HTT-AS

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Kenny Day

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Aug 18, 2016, 12:12:00 PM8/18/16
to gen...@soe.ucsc.edu
Dear UCSC,
 
I have lately been studying transcriptional elements within the HTT gene and noticed that the transcriptional start site and depiction of the HTT-AS nearby doesn't appear to agree with this manuscript that mapped the TSS, etc: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3153309/

Although the paper reports their coordinates relative to the TSS of HTT in build 36, regardless of build, the exon1 of HTT-AS is much further 5' to the 5'UTR of HTT.

Am I interpreting this incorrectly? The manuscript suggests the main TSS for the HTT-AS begins at +300 relative to the TSS of HTT (i.e. including antisense of HTT exon 1). In other words, they are showing that exon1 of the AS transcript is embedded within exon 1 of the HTT coding sequence.

Thanks!

Kenneth Day
HudsonAlpha Institute for Biotechnology

Matthew Speir

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Aug 19, 2016, 3:44:53 PM8/19/16
to Kenny Day, gen...@soe.ucsc.edu
Hi Kenneth,

Thank you for your question about the HTT-AS transcript in the UCSC
Genome Browser.

I'm unsure why the configuration of these transcripts is different from
that described in the paper you've linked. Assemblies and gene sets
change over time, so it's not too unbelievable that an annotation
produced 5 years ago is not the same as a current one.

Additionally, in many cases we're displaying annotations that others
have produced and mapped to the genome. For example, in hg38, the
primary default gene track was produced by the GENCODE group, which
displays these transcripts as non-overlapping:
https://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=mspeir&hgS_otherUserSessionName=hg38_HTT%2DAS_17920.
Same goes for the RefSeq Genes track displayed in that session.

You may want to contact the authors of the paper for more information
regarding their annotation of the HTT-AS gene and see if they can
provide any insight.

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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