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Old 07-01-2013, 03:39 AM   #1
Location: Sweden

Join Date: Jun 2013
Posts: 51
Default Annotation with refseq of transcripts


I would like to annotate or add description to my transcript for which I only have refseq number (accession number). I cannot find any database which provides data for transcriptional refseq (e.g. "NM_000537"). Could you help me with finding that?

Best regards,
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Old 07-01-2013, 04:39 AM   #2
Senior Member
Location: East Coast USA

Join Date: Feb 2008
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You can use the table browser from UCSC genome browser to do this. If you need help getting started with table browser look at this tutorial page:

Caveat: If your genome is not the list of supported genomes at UCSC then obviously this would not work.
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Old 07-01-2013, 04:44 AM   #3
Devon Ryan
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480

You should be able to find the files to do this on the UCSC table browser (I think kgXref has some conversions). You can also check out Biomart, which might prove simpler. You can also do this in R with some of the Annotation databases, if your data happens to already be in R for whatever reason.

Edit: I should have refreshed before posting, GenoMax beat me to it!
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Old 07-01-2013, 06:49 AM   #4
Location: Sweden

Join Date: Jun 2013
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Thanks both. I found the table that I was looking for but I couldn't download it, so I just copied the webpage, presenting the table. Anyway now it's working.
rozitaa is offline   Reply With Quote

annotations, refseq gtf

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