Hello, Parul,
You are correct, the txStart and txEnd are the coordinates that
define the transcript for genes in both the refGene and knownGene
tables. Please note that the txStart will always be less than
txEnd, irrespective of the strand from which the gene is
transcribed. That means that the actual start of transcription
for genes on the negative strand will be the txEnd coordinate.
This may sound confusing, but it greatly simplifies display in
the Genome Browser. Our software uses the txStart coord to
define the left side of an annotation for both positive- and
negative-strand genes.
regards,
--b0b kuhn
ucsc genome bioinformatics group
On 7/28/2011 11:01 PM, Parul Sagar wrote:
> dear sir/mam,
>
>
> I am Parul Sagar, Junior Research Fellow, *Institute of Cytology and
> Preventive Oncology*(ICMR).
>
> I am working on some project and i require gene coordinates of *Homo** **
> sapien*s. For that I used the Table Browser to download the RefSeq Genes
> set, and downloaded from
> http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/refGene.txt.gz. I
> also downloaded UCSC Genes track and knownGene table for hg19 database (
> http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/knownGene.txt.gz)<http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/knownGene.txt.gz>.
> In this table *txStart* ,*txEnd*, *cdsStart *and* cdsEnd* are given. so can
> i take *txStart *and *txEnd *as gene coordinates or is there any other table
> for that ? if yes then can you please send me the link or table name from
> where i can download all the genes coordinates.
>
> thank you.
>
>
>
> Parul Sagar
> Junior Research Fellow
> *Institute of Cytology and Preventive Oncology*(ICMR)
> _______________________________________________
> Genome maillist - [email protected]
> https://lists.soe.ucsc.edu/mailman/listinfo/genome
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