Question: Exon-Start Same As Exon-End From Ucsc Knowngene
3
gravatar for brentp
8.0 years ago by
brentp23k
Salt Lake City, UT
brentp23k wrote:

As an example, a single row from UCSC knownGene (hg19) like this:

SELECT cdsStart,cdsEnd,K.name,exonStarts,exonEnds FROM knownGene as K, kgXref as X WHERE
X.kgId=K.name and K.name='uc002imy.2'

The output (with new-lines added so that exonStarts and exonEnds line up):

cdsStart        cdsEnd  name    exonStarts      exonEnds
46103793        46115139        uc002imy.2      
46103534,46105837,46106490,46109521,46110051,46110576,46111228,46114216,46115032,46115092,46115124,   
46103841,46105876,46106542,46109599,46110107,46110668,46111310,46114291,46115092,46115122,46115152,

Note that the 2nd-from-last exonStart is the same as the 3rd-from-last exonEnd (46115092). What does this mean. A single row in knownGene is a single transcript, so what does it mean to have a zero-length intron? There are enough of these that I want to understand what is going on.

I have asked this question on the UCSC mailing list but no answer yet.

bed splicing exon transcript ucsc • 1.8k views
ADD COMMENTlink written 8.0 years ago by brentp23k

A response on the mailing list (https://lists.soe.ucsc.edu/pipermail/genome/2011-May/026016.html) explains that it's due to gaps on the query relative to the transcript sequence. I hadn't thought about these issues before now.

ADD REPLYlink written 8.0 years ago by brentp23k
1
gravatar for Scott Cain
8.0 years ago by
Scott Cain750
Scott Cain750 wrote:

I wonder if there is a CDS boundary there, like a stop codon. Sometimes I've seen data goofs where one exon is split into two when part of it is coding and the other isn't.

ADD COMMENTlink written 8.0 years ago by Scott Cain750

Could be... though this occurs even in transcripts that are (annotated as) non-coding.

ADD REPLYlink written 8.0 years ago by brentp23k
1
gravatar for Pi
8.0 years ago by
Pi510
Pi510 wrote:

Could it be intron retention?

ADD COMMENTlink written 8.0 years ago by Pi510
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