Get mRNA sequence from UCSC genome browser using coordinates
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2.2 years ago
Amos • 0

Hi.

I have a list of genome coordinates and I'm trying to get the sequences of those coordinates that are also on exons (almost all are but I need to make sure) I tried putting in the coordinates in the UCSC genome browser to make sure the area is on an exon. I then go to the table browser and put in the coordinates in the region option and choose sequence in the output format. After hitting the 'get sequence' button and chooseing either mRNA or genomic I get the sequence of the whole gene and not the coordinates I put in. If I hit the summery/statistics button it does tell me the correct size of the region I'm interested in (in the 'item bases' line) but the sequence I get is much larger than that.

How can I get the sequence of just the region I'm interested in?

sequence • 752 views
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See Pierre's answer using UCSC MySQL: C: Getting mRNA coding sequence for a UCSC accession

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2.1 years ago
piyushjo ▴ 560

Instead of UCSC browser you should try Ensembl Biomart. You can get mRNA sequence of each transcript of a gene. For few genes you can use their browser, for larger gene list you can use R library.

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