coordinates of exons in hg38

[Bogdan Tanasa]

Dear all,

I am sure that this question was asked before -- and -- I wish I could find a quick answer ;)

May I ask : how can we obtain the coordinates of exons of the RefSeq genes on hg38, where each coordinates (chr, start, end) also have assigned the gene name ?

thanks a lot, and a happy weekend,

-- bogdan

[Matthew Speir]

Hi Bogdan,

Thank you for your question about obtaining exon coordinates from the UCSC Genome Browser.

You can obtain this information from the Table Browser using steps 2 and 3 of the following video: https://youtu.be/6JoUqM1iKxQ (timestamps to these steps are in the description section of the video). The video focuses on using the hg19 assembly and UCSC Genes track, but that can be easily changed to fit your needs. For your purposes, you would want to select "hg38" from the "assembly" drop-down menu and then select the "NCBI RefSeq" track from the "track" drop-down menu. The NCBI RefSeq track for hg38 has several tables and you will need to choose the one which fits your needs:

• ncbiRefSeq – all curated and predicted annotations provided by RefSeq.
• ncbiRefSeqCurated – subset of RefSeq All that includes only those annotations whose accessions begin with NM, NR, or YP.
• ncbiRefSeqPredicted – subset of RefSeq All that includes those annotations whose accessions begin with XM or XR.
• refGene – annotations generated from UCSC's realignment of RNAs with NM and NR accessions to the human genome. This track was previously known as the "RefSeq Genes" track.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Matthew Speir
UCSC Genome Bioinformatics Group

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[Bogdan Tanasa]

Dear Matthew,

thank you very much ;)