Hello Hao Zheng,
All the genes in the knownCanonical.txt.gz file are referred to by their
UCSC genes identifier ("ucNNNabc.N"):
i.e.
chr1 1115 4272 1 uc009vip.1 uc009vip.1
chr1 4269 19221 2 uc009viw.1 uc009viw.1
chr1 19417 20957 3 uc009vjg.1 uc009vjg.1
So you would have to find the corresponding UCSC genes identifier for
these genes:
Alternate Gene Symbols: BCL5, BCL6_HUMAN, LAZ3, NM_001706, NP_001697,
P41182, S67779, uc003frp.1, ZBTB27, ZNF51
UCSC ID: uc003frp.2
Alternate Gene Symbols: MDS1_HUMAN, NM_004991, NP_004982, Q13465, Q13466
UCSC ID: uc003ffp.1
(TRD@)
Alternate Gene Symbols: AK310682, uc001wea.1
UCSC ID: uc010aju.1
The other gene you inquired about, "C12orf9" was not included in the
UCSC genes track. For more information about the criteria for
including/excluding genes from UCSC genes please see the track description:
http://genome.ucsc.edu/cgi-bin/hgGene?hgg_do_kgMethod=1
Hopefully this information was helpful and answers your question. If you
have further questions or require clarification feel free to contact the
mailing list at [email protected].
Best regards,
Pauline Fujita
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu
On 9/30/10 12:07 PM, [email protected] wrote:
> Dear Colleague,
>
> There are three genes called "BCL5", "MDS1" and "TRD@". However, I am not
> able to get the coordinates of these three genes from the
> knownCanonical table here:
> ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/knownCanonical.txt.gz.
>
> Do you have any suggestions?
>
> Thanks,
>
> Hao Zheng
>
> _______________________________________________
> Genome maillist - [email protected]
> https://lists.soe.ucsc.edu/mailman/listinfo/genome
>
_______________________________________________
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https://lists.soe.ucsc.edu/mailman/listinfo/genome
