[Genome] question about AI201163 human EST

[Silvia Anna Ciafrè]

I'm writing to ask a question about a human EST, present in the human database of UCSC genome browser. My question probably arises from a lack of comprehension, on my part, of the EST description: when reading the description of that EST, I find that it is on strand minus. But I also find that this must not bear any relationship with the direction of the transcription. So, may I infer that AI201163 EST is transcribed from the same DNA strand as CDKN1B mRNA, of which AI201163 EST seems to be an alternative splicing product? Or should I think that it's an antisense RNA with respect to CDKN1B mRNA?
Thank you very much for your help.
Sincerely,
Silvia Ciafrè


Silvia Anna Ciafrè
Dept. of Experimental Medicine and Biochemical Sciences
University of Rome Tor Vergata
Via Montpellier, 1
00133 Rome
Italy
tel +39 06 72596059
fax +39 06 72596053

[robert kuhn]

Dear Silvia,

The track description you describe comes from the EST track, which
includes all ESTs. We also have a track, Spliced ESTs that we consider
higher-quality, because the direction of transcription is more easily
ascertained.

Most ESTs are produced from cDNAs that have been clones into plasmid
vectors and are therefore double-stranded molecules when sequenced.
If an EST has no introns (aligns to the reference assembly as one
uninterrupted block), then it is not possible to determine the
transcription direction. That explains the statement that we display
only the direction of alignment, not transcription.

For ESTs that have been spliced, however, we can search for the gt----ag
canonical splice junctions and make a determination of transcription
direction. These ESTs are pulled out into the Spliced EST track, but
the information is also displayed with little arrows in the intron on
the browser graphic for the EST track containing non-spliced ESTs.

The AI201163 EST is transcribed in the forward direction (i.e., =from=
the reverse strand template), with the 5' end on the left in the
graphic. The mRNA for the CDKN1B gene is also transcribed in the
forward direction. Whether you should consider the EST to be an isoform
of CDKN1B is a decision you would have to make on your own. The EST
shares two of its exons with the gene, but it is the only transcript
among many in the EST and mRNA tracks with the two 5'-most exons. It is
not an anti-sense relative to the gene.

Best wishes,

--b0b kuhn
ucsc genome bioinformatics group

On 1/19/2011 2:29 AM, Silvia Anna Ciafr� wrote:
> I'm writing to ask a question about a human EST, present in the human database of UCSC genome browser. My question probably arises from a lack of comprehension, on my part, of the EST description: when reading the description of that EST, I find that it is on strand minus. But I also find that this must not bear any relationship with the direction of the transcription. So, may I infer that AI201163 EST is transcribed from the same DNA strand as CDKN1B mRNA, of which AI201163 EST seems to be an alternative splicing product? Or should I think that it's an antisense RNA with respect to CDKN1B mRNA?
> Thank you very much for your help.
> Sincerely,

> Silvia Ciafr�
>
>
> Silvia Anna Ciafr�

> Dept. of Experimental Medicine and Biochemical Sciences
> University of Rome Tor Vergata
> Via Montpellier, 1
> 00133 Rome
> Italy
> tel +39 06 72596059
> fax +39 06 72596053

> _______________________________________________
> Genome maillist - Gen...@soe.ucsc.edu
> https://lists.soe.ucsc.edu/mailman/listinfo/genome