REFSEQ genes are missing for chrM for GRCh38 on UCSC genome browser, why?

[Laura Smith]

Hi, 

I tried to review the chrM on UCSC genome browser, however the refseq genes returned no genes. Is this an error or is there no refseq genes available for GRCh38 on UCSC genome browser? 

http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=chrM%3A1-16569&hgsid=465431005_RoNFmTaJEpjtAupLY9OhYT8aOw3s

I appreciate your feedback. 

Thank you,

Laura

[Laura Smith]

Also, adding to my earlier email below, is UCSC genome browser going to have any chrM refseq annotations anytime soon ? If it does, this would be very helpful. Thank you. 

Laura 

[Robert Kuhn]

Hello, Laura,

Thanks for your report.  We are looking into it.  Things are slow here until January,

however, as the University is closed.

regards,

   --b0b kuhn
    ucsc genome bioinformatics group

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[Matthew Speir]

Hi Laura,

Thank you for your question about RefSeq annotations on chrM in the UCSC Genome Browser. The "RefSeq Genes" track, http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=refGene, in the UCSC Genome Browser, is based on mapping only a subset of those annotations from the RefSeq annotation database. To create our RefSeq Genes track, we only map those annotations with identifiers that start with NR_* or NM_*. RefSeq uses identifiers that begin with YP_* for mitochondrial annotations. Since we only map NM or NR identifiers, those RefSeq identifiers starting with YP will not be included in our RefSeq Genes track.

In the future, we do plan to create a track that includes all available RefSeq annotations, but I don't have an estimate on when that may be available. In the meantime, if you want to view gene annotations on chrM in the UCSC Genome Browser, you could use the "GENCODE Genes v22" track, http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=knownGene.

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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