UTR coordinates for any version of refseq transcripts
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Lachapelle, Josianne
Mar 24, 2021, 3:06:14 PM3/24/21
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Hello,
I’m trying to find the coordinates of 5’UTRs and 3’UTRs for >5000 genes, but for specific transcript versions. I’ve tried the NCBI RefSeq track with the RefSeq All (ncbiRefSeq) table, but it only lists the coordinates for one transcript version. Is there a way to export for all transcript versions? That way I could choose which version I need.
For example, gene BBIP1, the ncbiRefSeq table has transcript NM_001195306.1, but I’m looking for coordinates of transcript NM_001195306.2
Thank you,
Josianne
Josianne Lachapelle, PhD
Bioinformatics Programmer
LifeLabs Genetics | 175 Galaxy Blvd, Suite 105 | Toronto, ON M9W 0C9
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Brian Lee
Mar 25, 2021, 12:45:44 AM3/25/21
to Lachapelle, Josianne, gen...@soe.ucsc.edu
Dear Josianne,
Thank you for using the UCSC Genome Browser and your question about multiple versions of RefSeq transcripts.
One immediate solution for NM_001195306.2 would be to look to the hg38 which has this newer transcript: http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=NM_001195306.2
We don't have multiple versions of RefSeq transcripts available simultaneously on an assembly, adding support to older NM accessions is a feature we have considered adding. I added a note about the desire to compare UTR coordinates differences for any version of RefSeq transcripts as a scenario where such a feature would be helpful for users.
We do keep archives of older gene models for hg19 and hg38 for ncbiRefSeq that may be of interest for comparing older versions:
https://hgdownload.soe.ucsc.edu/goldenPath/archive/hg38/ncbiRefSeq/
https://hgdownload.soe.ucsc.edu/goldenPath/archive/hg19/ncbiRefSeq/
Thank you again for your inquiry and using the UCSC Genome Browser. If you have any further public questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
All the best,
Thank you for using the UCSC Genome Browser and your question about multiple versions of RefSeq transcripts.
One immediate solution for NM_001195306.2 would be to look to the hg38 which has this newer transcript: http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=NM_001195306.2
We don't have multiple versions of RefSeq transcripts available simultaneously on an assembly, adding support to older NM accessions is a feature we have considered adding. I added a note about the desire to compare UTR coordinates differences for any version of RefSeq transcripts as a scenario where such a feature would be helpful for users.
We do keep archives of older gene models for hg19 and hg38 for ncbiRefSeq that may be of interest for comparing older versions:
https://hgdownload.soe.ucsc.edu/goldenPath/archive/hg38/ncbiRefSeq/
https://hgdownload.soe.ucsc.edu/goldenPath/archive/hg19/ncbiRefSeq/
Thank you again for your inquiry and using the UCSC Genome Browser. If you have any further public questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
All the best,
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