REs relative to the genes (as compared with established p53 targets), their demonstrated activity, and the p53 responsiveness of the candidate genes, it is likely that the candidate polymorphic REs are involved directly in p53 transactivation." 28-Jun-2006 obig 28-Jun-2006 Cell type: Human RKO colon carcinoma cell line. Observed strong differences in p53 induced expression between p53 response element SNPs (strong/weak: G/C) (see figure 1). 28-Jun-2006 OREGEC00001 OREGES00026 OREGET00002 obig Cell type: Human RKO colon carcinoma cell line. The authors state (in results): "Of the genes examined, six exhibited increased expression after p53 induction in at least one cell type." However, it is difficult to determine how many or which of the cell lines (SaOS-2 osteosarcoma, RKO colon carcinoma, HT1080 fibrosarcoma and lymphoblastoid cells) showed a significant difference for any particular gene. I have reported as evidence only those that appeared significant by comparing the error bars (see figure 2). 28-Jun-2006 OREGEC00002 OREGES00007 OREGET00004 obig Cell type: Human GM15223 (PDR004) lymphoblastoid cells. The authors state (in results): "Of the genes examined, six exhibited increased expression after p53 induction in at least one cell type." However, it is difficult to determine how many or which of the cell lines (SaOS-2 osteosarcoma, RKO colon carcinoma, HT1080 fibrosarcoma and lymphoblastoid cells) showed a significant difference for any particular gene. I have reported as evidence only those that appeared significant by comparing the error bars (see figure 2). 28-Jun-2006 OREGEC00002 OREGES00007 OREGET00004 obig Cell type: Human HT1080 fibrosarcoma. The authors state (in results): "Of the genes examined, six exhibited increased expression after p53 induction in at least one cell type." However, it is difficult to determine how many or which of the cell lines (SaOS-2 osteosarcoma, RKO colon carcinoma, HT1080 fibrosarcoma and lymphoblastoid cells) showed a significant difference for any particular gene. I have reported as evidence only those that appeared significant by comparing the error bars (see figure 2). 28-Jun-2006 OREGEC00002 OREGES00007 OREGET00004 obig Cell type: Human SaOS-2 osteosarcoma cell line. The authors state (in results): "Of the genes examined, six exhibited increased expression after p53 induction in at least one cell type." However, it is difficult to determine how many or which of the cell lines (SaOS-2 osteosarcoma, RKO colon carcinoma, HT1080 fibrosarcoma and lymphoblastoid cells) showed a significant difference for any particular gene. I have reported as evidence only those that appeared significant by comparing the error bars (see figure 2). 28-Jun-2006 OREGEC00002 OREGES00007 OREGET00004 obig 29950 SERTAD1 NCBI 3255 POSITIVE OUTCOME 15843459 0 search_space EMPTY 0 false 0 sequence GGGCTTCAGGGCGCATGCCC 0 false 0 sequence_with_flank ggccctgcatggtgatgggcggagcttgtagggggcggattctgaaggagGGGCTTCAGGGCGCATGCCCgggcagctgcgcgagtgaggggtggaaagaggtggctttttactccgggg 0 false Homo sapiens OREG0002207 7157 TP53 NCBI TRANSCRIPTION FACTOR BINDING SITE From Results: "Although it is possible that the candidate REs are not specifically responsible for the observed expression changes, the transfection assays establish that the sites are strongly functional. Given the functional spacing of the REs relative to the genes (as compared with established p53 targets), their demonstrated activity, and the p53 responsiveness of the candidate genes, it is likely that the candidate polymorphic REs are involved directly in p53 transactivation." TLR8 mRNA was not detectable in any cell type tested by Rt-PCR after p53 induction. Therefore the evidence for P53 as its TF is less convincing. However, there was evidence for induction by P53 by luciferase assay and there does appear to be differential expression depending on which SNP variant is present. 28-Jun-2006 obig 28-Jun-2006 Cell type: Yeast. Observed strong differences in p53 induced expression between p53 response element SNPs (strong/weak: G/A) (see figure 1). 28-Jun-2006 OREGEC00001 OREGES00026 OREGET00002 obig Cell type: Human SaOS-2 osteosarcoma cell line. Observed strong differences in p53 induced expression between p53 response element SNPs (strong/weak: G/A) (see figure 1). 28-Jun-2006 OREGEC00001 OREGES00026 OREGET00002 obig Cell type: Human RKO colon carcinoma cell line. Observed strong differences in p53 induced expression between p53 response element SNPs (strong/weak: G/A) (see figure 1). 28-Jun-2006 OREGEC00001 OREGES00026 OREGET00002 obig 51311 TLR8 NCBI 3256 POSITIVE OUTCOME 15843459 0 search_space EMPTY 0 false 0 sequence AGGCAAGATGAAACATATCA 0 false 0 sequence_with_flank tctctgcccaccctgctgccaatttggttttctcccactcctggggtgtaAGGCAAGATGAAACATATCAcatcccgttctaaactttattcttgtggccaggggtcagcaaactttttc 0 false Homo sapiens OREG0002208 7157 TP53 NCBI TRANSCRIPTION FACTOR BINDING SITE From the abstract: "We identified a C-to-T SNP upstream of the transcriptional start site in {approx}6% of the people examined. The SNP is located within a putative p53 response element. Only the promoter with the T SNP (FLT1-T) was responsive to p53 when examined with reporter assays or by endogenous gene expression analysis in cell lines with different SNP status. In response to doxorubicin-induced DNA damage, there was clear allele discrimination based on p53 binding at the FLT1-T but not FLT1-C promoters as well as p53-dependent induction of flt-1 mRNA, which required the presence of FLT1-T. Our results establish that p53 can differentially stimulate transcription at a polymorphic variant of the flt-1 promoter and directly places the VEGF system in the p53 stress-response network via flt-1 in a significant fraction of the human population. We suggest that the p53-VEGF-flt-1 interaction is relevant to risks in angiogenesis-associated diseases, including cancer." 6-Jul-2006 obig 6-Jul-2006 From the results: "To assess the potential of the FLT1-T promoter variant to respond to p53-induced transactivation in human cells, the 1,196-bp promoter region of flt-1 described above containing either the FLT1-T or FLT1-C SNP was cloned into a pGL3 basic luciferase reporter plasmid (Fig. 2A). The constructs were transfected first into two different p53+/+ cell lines (HMEC and MCF7), both known to express endogenous flt-1. There was an at least 8-fold difference in transcriptional activity of the FLT1-T promoter when compared with FLT1-C (Fig. 2B)." 6-Jul-2006 OREGEC00001 OREGES00026 OREGET00002 obig From the results: "To further examine the impact of p53 expression on transactivation from the flt-1 promoter, MCF-7 cells were transfected with the FLT1-C or FLT1-T reporter constructs along with expression plasmids encoding either wtp53 or a truncation mutant (Q331stop, as shown in Fig. 2C). The addition of the wtp53 plasmid increased expression from the FLT1-T plasmid an additional 4-fold, whereas the truncated p53 had little if any effect. There was only minimal luciferase activity associated with the FLT1-C allele even when wtp53 was overexpressed." 6-Jul-2006 OREGEC00002 OREGES00026 OREGET00002 obig From the results: "We used a SaOS2 p53-null cell line to investigate more directly a role for p53 in transactivation of the FLT1-T promoter variant (Fig. 3). Cells were transfected with the FLT1-C and FLT1-T reporter plasmids along with the p53-expressing plasmid. In the absence of p53 (Fig. 3A) there was no induction of transcription from either the FLT1-C or FLT1-T plasmids (Fig. 3B). In contrast, cotransfection with a wtp53 expression plasmid led to an increase in transcriptional activity from the FLT1-T, but not the FLT1-C promoter (Fig. 3B). The efficiency of p53 transactivation from the FLT1-T promoter was {approx}25% of that from a reporter containing the strong p21-5'-p53 RE. (A direct comparison may not be possible because the p21 RE was not inserted in the context of the flt-1 promoter region.)" 6-Jul-2006 OREGEC00001 OREGES00026 OREGET00002 obig From the results: "The difference in p53-mediated transactivation from the flt-1 promoter alleles could be due to differences in binding. Therefore, lysates from SaOS2 cells that had been cotransfected with the reporter plasmids carrying the FLT1-C or -T alleles along with the wtp53 expression vector were subjected to chromatin immunoprecipitation (ChIP) with p53 antibody. As shown in Fig. 3C, the DNA from cells transfected with the FLT1-T promoter p53 RE exhibited p53 occupancy, whereas cells containing the FLT1-C promoter had little, if any, p53-specific binding." 6-Jul-2006 OREGEC00002 OREGES00005 OREGET00003 obig "Cells were exposed to the topoisomerase inhibitor doxorubicin (0.3 µg/ml for 24 h), a well established inducer of p53, as exemplified in Fig. 4A, and the consequences on induction of the endogenous flt-1 alleles were assessed. As shown in Fig. 4B, doxorubicin results in a 7-fold increase in flt-1 mRNA in the p53+/+ cells. This increase contrasts with the lack of flt-1 induction in the p53-null cell line." 6-Jul-2006 OREGEC00002 OREGES00007 OREGET00004 obig 2321 FLT1 NCBI 3295 POSITIVE OUTCOME 16432214 0 search_space EMPTY 0 false 0 sequence GGACACGCTCCCCTGGGACCTGAGC 0 false 0 search_space EMPTY 0 false Homo sapiens OREG0002251 7157 TP53 NCBI REGULATORY POLYMORPHISM 6-Jul-2006 0 reference_sequence aggaaatgacttgggcgggtgcatcaatgcggccgaaaaagacacggacaCgctcccctgggacctgagctggttcgcagtcttcccaaaggtgccaagca 0 false GERMLINE 0 variant_sequence aggaaatgacttgggcgggtgcatcaatgcggccgaaaaagacacggacaTgctcccctgggacctgagctggttcgcagtcttcccaaaggtgccaagca 0 false From abstract: "A single-nucleotide polymorphism (SNP), identified at nucleotide position -844 in the 5' promoter of the FasL gene, lies within a putative binding motif for CAAT/enhancer-binding protein {beta}. Electrophoretic mobility shift and supershift assays confirmed that this element binds specifically to C/EBP{beta} and demonstrated that the two alleles of this element have different affinities for C/EBP{beta}. In luciferase reporter assays, the -844C genotype had twice the basal activity of the -844T construct, and basal expression of Fas ligand (FasL) on peripheral blood fibrocytes was also significantly higher in -844C than in -844T homozygous donors. FasL is located on human chromosome 1q23, a region that shows linkage to the systemic lupus autoimmune phenotype. Analysis of 211 African American systemic lupus erythematosus patients revealed enrichment of the -844C homozygous genotype in these systemic lupus erythematosus patients compared with 150 ethnically matched normal controls (p = 0.024). The -844C homozygous genotype may lead to the increased expression of FasL, to altered FasL-mediated signaling in lymphocytes, and to enhanced risk for autoimmunity." 19-Jul-2006 obig 19-Jul-2006 labeled probe with the -844T allele (lane 6) bound but appeared to have much lower affinity for the transcription factor C/EBP{beta} than that of the -844C allele. 19-Jul-2006 OREGEC00001 OREGES00003 OREGET00001 obig 19-Jul-2006 OREGEC00001 OREGES00004 OREGET00002 obig 19-Jul-2006 OREGEC00001 OREGES00024 OREGET00005 obig 19-Jul-2006 OREGEC00001 OREGES00010 OREGET00006 obig 356 FASLG NCBI 3312 POSITIVE OUTCOME 12496392 0 search_space EMPTY 0 false 0 sequence ATTGCGAAAT 0 false 0 search_space EMPTY 0 false Homo sapiens OREG0002257 1051 CEBPB NCBI REGULATORY POLYMORPHISM 19-Jul-2006 0 reference_sequence ataaataagtaaataaataaactgggcaaacaatgaaaatgaaaacattgCgaaatacaaagcagctctgtgggttccactggtttgcagcctctgatcta 0 false rs763110 dbSNP GERMLINE 0 variant_sequence ataaataagtaaataaataaactgggcaaacaatgaaaatgaaaacattgTgaaatacaaagcagctctgtgggttccactggtttgcagcctctgatcta 0 false This binding site was also shown to have a functional rSNP which could be viewed as further evidence that the binding site is real (see: OREG0002257) 19-Jul-2006 obig 19-Jul-2006 Radiolabeled oligonucleotide probe containing the putative -848 to -839 C/EBP{beta} motif binds nuclear extract from activated Jurkat cells (Fig. 3, lane 2) and is inhibited both by the consensus CCAAT enhancer-binding oligonucleotide (lane 1) and by cold oligonucleotide containing the putative C/EBP{beta} motif (lane 3). 19-Jul-2006 OREGEC00001 OREGES00003 OREGET00001 obig Anti-C/EBP{beta} Ab can supershift the labeled probe/nuclear extract complexes (lane 4), providing further evidence that C/EBP{beta} is indeed the transcription factor that binds the region containing position -844. 19-Jul-2006 OREGEC00002 OREGES00002 OREGET00001 obig 356 FASLG NCBI 3313 POSITIVE OUTCOME 12496392 0 search_space EMPTY 0 false 0 sequence ATTGCGAAAT 0 false 0 sequence_with_flank ataaataagtaaataaataaactgggcaaacaatgaaaatgaaaacATTGCGAAATacaaagcagctctgtgggttccactggtttgcagcctctgatcta 0 false Homo sapiens OREG0002258 1051 CEBPB NCBI TRANSCRIPTION FACTOR BINDING SITE The authors have shown that members of the ATF/CREB family of transcription factors and c-Jun play important roles in mediating the transcriptional regulation of the SP-B gene via an SP-B CRE site in the proximal promoter. 20-Jul-2006 obig Record does not map due to the fact that a complete rabbit genome does not exist at this time. 23-Apr-2007 bcb 20-Jul-2006 Three bp overlapping mutations were introduced by PCR and their effect on SP-B promoter activity was investigated in NCI-H441 (ATCC HTB-174), a human pulmonary adenocarcinoma cell line. Results showed that mutations within the SP-B CRE element caused 40–70% decrease in SP-B promoter activity with the exception of one wherein substitution of TTG for GGT did not decrease promoter activity (Fig. 2). Mutation of each nucleotide within the SP-B CRE resulted in a decrease of SP-B promoter activity by 70%, whereas mutation to create a palindromic consensus CRE resulted in an increase of promoter activity by 100% (Fig. 2). 20-Jul-2006 OREGEC00001 OREGES00019 OREGET00002 obig EMSA of SP-B CRE in the presence of H441 nuclear proteins resulted in the formation of three major complexes designated I, II and III (Fig. 3A). Results showed (Fig. 3A) that formation of all the three complexes was reduced in the presence of excess SP-B CRE oligonucleotide but not mutant SP-B CRE oligonucleotide (M7) demonstrating the specificity of complex formation. In the presence of excess consensus CRE, the formation of complexes I and II but not that of complex III was completely abolished, whereas in the presence of excess mutant CRE the formation of complexes I and II was slightly reduced and that of complex III was abolished (Fig. 3A). Similar results were obtained when AP-1 consensus and mutant oligonucleotides were used as competitors in EMSA (data not shown). Reduced formation of complex III in the presence of excess mutant CRE oligonucleotide is most likely due to the presence of the sequence TGGTCA that matches the five nucleotides at the 3' end of the SP-B CRE sequence. Results showed that whereas wild type oligonucleotides and oligonucleotides containing mutations outside the AGGTCA sequence competed the formation of complex III, oligonucleotides containing mutations within the AGGTCA competed poorly (Fig. 3B). These data suggested that formation of complex III is likely the result of proteins binding to the AGGTCA sequence which is identical to the nuclear hormone receptor element binding half-site. 20-Jul-2006 OREGEC00001 OREGES00003 OREGET00001 obig Results showed that antibodies against CREB, CREB/CREM/ATF-1 and ATF-2 produced supershifted bands concomitantly reducing the levels of complexes I-III (Fig. 4A). An exception was in the case of antibodies against CREB which in addition to producing supershifted complexes, increased the levels of complexes I-III. These results indicated that proteins recognized by CREB, CREM, ATF-1 and ATF-2 antibodies are components of the DNA-protein complexes. Antibodies to c-Jun inhibited the formation of the DNA-protein complex indicating that c-Jun is also a component of the complexes (Fig. 4A). On the other hand antibodies to c-Fos and thyroid receptor did not have any effect on the complex formation (data not shown) indicating that they are not components of the DNA-protein complex. 20-Jul-2006 OREGEC00002 OREGES00002 OREGET00001 obig SP-B SP-B USER DEFINED 3320 POSITIVE OUTCOME 11368910 0 search_space EMPTY 0 false 0 sequence TGAGGTCA 0 false 0 sequence_with_flank aggggctggttcaaaacacctggagggctctccaggacaaaggcaaacacTGAGGTCAccactgcccccacagagccctgttccatgctcccgcccccagctataaga 0 false Oryctolagus cuniculus OREG0002267 multiple ATF/CREB family multiple ATF/CREB family USER DEFINED TRANSCRIPTION FACTOR BINDING SITE A 20-bp inhibitory element located between -362 and -343 in the upstream of NKX3.1 gene was identified by deletion and substitution mutation analysis and proven to be a functional inhibitory cis-element by EMSA and is likely to play an important role in downregulating NKX3.1 gene transcription. 24-Jul-2006 obig 24-Jul-2006 The results in Figure 2A showed that a 30 bp deletion from -367 to -338 enhanced the promoter activity 4.5-fold, while deletion from -391 to -368 had no significant effect on the promoter activity, which suggested that an important inhibitory cis element was located between -367 and -338 in the upstream of NKX3.1 gene. To further confirm the inhibitory element, three substitution mutant and one internal deletion construct were shown to significantly increase promoter activity. The 30bp element was also shown to significantly inhibit several other test promoters (SV40 and maspin). 24-Jul-2006 OREGEC00001 OREGES00004 OREGET00002 obig A specific DNA–protein complex was identified from LNCaP nuclear extracts (Lane 2 in Fig. 4A). The complex could be blocked by competition of 125-fold excess amount of unlabeled 30 bp oligonucleotides (Lane 3 in Fig. 4A), but not by competition of 125-fold excess amount of unlabeled ARE and E2F oligonucleotides (Lanes 4,5 in Fig. 4A) or consensus sequences for Cap, FHF2, and c-Myb (Lane 4–6 in Fig. 4B). In order to identify a crucial cis element within the 30-bp sequence, 5'-deletion probes and 3'-deletion probes of 30-bp sequence were synthesized (listed in Table II) and DIG-labeled and used to perform EMSA experiment. The results in Figure 4C showed that 30I-3'd1 (3'deletion from -342 to -338) and 30I-5'd1 (5' deletion from -367 to -363) did not reduce the binding activity to the nuclear extracts (Lanes 3, 6), the 30I-3'd2 (3'deletion from -347 to-343) and 30I-5'd2 (5'deletion from -362 to -358) partially reduced the binding activity (Lanes 4, 7), while the 30I-3'd3 (3'deletion from -352 to -348)and 30I-5'd3 (5' deletion from -357 to -353) lost the binding ability (Lanes 5, 8), which indicated that the sequences from -357 to -348 were critical for the binding activity. The DIG-labeled 20 bp-I sequence (-362 bp/-343 bp, listed in Table II) presented the same binding activity as the 30 bp-I sequence did (Lanes 9, 2). The results revealed that the sequences from -362 to -343, especially from -357 to -348 were very important for the inhibitory regulation. 24-Jul-2006 OREGEC00001 OREGES00003 OREGET00001 obig 4824 NKX3-1 NCBI 3338 POSITIVE OUTCOME 16845664 0 search_space EMPTY 0 false 0 sequence CTGGACTGTTTGTCTTGATC 0 false 0 sequence_with_flank gactgcgtgctcatcccctgtaattggctctgacggtcctgaagagctaaCTGGACTGTTTGTCTTGATCgtcccatccccaggagcttctctctgttgcgggtgggttggggcagagga 0 false Homo sapiens OREG0002292 REGULATORY REGION This record was updated to correct for an error upon entry (sequence did not match sequence with flank). The flanking sequence was also updated to the most recent version. 9-Aug-2006 obig 9-Aug-2006 25-Aug-2006 OREG0002313 obig deletion and substitution analyses 9-Aug-2006 OREGEC00001 OREGES00000 OREGET00000 obig methylation interference footprinting 9-Aug-2006 OREGEC00000 OREGES00000 OREGET00000 obig ENSGALG00000009844 Actin ENSEMBL gallus_gallus_core_40_1o 3360 POSITIVE OUTCOME 2552286 0 search_space EMPTY 0 false 0 sequence CCATTCATGG 0 false 0 sequence_with_flank tccgcacctgccttagatggccggacagccgcgccgcgccttgcgCCATTCATGGccgcgctgcgccgccatggcgccgagccggccaaataaggagaaggtggctgccccggcccgcga 0 false Gallus gallus OREG0002328 CArG2 CArG2 USER DEFINED TRANSCRIPTION FACTOR BINDING SITE This record was updated from OREG0000115 to make a minor correction to the sequence with flank. 10-Aug-2006 obig 10-Aug-2006 10-Aug-2007 OREG0004685 obig 10-Aug-2006 OREGEC00001 OREGES00000 OREGET00000 obig ENSMUSG00000068614 Actc1 ENSEMBL mus_musculus_core_40_36a 3364 POSITIVE OUTCOME 1570331 0 search_space EMPTY 0 false 0 sequence CAACTG 0 false 0 sequence_with_flank taaggcaaggtggcagatcaggggccccccacccctgcccccggctgctcCAACTGaccccgtccatcagagagctataaagctgcgctccaggcgactgacacccagtg 0 false Mus musculus OREG0002334 ENSMUSG00000009471 myoD ENSEMBL mus_musculus_core_40_36a TRANSCRIPTION FACTOR BINDING SITE This record was updated from OREG0000117 to update the sequence with flank and change the gene id to use the Entrez ID. 10-Aug-2006 obig 10-Aug-2006 DNA-binding studies; in vitro studies of synthetically engineered XMyoD. 10-Aug-2006 OREGEC00001 OREGES00000 OREGET00000 obig 394698 actc NCBI 3365 POSITIVE OUTCOME 1648530 0 search_space EMPTY 0 false 0 sequence CACCTG 0 false 0 sequence_with_flank tgccaaaaggcaggatgctccccccgtgttagtccccctgcacaattgtgctgCACCTGtctgctccatttgcagacccctgtgtctgtacaaactatttctttcattgt 0 false Xenopus tropicalis OREG0002335 MyoD MyoD USER DEFINED TRANSCRIPTION FACTOR BINDING SITE This record replaces OREG0000121 which had incorrect sequence with flank. The gene identifiers were also updated to Entrez IDs. This record was originally from MTIR http://www.cbil.upenn.edu/MTIR/alphaActin_C-sites.html#MARKER-9-42. 10-Aug-2006 obig 10-Aug-2006 mutation, promoter transfection 10-Aug-2006 OREGEC00001 OREGES00000 OREGET00000 obig 70 ACTC NCBI 3366 POSITIVE OUTCOME 2123467 0 search_space EMPTY 0 false 0 sequence GCCCCCCACCCCTGCCCC 0 false 0 sequence_with_flank tcctagcgggtgcgaaggggaccaaataaggcaaggtggcagaccggGCCCCCCACCCCTGCCCCcggctgctccaactgaccctgtccatcagcgttctataaagcggccctcct 0 false Homo sapiens OREG0002337 6667 SP1 NCBI TRANSCRIPTION FACTOR BINDING SITE 25-Aug-2006 deletion and substitution analyses 25-Aug-2006 OREGEC00001 OREGES00000 OREGET00000 obig methylation interference footprinting 25-Aug-2006 OREGEC00000 OREGES00000 OREGET00000 obig ENSGALG00000009844 Actin ENSEMBL gallus_gallus_core_40_1o 3390 POSITIVE OUTCOME 2552286 0 search_space EMPTY 0 false 0 sequence CCATTCATGG 0 false 0 sequence_with_flank tccgcacctgccttagatggccggacagccgcgccgcgccttgcgCCATTCATGGccgcgctgcgccgccatggcgccgagccggccaaataaggagaaggtggctgccccggcccgcga 0 false Gallus gallus OREG0002313 CArG2 CArG2 USER DEFINED TRANSCRIPTION FACTOR BINDING SITE This record replaced OREG0000112 which was found to have an error in the sequence with flank. The record was originally obtained from the MTIR page for Actin, Alpha-Cardiac. 25-Aug-2006 obig 25-Aug-2006 deletion and substitution analyses 25-Aug-2006 OREGEC00001 OREGES00000 OREGET00000 obig deletion and substitution analyses; EMSA; 25-Aug-2006 OREGEC00001 OREGES00013 OREGET00001 obig ENSGALG00000009844 Actin ENSEMBL gallus_gallus_core_40_1o 3391 POSITIVE OUTCOME 2552286 0 search_space EMPTY 0 false 0 sequence CTATAAA 0 false 0 sequence_with_flank caaataaggagaaggtggctgccccggcccgcgaaccgcccggccccgccgggggCTATAAAgcggcagcttcgcgccccgccggcacccaggcgctcctcggtaacctc 0 false Gallus gallus OREG0002318 TATA TATA USER DEFINED TRANSCRIPTION FACTOR BINDING SITE This record replaced OREG0000118 to update the sequence with flank and fix a taxon id problem. The record was originally created from the MTIR entry for Actin, Alpha-Cardiac. 25-Aug-2006 obig 25-Aug-2006 gel shift assay; transfection; methylation interference assay 25-Aug-2006 OREGEC00001 OREGES00000 OREGET00000 obig ENSGALG00000009844 Actin ENSEMBL gallus_gallus_core_40_1o 3392 POSITIVE OUTCOME 8175685 0 search_space EMPTY 0 false 0 sequence CATGTG 0 false 0 sequence_with_flank ctccgagcctcccctcccaccacgtcggcgggaggctccctatttggcCATGTGgcggcgggaccgcgctgctccgcacctgccttagatggccggacagccgcgccgcg 0 false Gallus gallus OREG0002323 c-E2 c-E2 USER DEFINED TRANSCRIPTION FACTOR BINDING SITE This record replaced OREG0000119 to update the sequence with flank and fix a taxon id problem. The sequence was originally obtained from the MTIR page for Actin, Alpha-Cardiac. 25-Aug-2006 obig 25-Aug-2006 methylation interference footprinting; 25-Aug-2006 OREGEC00000 OREGES00000 OREGET00000 obig site-directed mutation. 25-Aug-2006 OREGEC00001 OREGES00000 OREGET00000 obig ENSGALG00000009844 Actin ENSEMBL gallus_gallus_core_40_1o 3393 POSITIVE OUTCOME 1850096 0 search_space EMPTY 0 false 0 sequence CCTTAGATGG 0 false 0 sequence_with_flank aggctccctatttggccatgtggcggcgggaccgcgctgctccgcacctgCCTTAGATGGccggacagccgcgccgcgccttgcgccattcatggccgcgctgcgccgcc 0 false Gallus gallus OREG0002325 CArG3 CArG3 USER DEFINED TRANSCRIPTION FACTOR BINDING SITE This record replaced OREG0000120 to update the sequence with flank and fix a taxon id problem. The original sequence was obtained from the MTIR page for Actin, Alpha-Cardiac. 25-Aug-2006 obig 25-Aug-2006 EMSA 25-Aug-2006 OREGEC00001 OREGES00013 OREGET00001 obig methylation interference footprinting; 25-Aug-2006 OREGEC00000 OREGES00000 OREGET00000 obig mutation; contrasfection of myogenin and myf5(not MRF4). 25-Aug-2006 OREGEC00001 OREGES00000 OREGET00000 obig ENSGALG00000009844 Actin ENSEMBL gallus_gallus_core_40_1o 3394 POSITIVE OUTCOME 8175685 0 search_space EMPTY 0 false 0 sequence CACCTG 0 false 0 sequence_with_flank ggcgggaggctccctatttggccatgtggcggcgggaccgcgctgctccgCACCTGccttagatggccggacagccgcgccgcgccttgcgccattcatggccgcgctgc 0 false Gallus gallus OREG0002330 ENSGALG00000006216 c-MyoD1 ENSEMBL gallus_gallus_core_40_1o TRANSCRIPTION FACTOR BINDING SITE The record replace OREG0000137 with updated sequence with flank, corrected gene ID, and corrected taxon ID. The original sequence was obtained from the MTIR page for Caldesmon. 25-Aug-2006 obig 25-Aug-2006 deletion analysis. 25-Aug-2006 OREGEC00001 OREGES00000 OREGET00000 obig 373965 CALD1 NCBI 3396 POSITIVE OUTCOME 7559534 0 search_space EMPTY 0 false 0 sequence CCAAAAAAGG 0 false 0 sequence_with_flank atgattgttcctgacagaggatttactttcagaggccctgctaaggataaCCAAAAAAGGgcatgtagcaagacagttttggcagcttgcatgaattttcggagcttttt 0 false Gallus gallus OREG0002339 CArG-box CArG-box USER DEFINED TRANSCRIPTION FACTOR BINDING SITE This record replaced OREG0006424 (created by idonaldson) to update the gene id. 1-Sep-2006 obig 1-Sep-2006 7-Sep-2006 OREG0006432 idonaldson Cell type 416B multi-potent progenitor line 1-Sep-2006 OREGEC00001 OREGES00004 OREGET00002 obig 1-Sep-2006 OREGEC00001 OREGES00030 OREGET00002 obig 2313 FLI1 NCBI 4052 Fli-1 +12 POSITIVE OUTCOME 15649946 0 search_space EMPTY 0 false 0 sequence TCCTCGAAATCTTGCTCTCTTCTTCATTCTATTCCACTCATATACACACAAAACTATACACAATTTTTTTTAAAAAACATAACAGATTCAGGAGGTTATATAAAACACAAAGAAGGGAATGTTTTGCGAGGTTAAAAGGAAATCATTGAGTAGGGCTGACTTCAGGCTCCAGTTTCTCTTGAATAGCCTTTCTTGTTATTTCAAGGCTGATTGACTTATAACTGCATCCAAAGCTGCCTCACACCAGTTCCTTTTATCAGACCAAGTGAGACTTCCTGTGGACTGGCCCAGCTTCCTGATATATTTCCTTTTTCCTTTGGCAGAACAAAGAAAACCATAGCTCCAAGGATCCTTGGGAGCAAACACAATTTAGCCCTGAAGAACCTATTATTTTAAATTTTTCATTCTCAATGCGTAGGGCCAAGCGCCTGCCTTTGCTTTTTTTTTCCCCACAGCATTCTGTGTAATGTCCCGATGAACCCTATGTGCAATTACCAGGG 0 false 0 sequence_with_flank TCCTCCTCTACCCTTGTACCTTCGTTCTTTCTTCCTTTCCTCCTCGAAATCTTGCTCTCTTCTTCATTCTATTCCACTCATATACACACAAAACTATACACAATTTTTTTTAAAAAACATAACAGATTCAGGAGGTTATATAAAACACAAAGAAGGGAATGTTTTGCGAGGTTAAAAGGAAATCATTGAGTAGGGCTGACTTCAGGCTCCAGTTTCTCTTGAATAGCCTTTCTTGTTATTTCAAGGCTGATTGACTTATAACTGCATCCAAAGCTGCCTCACACCAGTTCCTTTTATCAGACCAAGTGAGACTTCCTGTGGACTGGCCCAGCTTCCTGATATATTTCCTTTTTCCTTTGGCAGAACAAAGAAAACCATAGCTCCAAGGATCCTTGGGAGCAAACACAATTTAGCCCTGAAGAACCTATTATTTTAAATTTTTCATTCTCAATGCGTAGGGCCAAGCGCCTGCCTTTGCTTTTTTTTTCCCCACAGCATTCTGTGTAATGTCCCGATGAACCCTATGTGCAATTACCAGGGGTCGATGAGCTACTTGAATTCATCCTAGTTGTAGTTTGAT 0 false Homo sapiens OREG0006427 REGULATORY REGION This record is referred to as the 'distal' element by the authors. There are a number of sequence discrepencies between the distal/proximal elements described in this paper and the HIV complete genome. This is not necessarily unexpected as the HIV genome is highly polymorphic. As HIV is not in UCSC or Ensembl it is difficult to visualize the sequence in relation to known polymorphisms. However, a blast against nr virus sequences identifies submitted sequences that match the elements with no discrepencies for the distal element (compared to EF090286) and only a single bp discrepency for the proximal element (compared to AF027806). Therefore, the bound sequence was entered as reported in the paper but with flanking sequence from the reference genome to facilitate mapping. 30-Nov-2006 obig 30-Nov-2006 From Results: "Competition analysis was performed to demonstrate the specificity of this binding. Oligonucleotides corresponding to either the distal ILF motif in the HIV LTR (Fig. 2, lanes 4 and 5) or the NFAT motif in the IL-2 promoter (Fig. 2, lanes 6 and 7) specifically blocked by competition the binding of the f3-galactosidase-ILF protein. Likewise, the proximal ILF motif in the HIV LTR also resulted in complete competition of ILF protein binding (data not shown). However, we note that in a number of different experiments both the proximal and distal HIV motifs served as better competitors for ILF binding than the NFAT motif." 30-Nov-2006 OREGEC00001 OREGES00003 OREGET00001 obig HIV LTR (long terminal repeat) HIV LTR (long terminal repeat) USER DEFINED 4251 POSITIVE OUTCOME 1909027 0 search_space EMPTY 0 false 0 sequence GAAGAGGCCAATGAAGGAGAGAACAACA 0 false 0 sequence_with_flank ctgacctttggatggtgcttcaagctagtaccagttgagcgagagcaggtaGAAGAGGCCAATGAAGGAGAGAACAACAgcctgttacaccctatgagcctgcatgggatggatgacccg 0 false Human immunodeficiency virus 1 OREG0002597 Human ILF (interleukin binding factor) Human ILF (interleukin binding factor) USER DEFINED TRANSCRIPTION FACTOR BINDING SITE This record is referred to as the 'proximal' element by the authors. There are a number of sequence discrepencies between the distal/proximal elements described in this paper and the HIV complete genome. This is not necessarily unexpected as the HIV genome is highly polymorphic. As HIV is not in UCSC or Ensembl it is difficult to visualize the sequence in relation to known polymorphisms. However, a blast against nr virus sequences identifies submitted sequences that match the elements with no discrepencies for the distal element (compared to EF090286) and only a single bp discrepency for the proximal element (compared to AF027806). Therefore, the bound sequence was entered as reported in the paper but with flanking sequence from the reference genome to facilitate mapping. 30-Nov-2006 obig 30-Nov-2006 From Results: "Competition analysis was performed to demonstrate the specificity of this binding. Oligonucleotides corresponding to either the distal ILF motif in the HIV LTR (Fig. 2, lanes 4 and 5) or the NFAT motif in the IL-2 promoter (Fig. 2, lanes 6 and 7) specifically blocked by competition the binding of the f3-galactosidase-ILF protein. Likewise, the proximal ILF motif in the HIV LTR also resulted in complete competition of ILF protein binding (data not shown). However, we note that in a number of different experiments both the proximal and distal HIV motifs served as better competitors for ILF binding than the NFAT motif." 30-Nov-2006 OREGEC00001 OREGES00003 OREGET00001 obig HIV LTR (long terminal repeat) HIV LTR (long terminal repeat) USER DEFINED 4254 POSITIVE OUTCOME 1909027 0 search_space EMPTY 0 false 0 sequence GAGGACGCGGAGAAAGAAGGTGTTAGTGTG 0 false 0 sequence_with_flank agaacaccagcttgttacaccctgtgagcctgcatgggatgGAGGACGCGGAGAAAGAAGGTGTTAGTGTGgaggtttgacagccgcctagcatttcatcacgtggcccgagagctgcat 0 false Human immunodeficiency virus 1 OREG0002614 Human ILF (interleukin binding factor) Human ILF (interleukin binding factor) USER DEFINED TRANSCRIPTION FACTOR BINDING SITE Foxa Site A is a Foxa1 binding site that is transactivated by Foxa2. 12-Jan-2007 obig 12-Jan-2007 Exogenously expressed Foxa1, Foxa2 or Foxa3 proteins have been shown to activate the rat glucagon gene promoter in the heterologous cell lines HepG2 or BHK (baby hamster kidney) in transient transfection assays. To investigate whether the human glucagon gene is transactivated by Foxa proteins like the rat gene, HepG2 cells were transfected with the human glucagon-reporter gene construct H-350GluLuc together with an expression plasmid for Foxa1 or Foxa2. The human glucagon gene promoter responded to Foxa1 and Foxa2 similarly to the rat promoter. To localize the cis-acting DNA sequence(s) of the human glucagon gene that mediate transcriptional activation by Foxa proteins, a 5' to 3' and internal-deletion analysis was performed. The combined results obtained with the 5' and 3' deletion analyses suggest that transactivation by Foxa2 of the human glucagon gene is conferred by element(s) located within the region encompassing bp -105 to -31. This region includes the predicted novel Foxa site A (Figures 4A and 4B). To examine their role more directly the Foxa site A was mutated in the context of the human glucagon gene promoter (Figure 5). The results show that the Foxa site A is essential for transactivation by Foxa2 of the human glucagon gene. These results demonstrate the functionality of the Foxa site A. For both the rat and the human genes, the activation of the glucagon promoter by Foxa2 in a heterologous cell line depends primarily on intact Foxa site A. 12-Jan-2007 OREGEC00001 OREGES00004 OREGET00002 obig Nuclear protein extract prepared from InR1G9 cells, which endogenously express the Foxa1 and Foxa2 isoforms, was probed with labeled oligonucleotides containing Foxa site A from either the rat or human glucagon promoter (Figure 7A). The rat G2 (Foxa site C) probe, which binds Foxa2 in InR1G9 extracts was included as a positive control. A retarded band with similar mobility was detected with all three probes (Figure 7A, indicated by an arrow). This complex with the rat or human site A probe was competed out by an excess of an unlabelled 'self' oligonucleotide (Figure 7A), suggesting that the retarded band represents specific interaction. 12-Jan-2007 OREGEC00001 OREGES00003 OREGET00001 obig To identify the protein that binds the Foxa site A, EMSAs were performed in the presence of preimmune goat IgG, antibodies recognizing specifically Foxa1 (anti-Foxa1)or antibodies recognizing Foxa1 and Foxa2 (anti-Foxa1/2) (see Figure 7C). The addition of the antibody specific for Foxa1 as well as the antibody recognizing Foxa1 and Foxa2 to the binding reaction inhibited the binding of the retarded complex to the rat and human Foxa siteA (Figure 7B, lanes 2 and 3 and lanes 5 and 6 respectively). Cell extracts were prepared in InR1G9 cells. 12-Jan-2007 OREGEC00002 OREGES00002 OREGET00001 obig 2641 GCG NCBI 4562 POSITIVE OUTCOME 15828872 0 search_space EMPTY 0 false 0 sequence GGCTAAACAGAGC 0 false 0 sequence_with_flank catttgtaacaaaaactcattatttacagatgagaaatttatattgtcagcgtaatatctgtgaGGCTAAACAGAGCtggagagtatataaaagcagtgc 0 false Homo sapiens OREG0002875 Foxa1/Foxa2 Foxa1/Foxa2 USER DEFINED TRANSCRIPTION FACTOR BINDING SITE These results demonstrate that the two Foxa-binding sites (A and B) regulate the vitronectin promoter in a cell-type dependent manner. 16-Jan-2007 obig 16-Jan-2007 The 101-bp promoter region (from 348 to +53 bp) in the mouse vitronectin gene has two consensus sequences of the Foxa-binding site (from 334 to 325, site A, and +15 to +26 bp, site B). Site B is the site which was the site which was analyzed. The construct, VN348/+53, which contains the 101-bp region, displayed promoter activity in Neuro2a cells. A promoter assay using 3'-successively deleted mutants of the 101-bp promoter region showed that elimination of the bp between +21 and +31 reduced the promoter activity to 2% in the construct VN348/+53. 16-Jan-2007 OREGEC00001 OREGES00004 OREGET00002 obig To examine whether site B binds to nuclear proteins, we performed EMSA using nuclear extracts from Neuro2a cells and a labeled site-B oligonucleotide as a probe. The assay revealed two shifted bands. The slow mobility band was out-competed by a 20-fold molar excess of unlabeled site-B oligonucleotides, but the fast mobility band was not, suggesting that the slow mobility band represents specifc binding of the nuclear protein to the site-B oligonucleotides. 16-Jan-2007 OREGEC00001 OREGES00003 OREGET00001 obig Site-directed mutagenesis for the Mut 3 site in site B (mtB, TTTCGGG) reduced the wild promoter activity to 4.6%, indicating that Site B acts as a transcription regulatory site in Neuro2a cells. 16-Jan-2007 OREGEC00001 OREGES00054 OREGET00009 obig In EMSA using the labeled site-B oligonucleotide as a probe a 30-fold molar excess of TTR-Foxa binding oligonucleotides completely inhibited the binding of nuclear extract from Neuro2a cells, suggesting that the nuclear proteins bind to the Foxa-binding DNA fragment. 16-Jan-2007 OREGEC00002 OREGES00003 OREGET00001 obig To identify the factor binding to the site-B oligonucleotide, we performed a supershift assay using antisera against Foxa1 and Foxa2. The band was supershifted by the antisera identifying the nuclear proteins on site B as Foxa1 and Foxa2 proteins. 16-Jan-2007 OREGEC00002 OREGES00002 OREGET00001 obig Overexpression of the Foxa1 protein increased the 101-bp promoter activity 8-fold, and overexpression of the Foxa2 protein increased the 101-bp promoter activity 2.6-fold. 16-Jan-2007 OREGEC00002 OREGES00004 OREGET00002 obig The site-B-mutated promoter (mtB) retained 38% of the wild promoter activity indicating that site B is not essential for the promoter activity in HepG2 cells. However, double mutation of sites A and B decreased the wild promoter activity to 5%, indicating that sites A and B contribute to the promoter activity in HepG2 cells. 16-Jan-2007 OREGEC00001 OREGES00004 OREGET00002 obig 22370 Vtn NCBI 4564 POSITIVE OUTCOME 11997100 0 search_space EMPTY 0 false 0 sequence CTGCTTCTTTTTT 0 false 0 sequence_with_flank aagggcagaaacccagggaactaggaactcttcttcagtCTGCTTCTTTTTTcaggcaggacagcgagattccagaagctccgcgcccag 0 false Mus musculus OREG0002878 Foxa1/Foxa2 Foxa1/Foxa2 USER DEFINED TRANSCRIPTION FACTOR BINDING SITE The BCL2-938AA genotype is associated with increased Bcl-2 expression and a novel unfavorable genetic marker in patients with B-CLL. 27-Feb-2007 obig 27-Feb-2007 A polymorphism upon promoter activity, we cloned fragments of the known BCL2 promoter region encompassing nt -690 to -1001 with regard to the translation initiation site and that carried either the C allele or the A allele into the pSEAP-basic reporter vector (Figure 1A). We pairwise transfected these constructs into otherwise identical batches of HEK293 cells, quantified secreted alkaline phosphatase, and corrected these values for transfection efficacy (Figure 1B). It can be seen that reporter activity was variable, but in 9 independently conducted paired experiments the activity associated with the C allele was always higher than that of the A allele. Normalized reporter activity increased by a factor of 3.2 +- 2.8 (mean +- SD) over baseline upon transfection of the BCL2 construct with the C allele, whereas the construct with the A allele increased reporter activity by only a factor of 2.3 +- 2.0 (mean +- SD; P = .004; Wilcoxon matched pairs test). Thus, in this assay the C allele was associated with a significantly higher activity, approximately 40%, compared with the A allele." ]]> 27-Feb-2007 OREGEC00001 OREGES00037 OREGET00002 obig From Results: "To confirm these results we repeated these experiments in Karpas 422 cells, a human follicular B-cell line (Figure 1C), using a different vector (pGL3) and reporter assay based on the luciferase system. In these experiments, reporter activity of the A allele was not significantly different from baseline (1.1 +- 0.19; mean +- SD; P = .22, Wilcoxon signed rank test). In contrast, we measured a significant activity associated with the C allele (1.3 +- 0.11; mean +- SD) that was statistically significantly different from baseline (P = .004; 1-sample t test) and significantly higher than that of the A allele (P = .03; Wilcoxon matched pairs test). Collectively, these data suggested an increased activity of the inhibitory P2 promoter associated with the C allele. This is suggestive of an overall reduced transcriptional activity of the BCL2 promoter in the presence of a C allele." 27-Feb-2007 OREGEC00001 OREGES00004 OREGET00002 obig From Results: "Because these differences in promoter activity suggested potentially different binding of transcription factors to the C and A alleles, respectively, we subsequently compared differential DNA-protein binding by means of electrophoretic mobility shift assays (EMSAs). Results are displayed in Figure 2 When oligonucleotides were incubated with nuclear proteins from Karpas 422 cells, we observed a significantly stronger band indicative of DNA-protein binding for the C allele compared with the A allele." 27-Feb-2007 OREGEC00001 OREGES00003 OREGET00001 obig From Results: "Specificity was confirmed through experiments in which a 100-fold molar excess of unlabeled nucleotide competed these bands away. Addition of an Sp-1 antibody competed this band almost completely away, indicating that this band was specific for Sp-1 binding sites." 27-Feb-2007 OREGEC00002 OREGES00002 OREGET00001 obig From Results: "One consequence of the increased activity of the inhibitory BCL2 promoter associated with the C allele should be a concomitant reduction in Bcl-2 protein expression in cells from C-allele carriers. To confirm this hypothesis, we investigated potential genotype-dependent Bcl-2 protein expression in B lymphocytes from patients with B-CLL. As chemotherapeutic agents may down-regulate Bcl-2 expression, samples were exclusively taken from patients who had never received antileukemic therapy. As shown in Figure 3A, expression of Bcl-2 in cells from 3 patients with -938AA genotype was increased compared with that in cells from 3 patients with CC genotypes. Protein expression associated with the AC genotype was somewhat more variable, showing low expression in 1 specimen comparable to that seen in CC genotypes, intermediate expression in another sample, and higher expression in 1 sample resembling the AA genotype. To correct for variations in total protein, blots were also probed with an antiactin antibody. After densitometry of Bcl-2- and actin-specific bands, the ratios of Bcl-2/actin were calculated and associated with BCL2 genotypes (Figure 3B). The ratios BCL2/actin were almost 2-fold higher comparing AA (0.75 +- 0.13) with CC genotypes (0.36 +- 0.14; P = .028; Student t test), whereas intermediate ratios were found associated with the AC genotype (0.61 +- 0.16). Assuming a gene-dose effect, expression levels across genotypes were also analyzed by linear ANOVA and found to be borderline significantly different (P = .048). Thus, an increased activity of the inhibitory P2 promoter appears to result in an accordingly reduced bcl-2 protein expression associated with the CC genotype." 27-Feb-2007 OREGEC00001 OREGES00008 OREGET00005 obig Genotype distribution between 123 CLL patients (42 AA, 55 AC, 26 CC) and 120 genotyped healthy controls (36 AA, 63 AC, 21 CC) was not significantly different, suggesting that genotypes of this polymorphism do not increase the susceptibility for B-CLL. However, median time from first diagnosis to initiation of chemotherapy and median overall survival were significantly shorter in patients with –938AA genotype (38 and 199 months, respectively) compared with AC/CC genotypes (120 and 321 months, respectively; P = .008 and P = .003, respectively). Multivariable Cox regression identified the BCL2–938AA genotype as an independent prognostic factor for the time to first treatment (hazard ratio [HR] 1.9; P = .034) together with disease stage at diagnosis (HR 2.5; P = .004) and ZAP-70 status (HR 3.0; P = .001). 27-Feb-2007 OREGEC00001 OREGES00010 OREGET00006 obig 596 BCL2 NCBI 4595 POSITIVE OUTCOME 16960146 0 search_space EMPTY 0 false 0 search_space EMPTY 0 false 0 search_space EMPTY 0 false Homo sapiens OREG0002918 UNKNOWN UNKNOWN USER DEFINED REGULATORY POLYMORPHISM 27-Feb-2007 0 reference_sequence agtttaatcagaagaggattcctgcctccgtccccggctccttcatcgtcccCtctcccctgtctctctcctggggaggcgtgaagcggtcccgtggata 0 false rs2279115 dbSNP NOT SPECIFIED 0 variant_sequence agtttaatcagaagaggattcctgcctccgtccccggctccttcatcgtcccAtctcccctgtctctctcctggggaggcgtgaagcggtcccgtggata 0 false Record created by bcb. Modified by obig to correct NCBI Gene ID. 11-Apr-2007 obig 11-Apr-2007 To determine whether HNF4alpha has the potential to activate the mouse BAT promoter, several BAT promoter-luciferase reporter plasmids were constructed. When HepG2 cells were used for transient transfections, the promoter activity of the -136-bp fragment containing a putative HNF4alpha-binding site was higher than that of the promoterless construct (pGL3/basic) and the -52-bp fragment. The promoter activities of the longer fragments were much higher than that of the -136-bp fragment. To determine whether this effect was due to HNF4alpha, CV-1 cells were used. The promoter activity of the -52-bp fragment was unchanged by cotransfection of the HNF4alpha-expression vector, consistent with the absence of an HNF4alpha- binding site. However, the promoter activity of the -136-bp fragment was increased by HNF4alpha. The same results were obtained from experiments using the longer fragments. 11-Apr-2007 OREGEC00001 OREGES00004 OREGET00002 obig To determine whether HNF4alpha can bind to the DR1-like elements in the mouse BAT promoter, gel shift analysis was performed. Liver nuclear extracts from H4Flox mice contained proteins that bound to the HNF4alpha-binding site. Binding was diminished by the addition of excess amounts of unlabeled BAT probe (wild-type) but not by the mutated probe, indicating that a protein specifically bound to this site. 11-Apr-2007 OREGEC00002 OREGES00001 OREGET00001 obig The bands were supershifted by the addition of anti-HNF4alpha antibody, indicating that the protein bound to this HNF4alpha- binding site was indeed HNF4alpha. Supershifted bands were not detected using liver nuclear extracts from H4LivKO mice. 11-Apr-2007 OREGEC00002 OREGES00002 OREGET00001 obig To determine whether disruption of the HNF4alpha-binding site decreases the promoter activity, mutations were introduced into the HNF4alpha -binding site in the mouse BAT (-602/-178)-luciferase construct when HepG2 cells were used for transient transfections, the promoter activity of the mutated -602-bp fragment (-602/Mut) was decreased to 25% as compared with the wild-type fragment (-602/WT). When CV-1 cells were used, the promoter activity of the mutated fragment was decreased to 15% by cotransfection of HNF4alpha as compared with the wildtype fragment, indicating that the HNF4alpha-binding site is important for activation of the mouse BAT promoter. 11-Apr-2007 OREGEC00001 OREGES00004 OREGET00002 obig 12012 Baat NCBI 4655 POSITIVE OUTCOME 14583614 0 search_space EMPTY 0 false 0 sequence AGTTCCAAGGTCT 0 false 0 sequence_with_flank ccgatgctttcatttttagatctttatctcaggcatttattcaaagtccaAGTTCCAAGGTCTtagtctcttctctgggttcagcctacttatatctggttgaggagggaaat 0 false Mus musculus OREG0002978 15378 Hnf4a NCBI TRANSCRIPTION FACTOR BINDING SITE This record was updated to increase sequence flank. This was necessary to resolve mapping ambiguity. 17-Apr-2007 obig 17-Apr-2007 17-Apr-2007 OREGEC00000 OREGES00000 OREGET00000 obig CBG23799 CBG23799 USER DEFINED 4672 POSITIVE OUTCOME 15790967 0 search_space EMPTY 0 false 0 sequence GTTACTATGGCAAC 0 false 0 sequence_with_flank ttttgaaccaattgaattatatttttgtagatctcggaagttgtgaactcccttcgaaaagatggagttcgtcgtgagaattgtcgaaagaatgtaggaaaaccagtctattcattcagtccattccaaatgcattttctaccgaaagtcttccgacctccatctggaacatatgcaaaaggagttgctagttaattataaaaatgtgtattttaataatgttcaataagttagtgtttattttcctattctttattttatattcaattttattcccaaattgtcacatttcccaaaccacggttcccaaattttgaccaatttctctttacatattccatctcacacactcgtcgatagatacttctttttcatatctttccccggtaataatgtgatgattgtttgaaatataatactgatgcaagatagagtttacataaattccttctccctttttctctatgctgtcgagtttacaccttGTTACTATGGCAACctgacacactcacgcgcctcgctgctcacgagccgtcttcattcgttcactcaaaatggagcgagtgaatggagaagatatttggcaggatcgcgaaattcgtttcgatgtggatcataagttagtttgaaaaactctaacatagaatctgaaaatcctttcagacttcttcgtatgatcaatggagaagtacaaattgctaaagtggagaatgtggaagacacgaaaggaaacaatggagataaaggtgaatatatttaggtcttcaattcaaaactaggtcgtttcaggggtaattcgagttaccaatcttcgtctgatctggtacgctatgagcatgccgcgcatcaacatcactattgggtggaatacgatcactggaacacaatcgaaaacatcgacatcggtaaaatatcattctggtacaaaaaatcggagctgtgaccaaaggtcccacagcgacatttacagtaacctgaatatatttttgcctgattgatt 0 false Caenorhabditis briggsae OREG0002999 F33H1.1 F33H1.1 USER DEFINED TRANSCRIPTION FACTOR BINDING SITE 1-May-2007 COS mouse cells 1-May-2007 OREGEC00001 OREGES00002 OREGET00001 obig ENSMUSG00000000440 Pparg ENSEMBL mus_musculus_core_41_36b 4764 POSITIVE OUTCOME 10862621 0 search_space EMPTY 0 false 0 sequence GCAAT 0 false 0 sequence_with_flank tggtgtgtattttactGCAATtttaaaaagcaatcaatattgaacaatct 0 false Mus musculus OREG0003016 ENSMUSG00000071637 NM_007679.2 ENSEMBL mus_musculus_core_41_36b TRANSCRIPTION FACTOR BINDING SITE This record was created to correct minor problems in OREG0002535. The sequence with flank was changed to use the proper upper/lower case convention. Some problem characters were also removed from evidence descriptions 10-May-2007 obig 10-May-2007 To study the contribution of Stat to the IFN-{alpha} action, we performed gel-shift analysis with the Stat motif using nuclear extracts from IFN-{alpha}-stimulated cells. IFN-{alpha} did, in fact, lead to a strong induction of a Stat binding protein (Fig. 5A, arrowhead). The specificity of this band has been demonstrated previously (10). There was a clear signal after 1 h of stimulation, sometimes with a decrease in binding activity at 2 h, as in this example. Later, the signal was strong again (Fig. 5A). To identify the proteins bound to the Stat3 motif after IFN-{alpha} stimulation by supershift analysis, the gels were again run for a longer period of time for better resolution of the bands (Fig. 5B). Here, anti-Stat1 Ab removed a minor high mobility band, while anti-Stat3 ablated the major low mobility band (lanes 3 and 5, respectively, in Fig. 5B). The combination of the Abs against Stat1 and Stat3 removed the entire specific complex (Fig. 5B, lane 6). The anti-Stat3 Ab induced the appearance of two supershifted bands (Fig. 5B, open arrows, lanes 5 and 6), while the anti-Stat1 Ab did not result in a visible band in the upper part of the gel. All other anti-Stat-Abs had no effect. These data suggest that the IFN-{alpha}-induced complex, which binds to the Stat3 motif, consists mainly of Stat3 homodimers (strong low mobility band) plus a small amount of Stat1 homodimers (weak higher mobility band). In gel-shift analysis using the Stat motif we observed induction of a minor band that was identified as Stat1 (see Fig. 5). 10-May-2007 OREGEC00001 OREGES00001 OREGET00001 obig To study the contribution of Stat to the IFN-{alpha} action, we performed gel-shift analysis with the Stat motif using nuclear extracts from IFN-{alpha}-stimulated cells. IFN-{alpha} did, in fact, lead to a strong induction of a Stat binding protein (Fig. 5A, arrowhead). The specificity of this band has been demonstrated previously (10). There was a clear signal after 1 h of stimulation, sometimes with a decrease in binding activity at 2 h, as in this example. Later, the signal was strong again (Fig. 5A). To identify the proteins bound to the Stat3 motif after IFN-{alpha} stimulation by supershift analysis, the gels were again run for a longer period of time for better resolution of the bands (Fig. 5B). Here, anti-Stat1 Ab removed a minor high mobility band, while anti-Stat3 ablated the major low mobility band (lanes 3 and 5, respectively, in Fig. 5B). The combination of the Abs against Stat1 and Stat3 removed the entire specific complex (Fig. 5B, lane 6). The anti-Stat3 Ab induced the appearance of two supershifted bands (Fig. 5B, open arrows, lanes 5 and 6), while the anti-Stat1 Ab did not result in a visible band in the upper part of the gel. All other anti-Stat-Abs had no effect. These data suggest that the IFN-{alpha}-induced complex, which binds to the Stat3 motif, consists mainly of Stat3 homodimers (strong low mobility band) plus a small amount of Stat1 homodimers (weak higher mobility band). In gel-shift analysis using the Stat motif we observed induction of a minor band that was identified as Stat1 (see Fig. 5) 10-May-2007 OREGEC00001 OREGES00002 OREGET00001 obig For these studies RPMI 8226 cells were transfected with the -195 fragment of the IL-10 promoter plus a total of 1 µg of expression plasmid. The experiments in Fig. 7 confirmed induction by Stat3, but Stat1 had no activity when added alone. When Stat1 was admixed with Stat3 expression plasmid, Stat1 was able to counteract the Stat3-mediated trans-activation at equal and 2/1 Stat1/Stat3 ratios (Fig. 7, right columns). These data demonstrate that Stat1 is able to counteract Stat3-mediated trans-activation of the human IL-10 promoter. FIGURE 7. Stat1 suppresses Stat3-mediated trans-activation of the human IL-10 promoter. Stat1 and Stat3 were cotransfected with the human -195 IL-10 promoter luciferase reporter plasmid into RPMI 8226 cells, and luciferase activity was determined after stimulation with IFN-{alpha} (100 U/ml for 6 h). Cells received an identical total amount of expression plasmid (1 µg). In the third column pair (Stat1 alone), Stat1 expression plasmid was at 0.3 µg. Stat3 was always at 0.3 µg, and in the combinations Stat1 was used at 0.6, 0.3, or 0.15 µg, with the remainder provided by pCAGGS. The data given are the averages of five experiments, n = 4 for the 1:1 and 0.5:1 cotransfection. 10-May-2007 OREGEC00001 OREGES00004 OREGET00002 obig When we mutated the Stat motif, the LPS-induced trans-activation was markedly reduced, but surprisingly the IFN-{alpha} activity was completely ablated (Fig. 4, third panel). Mutation of both sites resulted in a loss of trans-activation by any of the stimuli (Fig. 4, fourth panel). 10-May-2007 OREGEC00001 OREGES00055 OREGET00009 obig ENSG00000136634 IL10 ENSEMBL homo_sapiens_core_41_36c 4797 POSITIVE OUTCOME 12817009 0 search_space EMPTY 0 false 0 sequence TGCCGGGAA 0 false 0 sequence_with_flank gcttacgatgcaaaaattgaaaactaagtttattagagaggttagagaaggaggagctctaaggagaaaaaatcctgTGCCGGGAAaccttgattgtggctttttaatgaatgaagaggcctccctgagcttacaatataaaagggggacagagaggtgaaggtctacacatcaggggcttgctcttgcaaaaccaaaccacaagacagacttgcaaaagaaggc 0 false Homo sapiens OREG0003113 ENSG00000115415 STAT1 ENSEMBL homo_sapiens_core_41_36c TRANSCRIPTION FACTOR BINDING SITE Record deprecated to fix mapping issue. 17-Jul-2007 obig OREGDS00001 17-Jul-2007 Cell lines tested and results, HepG2: 2.946422012 HeLa: 2.956938783 HT1080: 2.375331235 MRC5: 1.429771351 JEG3: 2.82419135 U87: 1.601496896 G402: 2.419586707 HCT116: 2.357663188 CRL1690: 1.025913735 AGS: 1.842668838 Panc1: 1.935814982 HMCB: 1.531052194 MG63: 1.901190897 Snu-182: 2.512499604. Number of positive cell lines: 6. Mean: 3.694870348. Mean(log): 2.118610127. 17-Jul-2007 OREGEC00001 OREGES00004 OREGET00002 obig UNKNOWN UNKNOWN USER DEFINED 5054 NEGATIVE OUTCOME 12566409 0 search_space EMPTY 0 false 0 sequence CCTGGCAAGCCTCTATATTCTCATTCACACCCCAGTAAATCACTAAGAGATTATTGATGAAGATATGTGTATTTGGGTGTTTGAAGGATTGTAACAAAAATCAAAAGTAGAATAGAATTTTAGAATATATGCTTTCTGCATTGAGGACTTCATTTGCTTTATAGCCTTCTTTATATTTGTTGATATTCTTTCTTGCCCTGTGCCAACATTTTAGAAATACATTTTTAGAAATTTCTTACAAGATTTATCAGTATGCTACCAATAACAACACACACTCTCTCTCTCTcacacacacatacacacacacacacagacacaACTTTTTATCCATGTAATAACAAATATCTTGAATTTATAATGTGTATTTTGCCAGAAGTTAAGTGGTTATACATCATTGCTTTAGCTTTACAAAATCACTAGATCACTGACAGATTGTTCTTTTGGTTTTTTTTGTTTTGACATTTTTTCATATAGTTAAAACCCACAGCACTCAATTTCAT 0 false 0 search_space EMPTY 0 false Homo sapiens OREG0003365 REGULATORY REGION Record modified from OREG0000133 to update evidence. 31-Jul-2007 obig 31-Jul-2007 31-Jul-2007 OREGEC00001 OREGES00041 OREGET00009 obig Mutation of the E-box (from gacacatgtg to gaAGATCTCg) in human aldolase M-promoter resulted in a significant decrease in CAT activity in vastus lateralis and gastrocnemius fast muscle tissues and in slow muscle soleus tissues of transgenic mice. 31-Jul-2007 OREGEC00001 OREGES00019 OREGET00002 obig 226 ALDOA NCBI 7865 POSITIVE OUTCOME 8524331 0 search_space EMPTY 0 false 0 sequence CACATG 0 false 0 sequence_with_flank tcattagagaagatcggggaCACATGtggggcgggcaggagctgcc 0 false Homo sapiens OREG0003389 E-box E-box USER DEFINED TRANSCRIPTION FACTOR BINDING SITE Bergman DNAse I footprint sites: www.flyreg.org: FPID:006404 1-Aug-2007 obig OREGDS00000 1-Aug-2007 1-Aug-2007 OREGEC00001 OREGES00015 OREGET00003 obig CG31613 His3 ENSEMBL drosophila_melanogaster_core_45_43b 7885 POSITIVE OUTCOME 2781290 0 search_space EMPTY 0 false 0 sequence CCGAGAGAGTACG 0 false 0 sequence_with_flank ttggcgccaccctttcccaagcctttgcctcctttaccacgaccagtcatttttcactgttctatactattatacacgcacagcacgaaagtcactaaagaactaatttcaacgtttctgtgtgcccctatttataggtaaaacgacaaaaacCCGAGAGAGTACGaacgatatgttcgttcgcttttcgctcgtcaaatgaaatggcctccgtttttctctctctctctctctctctctctttcaccgtccacgattgctatataagtaggtagcaaatgctctgatcgtttattgtgttttcaaacgtg 0 false Drosophila melanogaster OREG0004663 Trl Trl USER DEFINED TRANSCRIPTION FACTOR BINDING SITE Bergman DNAse I footprint sites: www.flyreg.org: FPID:006405 1-Aug-2007 obig OREGDS00000 1-Aug-2007 2-Aug-2007 OREG0004677 obig 1-Aug-2007 OREGEC00001 OREGES00015 OREGET00003 obig CG31613 His3 ENSEMBL drosophila_melanogaster_core_45_43b 7886 POSITIVE OUTCOME 2781290 0 search_space EMPTY 0 false 0 sequence TTCTCTCTCTCTCTCTCTCTCTCTTTC 0 false 0 sequence_with_flank aaatgaaatggcctccgtttTTCTCTCTCTCTCTCTCTCTCTCTTTCaccgtccacgattgctatat 0 false Drosophila melanogaster OREG0004664 Trl Trl USER DEFINED TRANSCRIPTION FACTOR BINDING SITE Bergman DNAse I footprint sites: www.flyreg.org: FPID:006406 1-Aug-2007 obig OREGDS00000 1-Aug-2007 2-Aug-2007 OREG0004678 obig 1-Aug-2007 OREGEC00001 OREGES00015 OREGET00003 obig CG31613 His3 ENSEMBL drosophila_melanogaster_core_45_43b 7887 POSITIVE OUTCOME 6537904 0 search_space EMPTY 0 false 0 sequence CCACGATTGCTATATAAGTAGGTAGCAAATGC 0 false 0 sequence_with_flank ctctctctctctttcaccgtCCACGATTGCTATATAAGTAGGTAGCAAATGCtctgatcgtttattgtgttt 0 false Drosophila melanogaster OREG0004665 Unspecified Unspecified USER DEFINED TRANSCRIPTION FACTOR BINDING SITE Bergman DNAse I footprint sites: www.flyreg.org: FPID:006407 1-Aug-2007 obig OREGDS00000 1-Aug-2007 3-Aug-2007 OREG0004679 obig 1-Aug-2007 OREGEC00001 OREGES00015 OREGET00003 obig CG31613 His3 ENSEMBL drosophila_melanogaster_core_45_43b 7888 POSITIVE OUTCOME 6537904 0 search_space EMPTY 0 false 0 sequence GATCGTTTATTGTGTTTTCAAACGTGAAGTAGTGAACG 0 false 0 sequence_with_flank aagtaggtagcaaatgctctGATCGTTTATTGTGTTTTCAAACGTGAAGTAGTGAACGtgaactttagtgaaacccaa 0 false Drosophila melanogaster OREG0004666 Unspecified Unspecified USER DEFINED TRANSCRIPTION FACTOR BINDING SITE Bergman DNAse I footprint sites: www.flyreg.org: FPID:005502 2-Aug-2007 obig OREGDS00000 2-Aug-2007 2-Aug-2007 OREGEC00001 OREGES00015 OREGET00003 obig CG31366 Hsp70Ab ENSEMBL drosophila_melanogaster_core_45_43b 7889 POSITIVE OUTCOME 4028160 0 search_space EMPTY 0 false 0 sequence AAATAAAGCGAATATTCTAGAATCCC 0 false 0 sequence_with_flank tatttataaagaaatttccaAAATAAAGCGAATATTCTAGAATCCCaaaacaaactggttgttgcg 0 false Drosophila melanogaster OREG0004667 Hsf Hsf USER DEFINED TRANSCRIPTION FACTOR BINDING SITE Bergman DNAse I footprint sites: www.flyreg.org: FPID:005503 2-Aug-2007 obig OREGDS00000 2-Aug-2007 2-Aug-2007 OREGEC00001 OREGES00015 OREGET00003 obig CG31366 Hsp70Ab ENSEMBL drosophila_melanogaster_core_45_43b 7890 POSITIVE OUTCOME 4028160 0 search_space EMPTY 0 false 0 sequence AAACTCGAGAAATTTCTCTGGCCGT 0 false 0 sequence_with_flank tcatttgtttggcagaaagaAAACTCGAGAAATTTCTCTGGCCGTtattctctattcgttttgtg 0 false Drosophila melanogaster OREG0004668 Hsf Hsf USER DEFINED TRANSCRIPTION FACTOR BINDING SITE Bergman DNAse I footprint sites: www.flyreg.org: FPID:005504 2-Aug-2007 obig OREGDS00000 2-Aug-2007 2-Aug-2007 OREGEC00001 OREGES00015 OREGET00003 obig CG31366 Hsp70Ab ENSEMBL drosophila_melanogaster_core_45_43b 7891 POSITIVE OUTCOME 2781290 0 search_space EMPTY 0 false 0 sequence CGTTATTCTCTATTCGTTTT 0 false 0 sequence_with_flank actcgagaaatttctctggcCGTTATTCTCTATTCGTTTTgtgactctccctctttgtac 0 false Drosophila melanogaster OREG0004669 Trl Trl USER DEFINED TRANSCRIPTION FACTOR BINDING SITE Bergman DNAse I footprint sites: www.flyreg.org: FPID:005505 2-Aug-2007 obig OREGDS00000 2-Aug-2007 2-Aug-2007 OREGEC00001 OREGES00015 OREGET00003 obig CG31366 Hsp70Ab ENSEMBL drosophila_melanogaster_core_45_43b 7892 POSITIVE OUTCOME 2781290 0 search_space EMPTY 0 false 0 sequence TCTCCCTCTTTGTACTATTGCTCTCTCACTCTG 0 false 0 sequence_with_flank ttctctattcgttttgtgacTCTCCCTCTTTGTACTATTGCTCTCTCACTCTGtcacacagtaaacggcgcac 0 false Drosophila melanogaster OREG0004670 Trl Trl USER DEFINED TRANSCRIPTION FACTOR BINDING SITE Bergman DNAse I footprint sites: www.flyreg.org: FPID:005506 2-Aug-2007 obig OREGDS00000 2-Aug-2007 2-Aug-2007 OREGEC00001 OREGES00015 OREGET00003 obig CG31366 Hsp70Ab ENSEMBL drosophila_melanogaster_core_45_43b 7893 POSITIVE OUTCOME 4028160 0 search_space EMPTY 0 false 0 sequence CACTGTTCTCGTTGCTTCGAGAGAGCG 0 false 0 sequence_with_flank ctgtcacacagtaaacggcgCACTGTTCTCGTTGCTTCGAGAGAGCGcgcctcgaatgttcgcgaaa 0 false Drosophila melanogaster OREG0004671 Hsf Hsf USER DEFINED TRANSCRIPTION FACTOR BINDING SITE Bergman DNAse I footprint sites: www.flyreg.org: FPID:005507 2-Aug-2007 obig OREGDS00000 2-Aug-2007 2-Aug-2007 OREGEC00001 OREGES00015 OREGET00003 obig CG31366 Hsp70Ab ENSEMBL drosophila_melanogaster_core_45_43b 7894 POSITIVE OUTCOME 2781290 0 search_space EMPTY 0 false 0 sequence GCTTCGAGAGAGCGCGCC 0 false 0 sequence_with_flank aacggcgcactgttctcgttGCTTCGAGAGAGCGCGCCtcgaatgttcgcgaaaagag 0 false Drosophila melanogaster OREG0004672 Trl Trl USER DEFINED TRANSCRIPTION FACTOR BINDING SITE Bergman DNAse I footprint sites: www.flyreg.org: FPID:005508 2-Aug-2007 obig OREGDS00000 2-Aug-2007 2-Aug-2007 OREGEC00001 OREGES00015 OREGET00003 obig CG31366 Hsp70Ab ENSEMBL drosophila_melanogaster_core_45_43b 7895 POSITIVE OUTCOME 4028160 0 search_space EMPTY 0 false 0 sequence CGCCTCGAATGTTCGCGAAAAGAGCGC 0 false 0 sequence_with_flank ctcgttgcttcgagagagcgCGCCTCGAATGTTCGCGAAAAGAGCGCcggagtataaatagaggagc 0 false Drosophila melanogaster OREG0004673 Hsf Hsf USER DEFINED TRANSCRIPTION FACTOR BINDING SITE Bergman DNAse I footprint sites: www.flyreg.org: FPID:005509 2-Aug-2007 obig OREGDS00000 2-Aug-2007 2-Aug-2007 OREGEC00001 OREGES00015 OREGET00003 obig CG31366 Hsp70Ab ENSEMBL drosophila_melanogaster_core_45_43b 7896 POSITIVE OUTCOME 2781290 0 search_space EMPTY 0 false 0 sequence AAAGAGCGCCG 0 false 0 sequence_with_flank cgcgcctcgaatgttcgcgaAAAGAGCGCCGgagtataaatagaggagctt 0 false Drosophila melanogaster OREG0004674 Trl Trl USER DEFINED TRANSCRIPTION FACTOR BINDING SITE Bergman DNAse I footprint sites: www.flyreg.org: FPID:005510 2-Aug-2007 obig OREGDS00000 2-Aug-2007 2-Aug-2007 OREGEC00001 OREGES00015 OREGET00003 obig CG31366 Hsp70Ab ENSEMBL drosophila_melanogaster_core_45_43b 7897 POSITIVE OUTCOME 6722872 0 search_space EMPTY 0 false 0 sequence GGAGTATAAATAGAGGAGCTTCGTCGACGGAGAGTCAATTCTATTCAAACAAGCAAAGTGAACACAT 0 false 0 sequence_with_flank atgttcgcgaaaagagcgccGGAGTATAAATAGAGGAGCTTCGTCGACGGAGAGTCAATTCTATTCAAACAAGCAAAGTGAACACATcgctaagcgaaagctaagca 0 false Drosophila melanogaster OREG0004675 Unspecified Unspecified USER DEFINED TRANSCRIPTION FACTOR BINDING SITE Bergman DNAse I footprint sites: www.flyreg.org: FPID:005063 2-Aug-2007 obig OREGDS00000 2-Aug-2007 2-Aug-2007 OREGEC00001 OREGES00015 OREGET00003 obig CG3068 aur ENSEMBL drosophila_melanogaster_core_45_43b 7898 POSITIVE OUTCOME 9001253 0 search_space EMPTY 0 false 0 sequence AAGTCACGATATTC 0 false 0 sequence_with_flank taacattttctaacactacaAAGTCACGATATTCttcaaccaaccgatagtatc 0 false Drosophila melanogaster OREG0004676 Unspecified Unspecified USER DEFINED TRANSCRIPTION FACTOR BINDING SITE Bergman DNAse I footprint sites: www.flyreg.org: FPID:006405. The binding site appeared to have mistake (missing a single CT in the repetitive site) which was causing this sequence to map to the wrong gene. The sequence and sequence with flank were updated to correct this. 2-Aug-2007 obig OREGDS00000 2-Aug-2007 2-Aug-2007 OREGEC00001 OREGES00015 OREGET00003 obig CG31613 His3 ENSEMBL drosophila_melanogaster_core_45_43b 7899 POSITIVE OUTCOME 2781290 0 search_space EMPTY 0 false 0 sequence TTCTCTCTCTCTCTCTCTCTCTCTCTTTC 0 false 0 sequence_with_flank aaagaactaatttcaacgtttctgtgtgcccctatttataggtaaaacgacaaaaacccgagagagtacgaacgatatgttcgttcgcttttcgctcgtcaaatgaaatggcctccgtttTTCTCTCTCTCTCTCTCTCTCTCTCTTTCaccgtccacgattgctatataagtaggtagcaaatgctctgatcgtttattgtgttttcaaacgtgaagtagtgaacgtgaactttagtgaaacccaaatcggagatggctcgtaccaag 0 false Drosophila melanogaster OREG0004677 Trl Trl USER DEFINED TRANSCRIPTION FACTOR BINDING SITE Bergman DNAse I footprint sites: www.flyreg.org: FPID:006406. Fixed sequence with flank to prevent ambiguous mapping. 2-Aug-2007 obig OREGDS00000 2-Aug-2007 2-Aug-2007 OREGEC00001 OREGES00015 OREGET00003 obig CG31613 His3 ENSEMBL drosophila_melanogaster_core_45_43b 7900 POSITIVE OUTCOME 6537904 0 search_space EMPTY 0 false 0 sequence CCACGATTGCTATATAAGTAGGTAGCAAATGC 0 false 0 sequence_with_flank tttataggtaaaacgacaaaaacccgagagagtacgaacgatatgttcgttcgcttttcgctcgtcaaatgaaatggcctccgtttttctctctctctctctctctctctctttcaccgtCCACGATTGCTATATAAGTAGGTAGCAAATGCtctgatcgtttattgtgttttcaaacgtgaagtagtgaacgtgaactttagtgaaacccaaatcggagatggctcgtaccaagcaaactgctcgcaaatcgactggtggaaaggcgccac 0 false Drosophila melanogaster OREG0004678 Unspecified Unspecified USER DEFINED TRANSCRIPTION FACTOR BINDING SITE Bergman DNAse I footprint sites: www.flyreg.org: FPID:006407. Modified sequence with flank to prevent ambiguous mapping. 3-Aug-2007 obig OREGDS00000 3-Aug-2007 3-Aug-2007 OREGEC00001 OREGES00015 OREGET00003 obig CG31613 His3 ENSEMBL drosophila_melanogaster_core_45_43b 7901 POSITIVE OUTCOME 6537904 0 search_space EMPTY 0 false 0 sequence GATCGTTTATTGTGTTTTCAAACGTGAAGTAGTGAACG 0 false 0 sequence_with_flank gaacgatatgttcgttcgcttttcgctcgtcaaatgaaatggcctccgtttttctctctctctctctctctctctctttcaccgtccacgattgctatataagtaggtagcaaatgctctGATCGTTTATTGTGTTTTCAAACGTGAAGTAGTGAACGtgaactttagtgaaacccaaatcggagatggctcgtaccaagcaaactgctcgcaaatcgactggtggaaaggcgccacgcaaacaactggctactaaggccgctcgcaagagtgctcca 0 false Drosophila melanogaster OREG0004679 Unspecified Unspecified USER DEFINED TRANSCRIPTION FACTOR BINDING SITE Updated from previous record to change species and sequence to rat as indicated in original paper. 10-Aug-2007 obig 10-Aug-2007 10-Aug-2007 OREGEC00001 OREGES00000 OREGET00000 obig ENSRNOG00000008536 Actc1 ENSEMBL rattus_norvegicus_core_45_34o 7907 POSITIVE OUTCOME 1570331 0 search_space EMPTY 0 false 0 sequence CAACTG 0 false 0 sequence_with_flank ctaaggcgaccaaataaggcaaggtggcagctcaggggccctccacccctgcccccggctgctcCAACTGaccccgtccatcagcgcgctataaagccgcgctccaggcgactgtcacctagtgcctgccaccagcgccagcccagctga 0 false Rattus norvegicus OREG0004685 ENSRNOG00000011306 myoD ENSEMBL rattus_norvegicus_core_45_34o TRANSCRIPTION FACTOR BINDING SITE OREGDS00014 15-Sep-2008 EV:0200061 Chromatin immunoprecipitation (ChIP) was performed on Adult female C57Bl/6J mouse liver tissue using Foxa2 [HNF-3-beta (M-20): sc-6554, Santa Cruz] antibody. Foxa2-bound DNA (4.7 ng) was purified by SDS-PAGE to obtain 100-300 bp fragments and sequenced on an Illumina 1G sequencer. Resulting sequences were mapped to the NCBI Build 36 (mm8) reference mouse genome to produce 13 984 706 mapped reads that were extended to 200 bp length XSETs and overlapped to create peaks. To further define the peak dataset, each group of XSETs that represented DNA fragments with identical fragment start coordinates was collapsed to a single XSET. Peaks generated from the resulting filtered reads were thresholded at a peak height of 10, creating a high confidence set of 11475 Foxa2-binding sites with an estimated false discovery rate of 0.05. 15-Sep-2008 OREGEC00001 OREGES00059 OREGET00003 obig UNKNOWN UNKNOWN USER DEFINED 44826 POSITIVE OUTCOME 18611952 0 search_space EMPTY 0 false 100526312 mus_musculus_core_46_36g sequence GGTATGAGGACTATATGAGATTCCATAAGACAAGCTTAAAAAACGTGGGCTGCAAATTATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTTCATGTCTGTGTATGTGTCCATGAATGTGAAAGCCAGAGTTAACCTCCTGTGATCATCCTTATGATGTTTCTACATAGATTTTTGAGACTAGGTCTTTGGAGTCTACCTGTATCTTCCACCTACGTGTTGGAAGTATAAGCACATTCAACTACATGTGATTTTAATGAAGGTACATGCATGAAATCTTAATGTTGGCTAATTTTATAAGTACAATTTTTAGATACTCATTTAATTAGAATGTCACTATGACATTCTAATTAAAAGGCCAAGGAGAGAAAAAGAGATTCCAAATGAATGAAAATAAAGGTACTTTCTATTCTGTGCCTC 1 100525885 1 true 100526312 mus_musculus_core_46_36g sequence_with_flank GGTATGAGGACTATATGAGATTCCATAAGACAAGCTTAAAAAACGTGGGCTGCAAATTATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTTCATGTCTGTGTATGTGTCCATGAATGTGAAAGCCAGAGTTAACCTCCTGTGATCATCCTTATGATGTTTCTACATAGATTTTTGAGACTAGGTCTTTGGAGTCTACCTGTATCTTCCACCTACGTGTTGGAAGTATAAGCACATTCAACTACATGTGATTTTAATGAAGGTACATGCATGAAATCTTAATGTTGGCTAATTTTATAAGTACAATTTTTAGATACTCATTTAATTAGAATGTCACTATGACATTCTAATTAAAAGGCCAAGGAGAGAAAAAGAGATTCCAAATGAATGAAAATAAAGGTACTTTCTATTCTGTGCCTC 1 100525885 1 true Mus musculus OREG0040830 15376 Foxa2 NCBI REGULATORY REGION OREGDS00014 15-Sep-2008 EV:0200061 Chromatin immunoprecipitation (ChIP) was performed on Adult female C57Bl/6J mouse liver tissue using Foxa2 [HNF-3-beta (M-20): sc-6554, Santa Cruz] antibody. Foxa2-bound DNA (4.7 ng) was purified by SDS-PAGE to obtain 100-300 bp fragments and sequenced on an Illumina 1G sequencer. Resulting sequences were mapped to the NCBI Build 36 (mm8) reference mouse genome to produce 13 984 706 mapped reads that were extended to 200 bp length XSETs and overlapped to create peaks. To further define the peak dataset, each group of XSETs that represented DNA fragments with identical fragment start coordinates was collapsed to a single XSET. Peaks generated from the resulting filtered reads were thresholded at a peak height of 10, creating a high confidence set of 11475 Foxa2-binding sites with an estimated false discovery rate of 0.05. 15-Sep-2008 OREGEC00001 OREGES00059 OREGET00003 obig UNKNOWN UNKNOWN USER DEFINED 44843 POSITIVE OUTCOME 18611952 0 search_space EMPTY 0 false 106944117 mus_musculus_core_46_36g sequence CACTATTCTCACAGCAGCTGAATCTCAGCAAGAAAACCGAAAAAAAAAAGAAAACAAGCAAGTGTGTTTCACTATCATTTCTCATTTATACAAGCACAAGGCCCTTGTCAAAGAAAATCCTCCTGCAAATCACAATCAAAGAAGTCTCCATTGAAAAGAGCACATCTCCTCCTAGCCTGGAAACTGTTCCCACAGCATGATGGGTTTTCCTATCCACCTTGCACATACTCAACTCAAGGTTACAGAAAATATTTAATTATAAAATATCATCTTTCAATCTTTAGATTGCTTATCAAGGCCCAAAATATTGAGGGGGGGGGGGAGTCCTCACTGGCTGTTCACAGTTTACTCAATTTTCCTTGAACTCATTAGCAATGGGGAGGAAAACAACACTAGCAAGAATTAACTTAGGTGCTGGGTCCTGTTAACAGCTTTCTCCTACTTCGTCCAAGACCTTTAGTCCCTGTTGACTTTTGCGTTCCCACACTGCTATTCCCCTTTCACCTAAATCCCTCTGTGCACAGCAACTGGTAAGAAAAACATTTGTTTTATTTATATCTTTGTTTTTTAAAGCTTAATTAGTTCAAGTCTATTTATGTGC 1 106943517 1 true 106944117 mus_musculus_core_46_36g sequence_with_flank CACTATTCTCACAGCAGCTGAATCTCAGCAAGAAAACCGAAAAAAAAAAGAAAACAAGCAAGTGTGTTTCACTATCATTTCTCATTTATACAAGCACAAGGCCCTTGTCAAAGAAAATCCTCCTGCAAATCACAATCAAAGAAGTCTCCATTGAAAAGAGCACATCTCCTCCTAGCCTGGAAACTGTTCCCACAGCATGATGGGTTTTCCTATCCACCTTGCACATACTCAACTCAAGGTTACAGAAAATATTTAATTATAAAATATCATCTTTCAATCTTTAGATTGCTTATCAAGGCCCAAAATATTGAGGGGGGGGGGGAGTCCTCACTGGCTGTTCACAGTTTACTCAATTTTCCTTGAACTCATTAGCAATGGGGAGGAAAACAACACTAGCAAGAATTAACTTAGGTGCTGGGTCCTGTTAACAGCTTTCTCCTACTTCGTCCAAGACCTTTAGTCCCTGTTGACTTTTGCGTTCCCACACTGCTATTCCCCTTTCACCTAAATCCCTCTGTGCACAGCAACTGGTAAGAAAAACATTTGTTTTATTTATATCTTTGTTTTTTAAAGCTTAATTAGTTCAAGTCTATTTATGTGC 1 106943517 1 true Mus musculus OREG0040838 15376 Foxa2 NCBI REGULATORY REGION OREGDS00014 15-Sep-2008 EV:0200061 Chromatin immunoprecipitation (ChIP) was performed on Adult female C57Bl/6J mouse liver tissue using Foxa2 [HNF-3-beta (M-20): sc-6554, Santa Cruz] antibody. Foxa2-bound DNA (4.7 ng) was purified by SDS-PAGE to obtain 100-300 bp fragments and sequenced on an Illumina 1G sequencer. Resulting sequences were mapped to the NCBI Build 36 (mm8) reference mouse genome to produce 13 984 706 mapped reads that were extended to 200 bp length XSETs and overlapped to create peaks. To further define the peak dataset, each group of XSETs that represented DNA fragments with identical fragment start coordinates was collapsed to a single XSET. Peaks generated from the resulting filtered reads were thresholded at a peak height of 10, creating a high confidence set of 11475 Foxa2-binding sites with an estimated false discovery rate of 0.05. 15-Sep-2008 OREGEC00001 OREGES00059 OREGET00003 obig UNKNOWN UNKNOWN USER DEFINED 44842 POSITIVE OUTCOME 18611952 0 search_space EMPTY 0 false 106942819 mus_musculus_core_46_36g sequence TATCCATGGAGTTCCTTTTCATGGAAATGATGACTATGATGTCAACTGCCCATCAGGGAGTCTGGCTGAGACTCTGCATAGAATGTTCATCTGTAGCGCTTTTGTAGGGAACGTATTTTCAGAGTAAAGGTTCACAGGGGTGGGGTGGGGTGGGGTGGGGTATGGTGGGAGGGAGAGTAGAGGGAAATAGCACACCAATAGCAACCTCTCAGGCACTTCACGTCCACGCAGAACCTCAGAATGTGACCTCAATGGGAAACAGGGTCTTTGTTGGTTTGAGATAGGGCCATTTTGGATTTGAGTGGCTCCTACATACAATAACTGTCCATAAATGAGAGAGAACAGTATACACAAAGACACACAGGGAGAAGCCATGCATTCAGGAGATTGTAATAGAAGCCAGAAGCACTGGTAACCAGCAGAAGCCAGGGAAAGACAGTAGGTGTTCTTCATCACAGATTTCAGCCTCTTTAACTGTAGGAGAATACTCTGATGATGTTTCAGGCTCCCAGGTCTTGAAGTTTGTTACCTCAGCCCTAGGAAGCCAATAGGAGTGATCCTTTGGGCAGCTCCATGTCCCTGCCCTTATGAGTAGACCACAGCACGGACTCTCCTTTCTCTAGTTTACTCTTTTGTCCTAGGAAGAGAATATTTCAGGTAAGAGAAGAGTTCTTTCACATTTCCACTTTGGACCATGTGGATTACAGTCACAGTCCAAAAGCAAACAAAGCAAAAAATCAGAGGTTGTTGACCCAGAGAGTAAACATCCCATTGAGGTGAAAGCAGCAGACTGGAGCTGGAGAGGTGGCAGAGGTTAAGACGCACCCACCCCACCCACATCAGATGGCTCACAACTGTCTGTAACTCCTGCCCAGAGAATCCAAGGTCCTCTCTCACCTAGAATCCCTGCATTAAAGAGTACATACTCATACACCATTTAAAATAAAAGTAAGTCTAAAAAAAAAGGAGCACGAGAGCAAAAGAGGTTTTTTCCTTTTTCTTTCTTCTCTCTCTCTCTCTCT 1 106941798 1 true 106942819 mus_musculus_core_46_36g sequence_with_flank TATCCATGGAGTTCCTTTTCATGGAAATGATGACTATGATGTCAACTGCCCATCAGGGAGTCTGGCTGAGACTCTGCATAGAATGTTCATCTGTAGCGCTTTTGTAGGGAACGTATTTTCAGAGTAAAGGTTCACAGGGGTGGGGTGGGGTGGGGTGGGGTATGGTGGGAGGGAGAGTAGAGGGAAATAGCACACCAATAGCAACCTCTCAGGCACTTCACGTCCACGCAGAACCTCAGAATGTGACCTCAATGGGAAACAGGGTCTTTGTTGGTTTGAGATAGGGCCATTTTGGATTTGAGTGGCTCCTACATACAATAACTGTCCATAAATGAGAGAGAACAGTATACACAAAGACACACAGGGAGAAGCCATGCATTCAGGAGATTGTAATAGAAGCCAGAAGCACTGGTAACCAGCAGAAGCCAGGGAAAGACAGTAGGTGTTCTTCATCACAGATTTCAGCCTCTTTAACTGTAGGAGAATACTCTGATGATGTTTCAGGCTCCCAGGTCTTGAAGTTTGTTACCTCAGCCCTAGGAAGCCAATAGGAGTGATCCTTTGGGCAGCTCCATGTCCCTGCCCTTATGAGTAGACCACAGCACGGACTCTCCTTTCTCTAGTTTACTCTTTTGTCCTAGGAAGAGAATATTTCAGGTAAGAGAAGAGTTCTTTCACATTTCCACTTTGGACCATGTGGATTACAGTCACAGTCCAAAAGCAAACAAAGCAAAAAATCAGAGGTTGTTGACCCAGAGAGTAAACATCCCATTGAGGTGAAAGCAGCAGACTGGAGCTGGAGAGGTGGCAGAGGTTAAGACGCACCCACCCCACCCACATCAGATGGCTCACAACTGTCTGTAACTCCTGCCCAGAGAATCCAAGGTCCTCTCTCACCTAGAATCCCTGCATTAAAGAGTACATACTCATACACCATTTAAAATAAAAGTAAGTCTAAAAAAAAAGGAGCACGAGAGCAAAAGAGGTTTTTTCCTTTTTCTTTCTTCTCTCTCTCTCTCTCT 1 106941798 1 true Mus musculus OREG0040837 15376 Foxa2 NCBI REGULATORY REGION OREGDS00014 15-Sep-2008 EV:0200061 Chromatin immunoprecipitation (ChIP) was performed on Adult female C57Bl/6J mouse liver tissue using Foxa2 [HNF-3-beta (M-20): sc-6554, Santa Cruz] antibody. Foxa2-bound DNA (4.7 ng) was purified by SDS-PAGE to obtain 100-300 bp fragments and sequenced on an Illumina 1G sequencer. Resulting sequences were mapped to the NCBI Build 36 (mm8) reference mouse genome to produce 13 984 706 mapped reads that were extended to 200 bp length XSETs and overlapped to create peaks. To further define the peak dataset, each group of XSETs that represented DNA fragments with identical fragment start coordinates was collapsed to a single XSET. Peaks generated from the resulting filtered reads were thresholded at a peak height of 10, creating a high confidence set of 11475 Foxa2-binding sites with an estimated false discovery rate of 0.05. 15-Sep-2008 OREGEC00001 OREGES00059 OREGET00003 obig UNKNOWN UNKNOWN USER DEFINED 44841 POSITIVE OUTCOME 18611952 0 search_space EMPTY 0 false 106941114 mus_musculus_core_46_36g sequence GGCATCTCTAACCCAGGTTGCTTGCAACTGCTCACATGTTTAGTGCATGTACAAACAGAAAAATGTCAGTTGTGCTGTGGTTTAAGTTTTACCCATTCATTCAATATCTAAGTGACTTAAAAACTTACATTCATTTAAAAATAAATAAGAGAATGAAAATCTGAAATAGTGAAAATGAAGTAGAAAATTAAGCCTAGCTCTAAAAGAAGCCTGACTTCTGCCCTACATGTGTGACCAGAGATAATGCCTTTGGGAGTGATACACTGAGGGCAAGTGAGCCTTGGCAAGCAGAACTAACACTGAGGTTGATGGCTTTGAGTCAATAGAGAGTTGATAAGGACTGAAGACTGAGGTCCACCATGTCACTCATGTCTGTGTCATAGAGCCTCAATAAAAATTCAGGCCACCAATACTTCACACAGGACTTCCTGGTCCTCAGGTGTCAGTGCTGGGACAGCAATTCATTCTAACATAGGCCATGGTTTTCAACTTTCAGGGCTACAACAAGCTTTTCACAGGAGTCATATATCAGATAGGTTGCATATCAGATATTTTATATTATG 1 106940552 1 true 106941114 mus_musculus_core_46_36g sequence_with_flank GGCATCTCTAACCCAGGTTGCTTGCAACTGCTCACATGTTTAGTGCATGTACAAACAGAAAAATGTCAGTTGTGCTGTGGTTTAAGTTTTACCCATTCATTCAATATCTAAGTGACTTAAAAACTTACATTCATTTAAAAATAAATAAGAGAATGAAAATCTGAAATAGTGAAAATGAAGTAGAAAATTAAGCCTAGCTCTAAAAGAAGCCTGACTTCTGCCCTACATGTGTGACCAGAGATAATGCCTTTGGGAGTGATACACTGAGGGCAAGTGAGCCTTGGCAAGCAGAACTAACACTGAGGTTGATGGCTTTGAGTCAATAGAGAGTTGATAAGGACTGAAGACTGAGGTCCACCATGTCACTCATGTCTGTGTCATAGAGCCTCAATAAAAATTCAGGCCACCAATACTTCACACAGGACTTCCTGGTCCTCAGGTGTCAGTGCTGGGACAGCAATTCATTCTAACATAGGCCATGGTTTTCAACTTTCAGGGCTACAACAAGCTTTTCACAGGAGTCATATATCAGATAGGTTGCATATCAGATATTTTATATTATG 1 106940552 1 true Mus musculus OREG0040836 15376 Foxa2 NCBI REGULATORY REGION OREGDS00014 15-Sep-2008 EV:0200061 Chromatin immunoprecipitation (ChIP) was performed on Adult female C57Bl/6J mouse liver tissue using Foxa2 [HNF-3-beta (M-20): sc-6554, Santa Cruz] antibody. Foxa2-bound DNA (4.7 ng) was purified by SDS-PAGE to obtain 100-300 bp fragments and sequenced on an Illumina 1G sequencer. Resulting sequences were mapped to the NCBI Build 36 (mm8) reference mouse genome to produce 13 984 706 mapped reads that were extended to 200 bp length XSETs and overlapped to create peaks. To further define the peak dataset, each group of XSETs that represented DNA fragments with identical fragment start coordinates was collapsed to a single XSET. Peaks generated from the resulting filtered reads were thresholded at a peak height of 10, creating a high confidence set of 11475 Foxa2-binding sites with an estimated false discovery rate of 0.05. 15-Sep-2008 OREGEC00001 OREGES00059 OREGET00003 obig UNKNOWN UNKNOWN USER DEFINED 44840 POSITIVE OUTCOME 18611952 0 search_space EMPTY 0 false 106767580 mus_musculus_core_46_36g sequence GGGGAAGTGAGAGAAGGAATGTGAGCTTCAGCATTGATTCCACTTGACCGCAGCCAGCCTTATCAACCTCACAAAGCAGAGATGCCCTTCAGCACTGCTAGCTTTAAGCCTACTCCAAAGGCAGGCCACTCACACTTGGCCTGTGATGGCATCAATTGTGCTTTTAGTGTGTCAAGCTCTGCGTCCATCATAACTTGTCATACCTTAACTGTTTTATTGCAAATCAAATGCCATAGGCCATAAAGCTCTACATGTACATACACATATGAACAGATTTCTCACAATTTAAGAAACTTCTAAGTGTTTTGTCTTTCTCCTTCCAGTTCTGTTCCTCTACTCAGGAGCATATTTTCAGAGGGAATACATTTTTGTTTCTTGTACCCAGTTCCAAACTAAATGTCTTTTACTTCTATACAATAAGTTCTAAGCTTTTTCCCCATACTTTTTAAACTGCATAAATAGACTTTAGTAATAATAGTGTATATGGAATAAAGAAATATGAGAACACCATATTCTATATAGAATGCTTTTAAGCAAAAATAAATCCAAAGCTATTTGTGTGGGGGGGGTAATTTTATTCTCTAATTTCCATTTTGTAGATAAGACACAGCTTGGCTCCTTGGTTGGCCTGGAATAAGTTTGAGATTAGCCCAAAACTAGTGCCAAAATTTGAAGCCATCCCTGTCTGAGGAGGCTATGAACACTTTCAGGTGTCCCTTAAGCACCAAAGTTCACAAGATTAAGTCAATAGGCAGTGTCCCTGCACTTTAACCTCAGTGGAGCAGGGCCAGGGCCCTTCCAATTCTGCAGGGACTTTAACCATTAAGCTGTGCATAACAACAAGGCCTTTAGCTTAGTTTTACTCCTGGAGGCTTGAAGAGAGCAGATAAGAGATGAATATATTAATATCCTTTCTCTCTGTAGGTATGTCATATATCATCACCATAATTGGCCCCATTTATAGCTATCCTACTACAGGAAAGAAACAGTCCTCTGTACTTTACATATGTTAGTCTTTAATGATCCCAGAAACTCTTGGAAATAAGAATTAATGCTGCTCTCCATTTATAATAAAAGGAAATTAAGGGTTTTGACAGTATATTTACTCATGTCAAAGACACTCAGCTGAAAACTGACACAGACCATATTCAGGTCAGATATGTTAGGCTTGCAGCATTAAGCCTAACACTTGTCTGTCTATTGACTTAATCTTGGGAACTTTAGTGTTTAAGTATGCTAGTGCTGAAAACAAACAACAACAAAGTTAGAAGTACTAGTTAAACTTAATGTTTGTGCTGATTCTTTAGAAATATACCTAAATGAGAACCCCAAACCCCAACCTTCTTGCTGCCCATTTGCATTACGTGCAATTATCAAGTCAGATATGTTTCTAGGCTAAGGTCAAATTGTGCTTACAGATGGTTCTGGAGAATTCTTACAAAAGAATATG 1 106766131 1 true 106767580 mus_musculus_core_46_36g sequence_with_flank GGGGAAGTGAGAGAAGGAATGTGAGCTTCAGCATTGATTCCACTTGACCGCAGCCAGCCTTATCAACCTCACAAAGCAGAGATGCCCTTCAGCACTGCTAGCTTTAAGCCTACTCCAAAGGCAGGCCACTCACACTTGGCCTGTGATGGCATCAATTGTGCTTTTAGTGTGTCAAGCTCTGCGTCCATCATAACTTGTCATACCTTAACTGTTTTATTGCAAATCAAATGCCATAGGCCATAAAGCTCTACATGTACATACACATATGAACAGATTTCTCACAATTTAAGAAACTTCTAAGTGTTTTGTCTTTCTCCTTCCAGTTCTGTTCCTCTACTCAGGAGCATATTTTCAGAGGGAATACATTTTTGTTTCTTGTACCCAGTTCCAAACTAAATGTCTTTTACTTCTATACAATAAGTTCTAAGCTTTTTCCCCATACTTTTTAAACTGCATAAATAGACTTTAGTAATAATAGTGTATATGGAATAAAGAAATATGAGAACACCATATTCTATATAGAATGCTTTTAAGCAAAAATAAATCCAAAGCTATTTGTGTGGGGGGGGTAATTTTATTCTCTAATTTCCATTTTGTAGATAAGACACAGCTTGGCTCCTTGGTTGGCCTGGAATAAGTTTGAGATTAGCCCAAAACTAGTGCCAAAATTTGAAGCCATCCCTGTCTGAGGAGGCTATGAACACTTTCAGGTGTCCCTTAAGCACCAAAGTTCACAAGATTAAGTCAATAGGCAGTGTCCCTGCACTTTAACCTCAGTGGAGCAGGGCCAGGGCCCTTCCAATTCTGCAGGGACTTTAACCATTAAGCTGTGCATAACAACAAGGCCTTTAGCTTAGTTTTACTCCTGGAGGCTTGAAGAGAGCAGATAAGAGATGAATATATTAATATCCTTTCTCTCTGTAGGTATGTCATATATCATCACCATAATTGGCCCCATTTATAGCTATCCTACTACAGGAAAGAAACAGTCCTCTGTACTTTACATATGTTAGTCTTTAATGATCCCAGAAACTCTTGGAAATAAGAATTAATGCTGCTCTCCATTTATAATAAAAGGAAATTAAGGGTTTTGACAGTATATTTACTCATGTCAAAGACACTCAGCTGAAAACTGACACAGACCATATTCAGGTCAGATATGTTAGGCTTGCAGCATTAAGCCTAACACTTGTCTGTCTATTGACTTAATCTTGGGAACTTTAGTGTTTAAGTATGCTAGTGCTGAAAACAAACAACAACAAAGTTAGAAGTACTAGTTAAACTTAATGTTTGTGCTGATTCTTTAGAAATATACCTAAATGAGAACCCCAAACCCCAACCTTCTTGCTGCCCATTTGCATTACGTGCAATTATCAAGTCAGATATGTTTCTAGGCTAAGGTCAAATTGTGCTTACAGATGGTTCTGGAGAATTCTTACAAAAGAATATG 1 106766131 1 true Mus musculus OREG0040835 15376 Foxa2 NCBI REGULATORY REGION OREGDS00014 15-Sep-2008 EV:0200061 Chromatin immunoprecipitation (ChIP) was performed on Adult female C57Bl/6J mouse liver tissue using Foxa2 [HNF-3-beta (M-20): sc-6554, Santa Cruz] antibody. Foxa2-bound DNA (4.7 ng) was purified by SDS-PAGE to obtain 100-300 bp fragments and sequenced on an Illumina 1G sequencer. Resulting sequences were mapped to the NCBI Build 36 (mm8) reference mouse genome to produce 13 984 706 mapped reads that were extended to 200 bp length XSETs and overlapped to create peaks. To further define the peak dataset, each group of XSETs that represented DNA fragments with identical fragment start coordinates was collapsed to a single XSET. Peaks generated from the resulting filtered reads were thresholded at a peak height of 10, creating a high confidence set of 11475 Foxa2-binding sites with an estimated false discovery rate of 0.05. 15-Sep-2008 OREGEC00001 OREGES00059 OREGET00003 obig UNKNOWN UNKNOWN USER DEFINED 44839 POSITIVE OUTCOME 18611952 0 search_space EMPTY 0 false 105443638 mus_musculus_core_46_36g sequence GTTAATTAGCCAATTAATTAATTAAATTTCTGAGACATGGCTTCTCTGTATAGCCATGGTTGTCCAGGAACTCACTTTGTAGACCAGGCTTGCCTCAAATTCAGAAATCTGCCTGCCTCTGCCTCCCGAGTGCTGGGATTAAAGGCATGCACCACCATGCCCAGCTAATTTATTTATATATATATATATTTTATTTTAGCTTATGACTTGTTTTAGTGTCTATCTGTCCTGAACGAATATTTATATTTTCTGTTAACAGCTGGTGTCCCTGGACACCAACCGAAATCATTAGATAGATATAGTCATTCCTGTAAGATAACATGGAAGTAT 1 105443309 1 true 105443638 mus_musculus_core_46_36g sequence_with_flank GTTAATTAGCCAATTAATTAATTAAATTTCTGAGACATGGCTTCTCTGTATAGCCATGGTTGTCCAGGAACTCACTTTGTAGACCAGGCTTGCCTCAAATTCAGAAATCTGCCTGCCTCTGCCTCCCGAGTGCTGGGATTAAAGGCATGCACCACCATGCCCAGCTAATTTATTTATATATATATATATTTTATTTTAGCTTATGACTTGTTTTAGTGTCTATCTGTCCTGAACGAATATTTATATTTTCTGTTAACAGCTGGTGTCCCTGGACACCAACCGAAATCATTAGATAGATATAGTCATTCCTGTAAGATAACATGGAAGTAT 1 105443309 1 true Mus musculus OREG0040834 15376 Foxa2 NCBI REGULATORY REGION OREGDS00014 15-Sep-2008 EV:0200061 Chromatin immunoprecipitation (ChIP) was performed on Adult female C57Bl/6J mouse liver tissue using Foxa2 [HNF-3-beta (M-20): sc-6554, Santa Cruz] antibody. Foxa2-bound DNA (4.7 ng) was purified by SDS-PAGE to obtain 100-300 bp fragments and sequenced on an Illumina 1G sequencer. Resulting sequences were mapped to the NCBI Build 36 (mm8) reference mouse genome to produce 13 984 706 mapped reads that were extended to 200 bp length XSETs and overlapped to create peaks. To further define the peak dataset, each group of XSETs that represented DNA fragments with identical fragment start coordinates was collapsed to a single XSET. Peaks generated from the resulting filtered reads were thresholded at a peak height of 10, creating a high confidence set of 11475 Foxa2-binding sites with an estimated false discovery rate of 0.05. 15-Sep-2008 OREGEC00001 OREGES00059 OREGET00003 obig UNKNOWN UNKNOWN USER DEFINED 44838 POSITIVE OUTCOME 18611952 0 search_space EMPTY 0 false 104232618 mus_musculus_core_46_36g sequence ATGAATTTTGTTTTATGAGTCATGAGATGTGCAAATATAAAGTCTTCAATTAGCTATATTGTGTTTAAAAGTATTCCTATTTCTTGCTCAGTCCTCATTTTTATTTTGTATATTTTATTTTAATACATAAGATCTTCTGTTTTATAAGCTTGAAACTCCCAGGCTCAAGCAATTCTCATGACTCAGCCTCCTAAGTAAATGGCTATACTGGTACAACCAGTCAGAACTCTTCTATAAAGATTTGTGCTTGCATCTGGGGAGATGAACAATGTGTGAAAGTGTGTAAGGTCAGGAATGAAAATAGTGTTTTTTTTTTCCTTCGGAGCTATTCTCATAATTATTCT 1 104232275 1 true 104232618 mus_musculus_core_46_36g sequence_with_flank ATGAATTTTGTTTTATGAGTCATGAGATGTGCAAATATAAAGTCTTCAATTAGCTATATTGTGTTTAAAAGTATTCCTATTTCTTGCTCAGTCCTCATTTTTATTTTGTATATTTTATTTTAATACATAAGATCTTCTGTTTTATAAGCTTGAAACTCCCAGGCTCAAGCAATTCTCATGACTCAGCCTCCTAAGTAAATGGCTATACTGGTACAACCAGTCAGAACTCTTCTATAAAGATTTGTGCTTGCATCTGGGGAGATGAACAATGTGTGAAAGTGTGTAAGGTCAGGAATGAAAATAGTGTTTTTTTTTTCCTTCGGAGCTATTCTCATAATTATTCT 1 104232275 1 true Mus musculus OREG0040833 15376 Foxa2 NCBI REGULATORY REGION OREGDS00014 15-Sep-2008 EV:0200061 Chromatin immunoprecipitation (ChIP) was performed on Adult female C57Bl/6J mouse liver tissue using Foxa2 [HNF-3-beta (M-20): sc-6554, Santa Cruz] antibody. Foxa2-bound DNA (4.7 ng) was purified by SDS-PAGE to obtain 100-300 bp fragments and sequenced on an Illumina 1G sequencer. Resulting sequences were mapped to the NCBI Build 36 (mm8) reference mouse genome to produce 13 984 706 mapped reads that were extended to 200 bp length XSETs and overlapped to create peaks. To further define the peak dataset, each group of XSETs that represented DNA fragments with identical fragment start coordinates was collapsed to a single XSET. Peaks generated from the resulting filtered reads were thresholded at a peak height of 10, creating a high confidence set of 11475 Foxa2-binding sites with an estimated false discovery rate of 0.05. 15-Sep-2008 OREGEC00001 OREGES00059 OREGET00003 obig UNKNOWN UNKNOWN USER DEFINED 44837 POSITIVE OUTCOME 18611952 0 search_space EMPTY 0 false 102895017 mus_musculus_core_46_36g sequence CAGTGATGGTCGATGATTCCCAAGGTATGTTCACATTCTTATGTCTGAGATGAGAGAGTGACACACTTAGTTTAGTTTTAGTCAAATTCTGGCTGGAAAGGATACTCTAAATGTATCAAACAGAGTGTATTCAATATTCTATTCCAGTTTGTATTCTAATAAATATATACTATAATAATATATGATTATATAATTTATTATATGATATATATATAATATATTCATATGCTATATCTTTTATTTACACTATAGAATATATAATTGTGTGTTATATAATTATTATACTTATTGTAATATAATGTATAACAATGTATTGTTGCTATAATTATCATATACTATGCAATATATTATATAATCATATGATATATATATAACATAAAACACATGATAGAATATTTGATCTATTTACTTATTTATGTATAATGGAAAATAGAAACAGCCTAACAGTAATAAATCCTTGAGAGATTAAGAAATATTATATCAGAAAGAATTAAACAGAGCAAAAAATATTCAGTTATCTTTGAATATGAGAGGTTGCTCTTGATATAATGTTGTCTGGTGGTAACAAGGAATCTAATAAGATATTCTGAACTGTAACACATATGTGGTCACACACAGTCACATTTGTATAGATATACATCAACATGTGCAAGCACCCAGACACTATGACACCTGTATGGACACATACAGACACAGAAACACAAA 1 102894313 1 true 102895017 mus_musculus_core_46_36g sequence_with_flank CAGTGATGGTCGATGATTCCCAAGGTATGTTCACATTCTTATGTCTGAGATGAGAGAGTGACACACTTAGTTTAGTTTTAGTCAAATTCTGGCTGGAAAGGATACTCTAAATGTATCAAACAGAGTGTATTCAATATTCTATTCCAGTTTGTATTCTAATAAATATATACTATAATAATATATGATTATATAATTTATTATATGATATATATATAATATATTCATATGCTATATCTTTTATTTACACTATAGAATATATAATTGTGTGTTATATAATTATTATACTTATTGTAATATAATGTATAACAATGTATTGTTGCTATAATTATCATATACTATGCAATATATTATATAATCATATGATATATATATAACATAAAACACATGATAGAATATTTGATCTATTTACTTATTTATGTATAATGGAAAATAGAAACAGCCTAACAGTAATAAATCCTTGAGAGATTAAGAAATATTATATCAGAAAGAATTAAACAGAGCAAAAAATATTCAGTTATCTTTGAATATGAGAGGTTGCTCTTGATATAATGTTGTCTGGTGGTAACAAGGAATCTAATAAGATATTCTGAACTGTAACACATATGTGGTCACACACAGTCACATTTGTATAGATATACATCAACATGTGCAAGCACCCAGACACTATGACACCTGTATGGACACATACAGACACAGAAACACAAA 1 102894313 1 true Mus musculus OREG0040832 15376 Foxa2 NCBI REGULATORY REGION OREGDS00014 15-Sep-2008 EV:0200061 Chromatin immunoprecipitation (ChIP) was performed on Adult female C57Bl/6J mouse liver tissue using Foxa2 [HNF-3-beta (M-20): sc-6554, Santa Cruz] antibody. Foxa2-bound DNA (4.7 ng) was purified by SDS-PAGE to obtain 100-300 bp fragments and sequenced on an Illumina 1G sequencer. Resulting sequences were mapped to the NCBI Build 36 (mm8) reference mouse genome to produce 13 984 706 mapped reads that were extended to 200 bp length XSETs and overlapped to create peaks. To further define the peak dataset, each group of XSETs that represented DNA fragments with identical fragment start coordinates was collapsed to a single XSET. Peaks generated from the resulting filtered reads were thresholded at a peak height of 10, creating a high confidence set of 11475 Foxa2-binding sites with an estimated false discovery rate of 0.05. 15-Sep-2008 OREGEC00001 OREGES00059 OREGET00003 obig UNKNOWN UNKNOWN USER DEFINED 44836 POSITIVE OUTCOME 18611952 0 search_space EMPTY 0 false 102537637 mus_musculus_core_46_36g sequence CCCTGTACAGGGGAATGCCAGGGCCAAAATATGGGAATGGGTGGGTAGGGAAGTAGAGGGGAGGGTATGGGGGACTTTTGGGATAGCATTGGAAATGTAATTGAGGAAAATACGTAATAAAAATATTTAAAAAAAAGAATAAAGCCATTAATTACAATGTTGTCAGCAGGAAAGAGAAAGTAAATATTTGAATTTCTTTGCTACTCATTCCACACAATGCTTCTTTCAGGTCCAAAGTACCTGGACCTTGGTGTGTGATGCAATAATTGTTTGTCCTGAGTGGCACACTGGATGGGCAGAGAGGGGTCTGAGTTATTGAGATCAAATTGACTCTTTTTCTTCTGAGTTAGAAGCCTGGTCTACCTTGCAATTGTGCAAAAGTAAGATTGTATGGTAATGATAAAATAGTTAAACAGGTGAAACTCACGCTCAGATTGCATAACAGCCTGGGCTCGCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCATCCCTCCCTTCCTCCCTCCCTTCTTTGTGACTTATACACAGAATCATCTGCCAGCTCAGGAGAGAAATGTTTTGTGTTGTGGATGGGAGAGACTGAGTTAGAGATGCTGCCCTGTGTTTGTAGACAGATTGAGTGATGTCTGAGTAGATCAGTGCCTCTCTCTTTCTGACTTTCTGC 1 102536974 1 true 102537637 mus_musculus_core_46_36g sequence_with_flank CCCTGTACAGGGGAATGCCAGGGCCAAAATATGGGAATGGGTGGGTAGGGAAGTAGAGGGGAGGGTATGGGGGACTTTTGGGATAGCATTGGAAATGTAATTGAGGAAAATACGTAATAAAAATATTTAAAAAAAAGAATAAAGCCATTAATTACAATGTTGTCAGCAGGAAAGAGAAAGTAAATATTTGAATTTCTTTGCTACTCATTCCACACAATGCTTCTTTCAGGTCCAAAGTACCTGGACCTTGGTGTGTGATGCAATAATTGTTTGTCCTGAGTGGCACACTGGATGGGCAGAGAGGGGTCTGAGTTATTGAGATCAAATTGACTCTTTTTCTTCTGAGTTAGAAGCCTGGTCTACCTTGCAATTGTGCAAAAGTAAGATTGTATGGTAATGATAAAATAGTTAAACAGGTGAAACTCACGCTCAGATTGCATAACAGCCTGGGCTCGCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCATCCCTCCCTTCCTCCCTCCCTTCTTTGTGACTTATACACAGAATCATCTGCCAGCTCAGGAGAGAAATGTTTTGTGTTGTGGATGGGAGAGACTGAGTTAGAGATGCTGCCCTGTGTTTGTAGACAGATTGAGTGATGTCTGAGTAGATCAGTGCCTCTCTCTTTCTGACTTTCTGC 1 102536974 1 true Mus musculus OREG0040831 15376 Foxa2 NCBI REGULATORY REGION OREGDS00014 15-Sep-2008 EV:0200061 Chromatin immunoprecipitation (ChIP) was performed on Adult female C57Bl/6J mouse liver tissue using Foxa2 [HNF-3-beta (M-20): sc-6554, Santa Cruz] antibody. Foxa2-bound DNA (4.7 ng) was purified by SDS-PAGE to obtain 100-300 bp fragments and sequenced on an Illumina 1G sequencer. Resulting sequences were mapped to the NCBI Build 36 (mm8) reference mouse genome to produce 13 984 706 mapped reads that were extended to 200 bp length XSETs and overlapped to create peaks. To further define the peak dataset, each group of XSETs that represented DNA fragments with identical fragment start coordinates was collapsed to a single XSET. Peaks generated from the resulting filtered reads were thresholded at a peak height of 10, creating a high confidence set of 11475 Foxa2-binding sites with an estimated false discovery rate of 0.05. 15-Sep-2008 OREGEC00001 OREGES00059 OREGET00003 obig UNKNOWN UNKNOWN USER DEFINED 44844 POSITIVE OUTCOME 18611952 0 search_space EMPTY 0 false 107003621 mus_musculus_core_46_36g sequence GGTGCCAGGCCACTGTCTCCTTGACTTTGAGGGGTCTTTAGAGGAAACAAACCTGAGGATGTTCTCATCCAGAATCTCCTTGTGTCACTCACTGTTCCTTCAAGCACTGTTCCCAGAGAAGAACTCCAACTAGAAACTCATAAGCAAGGTCCTGTGGTGAGAGGGATTATGTCAGTGGTATCAGGAGCCACACATCATGGACAGCCTATGGACTGGCGTTCAGCATAGCTTTTCATTTCCCCACCCTCTCTCTGTGCAATGCTGGGAACTGAATCCAGGCCCTTGCACATCCTAGACAAGCCTCTACCACCAGCTCTATCTCTATTGTCTAACAGTCACTCCAAAAATACCCAGAGTTGGAAAAAGAACAGTTGGGTATTTTTGCTGACTAAACCCACTATCTATTTTACAATTCTTCCCTCCTAGAGTAACCTGGTATAACTGAATGTAGCTGGCTGAAAAGATTCAATGTCCAGCCTCCGACAGAGAAGAGATACAGTGTCCACAGGACACAGTTCAAACAAATATGAGTTAAGCAGAGGTCATTGATTGGGTTTTGGAGTCATTTCCTTTTCCAGCACAAGGCAGCCTTCCTTCAGCCACTGTCTTGTAACTGACACTTAGAGAAAAGCCAGGGTCTCACAGAAACTCTTGCCTGGTACCTTGGTTACCAATCATGTCCAGATGCTGTCTAGCTCATATGAGAAAAAAACAATCCTAAAGTTGTTTCAAGATACTGTTTA 1 107002879 1 true 107003621 mus_musculus_core_46_36g sequence_with_flank GGTGCCAGGCCACTGTCTCCTTGACTTTGAGGGGTCTTTAGAGGAAACAAACCTGAGGATGTTCTCATCCAGAATCTCCTTGTGTCACTCACTGTTCCTTCAAGCACTGTTCCCAGAGAAGAACTCCAACTAGAAACTCATAAGCAAGGTCCTGTGGTGAGAGGGATTATGTCAGTGGTATCAGGAGCCACACATCATGGACAGCCTATGGACTGGCGTTCAGCATAGCTTTTCATTTCCCCACCCTCTCTCTGTGCAATGCTGGGAACTGAATCCAGGCCCTTGCACATCCTAGACAAGCCTCTACCACCAGCTCTATCTCTATTGTCTAACAGTCACTCCAAAAATACCCAGAGTTGGAAAAAGAACAGTTGGGTATTTTTGCTGACTAAACCCACTATCTATTTTACAATTCTTCCCTCCTAGAGTAACCTGGTATAACTGAATGTAGCTGGCTGAAAAGATTCAATGTCCAGCCTCCGACAGAGAAGAGATACAGTGTCCACAGGACACAGTTCAAACAAATATGAGTTAAGCAGAGGTCATTGATTGGGTTTTGGAGTCATTTCCTTTTCCAGCACAAGGCAGCCTTCCTTCAGCCACTGTCTTGTAACTGACACTTAGAGAAAAGCCAGGGTCTCACAGAAACTCTTGCCTGGTACCTTGGTTACCAATCATGTCCAGATGCTGTCTAGCTCATATGAGAAAAAAACAATCCTAAAGTTGTTTCAAGATACTGTTTA 1 107002879 1 true Mus musculus OREG0040839 15376 Foxa2 NCBI REGULATORY REGION OREGDS00014 15-Sep-2008 EV:0200061 Chromatin immunoprecipitation (ChIP) was performed on Adult female C57Bl/6J mouse liver tissue using Foxa2 [HNF-3-beta (M-20): sc-6554, Santa Cruz] antibody. Foxa2-bound DNA (4.7 ng) was purified by SDS-PAGE to obtain 100-300 bp fragments and sequenced on an Illumina 1G sequencer. Resulting sequences were mapped to the NCBI Build 36 (mm8) reference mouse genome to produce 13 984 706 mapped reads that were extended to 200 bp length XSETs and overlapped to create peaks. To further define the peak dataset, each group of XSETs that represented DNA fragments with identical fragment start coordinates was collapsed to a single XSET. Peaks generated from the resulting filtered reads were thresholded at a peak height of 10, creating a high confidence set of 11475 Foxa2-binding sites with an estimated false discovery rate of 0.05. 15-Sep-2008 OREGEC00001 OREGES00059 OREGET00003 obig UNKNOWN UNKNOWN USER DEFINED 44845 POSITIVE OUTCOME 18611952 0 search_space EMPTY 0 false 107006693 mus_musculus_core_46_36g sequence ACTTCAATCTGGGATGCAAACTGGGAAGAACTCTGTTGTTGACTAGAAGAAATCAGGGAAATGAGCAGGCCAGCTAATTGTGAAACAATTTAACAAAGCTAAATTAGCAATAAGAAGAGGCAAAAGGATTTCTAGAGCCACTCGGGTATCCAGGGTGAAGTAAGAAGGCAATGAAGTTAGAAGAGAGCAATTTAAAAATTAACCCGTGTGTGAACTTACTCTGTTCAGAACAGGAATTCGAAAGCAAACAAAGACCAGTTGAGGCCCTCCTCCCTCCGGAGCAGGATTGGCATTTTAGAGGAGAAATTGATTGGTGGAGAACCCACTCTGCTGGGTAATTAAACAAGTATGCCGATCAATAGTCAGTATCTGGGATTTGGAAGCTCACTGCAAGCTAACACAGGGACACAGAAGGGAGGGGGAGGAACTGCTGGTTGCTTCGGGCAAGGCTAGAGCTTTAAGGGTTTTACA 1 107006223 1 true 107006693 mus_musculus_core_46_36g sequence_with_flank ACTTCAATCTGGGATGCAAACTGGGAAGAACTCTGTTGTTGACTAGAAGAAATCAGGGAAATGAGCAGGCCAGCTAATTGTGAAACAATTTAACAAAGCTAAATTAGCAATAAGAAGAGGCAAAAGGATTTCTAGAGCCACTCGGGTATCCAGGGTGAAGTAAGAAGGCAATGAAGTTAGAAGAGAGCAATTTAAAAATTAACCCGTGTGTGAACTTACTCTGTTCAGAACAGGAATTCGAAAGCAAACAAAGACCAGTTGAGGCCCTCCTCCCTCCGGAGCAGGATTGGCATTTTAGAGGAGAAATTGATTGGTGGAGAACCCACTCTGCTGGGTAATTAAACAAGTATGCCGATCAATAGTCAGTATCTGGGATTTGGAAGCTCACTGCAAGCTAACACAGGGACACAGAAGGGAGGGGGAGGAACTGCTGGTTGCTTCGGGCAAGGCTAGAGCTTTAAGGGTTTTACA 1 107006223 1 true Mus musculus OREG0040840 15376 Foxa2 NCBI REGULATORY REGION OREGDS00014 15-Sep-2008 EV:0200061 Chromatin immunoprecipitation (ChIP) was performed on Adult female C57Bl/6J mouse liver tissue using Foxa2 [HNF-3-beta (M-20): sc-6554, Santa Cruz] antibody. Foxa2-bound DNA (4.7 ng) was purified by SDS-PAGE to obtain 100-300 bp fragments and sequenced on an Illumina 1G sequencer. Resulting sequences were mapped to the NCBI Build 36 (mm8) reference mouse genome to produce 13 984 706 mapped reads that were extended to 200 bp length XSETs and overlapped to create peaks. To further define the peak dataset, each group of XSETs that represented DNA fragments with identical fragment start coordinates was collapsed to a single XSET. Peaks generated from the resulting filtered reads were thresholded at a peak height of 10, creating a high confidence set of 11475 Foxa2-binding sites with an estimated false discovery rate of 0.05. 15-Sep-2008 OREGEC00001 OREGES00059 OREGET00003 obig UNKNOWN UNKNOWN USER DEFINED 44846 POSITIVE OUTCOME 18611952 0 search_space EMPTY 0 false 107212692 mus_musculus_core_46_36g sequence AAGAAAGAAGGAAGCCCTGATCCTTCCCATTGTATCTTTAAGCCTCATCTGACACCAGAGATAGGGAGGAAGCAGCTTGTCTCAAATGGAAGACAGTTTAGATCAGAACTAGAAAAAACATTATAGCTCCTGAAAATGCTTAAAGCTTCCTAAGTAAGACTGCCTTTATAATAGACAGCTATTAGAAGGCACCAGAGTCTGTGCAGGGTACTCTGCTGGGTCAGGAGACAGGATTCCAACAAGGCCACGAAGAGAAAGTAAATAACCCCATGTGTTGTTTGTACCTAGTTCCACTTAATAAATAGCAACGGATCCTTAAAACACAGGCTTGTTTGTCTTTACATGGCCAAAATAAATAGACTACTACATAGTTTATTCTGTGAGGGGCTGTAATGATTAAATTGACTTAGCAGCATACTAATCCAAATACCATGCAAAAATCAACTGTAATTGTTGTTGAAAACTCTAAATAACCACACAGACATTGAGTAAATGGTCCTGTACGGCTACAGTATGAAACTTATCCTCCTGTTTTCTCACACAGTAACTCAATAAAACTAAAGGATGAAATGGCAACCATGCTGTCATTAACATGACACTACATCTAGTTTGGATAATGAAAACCTGGCAGACAGTCCATGAGTTGCTGTCATTCTAAACAAACACTTCCAGTTTTCCACTGGGACACAGGCCAAGTGACTAACCCCAAAGACTATTAAGGACAAAGTTTAGCTGGAGAAATAACTTCCCACCAGTCAACCCTTCAGAGGTCCCAAACTCCAACCTCGCTTTGAAAGAATTTATGTACTTATTTGCATGTATCTGTATGTGGTGTGCACACTTGCCTATGCATGTTCACATGTGTCATTGCATGCAGGTGTGCATACATACATGTGCCTGTGTGTGTGTGTGGTGTGTGTGTAGAGGCCTGAGACTGACATCAGGTACCTTCCTTGATCACTCTCAAGATTATGTATAGAAGCAGGCTCTCTCTCTCTGGGTCTGAAGGTTGCTGTTTCAGAACCTGAATTAGTGCTGTTGGGGTTGCCAACTGTAGAGCTAG 1 107211630 1 true 107212692 mus_musculus_core_46_36g sequence_with_flank AAGAAAGAAGGAAGCCCTGATCCTTCCCATTGTATCTTTAAGCCTCATCTGACACCAGAGATAGGGAGGAAGCAGCTTGTCTCAAATGGAAGACAGTTTAGATCAGAACTAGAAAAAACATTATAGCTCCTGAAAATGCTTAAAGCTTCCTAAGTAAGACTGCCTTTATAATAGACAGCTATTAGAAGGCACCAGAGTCTGTGCAGGGTACTCTGCTGGGTCAGGAGACAGGATTCCAACAAGGCCACGAAGAGAAAGTAAATAACCCCATGTGTTGTTTGTACCTAGTTCCACTTAATAAATAGCAACGGATCCTTAAAACACAGGCTTGTTTGTCTTTACATGGCCAAAATAAATAGACTACTACATAGTTTATTCTGTGAGGGGCTGTAATGATTAAATTGACTTAGCAGCATACTAATCCAAATACCATGCAAAAATCAACTGTAATTGTTGTTGAAAACTCTAAATAACCACACAGACATTGAGTAAATGGTCCTGTACGGCTACAGTATGAAACTTATCCTCCTGTTTTCTCACACAGTAACTCAATAAAACTAAAGGATGAAATGGCAACCATGCTGTCATTAACATGACACTACATCTAGTTTGGATAATGAAAACCTGGCAGACAGTCCATGAGTTGCTGTCATTCTAAACAAACACTTCCAGTTTTCCACTGGGACACAGGCCAAGTGACTAACCCCAAAGACTATTAAGGACAAAGTTTAGCTGGAGAAATAACTTCCCACCAGTCAACCCTTCAGAGGTCCCAAACTCCAACCTCGCTTTGAAAGAATTTATGTACTTATTTGCATGTATCTGTATGTGGTGTGCACACTTGCCTATGCATGTTCACATGTGTCATTGCATGCAGGTGTGCATACATACATGTGCCTGTGTGTGTGTGTGGTGTGTGTGTAGAGGCCTGAGACTGACATCAGGTACCTTCCTTGATCACTCTCAAGATTATGTATAGAAGCAGGCTCTCTCTCTCTGGGTCTGAAGGTTGCTGTTTCAGAACCTGAATTAGTGCTGTTGGGGTTGCCAACTGTAGAGCTAG 1 107211630 1 true Mus musculus OREG0040841 15376 Foxa2 NCBI REGULATORY REGION OREGDS00014 15-Sep-2008 EV:0200061 Chromatin immunoprecipitation (ChIP) was performed on Adult female C57Bl/6J mouse liver tissue using Foxa2 [HNF-3-beta (M-20): sc-6554, Santa Cruz] antibody. Foxa2-bound DNA (4.7 ng) was purified by SDS-PAGE to obtain 100-300 bp fragments and sequenced on an Illumina 1G sequencer. Resulting sequences were mapped to the NCBI Build 36 (mm8) reference mouse genome to produce 13 984 706 mapped reads that were extended to 200 bp length XSETs and overlapped to create peaks. To further define the peak dataset, each group of XSETs that represented DNA fragments with identical fragment start coordinates was collapsed to a single XSET. Peaks generated from the resulting filtered reads were thresholded at a peak height of 10, creating a high confidence set of 11475 Foxa2-binding sites with an estimated false discovery rate of 0.05. 15-Sep-2008 OREGEC00001 OREGES00059 OREGET00003 obig UNKNOWN UNKNOWN USER DEFINED 44847 POSITIVE OUTCOME 18611952 0 search_space EMPTY 0 false 107546742 mus_musculus_core_46_36g sequence CATAAATACAATCAGCTCATAGTCTTAAATGTTTGCGGTGTTCACTTAAGAAGACTTAATAAAAAGTCAAAACAAAAGCCAGGTCTGTGTTTTTATTTTATTCTGTTTATTATGTATTTTAAAGATTCCAAAACAAGCTTAGGCTTGATTAATTTTATACCTTGAACAAGTTTCAATAACTACAAAGAAGGATATGAACTTGGATATTGATAACTTTATTTTTTATGATTTTTTAAATTGTGTGTAAAGACAGGGATAGGGGCTACACATGAATGCAATTGTTCAAGGAGGCAATATTCATACCTATATAGCTATAGTTAACAGATGATTTTGAGCTGCCTGACATATGGAATAGAACTCCAGTCCTGTAACAGCAGGACAGGGCTTCAACCACTGAGCTATCTCTTCAGCCCCTGATAACTTAATTTTAATCTCATCCTTTAAGCTGATTTTTAACATAACTGGGAACACTAGTAGTGTGGGGTGCTGGAGAGTTAGCTCAGTTTTAAGCCCTGCCTGGCATTCATGTAACTCTAGGTTTCCAGCATTCACACCAAGTGTTTCGCAACCATCTCTAAATCCAGTTGTAGGGGATCCAAGTTCTCTGGCTATCACAGGCAATGATGCAGTGTACACAAGCCCACACACTCACACACACATACCACTTATAAATCAATGAAAAGAAGTTGGATTAAAAGTAAGATAAGGCACAGCTGTAATTGACATTGTTATTAAGTATTATACTAAATAACATAAATAAATCATAAAAAAATATTGGTTATTTTCAGAAAGAAATCCGTAGTTCCCTGGTTCTTTCAATGTTGCAACAGATGTTAATGGAAGATAAGGCTGATTTGGTAAGAGAAGCTGTGATTAAAAGCCTGGGTATCATTATGGGCTACATTGATGATCCTGACAAATATCAACAGGTATGCTTTTCAGCGGAAACTTCTTTTACCCTGTTATCAATTTTTAAGAAATGTACTGATTCAGACATTTGGTTGTCTGCAAGTGAGGTGGTGTATCTAAGCAGTCAATGAAAAAGACAGCTGCGGGGCTGGTGAGATGGCTCAGTGGGTAAGAGCACCCGACTGCTCTTCCGAAGGTCCGAAGTTCAAATCCCAGCAACCACATGGTGGCTCACAACCATCCGTAATGAGATCTGACTCCCTCTTCTGGAGTGTCTGAAGACAGCTCAGTGTACTTATA 1 107545534 1 true 107546742 mus_musculus_core_46_36g sequence_with_flank CATAAATACAATCAGCTCATAGTCTTAAATGTTTGCGGTGTTCACTTAAGAAGACTTAATAAAAAGTCAAAACAAAAGCCAGGTCTGTGTTTTTATTTTATTCTGTTTATTATGTATTTTAAAGATTCCAAAACAAGCTTAGGCTTGATTAATTTTATACCTTGAACAAGTTTCAATAACTACAAAGAAGGATATGAACTTGGATATTGATAACTTTATTTTTTATGATTTTTTAAATTGTGTGTAAAGACAGGGATAGGGGCTACACATGAATGCAATTGTTCAAGGAGGCAATATTCATACCTATATAGCTATAGTTAACAGATGATTTTGAGCTGCCTGACATATGGAATAGAACTCCAGTCCTGTAACAGCAGGACAGGGCTTCAACCACTGAGCTATCTCTTCAGCCCCTGATAACTTAATTTTAATCTCATCCTTTAAGCTGATTTTTAACATAACTGGGAACACTAGTAGTGTGGGGTGCTGGAGAGTTAGCTCAGTTTTAAGCCCTGCCTGGCATTCATGTAACTCTAGGTTTCCAGCATTCACACCAAGTGTTTCGCAACCATCTCTAAATCCAGTTGTAGGGGATCCAAGTTCTCTGGCTATCACAGGCAATGATGCAGTGTACACAAGCCCACACACTCACACACACATACCACTTATAAATCAATGAAAAGAAGTTGGATTAAAAGTAAGATAAGGCACAGCTGTAATTGACATTGTTATTAAGTATTATACTAAATAACATAAATAAATCATAAAAAAATATTGGTTATTTTCAGAAAGAAATCCGTAGTTCCCTGGTTCTTTCAATGTTGCAACAGATGTTAATGGAAGATAAGGCTGATTTGGTAAGAGAAGCTGTGATTAAAAGCCTGGGTATCATTATGGGCTACATTGATGATCCTGACAAATATCAACAGGTATGCTTTTCAGCGGAAACTTCTTTTACCCTGTTATCAATTTTTAAGAAATGTACTGATTCAGACATTTGGTTGTCTGCAAGTGAGGTGGTGTATCTAAGCAGTCAATGAAAAAGACAGCTGCGGGGCTGGTGAGATGGCTCAGTGGGTAAGAGCACCCGACTGCTCTTCCGAAGGTCCGAAGTTCAAATCCCAGCAACCACATGGTGGCTCACAACCATCCGTAATGAGATCTGACTCCCTCTTCTGGAGTGTCTGAAGACAGCTCAGTGTACTTATA 1 107545534 1 true Mus musculus OREG0040842 15376 Foxa2 NCBI REGULATORY REGION OREGDS00014 15-Sep-2008 EV:0200061 Chromatin immunoprecipitation (ChIP) was performed on Adult female C57Bl/6J mouse liver tissue using Foxa2 [HNF-3-beta (M-20): sc-6554, Santa Cruz] antibody. Foxa2-bound DNA (4.7 ng) was purified by SDS-PAGE to obtain 100-300 bp fragments and sequenced on an Illumina 1G sequencer. Resulting sequences were mapped to the NCBI Build 36 (mm8) reference mouse genome to produce 13 984 706 mapped reads that were extended to 200 bp length XSETs and overlapped to create peaks. To further define the peak dataset, each group of XSETs that represented DNA fragments with identical fragment start coordinates was collapsed to a single XSET. Peaks generated from the resulting filtered reads were thresholded at a peak height of 10, creating a high confidence set of 11475 Foxa2-binding sites with an estimated false discovery rate of 0.05. 15-Sep-2008 OREGEC00001 OREGES00059 OREGET00003 obig UNKNOWN UNKNOWN USER DEFINED 44848 POSITIVE OUTCOME 18611952 0 search_space EMPTY 0 false 107555218 mus_musculus_core_46_36g sequence TTTAATAAGTTAAGTAATTATTAGTGTTTTGCGAAATGAAGAGATTCAGTATTAGTTCTATGATTCTGCAGATTAATCTTTCCCCAGTGTTCTTCCTTTTAGTCTGCATTAAATATGTGAATTAAAAAGACTGAGATGCTGACAAGAAAGCAAAATCCTTTTACCTCTTCCCCAGTCTGTTACCATTATCATTGGAAATTGCTCAATAGTTCCTGAGTAAATAGCTAGCTGTATGGGTTCAGAAAAACATTTAGGAGTCATTTAAATATTGAACACTGCAGAATTGTCTTCAGTAGTTTGAAATCTATGATAATTCCATTTTTAAAAACCTGAGCATTTGCTCTACCTTAAGATAGTGAAGAAAAAAATCTTACTTGAAGGAATTTATTGATTGTGAACATGCTAACCATGACAATTCTAAAGGAGACTTTTTTTTCAAATATAGCCAGATGCTTTTTCCAATAATTCTAATCATATTATGGTGATATAATATTTACTCATGT 1 107554716 1 true 107555218 mus_musculus_core_46_36g sequence_with_flank TTTAATAAGTTAAGTAATTATTAGTGTTTTGCGAAATGAAGAGATTCAGTATTAGTTCTATGATTCTGCAGATTAATCTTTCCCCAGTGTTCTTCCTTTTAGTCTGCATTAAATATGTGAATTAAAAAGACTGAGATGCTGACAAGAAAGCAAAATCCTTTTACCTCTTCCCCAGTCTGTTACCATTATCATTGGAAATTGCTCAATAGTTCCTGAGTAAATAGCTAGCTGTATGGGTTCAGAAAAACATTTAGGAGTCATTTAAATATTGAACACTGCAGAATTGTCTTCAGTAGTTTGAAATCTATGATAATTCCATTTTTAAAAACCTGAGCATTTGCTCTACCTTAAGATAGTGAAGAAAAAAATCTTACTTGAAGGAATTTATTGATTGTGAACATGCTAACCATGACAATTCTAAAGGAGACTTTTTTTTCAAATATAGCCAGATGCTTTTTCCAATAATTCTAATCATATTATGGTGATATAATATTTACTCATGT 1 107554716 1 true Mus musculus OREG0040843 15376 Foxa2 NCBI REGULATORY REGION OREGDS00014 15-Sep-2008 EV:0200061 Chromatin immunoprecipitation (ChIP) was performed on Adult female C57Bl/6J mouse liver tissue using Foxa2 [HNF-3-beta (M-20): sc-6554, Santa Cruz] antibody. Foxa2-bound DNA (4.7 ng) was purified by SDS-PAGE to obtain 100-300 bp fragments and sequenced on an Illumina 1G sequencer. Resulting sequences were mapped to the NCBI Build 36 (mm8) reference mouse genome to produce 13 984 706 mapped reads that were extended to 200 bp length XSETs and overlapped to create peaks. To further define the peak dataset, each group of XSETs that represented DNA fragments with identical fragment start coordinates was collapsed to a single XSET. Peaks generated from the resulting filtered reads were thresholded at a peak height of 10, creating a high confidence set of 11475 Foxa2-binding sites with an estimated false discovery rate of 0.05. 15-Sep-2008 OREGEC00001 OREGES00059 OREGET00003 obig UNKNOWN UNKNOWN USER DEFINED 44849 POSITIVE OUTCOME 18611952 0 search_space EMPTY 0 false 107734099 mus_musculus_core_46_36g sequence ACTCTCACCCCCAAACACTCACACACCTTATCTACCAAGCACAGGCCTTTGCGTATGGGAAGTATCCATCATGTAACTAATGCTTTGTTCATTAATATTTAAACATGGACCCTGGCAAATTAGTGTATATCTTTGCCAGTTTTCATCTTGAACCAATGCCCTGTCCTGTGTGCTTTTCTAATTATCTGAACTTGTAATTATTCGAAGAGCTTCCTCCCTTCTGTCACAAGTGATGAATTCATTGTTGGTTCAGCTTCGAGCACCGCCACCACCTCCCAGCCTTTGCCAACTGTGGCTAACGGTGGCTGGGCCCACATCCCTGTTTGTTTGTCCTAATGCTCGTTACTGTTTGGCTCTCCTCTACCTGCTGCCAATGCAGAACTATTTATATCAACACAGAGACGCCTTGGTGAGCTTCGCTGTGATAACACATCCTCAGAAATCCTTCCATCACAAAGGACTTTGCCCCAGTTCTCCTCCTAGAACTCCTCTCCTGGCACTGACCCAGGGACCCTCCCCAAGAGGAACTCCTGGCTTCCCCAGGGGAAGTGGCAGCCACTGGTCCATCAGCTTGGATGATAAGTCTTTGCCTTCCAACTGAAGGCCC 1 107733493 1 true 107734099 mus_musculus_core_46_36g sequence_with_flank ACTCTCACCCCCAAACACTCACACACCTTATCTACCAAGCACAGGCCTTTGCGTATGGGAAGTATCCATCATGTAACTAATGCTTTGTTCATTAATATTTAAACATGGACCCTGGCAAATTAGTGTATATCTTTGCCAGTTTTCATCTTGAACCAATGCCCTGTCCTGTGTGCTTTTCTAATTATCTGAACTTGTAATTATTCGAAGAGCTTCCTCCCTTCTGTCACAAGTGATGAATTCATTGTTGGTTCAGCTTCGAGCACCGCCACCACCTCCCAGCCTTTGCCAACTGTGGCTAACGGTGGCTGGGCCCACATCCCTGTTTGTTTGTCCTAATGCTCGTTACTGTTTGGCTCTCCTCTACCTGCTGCCAATGCAGAACTATTTATATCAACACAGAGACGCCTTGGTGAGCTTCGCTGTGATAACACATCCTCAGAAATCCTTCCATCACAAAGGACTTTGCCCCAGTTCTCCTCCTAGAACTCCTCTCCTGGCACTGACCCAGGGACCCTCCCCAAGAGGAACTCCTGGCTTCCCCAGGGGAAGTGGCAGCCACTGGTCCATCAGCTTGGATGATAAGTCTTTGCCTTCCAACTGAAGGCCC 1 107733493 1 true Mus musculus OREG0040844 15376 Foxa2 NCBI REGULATORY REGION OREGDS00014 15-Sep-2008 EV:0200061 Chromatin immunoprecipitation (ChIP) was performed on Adult female C57Bl/6J mouse liver tissue using Foxa2 [HNF-3-beta (M-20): sc-6554, Santa Cruz] antibody. Foxa2-bound DNA (4.7 ng) was purified by SDS-PAGE to obtain 100-300 bp fragments and sequenced on an Illumina 1G sequencer. Resulting sequences were mapped to the NCBI Build 36 (mm8) reference mouse genome to produce 13 984 706 mapped reads that were extended to 200 bp length XSETs and overlapped to create peaks. To further define the peak dataset, each group of XSETs that represented DNA fragments with identical fragment start coordinates was collapsed to a single XSET. Peaks generated from the resulting filtered reads were thresholded at a peak height of 10, creating a high confidence set of 11475 Foxa2-binding sites with an estimated false discovery rate of 0.05. 15-Sep-2008 OREGEC00001 OREGES00059 OREGET00003 obig UNKNOWN UNKNOWN USER DEFINED 44850 POSITIVE OUTCOME 18611952 0 search_space EMPTY 0 false 107736485 mus_musculus_core_46_36g sequence TGAACTGAACACATTTGTATTCTTGTTAGCATTCACAGCAGGTGATGTATGAAGGATGCCTGGGAGCTGGGCCAAAGAGACATTTTAAGACCTAGCATGATTTTGTGCTAAAAATAAAACTACCAGTCAAATTTACTTATTTATAAGTCAGTTGTGCCACTACCGGGGCAATGTGAGACCTACTCCGGGGAAGCTGCTCATCTCTAGCCTCGGGCCCACGTTTCTAACAGGGGAATATCCACATTGCACCACTGGGTCAGGGTTGAAAATCAGTGGGTGGTAAGTTTCAACACACTCGCCTAGAAACAGCCCCAGGGCTGCTCACACACTGGGGCCTGGCAGGATACTGGTGCTATTTACATCCTTGTGAAGGTTACTGCTCCTGCCATAAACACAGTATGCGGTCCATAAGCACAAACCTCCAGCTCCTGGCCCCACCCTTTCTTCTCTGCATCACTGGCTACAGTGCACTGCCCTAGGTTAAGCTTCCCTCTGCTCTGAAGGGGTCGCTTTTCTGAAGGTCACTGGAATCAATATGACAGTGTGGACTTTCAGCTTGGAACAAGCAGGCAGATGTCAGTTGTCCCGTTCTACTCATTTCCAAAGAAAGGTAAACAGACAGTGTCACGGGGTCTGTGGGATCCAATGCGTACTTACACCAGCTGCTCTTAACACACCAGCGTCTCCAGGAAAAACAGGCAACAGTATCTACCTCCCGCCTTTGTTCATTAATAAACATTTTAAGGGATTCCTCTCACTTGATTTTTAT 1 107735717 1 true 107736485 mus_musculus_core_46_36g sequence_with_flank TGAACTGAACACATTTGTATTCTTGTTAGCATTCACAGCAGGTGATGTATGAAGGATGCCTGGGAGCTGGGCCAAAGAGACATTTTAAGACCTAGCATGATTTTGTGCTAAAAATAAAACTACCAGTCAAATTTACTTATTTATAAGTCAGTTGTGCCACTACCGGGGCAATGTGAGACCTACTCCGGGGAAGCTGCTCATCTCTAGCCTCGGGCCCACGTTTCTAACAGGGGAATATCCACATTGCACCACTGGGTCAGGGTTGAAAATCAGTGGGTGGTAAGTTTCAACACACTCGCCTAGAAACAGCCCCAGGGCTGCTCACACACTGGGGCCTGGCAGGATACTGGTGCTATTTACATCCTTGTGAAGGTTACTGCTCCTGCCATAAACACAGTATGCGGTCCATAAGCACAAACCTCCAGCTCCTGGCCCCACCCTTTCTTCTCTGCATCACTGGCTACAGTGCACTGCCCTAGGTTAAGCTTCCCTCTGCTCTGAAGGGGTCGCTTTTCTGAAGGTCACTGGAATCAATATGACAGTGTGGACTTTCAGCTTGGAACAAGCAGGCAGATGTCAGTTGTCCCGTTCTACTCATTTCCAAAGAAAGGTAAACAGACAGTGTCACGGGGTCTGTGGGATCCAATGCGTACTTACACCAGCTGCTCTTAACACACCAGCGTCTCCAGGAAAAACAGGCAACAGTATCTACCTCCCGCCTTTGTTCATTAATAAACATTTTAAGGGATTCCTCTCACTTGATTTTTAT 1 107735717 1 true Mus musculus OREG0040845 15376 Foxa2 NCBI REGULATORY REGION OREGDS00014 15-Sep-2008 EV:0200061 Chromatin immunoprecipitation (ChIP) was performed on Adult female C57Bl/6J mouse liver tissue using Foxa2 [HNF-3-beta (M-20): sc-6554, Santa Cruz] antibody. Foxa2-bound DNA (4.7 ng) was purified by SDS-PAGE to obtain 100-300 bp fragments and sequenced on an Illumina 1G sequencer. Resulting sequences were mapped to the NCBI Build 36 (mm8) reference mouse genome to produce 13 984 706 mapped reads that were extended to 200 bp length XSETs and overlapped to create peaks. To further define the peak dataset, each group of XSETs that represented DNA fragments with identical fragment start coordinates was collapsed to a single XSET. Peaks generated from the resulting filtered reads were thresholded at a peak height of 10, creating a high confidence set of 11475 Foxa2-binding sites with an estimated false discovery rate of 0.05. 15-Sep-2008 OREGEC00001 OREGES00059 OREGET00003 obig UNKNOWN UNKNOWN USER DEFINED 44851 POSITIVE OUTCOME 18611952 0 search_space EMPTY 0 false 107753710 mus_musculus_core_46_36g sequence ACACACAGTCATCTGATTGGTTCTGTTTTCCAGAGAACCCTGACAAGTCCATCTCAATGAGACGCTGCCCCAAAGTTTCCCTGAAAGTCAACTATTTCTTCACTGTTTCCCATAAGTCTCATTTTAAATGTAGGGGATGTGCTGTACATAATTGTGCAGACAGACTTTCACTTTCACACTATCTGAAGTCCCAGAGCATTAGTGCTACTGTGCATTCCAGACCCATCCATGTTTGCTGACTCGTCATGCTCAGCACAGTAGAAACACTATCGCTCACTTGCCTTCATTTCCTGGTACAAATACCAACAGGAAGGATTTCCCTGTGAGAGTTGTGTTCTGGTGTTTGAGTATTACTTAGGAAAATTCCTAGCCTCATAATGATTGGCCTGGTGAGAATTTGTCTTATTTGCTCTCTGTGAGTTGAAATGAGTTTTCGTTGGAAAATTTCATAATAGCTCTGGAGGTCACAGGGAGCATGAGGCTGTTGCAGAACCAAGGCTGCTGACCCAGTGGCTGGCACTGAGTGTGCTCAGGCCACTCTTCATCAACAGAGGAGTGTTTTAAAGTCACATTCAGTAAAGGAGAGTTGTCTGAGACAATCCAAAAACAGCTTACAAATGGCTAAGAAAGCCATTTTTTACCTTCAGTGACTTTTTTTTCTGTTGTCATACAGTGTTTTATGAAAATAAAAAGTAAAGTGTTTGCTATT 1 107753002 1 true 107753710 mus_musculus_core_46_36g sequence_with_flank ACACACAGTCATCTGATTGGTTCTGTTTTCCAGAGAACCCTGACAAGTCCATCTCAATGAGACGCTGCCCCAAAGTTTCCCTGAAAGTCAACTATTTCTTCACTGTTTCCCATAAGTCTCATTTTAAATGTAGGGGATGTGCTGTACATAATTGTGCAGACAGACTTTCACTTTCACACTATCTGAAGTCCCAGAGCATTAGTGCTACTGTGCATTCCAGACCCATCCATGTTTGCTGACTCGTCATGCTCAGCACAGTAGAAACACTATCGCTCACTTGCCTTCATTTCCTGGTACAAATACCAACAGGAAGGATTTCCCTGTGAGAGTTGTGTTCTGGTGTTTGAGTATTACTTAGGAAAATTCCTAGCCTCATAATGATTGGCCTGGTGAGAATTTGTCTTATTTGCTCTCTGTGAGTTGAAATGAGTTTTCGTTGGAAAATTTCATAATAGCTCTGGAGGTCACAGGGAGCATGAGGCTGTTGCAGAACCAAGGCTGCTGACCCAGTGGCTGGCACTGAGTGTGCTCAGGCCACTCTTCATCAACAGAGGAGTGTTTTAAAGTCACATTCAGTAAAGGAGAGTTGTCTGAGACAATCCAAAAACAGCTTACAAATGGCTAAGAAAGCCATTTTTTACCTTCAGTGACTTTTTTTTCTGTTGTCATACAGTGTTTTATGAAAATAAAAAGTAAAGTGTTTGCTATT 1 107753002 1 true Mus musculus OREG0040846 15376 Foxa2 NCBI REGULATORY REGION OREGDS00014 15-Sep-2008 EV:0200061 Chromatin immunoprecipitation (ChIP) was performed on Adult female C57Bl/6J mouse liver tissue using Foxa2 [HNF-3-beta (M-20): sc-6554, Santa Cruz] antibody. Foxa2-bound DNA (4.7 ng) was purified by SDS-PAGE to obtain 100-300 bp fragments and sequenced on an Illumina 1G sequencer. Resulting sequences were mapped to the NCBI Build 36 (mm8) reference mouse genome to produce 13 984 706 mapped reads that were extended to 200 bp length XSETs and overlapped to create peaks. To further define the peak dataset, each group of XSETs that represented DNA fragments with identical fragment start coordinates was collapsed to a single XSET. Peaks generated from the resulting filtered reads were thresholded at a peak height of 10, creating a high confidence set of 11475 Foxa2-binding sites with an estimated false discovery rate of 0.05. 15-Sep-2008 OREGEC00001 OREGES00059 OREGET00003 obig UNKNOWN UNKNOWN USER DEFINED 44852 POSITIVE OUTCOME 18611952 0 search_space EMPTY 0 false 107755187 mus_musculus_core_46_36g sequence AAGTGCTTGCAGTACAGGCATGAGAACCAGAGTTCAGATCCTCAGCACTCATGCAGAATCCAGGCTTTGTGGCATGTGTTTGTAAGCCCTGTGTTGGGAAATAGAGACAGAAAGATCTCCAGGAATTGCAGGCCAGCCAGATGAGCCAAAACAACAAACAGGTTCAGTGATACACCCTGTCTGAAGAAGACACTTAATATCAACAACCTCTGGCCTTCGCATGTCCAAATACAACACACACACACACACACACACACACACACACACACACACACACACAGGGACACACACGGACAATGAATGCACATGCTTATACATCCATGAGCACACACATGCATATACACGTGTGCACACACAGTTTTTTTTTAACATTTAAGTTTGGTTAGTTTTAAGTGTCAGCACAGTCTAGCATTCCCTGAGAAAGGAGTCTCAACTGAGGAATTACCTAGATGAGACTGGCCTGTGGGAATGTCTTTAGGGGGTCATTTTGTATGTTAGTTGGTGCAGGAGAGCTCAGTCCACTGTGTGTGCATGTGTGTGGGGTTACATCTTTAGGCAAGGGCTCCACGATTATATGAGAAAACAAGTTAAGTAAAATCCAGCCTGAATGCTAACAAGCAGCATTCTCCATGGTTTCTGCTGAACTTTGACAGTGAGTT 1 107754529 1 true 107755187 mus_musculus_core_46_36g sequence_with_flank AAGTGCTTGCAGTACAGGCATGAGAACCAGAGTTCAGATCCTCAGCACTCATGCAGAATCCAGGCTTTGTGGCATGTGTTTGTAAGCCCTGTGTTGGGAAATAGAGACAGAAAGATCTCCAGGAATTGCAGGCCAGCCAGATGAGCCAAAACAACAAACAGGTTCAGTGATACACCCTGTCTGAAGAAGACACTTAATATCAACAACCTCTGGCCTTCGCATGTCCAAATACAACACACACACACACACACACACACACACACACACACACACACACACAGGGACACACACGGACAATGAATGCACATGCTTATACATCCATGAGCACACACATGCATATACACGTGTGCACACACAGTTTTTTTTTAACATTTAAGTTTGGTTAGTTTTAAGTGTCAGCACAGTCTAGCATTCCCTGAGAAAGGAGTCTCAACTGAGGAATTACCTAGATGAGACTGGCCTGTGGGAATGTCTTTAGGGGGTCATTTTGTATGTTAGTTGGTGCAGGAGAGCTCAGTCCACTGTGTGTGCATGTGTGTGGGGTTACATCTTTAGGCAAGGGCTCCACGATTATATGAGAAAACAAGTTAAGTAAAATCCAGCCTGAATGCTAACAAGCAGCATTCTCCATGGTTTCTGCTGAACTTTGACAGTGAGTT 1 107754529 1 true Mus musculus OREG0040847 15376 Foxa2 NCBI REGULATORY REGION OREGDS00014 15-Sep-2008 EV:0200061 Chromatin immunoprecipitation (ChIP) was performed on Adult female C57Bl/6J mouse liver tissue using Foxa2 [HNF-3-beta (M-20): sc-6554, Santa Cruz] antibody. Foxa2-bound DNA (4.7 ng) was purified by SDS-PAGE to obtain 100-300 bp fragments and sequenced on an Illumina 1G sequencer. Resulting sequences were mapped to the NCBI Build 36 (mm8) reference mouse genome to produce 13 984 706 mapped reads that were extended to 200 bp length XSETs and overlapped to create peaks. To further define the peak dataset, each group of XSETs that represented DNA fragments with identical fragment start coordinates was collapsed to a single XSET. Peaks generated from the resulting filtered reads were thresholded at a peak height of 10, creating a high confidence set of 11475 Foxa2-binding sites with an estimated false discovery rate of 0.05. 15-Sep-2008 OREGEC00001 OREGES00059 OREGET00003 obig UNKNOWN UNKNOWN USER DEFINED 44853 POSITIVE OUTCOME 18611952 0 search_space EMPTY 0 false 107782291 mus_musculus_core_46_36g sequence GGGTCCTGAGGAAGGAGTGAATAGGAGTGGTGAACAAATGACTTGGAGTCAGTGATGGATGCAAGCTGACAGCTCTGGGTTCTGCTCAAGATAAGCTACTTTCTTAGGAAATGCATATCAATTCAAGCATTTACCCTATGTTCCCTTTTGATTATTCCATAAATCAGCATTTTATGACCTTAGCTCCTTGACTCTAAAGACAGAGCCACAAGGCCAAAGTTGCTGAAAAAAGTTCTGCTGTTTGCTGGAGCTGGAACACTGCCCCATTGTTCTATTACATTATTACCACCTTTTTGTTTTCCAATTCACTGCCTAACTTGACTGTCCTGCTCTGTAAACAGACCTTGCTCTGTAAACAGACCTTGAACCCAGAGATCTGCATGGCTCTGTCTCCTGAACACTGGGATTAAAGGCATGTACCTCCATGCCTAGACTTAAGCTTTTCTTTACCTAGAACTTGCTCTGTCCCAGGCTGGCCTTTAATTAAGAAATCTGATTTCTTTAGTCTTCTGGGATTAAAGGTGTACACCACCATGCCTGGGCCTAAGCTTTTCATGGCCATTTTTGCTCAAGATCCAGATCAAAAGCCTGTGTCTTCCAGCCACAAATGTGATCTGAATCTTGAGGCTTCATTTCTGGATTGTAGTTCATTCCAGATTAAAAGTCCAAACTATTCCTTGTTCAACTACAAACAAACAATAAGCTAACCTGGGTGGGATCTTGCCCTTACATCACTATCCCCTAAATCTCTTTATCTCCTTCTTTAATATCTTTCTGACAAAGCTGGCTCATTAGTACAGATGTCTCT 1 107781484 1 true 107782291 mus_musculus_core_46_36g sequence_with_flank GGGTCCTGAGGAAGGAGTGAATAGGAGTGGTGAACAAATGACTTGGAGTCAGTGATGGATGCAAGCTGACAGCTCTGGGTTCTGCTCAAGATAAGCTACTTTCTTAGGAAATGCATATCAATTCAAGCATTTACCCTATGTTCCCTTTTGATTATTCCATAAATCAGCATTTTATGACCTTAGCTCCTTGACTCTAAAGACAGAGCCACAAGGCCAAAGTTGCTGAAAAAAGTTCTGCTGTTTGCTGGAGCTGGAACACTGCCCCATTGTTCTATTACATTATTACCACCTTTTTGTTTTCCAATTCACTGCCTAACTTGACTGTCCTGCTCTGTAAACAGACCTTGCTCTGTAAACAGACCTTGAACCCAGAGATCTGCATGGCTCTGTCTCCTGAACACTGGGATTAAAGGCATGTACCTCCATGCCTAGACTTAAGCTTTTCTTTACCTAGAACTTGCTCTGTCCCAGGCTGGCCTTTAATTAAGAAATCTGATTTCTTTAGTCTTCTGGGATTAAAGGTGTACACCACCATGCCTGGGCCTAAGCTTTTCATGGCCATTTTTGCTCAAGATCCAGATCAAAAGCCTGTGTCTTCCAGCCACAAATGTGATCTGAATCTTGAGGCTTCATTTCTGGATTGTAGTTCATTCCAGATTAAAAGTCCAAACTATTCCTTGTTCAACTACAAACAAACAATAAGCTAACCTGGGTGGGATCTTGCCCTTACATCACTATCCCCTAAATCTCTTTATCTCCTTCTTTAATATCTTTCTGACAAAGCTGGCTCATTAGTACAGATGTCTCT 1 107781484 1 true Mus musculus OREG0040848 15376 Foxa2 NCBI REGULATORY REGION OREGDS00014 15-Sep-2008 EV:0200061 Chromatin immunoprecipitation (ChIP) was performed on Adult female C57Bl/6J mouse liver tissue using Foxa2 [HNF-3-beta (M-20): sc-6554, Santa Cruz] antibody. Foxa2-bound DNA (4.7 ng) was purified by SDS-PAGE to obtain 100-300 bp fragments and sequenced on an Illumina 1G sequencer. Resulting sequences were mapped to the NCBI Build 36 (mm8) reference mouse genome to produce 13 984 706 mapped reads that were extended to 200 bp length XSETs and overlapped to create peaks. To further define the peak dataset, each group of XSETs that represented DNA fragments with identical fragment start coordinates was collapsed to a single XSET. Peaks generated from the resulting filtered reads were thresholded at a peak height of 10, creating a high confidence set of 11475 Foxa2-binding sites with an estimated false discovery rate of 0.05. 15-Sep-2008 OREGEC00001 OREGES00059 OREGET00003 obig UNKNOWN UNKNOWN USER DEFINED 44854 POSITIVE OUTCOME 18611952 0 search_space EMPTY 0 false 107983626 mus_musculus_core_46_36g sequence GGGAAGAAGGCGACATTTGTTACCAATTATGCTGTTGGTTGGAAGCCAAGTCCTGAGTTCGAAATTAACAAAAACAGATAAGGAGTCCTCCAGGAAGCTCACTTTCATCTCACGATGAAATTTAATCTAACATTTGGTAGCTTGAGTGTAGCCTTTGACTCATCAGCAAGGAAAAGCAGCTTGGCCTTGTTTGTTTTCCCTGCTTGCGCCTTGTTTGGGGTGTCAATAGTGCAGAGCCTGTGACAGGCAGCTGATCTCTGGGGAAGCGCAGCCAAACGGAAGATCCCAGCCAAGCCAGGAACTTCAGCTCAAACACTCATCTCAGGCACACAATGCCGCCCCTTGTGCGGCTAAAGAACAGGGCCAGGGCTTTGTACCAGGATAGGAATGACAATATGCCCTAAGATTCACTTTCTTAATACAGGGTTTGTGTTTCTGTCCCATGAAAGACAACTGTGTGTCCACTGAAAACAGGGTCATATTCTTTGTGTGGTGTCCTGGAAAAATACACAATCATTCTAAAACTCCAAATATTTTTTTACTATAAGGCTCATTAAAGAATTTGAACTTAATTCTTATATTCTAACACCCTGGTTAGAAATGTCTGTAACGAGTATTCTAATAACCTTGATTGCAGCTTCAGTCCAATCACTGAACTACTAGCCTGGGGTTCTTGACTGCTCTTTTACTGGAGTGTCTCTCTGGACACTCCAGATGACACTTATGAAATGTTTGTTTCCAAGCCTCCTTTGGTGATTTCTCAATGCCACGTTTGCTGTAGAGCTACCAACCTTCCAGCTTTAGTAACTATAAAATCTTCACCACAAGCTACTGCGTCCTGCTTGAGCGCTGTTCCGTTCATGGAATTATCTCAATATATTGCTTCTGCCGTTCCCTCCT 1 107982727 1 true 107983626 mus_musculus_core_46_36g sequence_with_flank GGGAAGAAGGCGACATTTGTTACCAATTATGCTGTTGGTTGGAAGCCAAGTCCTGAGTTCGAAATTAACAAAAACAGATAAGGAGTCCTCCAGGAAGCTCACTTTCATCTCACGATGAAATTTAATCTAACATTTGGTAGCTTGAGTGTAGCCTTTGACTCATCAGCAAGGAAAAGCAGCTTGGCCTTGTTTGTTTTCCCTGCTTGCGCCTTGTTTGGGGTGTCAATAGTGCAGAGCCTGTGACAGGCAGCTGATCTCTGGGGAAGCGCAGCCAAACGGAAGATCCCAGCCAAGCCAGGAACTTCAGCTCAAACACTCATCTCAGGCACACAATGCCGCCCCTTGTGCGGCTAAAGAACAGGGCCAGGGCTTTGTACCAGGATAGGAATGACAATATGCCCTAAGATTCACTTTCTTAATACAGGGTTTGTGTTTCTGTCCCATGAAAGACAACTGTGTGTCCACTGAAAACAGGGTCATATTCTTTGTGTGGTGTCCTGGAAAAATACACAATCATTCTAAAACTCCAAATATTTTTTTACTATAAGGCTCATTAAAGAATTTGAACTTAATTCTTATATTCTAACACCCTGGTTAGAAATGTCTGTAACGAGTATTCTAATAACCTTGATTGCAGCTTCAGTCCAATCACTGAACTACTAGCCTGGGGTTCTTGACTGCTCTTTTACTGGAGTGTCTCTCTGGACACTCCAGATGACACTTATGAAATGTTTGTTTCCAAGCCTCCTTTGGTGATTTCTCAATGCCACGTTTGCTGTAGAGCTACCAACCTTCCAGCTTTAGTAACTATAAAATCTTCACCACAAGCTACTGCGTCCTGCTTGAGCGCTGTTCCGTTCATGGAATTATCTCAATATATTGCTTCTGCCGTTCCCTCCT 1 107982727 1 true Mus musculus OREG0040849 15376 Foxa2 NCBI REGULATORY REGION OREGDS00014 15-Sep-2008 EV:0200061 Chromatin immunoprecipitation (ChIP) was performed on Adult female C57Bl/6J mouse liver tissue using Foxa2 [HNF-3-beta (M-20): sc-6554, Santa Cruz] antibody. Foxa2-bound DNA (4.7 ng) was purified by SDS-PAGE to obtain 100-300 bp fragments and sequenced on an Illumina 1G sequencer. Resulting sequences were mapped to the NCBI Build 36 (mm8) reference mouse genome to produce 13 984 706 mapped reads that were extended to 200 bp length XSETs and overlapped to create peaks. To further define the peak dataset, each group of XSETs that represented DNA fragments with identical fragment start coordinates was collapsed to a single XSET. Peaks generated from the resulting filtered reads were thresholded at a peak height of 10, creating a high confidence set of 11475 Foxa2-binding sites with an estimated false discovery rate of 0.05. 15-Sep-2008 OREGEC00001 OREGES00059 OREGET00003 obig UNKNOWN UNKNOWN USER DEFINED 44855 POSITIVE OUTCOME 18611952 0 search_space EMPTY 0 false 108016992 mus_musculus_core_46_36g sequence AGGATTGTGGGTCAATTTATGAAAGTAGTAGGTATGAGGTGTCACACATTTAGTAAGATGTATGGACTGGGCATGTAGTTAGAGGCTGGCGGCATAATGAGTGACGGTTTGCCTCCTGCTCTGTTTCACAGATGGCACATTGCCTTTGCTGAGACATGAGTGAGCTGGTTGCTGTCCTCCCCTTAGCTGGCAGCCTTCCTTGGTTTACACCAGCTTCTAAGAATTGGTCCAACTTTGTTGTTTACTATTGGTTAGTGTAAGCGTTGACTCAGGAAGATGGTAGAAATGTTGCCTAGTTGTCTTACAAGAGTCCATTTTAAAAATACAAAATAAATGTGAGTACTGGCTATGGCTATGGGACACAAGTGAAGAGATCTAAGAAGAATATTTTATTTATGGAATTCTTAGGTTGTATTATTTTAAATGGCAATGCTTTCCTTTATAGTGGGGTGGGGACTTATATAAACAATTACCACCCTGCTTCCTGAAAGTAGAATGATTCTACTTTGTGGACTGGATATGAAAGGTATAGAAGTGTTGACCATTGTTCTCCAAGCAGAGTAGATGCAGTTCTCATCAGAACAGCTCTAACTACTTGCAAGAGACCCTGGAGTCCATTGACTGGTGACCTTTCTTCAT 1 108016354 1 true 108016992 mus_musculus_core_46_36g sequence_with_flank AGGATTGTGGGTCAATTTATGAAAGTAGTAGGTATGAGGTGTCACACATTTAGTAAGATGTATGGACTGGGCATGTAGTTAGAGGCTGGCGGCATAATGAGTGACGGTTTGCCTCCTGCTCTGTTTCACAGATGGCACATTGCCTTTGCTGAGACATGAGTGAGCTGGTTGCTGTCCTCCCCTTAGCTGGCAGCCTTCCTTGGTTTACACCAGCTTCTAAGAATTGGTCCAACTTTGTTGTTTACTATTGGTTAGTGTAAGCGTTGACTCAGGAAGATGGTAGAAATGTTGCCTAGTTGTCTTACAAGAGTCCATTTTAAAAATACAAAATAAATGTGAGTACTGGCTATGGCTATGGGACACAAGTGAAGAGATCTAAGAAGAATATTTTATTTATGGAATTCTTAGGTTGTATTATTTTAAATGGCAATGCTTTCCTTTATAGTGGGGTGGGGACTTATATAAACAATTACCACCCTGCTTCCTGAAAGTAGAATGATTCTACTTTGTGGACTGGATATGAAAGGTATAGAAGTGTTGACCATTGTTCTCCAAGCAGAGTAGATGCAGTTCTCATCAGAACAGCTCTAACTACTTGCAAGAGACCCTGGAGTCCATTGACTGGTGACCTTTCTTCAT 1 108016354 1 true Mus musculus OREG0040850 15376 Foxa2 NCBI REGULATORY REGION OREGDS00014 15-Sep-2008 EV:0200061 Chromatin immunoprecipitation (ChIP) was performed on Adult female C57Bl/6J mouse liver tissue using Foxa2 [HNF-3-beta (M-20): sc-6554, Santa Cruz] antibody. Foxa2-bound DNA (4.7 ng) was purified by SDS-PAGE to obtain 100-300 bp fragments and sequenced on an Illumina 1G sequencer. Resulting sequences were mapped to the NCBI Build 36 (mm8) reference mouse genome to produce 13 984 706 mapped reads that were extended to 200 bp length XSETs and overlapped to create peaks. To further define the peak dataset, each group of XSETs that represented DNA fragments with identical fragment start coordinates was collapsed to a single XSET. Peaks generated from the resulting filtered reads were thresholded at a peak height of 10, creating a high confidence set of 11475 Foxa2-binding sites with an estimated false discovery rate of 0.05. 15-Sep-2008 OREGEC00001 OREGES00059 OREGET00003 obig UNKNOWN UNKNOWN USER DEFINED 44856 POSITIVE OUTCOME 18611952 0 search_space EMPTY 0 false 108021214 mus_musculus_core_46_36g sequence AAACTAATGAACATGTGATTTTCCTTAATTATAAGCATAGAATTCCTATTTTGTGTTCATTATTGGACTATATGCAGAGATTTCAAAATGAGTTTTTGACATTATTTTGATTGCTTTTAAGAATAAATTCCTCAAATATGTATAAAATTTCCTAGATCATTTGGCTATTTTATGTTCAAGTTCCAATATTTTTATATATTTCTTATCTGCATGTATATGTGTATGGAAATCAGTGGTCAGTCGTGGGTGTGTCCACCTCTTTTTGAGAGCCTCTCTCTTCCTGGGGCTCTAGTCGAGCTGGAGTAGCCAGCAAGCCTTAGGGACCCTGCCTCTGCCTCTCCAGTGCTGGCTTCCAAGCGCTTGTGTGTGACAAGCACTTTACTAGTTGTCCCATCTCCCCTGCCCTGGCTTCCATAAATTTCTAGTAATAAACTTCTTAAGGACTATGGAAGAAACTCTTGCACGTGCCCCCGTGGCCAGCATGTGCCCCCTGTACGTCACTTGCTAAGCAGCAGGCTGTGTCTTCACCCTGTGCACACACTCTTTACTGACTGAACCACCTCCCTAACCCCAGCTTCCATAATTTCTAGTTCATTGCTTAACCACTTGGCTACAACTACAACTACAGGGTTTTAAACCGGCCATTCAGAAGAACCGTGAGTGTTAATTCTTCACCCGAAGCTGATGGATCGCCAGACAGAATGGTTGGGGAATTGAGCTTAATTTACCAGGACCTGGAATCCTGACAGGACTGCCCCCTGCTCAGGATAGCTGCACAGTTTTGCTGTTATTCACACAGGAACTTTGTTATTTACAGGCTTAGCAGTTTCTGGCATGAAGTTTTATTTGTGTTCAAAAGTCACTGATCAGTGGTAACAGGAACTTTAAAAATATGAGATACTGTTGTGCCCCTACCCACTCTGTCATCTCAAACAGTTATAGAGTGCTTGCCTTTGCTTTCAAGGTGGTATAAGGTGTTTTGGAGGTGGAGGGAAAACTTGAATCGGCCCCAGCTTTTTCAGAAGATTAACCAATTTGAACAAGGACACTGATTGTCATGAGAAAAGCACCAGGAGCATTCTTCCTCTTTCCTTTATGGTTTCTTGAACTTGGTGCTTGTAAAATGTCAGTCTATAA 1 108020078 1 true 108021214 mus_musculus_core_46_36g sequence_with_flank AAACTAATGAACATGTGATTTTCCTTAATTATAAGCATAGAATTCCTATTTTGTGTTCATTATTGGACTATATGCAGAGATTTCAAAATGAGTTTTTGACATTATTTTGATTGCTTTTAAGAATAAATTCCTCAAATATGTATAAAATTTCCTAGATCATTTGGCTATTTTATGTTCAAGTTCCAATATTTTTATATATTTCTTATCTGCATGTATATGTGTATGGAAATCAGTGGTCAGTCGTGGGTGTGTCCACCTCTTTTTGAGAGCCTCTCTCTTCCTGGGGCTCTAGTCGAGCTGGAGTAGCCAGCAAGCCTTAGGGACCCTGCCTCTGCCTCTCCAGTGCTGGCTTCCAAGCGCTTGTGTGTGACAAGCACTTTACTAGTTGTCCCATCTCCCCTGCCCTGGCTTCCATAAATTTCTAGTAATAAACTTCTTAAGGACTATGGAAGAAACTCTTGCACGTGCCCCCGTGGCCAGCATGTGCCCCCTGTACGTCACTTGCTAAGCAGCAGGCTGTGTCTTCACCCTGTGCACACACTCTTTACTGACTGAACCACCTCCCTAACCCCAGCTTCCATAATTTCTAGTTCATTGCTTAACCACTTGGCTACAACTACAACTACAGGGTTTTAAACCGGCCATTCAGAAGAACCGTGAGTGTTAATTCTTCACCCGAAGCTGATGGATCGCCAGACAGAATGGTTGGGGAATTGAGCTTAATTTACCAGGACCTGGAATCCTGACAGGACTGCCCCCTGCTCAGGATAGCTGCACAGTTTTGCTGTTATTCACACAGGAACTTTGTTATTTACAGGCTTAGCAGTTTCTGGCATGAAGTTTTATTTGTGTTCAAAAGTCACTGATCAGTGGTAACAGGAACTTTAAAAATATGAGATACTGTTGTGCCCCTACCCACTCTGTCATCTCAAACAGTTATAGAGTGCTTGCCTTTGCTTTCAAGGTGGTATAAGGTGTTTTGGAGGTGGAGGGAAAACTTGAATCGGCCCCAGCTTTTTCAGAAGATTAACCAATTTGAACAAGGACACTGATTGTCATGAGAAAAGCACCAGGAGCATTCTTCCTCTTTCCTTTATGGTTTCTTGAACTTGGTGCTTGTAAAATGTCAGTCTATAA 1 108020078 1 true Mus musculus OREG0040851 15376 Foxa2 NCBI REGULATORY REGION OREGDS00014 15-Sep-2008 EV:0200061 Chromatin immunoprecipitation (ChIP) was performed on Adult female C57Bl/6J mouse liver tissue using Foxa2 [HNF-3-beta (M-20): sc-6554, Santa Cruz] antibody. Foxa2-bound DNA (4.7 ng) was purified by SDS-PAGE to obtain 100-300 bp fragments and sequenced on an Illumina 1G sequencer. Resulting sequences were mapped to the NCBI Build 36 (mm8) reference mouse genome to produce 13 984 706 mapped reads that were extended to 200 bp length XSETs and overlapped to create peaks. To further define the peak dataset, each group of XSETs that represented DNA fragments with identical fragment start coordinates was collapsed to a single XSET. Peaks generated from the resulting filtered reads were thresholded at a peak height of 10, creating a high confidence set of 11475 Foxa2-binding sites with an estimated false discovery rate of 0.05. 15-Sep-2008 OREGEC00001 OREGES00059 OREGET00003 obig UNKNOWN UNKNOWN USER DEFINED 44857 POSITIVE OUTCOME 18611952 0 search_space EMPTY 0 false 109442095 mus_musculus_core_46_36g sequence GTTCCATCTTGCGTAGTAGGCTCTAAGTTAAATCAGACCCGGGTTGGTTACTCCCTCCCACAAACTTTGTTCCTGCTTTACACTAGCATATTTTGCATTCAGGACAGACTGAAGATCAGAAGTATTGTGGCTGGGCTGGTGTTTATGTTTTTCTTCTGTTAGCCTGCAGACTACCTTCCCAACACTCAAGCTTAGAGGTGAAGGTTCTACGCAGGCTCCATCTCGACTTTTCCATGTTCACTGAGTTCTGTGGGTGTTGTCTTCAGCAATGGGACTTTGCTGTCTCTGTGGAGAGCAACCTTTGGTCTTATCAACAGTCTAGGTTGTTTGGGGATTTCTCAACTCTTTTGGCCAACAATTCAATTGGATGAAACCCAGTCCCCATACTGGAAGTTTTGTTCAGGGACAAAATTTAGCCAGTTGGGTTTGGTCTCCCTCATTATTTGGAAATTTTGTTAGGATGGCACTCATATGCTACATGAAGTTTCTACCTACTAGATTTCTAAACCACCCATAAACTGCTTTTCAATTTTAACTCTTTTCATTTACTTCCTCAATCCCCTCCC 1 109441530 1 true 109442095 mus_musculus_core_46_36g sequence_with_flank GTTCCATCTTGCGTAGTAGGCTCTAAGTTAAATCAGACCCGGGTTGGTTACTCCCTCCCACAAACTTTGTTCCTGCTTTACACTAGCATATTTTGCATTCAGGACAGACTGAAGATCAGAAGTATTGTGGCTGGGCTGGTGTTTATGTTTTTCTTCTGTTAGCCTGCAGACTACCTTCCCAACACTCAAGCTTAGAGGTGAAGGTTCTACGCAGGCTCCATCTCGACTTTTCCATGTTCACTGAGTTCTGTGGGTGTTGTCTTCAGCAATGGGACTTTGCTGTCTCTGTGGAGAGCAACCTTTGGTCTTATCAACAGTCTAGGTTGTTTGGGGATTTCTCAACTCTTTTGGCCAACAATTCAATTGGATGAAACCCAGTCCCCATACTGGAAGTTTTGTTCAGGGACAAAATTTAGCCAGTTGGGTTTGGTCTCCCTCATTATTTGGAAATTTTGTTAGGATGGCACTCATATGCTACATGAAGTTTCTACCTACTAGATTTCTAAACCACCCATAAACTGCTTTTCAATTTTAACTCTTTTCATTTACTTCCTCAATCCCCTCCC 1 109441530 1 true Mus musculus OREG0040852 15376 Foxa2 NCBI REGULATORY REGION OREGDS00014 15-Sep-2008 EV:0200061 Chromatin immunoprecipitation (ChIP) was performed on Adult female C57Bl/6J mouse liver tissue using Foxa2 [HNF-3-beta (M-20): sc-6554, Santa Cruz] antibody. Foxa2-bound DNA (4.7 ng) was purified by SDS-PAGE to obtain 100-300 bp fragments and sequenced on an Illumina 1G sequencer. Resulting sequences were mapped to the NCBI Build 36 (mm8) reference mouse genome to produce 13 984 706 mapped reads that were extended to 200 bp length XSETs and overlapped to create peaks. To further define the peak dataset, each group of XSETs that represented DNA fragments with identical fragment start coordinates was collapsed to a single XSET. Peaks generated from the resulting filtered reads were thresholded at a peak height of 10, creating a high confidence set of 11475 Foxa2-binding sites with an estimated false discovery rate of 0.05. 15-Sep-2008 OREGEC00001 OREGES00059 OREGET00003 obig UNKNOWN UNKNOWN USER DEFINED 44858 POSITIVE OUTCOME 18611952 0 search_space EMPTY 0 false 110324727 mus_musculus_core_46_36g sequence GAGTGGGGTCATACAGCTTCTCACAGCCTAACGTCCTCCTAGCTTTATGGAGTGCGCACAGTCGAATTTCCTGTCCCCAACCCCCCAGTCCTTTGGCAGGCTGGGCTCAGGACACTATTTTAATCAACTTACGTGTGGGTGCAACCTACTGAGTTCATTTAACCCTACCTACATGTACATATGTGCTCATCTTGAGATTGGATGATGATGGCTCTAATGCATTATTTTTTTAATTCGGCTCCCCAAATCACATGGGAATCTGCAAGTCCTGACACTGAGGGTCCCTGTCCCCAATTACTTCTTGATTAATCAATAAAAACTCAACTGCCAATTGCTGGGCATAGTGAAAGTGACAG 1 110324372 1 true 110324727 mus_musculus_core_46_36g sequence_with_flank GAGTGGGGTCATACAGCTTCTCACAGCCTAACGTCCTCCTAGCTTTATGGAGTGCGCACAGTCGAATTTCCTGTCCCCAACCCCCCAGTCCTTTGGCAGGCTGGGCTCAGGACACTATTTTAATCAACTTACGTGTGGGTGCAACCTACTGAGTTCATTTAACCCTACCTACATGTACATATGTGCTCATCTTGAGATTGGATGATGATGGCTCTAATGCATTATTTTTTTAATTCGGCTCCCCAAATCACATGGGAATCTGCAAGTCCTGACACTGAGGGTCCCTGTCCCCAATTACTTCTTGATTAATCAATAAAAACTCAACTGCCAATTGCTGGGCATAGTGAAAGTGACAG 1 110324372 1 true Mus musculus OREG0040853 15376 Foxa2 NCBI REGULATORY REGION OREGDS00014 15-Sep-2008 EV:0200061 Chromatin immunoprecipitation (ChIP) was performed on Adult female C57Bl/6J mouse liver tissue using Foxa2 [HNF-3-beta (M-20): sc-6554, Santa Cruz] antibody. Foxa2-bound DNA (4.7 ng) was purified by SDS-PAGE to obtain 100-300 bp fragments and sequenced on an Illumina 1G sequencer. Resulting sequences were mapped to the NCBI Build 36 (mm8) reference mouse genome to produce 13 984 706 mapped reads that were extended to 200 bp length XSETs and overlapped to create peaks. To further define the peak dataset, each group of XSETs that represented DNA fragments with identical fragment start coordinates was collapsed to a single XSET. Peaks generated from the resulting filtered reads were thresholded at a peak height of 10, creating a high confidence set of 11475 Foxa2-binding sites with an estimated false discovery rate of 0.05. 15-Sep-2008 OREGEC00001 OREGES00059 OREGET00003 obig UNKNOWN UNKNOWN USER DEFINED 44859 POSITIVE OUTCOME 18611952 0 search_space EMPTY 0 false 112103598 mus_musculus_core_46_36g sequence TGTAGAACACTTCTACAACAGACCTTTGCACACAACCTCCTTTCTTTGGGAAAGATGTCTTTAGTTTTTTTATGTTTTTCATTCCCCAAACTTTGTAAATTTTCTAGCCATAATTAACTTAAAAAAAAACTTTTTGCTTCTGGATGTGTTATTAAAAAAAAATCACTGTTTTGTGAGTATCTATTCTTTACTTTTAAAAAGTAAGAGGATTTACTTTCTAATATAATGAATATATTATTCATTTTTCTCATTTCCCTAGCTTCTCATAATAATGCAAGTTCTATAAGGGAGTTTTGTCTTTTGTCCAGTGTCATCTCATGTGCCTTTG 1 112103271 1 true 112103598 mus_musculus_core_46_36g sequence_with_flank TGTAGAACACTTCTACAACAGACCTTTGCACACAACCTCCTTTCTTTGGGAAAGATGTCTTTAGTTTTTTTATGTTTTTCATTCCCCAAACTTTGTAAATTTTCTAGCCATAATTAACTTAAAAAAAAACTTTTTGCTTCTGGATGTGTTATTAAAAAAAAATCACTGTTTTGTGAGTATCTATTCTTTACTTTTAAAAAGTAAGAGGATTTACTTTCTAATATAATGAATATATTATTCATTTTTCTCATTTCCCTAGCTTCTCATAATAATGCAAGTTCTATAAGGGAGTTTTGTCTTTTGTCCAGTGTCATCTCATGTGCCTTTG 1 112103271 1 true Mus musculus OREG0040854 15376 Foxa2 NCBI REGULATORY REGION OREGDS00014 15-Sep-2008 EV:0200061 Chromatin immunoprecipitation (ChIP) was performed on Adult female C57Bl/6J mouse liver tissue using Foxa2 [HNF-3-beta (M-20): sc-6554, Santa Cruz] antibody. Foxa2-bound DNA (4.7 ng) was purified by SDS-PAGE to obtain 100-300 bp fragments and sequenced on an Illumina 1G sequencer. Resulting sequences were mapped to the NCBI Build 36 (mm8) reference mouse genome to produce 13 984 706 mapped reads that were extended to 200 bp length XSETs and overlapped to create peaks. To further define the peak dataset, each group of XSETs that represented DNA fragments with identical fragment start coordinates was collapsed to a single XSET. Peaks generated from the resulting filtered reads were thresholded at a peak height of 10, creating a high confidence set of 11475 Foxa2-binding sites with an estimated false discovery rate of 0.05. 15-Sep-2008 OREGEC00001 OREGES00059 OREGET00003 obig UNKNOWN UNKNOWN USER DEFINED 44860 POSITIVE OUTCOME 18611952 0 search_space EMPTY 0 false 11390230 mus_musculus_core_46_36g sequence GAGAGTAGCATTGACATTACTAATCCATTTGCTTCTGGTTTCTCCTTTTTACTCTCTGCCTGTAAAGCCAGCACTTGGCTCAGTTTCCTCTTGTCCTTTTCCATTTTATTGGCAAGTTGATGCCCAGTTCATGAACTGCTAATTAAAATAAATTGGTTTGTTAAAAAGAAATTTGTTAAATTTTTGCTTTTTGACAGAAATTCAGGATGTTGACAATGTATGATAAAATAGAATAAGTAACTTAAGATACTTAAGTGTTCCATCCTTGCAAAGGGTCATACTCCAAGATACAGGCTACTCACAGCCTGAGCAGCCTCACACGTGGTAATTGCCTGGGCAGCCTGAAAAGACCTTTTTATTCAGTCTAGGAGAGTGATTCTCAACCTTCCTCAGAAGCACTATGACCTTTTAATACAGTTCTTCACGCTGTGGTGACTCCCAACCACGAATTATTTTGTTGCTACTTCATAACTGTAATTT 1 11389751 1 true 11390230 mus_musculus_core_46_36g sequence_with_flank GAGAGTAGCATTGACATTACTAATCCATTTGCTTCTGGTTTCTCCTTTTTACTCTCTGCCTGTAAAGCCAGCACTTGGCTCAGTTTCCTCTTGTCCTTTTCCATTTTATTGGCAAGTTGATGCCCAGTTCATGAACTGCTAATTAAAATAAATTGGTTTGTTAAAAAGAAATTTGTTAAATTTTTGCTTTTTGACAGAAATTCAGGATGTTGACAATGTATGATAAAATAGAATAAGTAACTTAAGATACTTAAGTGTTCCATCCTTGCAAAGGGTCATACTCCAAGATACAGGCTACTCACAGCCTGAGCAGCCTCACACGTGGTAATTGCCTGGGCAGCCTGAAAAGACCTTTTTATTCAGTCTAGGAGAGTGATTCTCAACCTTCCTCAGAAGCACTATGACCTTTTAATACAGTTCTTCACGCTGTGGTGACTCCCAACCACGAATTATTTTGTTGCTACTTCATAACTGTAATTT 1 11389751 1 true Mus musculus OREG0040855 15376 Foxa2 NCBI REGULATORY REGION OREGDS00014 15-Sep-2008 EV:0200061 Chromatin immunoprecipitation (ChIP) was performed on Adult female C57Bl/6J mouse liver tissue using Foxa2 [HNF-3-beta (M-20): sc-6554, Santa Cruz] antibody. Foxa2-bound DNA (4.7 ng) was purified by SDS-PAGE to obtain 100-300 bp fragments and sequenced on an Illumina 1G sequencer. Resulting sequences were mapped to the NCBI Build 36 (mm8) reference mouse genome to produce 13 984 706 mapped reads that were extended to 200 bp length XSETs and overlapped to create peaks. To further define the peak dataset, each group of XSETs that represented DNA fragments with identical fragment start coordinates was collapsed to a single XSET. Peaks generated from the resulting filtered reads were thresholded at a peak height of 10, creating a high confidence set of 11475 Foxa2-binding sites with an estimated false discovery rate of 0.05. 15-Sep-2008 OREGEC00001 OREGES00059 OREGET00003 obig UNKNOWN UNKNOWN USER DEFINED 44861 POSITIVE OUTCOME 18611952 0 search_space EMPTY 0 false 114017217 mus_musculus_core_46_36g sequence ATATAATTTGACATGTAGTATTTTTTAAAAATCTAGTAGATTAAGCAATGGAATGCTTTGGAATTCATTTGGGAGTTGAAGTAGGTTGAAAATAGTGAACCAAACAAATGAAATGAGTCTGAAGACAAACCAAAGAAGGAAGGAGATGGTTCAAAGGGAGATGATTAAATGATAGCATCTTTAGCTAAAATGTTCTTCAGCTGATAATACTATAAAAAAATGAGCAGTCCATTGCCTTAATCACTCAGTCACCTTGGACACATACCATCCCTGACCTCAAGTTATATTATAGAGCAATGGTGATAAAAACTTCACGGGATTGATACAGAAACAAGAAAGTAGATCAATGAATTGAATTGAAGACCCAGAAATGAACTCACACATCTACGGTCACTTGACCTTTGACAAAGAAACTAAAATCATTCAATG 1 114016789 1 true 114017217 mus_musculus_core_46_36g sequence_with_flank ATATAATTTGACATGTAGTATTTTTTAAAAATCTAGTAGATTAAGCAATGGAATGCTTTGGAATTCATTTGGGAGTTGAAGTAGGTTGAAAATAGTGAACCAAACAAATGAAATGAGTCTGAAGACAAACCAAAGAAGGAAGGAGATGGTTCAAAGGGAGATGATTAAATGATAGCATCTTTAGCTAAAATGTTCTTCAGCTGATAATACTATAAAAAAATGAGCAGTCCATTGCCTTAATCACTCAGTCACCTTGGACACATACCATCCCTGACCTCAAGTTATATTATAGAGCAATGGTGATAAAAACTTCACGGGATTGATACAGAAACAAGAAAGTAGATCAATGAATTGAATTGAAGACCCAGAAATGAACTCACACATCTACGGTCACTTGACCTTTGACAAAGAAACTAAAATCATTCAATG 1 114016789 1 true Mus musculus OREG0040856 15376 Foxa2 NCBI REGULATORY REGION OREGDS00014 15-Sep-2008 EV:0200061 Chromatin immunoprecipitation (ChIP) was performed on Adult female C57Bl/6J mouse liver tissue using Foxa2 [HNF-3-beta (M-20): sc-6554, Santa Cruz] antibody. Foxa2-bound DNA (4.7 ng) was purified by SDS-PAGE to obtain 100-300 bp fragments and sequenced on an Illumina 1G sequencer. Resulting sequences were mapped to the NCBI Build 36 (mm8) reference mouse genome to produce 13 984 706 mapped reads that were extended to 200 bp length XSETs and overlapped to create peaks. To further define the peak dataset, each group of XSETs that represented DNA fragments with identical fragment start coordinates was collapsed to a single XSET. Peaks generated from the resulting filtered reads were thresholded at a peak height of 10, creating a high confidence set of 11475 Foxa2-binding sites with an estimated false discovery rate of 0.05. 15-Sep-2008 OREGEC00001 OREGES00059 OREGET00003 obig UNKNOWN UNKNOWN USER DEFINED 44862 POSITIVE OUTCOME 18611952 0 search_space EMPTY 0 false 115868993 mus_musculus_core_46_36g sequence GCTTGGTGTTGTCTGTGAATTCTGTCTTGAGTATTCTGAACTTTGGTGCTAATATCCACTTATCAGTGAGTGCATACCATATATGTTCTTTTGTGATTGGGTTACCTCACACAGGGTGATATTTTCCAGTTCCATCCATTTGCCTAAGAATTTCATGAACTCATCATTTTTTATAGCTGAGTACTACTCCATTGTGTAAATGTACCATATTTTCTGTATCGATTCCTATGTTAAAAGGCATCTGGGTTCTTTCCAGCTTCTGGCTATTATAAATAAGGCTGTCATGAGCATAGTAGAGCATGTGTCCTTGTTATATGTTGGAGCATCTTTT 1 115868663 1 true 115868993 mus_musculus_core_46_36g sequence_with_flank GCTTGGTGTTGTCTGTGAATTCTGTCTTGAGTATTCTGAACTTTGGTGCTAATATCCACTTATCAGTGAGTGCATACCATATATGTTCTTTTGTGATTGGGTTACCTCACACAGGGTGATATTTTCCAGTTCCATCCATTTGCCTAAGAATTTCATGAACTCATCATTTTTTATAGCTGAGTACTACTCCATTGTGTAAATGTACCATATTTTCTGTATCGATTCCTATGTTAAAAGGCATCTGGGTTCTTTCCAGCTTCTGGCTATTATAAATAAGGCTGTCATGAGCATAGTAGAGCATGTGTCCTTGTTATATGTTGGAGCATCTTTT 1 115868663 1 true Mus musculus OREG0040857 15376 Foxa2 NCBI REGULATORY REGION OREGDS00014 15-Sep-2008 EV:0200061 Chromatin immunoprecipitation (ChIP) was performed on Adult female C57Bl/6J mouse liver tissue using Foxa2 [HNF-3-beta (M-20): sc-6554, Santa Cruz] antibody. Foxa2-bound DNA (4.7 ng) was purified by SDS-PAGE to obtain 100-300 bp fragments and sequenced on an Illumina 1G sequencer. Resulting sequences were mapped to the NCBI Build 36 (mm8) reference mouse genome to produce 13 984 706 mapped reads that were extended to 200 bp length XSETs and overlapped to create peaks. To further define the peak dataset, each group of XSETs that represented DNA fragments with identical fragment start coordinates was collapsed to a single XSET. Peaks generated from the resulting filtered reads were thresholded at a peak height of 10, creating a high confidence set of 11475 Foxa2-binding sites with an estimated false discovery rate of 0.05. 15-Sep-2008 OREGEC00001 OREGES00059 OREGET00003 obig UNKNOWN UNKNOWN USER DEFINED 44863 POSITIVE OUTCOME 18611952 0 search_space EMPTY 0 false 116691873 mus_musculus_core_46_36g sequence AAGCAAATACCTTGCCAAGCAATCTGTGCAGATTATAAAAGGTATAAGCTGAGCAACTGAGAACTGCTAGTCACATGCCAGATTTCAGGGCCTCAGTTCTGACTGTGAGAATTCTCAGAAACGACTTTATGGAAAGCAAACATTTGGCAGGCATTTAAATAGAAGTAGCAGCCAAGATATTGGCCTTGCAGATTTGAAAATGCATAAATCTATACCTTAGGATCAAAAAACAGATTCTTCTATTCTGAAAGGAAGAGATTTAACTACCTATCCAGCAAGAGACCAGATGGTGTTTGCTGTAGCTGGCAGACCAGGAACAAATGACTTTTTTTAAAAGTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAGAAGAAGGGGAAAACTAACAATGACAAGAACAGTGACAAGTTTGTTCATGTGATGAGTATGTGTACCATAAACACTGGGCATGGGAATTATGGAGAAGGCTAGGTAAGTAAAGTGCTTCCTTGCTAACATGCAGACCTTAGTTCAAATCTGAAATTGTATGTAACACTTACAATTTTACTGCTGTGGTTTATATGCATAACTCCAGCAATGGGGGGGGGGGGCAGAAACAAGTGGATCTCTGGAATGAACAGGCTCACCAATTTAGCCTAATTGTTGAACTCAAGGCCTTGATAAACAATCTTCTATTCACCTTGTACCATAATACTACCCACAACCAAAACCCCCACTCACTAATCTTACACAAAAACTACATACAAAGATATGTATATATACAAGCAAAATAAACAAAAATAACATATTAAGCATGATACAGCACAGAAAACACAACATAACATAACAAACATAATCAAACACTTCTCTGAGACAGCTAAAGTTTGCCAAAGTCTGCTTTGTCTTAGAAAGACCAATACAGTCTGATTCACCTCAAGAAAATTTTAATCTTGTATTATATTCCTGGGAAGAGTTAGGAGAGTAAATATTTTAATTTAGAGTCATTTTAGAGCTACAGTTAGCATAGATATAAATGTATTGTTTCACAGTTATAGAGTTTTGAGATTTAATTAGGAGAATCCTTCCTATTATGCAGGGACTTTTGCATGGAAGTAGGCTGACCTGATTTGAATTAATGTACTTTAAGTAATTTTTACTGAATTTCCTGATGTGAATATCTAACCAGAAT 1 116690703 1 true 116691873 mus_musculus_core_46_36g sequence_with_flank AAGCAAATACCTTGCCAAGCAATCTGTGCAGATTATAAAAGGTATAAGCTGAGCAACTGAGAACTGCTAGTCACATGCCAGATTTCAGGGCCTCAGTTCTGACTGTGAGAATTCTCAGAAACGACTTTATGGAAAGCAAACATTTGGCAGGCATTTAAATAGAAGTAGCAGCCAAGATATTGGCCTTGCAGATTTGAAAATGCATAAATCTATACCTTAGGATCAAAAAACAGATTCTTCTATTCTGAAAGGAAGAGATTTAACTACCTATCCAGCAAGAGACCAGATGGTGTTTGCTGTAGCTGGCAGACCAGGAACAAATGACTTTTTTTAAAAGTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAGAAGAAGGGGAAAACTAACAATGACAAGAACAGTGACAAGTTTGTTCATGTGATGAGTATGTGTACCATAAACACTGGGCATGGGAATTATGGAGAAGGCTAGGTAAGTAAAGTGCTTCCTTGCTAACATGCAGACCTTAGTTCAAATCTGAAATTGTATGTAACACTTACAATTTTACTGCTGTGGTTTATATGCATAACTCCAGCAATGGGGGGGGGGGGCAGAAACAAGTGGATCTCTGGAATGAACAGGCTCACCAATTTAGCCTAATTGTTGAACTCAAGGCCTTGATAAACAATCTTCTATTCACCTTGTACCATAATACTACCCACAACCAAAACCCCCACTCACTAATCTTACACAAAAACTACATACAAAGATATGTATATATACAAGCAAAATAAACAAAAATAACATATTAAGCATGATACAGCACAGAAAACACAACATAACATAACAAACATAATCAAACACTTCTCTGAGACAGCTAAAGTTTGCCAAAGTCTGCTTTGTCTTAGAAAGACCAATACAGTCTGATTCACCTCAAGAAAATTTTAATCTTGTATTATATTCCTGGGAAGAGTTAGGAGAGTAAATATTTTAATTTAGAGTCATTTTAGAGCTACAGTTAGCATAGATATAAATGTATTGTTTCACAGTTATAGAGTTTTGAGATTTAATTAGGAGAATCCTTCCTATTATGCAGGGACTTTTGCATGGAAGTAGGCTGACCTGATTTGAATTAATGTACTTTAAGTAATTTTTACTGAATTTCCTGATGTGAATATCTAACCAGAAT 1 116690703 1 true Mus musculus OREG0040858 15376 Foxa2 NCBI REGULATORY REGION OREGDS00014 15-Sep-2008 EV:0200061 Chromatin immunoprecipitation (ChIP) was performed on Adult female C57Bl/6J mouse liver tissue using Foxa2 [HNF-3-beta (M-20): sc-6554, Santa Cruz] antibody. Foxa2-bound DNA (4.7 ng) was purified by SDS-PAGE to obtain 100-300 bp fragments and sequenced on an Illumina 1G sequencer. Resulting sequences were mapped to the NCBI Build 36 (mm8) reference mouse genome to produce 13 984 706 mapped reads that were extended to 200 bp length XSETs and overlapped to create peaks. To further define the peak dataset, each group of XSETs that represented DNA fragments with identical fragment start coordinates was collapsed to a single XSET. Peaks generated from the resulting filtered reads were thresholded at a peak height of 10, creating a high confidence set of 11475 Foxa2-binding sites with an estimated false discovery rate of 0.05. 15-Sep-2008 OREGEC00001 OREGES00059 OREGET00003 obig UNKNOWN UNKNOWN USER DEFINED 44864 POSITIVE OUTCOME 18611952 0 search_space EMPTY 0 false 118076384 mus_musculus_core_46_36g sequence GTGAAAATATAAAGTCCTTCATTAGTTCTAAAGGAGTCAATATTAAGTTATAGAGTGCTTAAAGTATTCCTGCGTCATGTTTAGTACTCATTTTTAATTGCATATTTCATTTTATGAAATAAGATCTGTTTTCTAGGCTTGAAAATACTATTAGGCTCAAGCAATTCTCCTGCCTCAGCCTCCTAAGTCACTGGAACTACCTGGGTATCCAGTCAAACTTCTTTTTATAAAGATTTACACTTGCAAGTGGGAAGAAAAACATATGTGTGAAGGTGTGGAGGTCAGAAGTCAAACTAGTGTTGTTGGTTTTTTTCCTTAGAAGATGTCCACATAGTTTTTCAAGGCAGGG 1 118076036 1 true 118076384 mus_musculus_core_46_36g sequence_with_flank GTGAAAATATAAAGTCCTTCATTAGTTCTAAAGGAGTCAATATTAAGTTATAGAGTGCTTAAAGTATTCCTGCGTCATGTTTAGTACTCATTTTTAATTGCATATTTCATTTTATGAAATAAGATCTGTTTTCTAGGCTTGAAAATACTATTAGGCTCAAGCAATTCTCCTGCCTCAGCCTCCTAAGTCACTGGAACTACCTGGGTATCCAGTCAAACTTCTTTTTATAAAGATTTACACTTGCAAGTGGGAAGAAAAACATATGTGTGAAGGTGTGGAGGTCAGAAGTCAAACTAGTGTTGTTGGTTTTTTTCCTTAGAAGATGTCCACATAGTTTTTCAAGGCAGGG 1 118076036 1 true Mus musculus OREG0040859 15376 Foxa2 NCBI REGULATORY REGION OREGDS00014 15-Sep-2008 EV:0200061 Chromatin immunoprecipitation (ChIP) was performed on Adult female C57Bl/6J mouse liver tissue using Foxa2 [HNF-3-beta (M-20): sc-6554, Santa Cruz] antibody. Foxa2-bound DNA (4.7 ng) was purified by SDS-PAGE to obtain 100-300 bp fragments and sequenced on an Illumina 1G sequencer. Resulting sequences were mapped to the NCBI Build 36 (mm8) reference mouse genome to produce 13 984 706 mapped reads that were extended to 200 bp length XSETs and overlapped to create peaks. To further define the peak dataset, each group of XSETs that represented DNA fragments with identical fragment start coordinates was collapsed to a single XSET. Peaks generated from the resulting filtered reads were thresholded at a peak height of 10, creating a high confidence set of 11475 Foxa2-binding sites with an estimated false discovery rate of 0.05. 15-Sep-2008 OREGEC00001 OREGES00059 OREGET00003 obig UNKNOWN UNKNOWN USER DEFINED 44865 POSITIVE OUTCOME 18611952 0 search_space EMPTY 0 false 119322163 mus_musculus_core_46_36g sequence TATTATAATCCCTTTCTTCTCCTAAATTGCTTTTGCTCAAAGTATTTTATCATAGTAACAGAAGTTAAATTAGAACAGGAGGTATAATATTGTGTTGCCAGGTGTGTTTACATAAAGCACTTCTAGGGCTGGGAAGATTGCTCAGCTAATAAAGTGCTTGCTGTGAAAGCATGATGAGTGGATTGAACCAGCTTAGCCTAATCAGTGAGACCACATCTCTAAGAAACCTTGTTTCAAACAACTGGGTAGGTGGCTCCTGTAGAACAACACCCACAGTTTGACCTCTATCTTCTACCTGCATGTGCACATAAATGCACACACACATCCTCTCATGCATACACATAAACTCATTCAAACATACAGAGAAAGTGAGAAACACAGAAACAGACAGAGACAGTGACAGTGACAGAGTTGTGCTGCAAACAACAAGCAGTCATTGTTTTAATTTCAAGATGTATTATTTTGACGTGGTCATTTATTTATTGTTTCATTAGTTTGCATTTAATTCTTCTTTTGATGCTGTCATGCTATAAAACATCATGTTTATTTCTTCATTTCTGTTTTCTGCTATGATCTTATTTACTGTAAGTGAAAAGAGATTTTTGTGGCATTTTTTTTCTTTTATTAAGTAGGTTTCCATTTGGGACATGAAAGGAACTTGAAAAGGAAGAGAGAATGAAATAATCATTATAAGAACACCAGAAAGATTATGTAATTAACCATGCTGCATTGTGGATGTTTAGTTGTTTGTAGAATTAAAATTTCCATAGAGGCAATAGAACATTCTGGAAAGGAGACCATACACAGTAAGAGTATAGACCATTTAATAAATCACACACCATTTAGATAGGTTTAAAAGCCATATAAAATATGTTAGAGCACAAGACAACATTGAATAGGTGAGGAGGGGTAATGAACAGAAGCAAATATTGGCAAATGAGCATTCTAAAGAGAGGGTGGTGTCAGCATTTGCAGAACTGAAAAACATCTGTGAGTCAATCTGTACTAGAATTTTTTCA 1 119321145 1 true 119322163 mus_musculus_core_46_36g sequence_with_flank TATTATAATCCCTTTCTTCTCCTAAATTGCTTTTGCTCAAAGTATTTTATCATAGTAACAGAAGTTAAATTAGAACAGGAGGTATAATATTGTGTTGCCAGGTGTGTTTACATAAAGCACTTCTAGGGCTGGGAAGATTGCTCAGCTAATAAAGTGCTTGCTGTGAAAGCATGATGAGTGGATTGAACCAGCTTAGCCTAATCAGTGAGACCACATCTCTAAGAAACCTTGTTTCAAACAACTGGGTAGGTGGCTCCTGTAGAACAACACCCACAGTTTGACCTCTATCTTCTACCTGCATGTGCACATAAATGCACACACACATCCTCTCATGCATACACATAAACTCATTCAAACATACAGAGAAAGTGAGAAACACAGAAACAGACAGAGACAGTGACAGTGACAGAGTTGTGCTGCAAACAACAAGCAGTCATTGTTTTAATTTCAAGATGTATTATTTTGACGTGGTCATTTATTTATTGTTTCATTAGTTTGCATTTAATTCTTCTTTTGATGCTGTCATGCTATAAAACATCATGTTTATTTCTTCATTTCTGTTTTCTGCTATGATCTTATTTACTGTAAGTGAAAAGAGATTTTTGTGGCATTTTTTTTCTTTTATTAAGTAGGTTTCCATTTGGGACATGAAAGGAACTTGAAAAGGAAGAGAGAATGAAATAATCATTATAAGAACACCAGAAAGATTATGTAATTAACCATGCTGCATTGTGGATGTTTAGTTGTTTGTAGAATTAAAATTTCCATAGAGGCAATAGAACATTCTGGAAAGGAGACCATACACAGTAAGAGTATAGACCATTTAATAAATCACACACCATTTAGATAGGTTTAAAAGCCATATAAAATATGTTAGAGCACAAGACAACATTGAATAGGTGAGGAGGGGTAATGAACAGAAGCAAATATTGGCAAATGAGCATTCTAAAGAGAGGGTGGTGTCAGCATTTGCAGAACTGAAAAACATCTGTGAGTCAATCTGTACTAGAATTTTTTCA 1 119321145 1 true Mus musculus OREG0040860 15376 Foxa2 NCBI REGULATORY REGION OREGDS00014 15-Sep-2008 EV:0200061 Chromatin immunoprecipitation (ChIP) was performed on Adult female C57Bl/6J mouse liver tissue using Foxa2 [HNF-3-beta (M-20): sc-6554, Santa Cruz] antibody. Foxa2-bound DNA (4.7 ng) was purified by SDS-PAGE to obtain 100-300 bp fragments and sequenced on an Illumina 1G sequencer. Resulting sequences were mapped to the NCBI Build 36 (mm8) reference mouse genome to produce 13 984 706 mapped reads that were extended to 200 bp length XSETs and overlapped to create peaks. To further define the peak dataset, each group of XSETs that represented DNA fragments with identical fragment start coordinates was collapsed to a single XSET. Peaks generated from the resulting filtered reads were thresholded at a peak height of 10, creating a high confidence set of 11475 Foxa2-binding sites with an estimated false discovery rate of 0.05. 15-Sep-2008 OREGEC00001 OREGES00059 OREGET00003 obig UNKNOWN UNKNOWN USER DEFINED 44866 POSITIVE OUTCOME 18611952 0 search_space EMPTY 0 false 120286927 mus_musculus_core_46_36g sequence CGGGAAGTGGTACATGCCTTTAATTTTAGCAGTCGGGAGCTACAAGTTTGAGGCCAGCAGGGGCTACATGCTAAGGGCTACATAGACTCTGCGCCTCAAAAGAATTATACACTTTCAAGTATCTAATTCCTCCCAGTGCTGGCTTGGTGTTTGAATTAGTATATAGATTTACTTGTAAGCTGGATGAAAACCCAAATACGGAACCCTTTATCTGTATTACAACATTTTCCAAAGGGAGCGCTTCTTAGTGTATCACAGTCTTAGGGCAGCGGTGAGAAAGCTGGTCTCCAGTAATTACTGTCCGGCTGCCCTCTAGCATACAATAAAGGAACTGCGAGGAGGGCAACAGTACACACGCGGCTACTTTAATCTTTAAATGTTTAGGTAAGGAAGAGAGGTTTTGTGGTTTTTTCCAAAAATTGCACCAAGGTAAAGCAGAGCTCTAACCGATGCAGGTGTGTTGTCAGGCGTTAGCAGTACTGCCCTCACTACGCGTTCATTGGACAGTAGCGCAACCCCAAGAAAAGGATGGTTGCTTGCAACCACGCGCGCCCGGCAGCCAGAAAGCTCTAAGTCCGGGTTTGGTTGCGGTGACCACCGCAGGAGGCCTACCCCAACCTGCCCGGTGTACAGTATTTTCTTCGACTGC 1 120286279 1 true 120286927 mus_musculus_core_46_36g sequence_with_flank CGGGAAGTGGTACATGCCTTTAATTTTAGCAGTCGGGAGCTACAAGTTTGAGGCCAGCAGGGGCTACATGCTAAGGGCTACATAGACTCTGCGCCTCAAAAGAATTATACACTTTCAAGTATCTAATTCCTCCCAGTGCTGGCTTGGTGTTTGAATTAGTATATAGATTTACTTGTAAGCTGGATGAAAACCCAAATACGGAACCCTTTATCTGTATTACAACATTTTCCAAAGGGAGCGCTTCTTAGTGTATCACAGTCTTAGGGCAGCGGTGAGAAAGCTGGTCTCCAGTAATTACTGTCCGGCTGCCCTCTAGCATACAATAAAGGAACTGCGAGGAGGGCAACAGTACACACGCGGCTACTTTAATCTTTAAATGTTTAGGTAAGGAAGAGAGGTTTTGTGGTTTTTTCCAAAAATTGCACCAAGGTAAAGCAGAGCTCTAACCGATGCAGGTGTGTTGTCAGGCGTTAGCAGTACTGCCCTCACTACGCGTTCATTGGACAGTAGCGCAACCCCAAGAAAAGGATGGTTGCTTGCAACCACGCGCGCCCGGCAGCCAGAAAGCTCTAAGTCCGGGTTTGGTTGCGGTGACCACCGCAGGAGGCCTACCCCAACCTGCCCGGTGTACAGTATTTTCTTCGACTGC 1 120286279 1 true Mus musculus OREG0040861 15376 Foxa2 NCBI REGULATORY REGION OREGDS00014 15-Sep-2008 EV:0200061 Chromatin immunoprecipitation (ChIP) was performed on Adult female C57Bl/6J mouse liver tissue using Foxa2 [HNF-3-beta (M-20): sc-6554, Santa Cruz] antibody. Foxa2-bound DNA (4.7 ng) was purified by SDS-PAGE to obtain 100-300 bp fragments and sequenced on an Illumina 1G sequencer. Resulting sequences were mapped to the NCBI Build 36 (mm8) reference mouse genome to produce 13 984 706 mapped reads that were extended to 200 bp length XSETs and overlapped to create peaks. To further define the peak dataset, each group of XSETs that represented DNA fragments with identical fragment start coordinates was collapsed to a single XSET. Peaks generated from the resulting filtered reads were thresholded at a peak height of 10, creating a high confidence set of 11475 Foxa2-binding sites with an estimated false discovery rate of 0.05. 15-Sep-2008 OREGEC00001 OREGES00059 OREGET00003 obig UNKNOWN UNKNOWN USER DEFINED 44867 POSITIVE OUTCOME 18611952 0 search_space EMPTY 0 false 120634714 mus_musculus_core_46_36g sequence CTACTACAGTGGGCTCTACCTCATCTCTGTAAACTCAGGACAGCAAGTCCAGTGTTGGGGTGACTGTGAGCATTGCAGGAGCTTATCAGAGAGTATTTTCCCCAATAGTACTTTCCTGGATTTGCACCTGAGAGTTGTGTATAGTCTGGTGTGGGGAAGAGTGGTGTAGTGTGGTATGGATAGTGTGGTGTGGTGTGGTGTGGCGTGGGGTGCTGTGGTGTGGAGTGGGGTAATGTGGTATGGTGTGGTGTGGTGTAGTATAGTGTGGTGTGGTGTGGCGTGGGGTGCTGTGGTGTGGAGTGGGGTAGTGTGGTGTGGTGTGCTGTAGGGTGGGGTGGGGTGGTGTGATGTGGGCTGCGGTGGCATGTGTGTGTACCTGTGCTTGTTTGAGCACATGTACTTATGGATGTGTTTCTGTGGAGGCTAGAGGACAACCTCAACCTCAGGCACTCTCCATCTTTTTGTTAGAGATAGAGTCTCTCT 1 120634232 1 true 120634714 mus_musculus_core_46_36g sequence_with_flank CTACTACAGTGGGCTCTACCTCATCTCTGTAAACTCAGGACAGCAAGTCCAGTGTTGGGGTGACTGTGAGCATTGCAGGAGCTTATCAGAGAGTATTTTCCCCAATAGTACTTTCCTGGATTTGCACCTGAG