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EnsEMBL Sequence Scanner

Description:

With an EnsEMBL transcript ID (ENST), locate a subsequence within an upstream sequence at a specific relative distance from the transcription start site.

Rationale:

Many publications describe sequences in a genome that are regulatory however, these sequences may have moved between genomic builds or may not be easy to locate within the upstream sequence. This script takes an EnsEMBL transcript ID and interrogates a genomic region relative to the start of transcription for matches to small input sequences. For instance, if a publication reports the sequence "ATATATAT" as regulatory and upstream of the transcription start site, this script will find all matches within a specified region of the sequence and report them (for both strands).

Script:

EnsEMBL Database version:
Enter Transcript ID:
ID must match selected database
HELP: Find EnsEMBL Transcript IDs
EXAMPLE:
ENST00000236291 (Human)
Relative Start:
EXAMPLE: -1000
Relative End:
EXAMPLE: -1
Strand:
Scan Sequence 1:
EXAMPLE: CGCGCGCG
Scan Sequence 2 (optional):
EXAMPLE: ATATATAT
 

Questions or comments to oreganno@bcgsc.ca. (Archived here)