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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