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EnsEMBL Sequence Fetcher

Description:

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

Rationale:

Many publications describe transcription factor binding sites occuring at a specific distance from the transcription start site. Finding these sequences in a genomic build can be time-consuming and error-prone. This script takes in relative coordinates and gather sequence which can be inspected for the presence of reported sequences. If the sequence desired, is not found on either strand, try the EnsEMBL Sequence Scanner to help find the location of your desired sequence.

Script:

EnsEMBL Database version:
Enter Transcript ID:
ID must match selected database
HELP: Find EnsEMBL Transcript IDs
EXAMPLE:
ENST00000236291 (Human)
Relative Start:
EXAMPLE: -100
Relative End:
EXAMPLE: -90
Strand:

 

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