Dear Lionel/Lee,
Our database includes non-protein-coding genes as well as coding.
In that case, we represent thickStart = thinkEnd (startCodon =
endCodon) in the database. Our software then displays the item with
no translation, showing the gene entirely as a half-height box, the
same way we represent the 5' and 3' untranslated regions (UTRs) of
coding genes.
Regarding your second question, we represent blockCount = 1 if there
are no introns removed in the mature transcript. An exon need not be
translated (or entirely translated), and there are coding genes with
exons that are entirely part of a UTR.
Thanks for being a Browser user.
Best wishes,
--b0b kuhn
ucsc genome bioinformatics group
On 1/18/2011 10:31 AM, Lionel (Lee) Brooks 3rd wrote:
> Hello Gentlepeople,
>
> I have been working with the knownGene table and I am confused about
> some of the rows in this table.
> Here, I'll submit an exceptionally confusing entry from the table. It
> was exported as bed format file:
>
> ['chr1', '149397113', '149399229', 'uc010pbi.1', '0', '-', '149397113',
> '149397113', '0', '1', '2116,', '0,']
>
> According to the bed file format we know that the fields represent the
> following values:
> chromosome, chromStart, chromEnd, name, score, strand, thickStart (start
> codon), thickEnd (stop codon), itemRgb, blockCount (number of exons),
> blockSizes (exon sizes), blockStarts (exons starts)
>
> My confusion has arisen from the fact that thickStart == thickEnd.
> This would mean that the start and stop codon are one and the same?
>
> Also confusing is that blockCount == 1.
> How can there be an exon if the start and end codon are at the same spot?
> In fact, the blockSizes field indicates that the exon is 2116 bases long.
> How can this be?
>
> Am I misinterpreting these values?
> What am I missing?
> If this is not the right forum to ask this question then can you guide
> me to a suitable resource?
>
>
> TIA,
> Lionel "Lee" Brooks 3rd
> Dartmouth Genetics Graduate Student
> _______________________________________________
> Genome maillist - [email protected]
> https://lists.soe.ucsc.edu/mailman/listinfo/genome
_______________________________________________
Genome maillist - [email protected]
https://lists.soe.ucsc.edu/mailman/listinfo/genome
