Does RefSeq DB have a CDS file for its transcripts?
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6.6 years ago
pwg46 ▴ 460

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?

 

nm refseq cds sequence coding • 2.5k views
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Entering edit mode
6.6 years ago
Irsan ★ 7.4k
  1. Go to UCSC table browser
  2. Select genes and gene prediction tracks
  3. Select RefSeq genes
  4. select table refGene
  5. region: genome
  6. output format: bed
  7. refGene-CDS.bed
  8. Click on get output
  9. select coding exons
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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?

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