Does RefSeq DB have a CDS file for its transcripts? · Biostar

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Does RefSeq DB have a CDS file for its transcripts?

Hello,

I am looking for a file which contains all CDS for their NM (coding transcript) identifiers. Ensembl has one which maps each of its ENST's to their CDS, however I have been unable to find the same for Refseq's coding transcripts (NM). If anyone knows of and could point me to such a file, that would be great. It doesn't even have to come from RefSeq databases. Perhaps there are other NCBI db's which have the file I'm looking for?

cds refseq nm coding-sequence

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updated 4.5 years ago by Ram

• written 11.7 years ago by pwg46

1 answer

Go to UCSC table browser
Select genes and gene prediction tracks
Select RefSeq genes
select table refGene
region: genome
output format: bed
refGene-CDS.bed
Click on get output
select coding exons

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updated 4.5 years ago by Ram

• written 11.7 years ago by Irsan

Hmm, I looked into that. However the data file it outputs doesn't give the actual sequences. Are there any adjustments I could make to get the actual sequence?

• 0 views • link

updated 4.5 years ago by Ram

• written 11.7 years ago by pwg46

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