Question Regarding U2AF1L5

[Vora, Shailee]

Hello,

I am a PhD Student at Mount Sinai in New York. I am currently working on the U2AF1 splicing factor and have some questions regarding this gene in the UCSC Browser. 

In hg38, there appears to be a duplication of this gene that is referred to as U2AF1l5 (like-5). Both are on chromosome 21, but at opposite ends. 

I am having trouble understanding whether this is an inactive pseudogene or a duplication of the gene that is actually expressed as protein?

Would you have any information regarding this duplication? Any input would be much appreciated, as it doesn't seem to be well documented elsewhere. 

Thank you for your time. 

Best regards, 

Shailee Vora

U2AF1L5:

http://genome.ucsc.edu/cgi-bin/hgGene?hgg_gene=uc032prm.2&hgg_prot=ENST00000610664.4&hgg_chrom=chr21&hgg_start=6484622&hgg_end=6499200&hgg_type=knownGene&db=hg38&hgsid=650323975_JqatNUz86bQYwivnqTqF8TDJHtB3

U2AF1:

http://genome.ucsc.edu/cgi-bin/hgGene?hgg_gene=uc002zda.2&hgg_prot=ENST00000380276.6&hgg_chrom=chr21&hgg_start=43092955&hgg_end=43107565&hgg_type=knownGene&db=hg38&hgsid=650323975_JqatNUz86bQYwivnqTqF8TDJHtB3

[Christopher Lee]

Hi Shailee,

Thank you for your question about U2AF1L5. As this forum is not
intended for general scientific advice, I cannot tell you with
certainty whether or not both copies of the U2AF1 transcript are
expressed or are pseudogenes, etc. However, if you take the mRNA for
the uc002zdb.2 transcript and BLAT it against the hg38 genome, you can
see that the mRNA sequence aligns almost perfectly to both ends of the
chromosome:
http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=chmalee&hgS_otherUserSessionName=hg38_u2af1_blat

In the above session I have saved the BLAT results as a custom track,
and used the multi-region feature to chop the chromosome down to both
ends so you can compare the mRNA BLAT results to the predicted
transcripts in various gene tracks. Since the mRNA aligns so well to
both locations, it does not surprise me that the transcript prediction
shows up in both locations, however I cannot say for sure if one,
both, or none of the transcripts are actually expressed.

Unfortunately, since I cannot tell you whether these transcripts are
expressed or not you will have to inspect the various gene tracks and
decide for yourself whether or not one is a pseudogene.

Please let us know if you have any further questions!

Christopher Lee
UCSC Genomics Institute

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