Genome Browser Result annotation

[Quartuccia, Gabriella I.]

Hello,

My name is Gabriella and I'm a technician in a research lab at Columbia University. I used the BLAT feature today and I was wondering gif you guys could clarify something for me, an alternate location named "15_KI270850v1_alt" as the chromosome. I'm assuming this is one of the pseudogenes tied to the sequence I BLAT'ed, but I'm a little confused about why it's annotated as an alternate sequence, and what that even means.

Thank you.

Best,

Gabriella

[Chris Villarreal]

Dear Gabriella,

Thank you for your question about your BLAT results. The chr*_alt chromosomes are alternative sequences for different regions in the human genome. You can read more about them on the GRCh38/hg38 Gateway page, http://genome.ucsc.edu/cgi-bin/hgGateway?db=hg38, under the section titled " GRCh38 Highlights". You can also find more information on these alternate loci on the Genome Reference Consortium (GRC) website: http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/info/definitions.shtml#ALTERNATE. You can see what regions these alternate sequences correspond to in the genome by using the "Alt Map Super-track", http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=altSequence.

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.

-Chris V
UCSC Genome Browser

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