[Genome] Coding exons of genes in the human genome

[Brooke Rhead]

Hi Siddarth,

Are you using the hg18 database?  I do not see any entries in the 
hg18.kgXref table like '1-Mar' or 'C10orf10'.

Is the kgXref table you are using identical to the one located here?:
http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/kgXref.txt.gz

--
Brooke Rhead
UCSC Genome Bioinformatics Group


SiddarthGautham Selvaraj wrote:
> Hi,
> 
> 
> I am a graduate student from Arizona State University. I am trying to
> extract the list of canonical genes from KnownCanonical table. To do that, I
> first need to organize genes based on gene symbols.
> 
> The values contained as gene symbol in kgXref table are not very precise. It
> has entries like
> 
>  1-Mar  2-Mar  3-Mar  4-Mar  5-Mar  6-Mar  7-Mar  8-Mar  9-Mar  1-Sep  2-Sep
> 3-Sep  4-Sep  5-Sep  6-Sep  7-Sep  8-Sep  9-Sep  10-Sep  11-Sep  12-Sep
> 15-Sep  1-Dec and
> 
>  C10orf10  C10orf104  C10orf107  C10orf108  C10orf11  C10orf110  C10orf111
> C10orf113  C10orf114  C10orf116  C10orf118  C10orf119  C10orf12  C10orf120
> C10orf122  C10orf125  C10orf129  C10orf130  C10orf132  C10orf137  C10orf18
> C10orf22  C10orf25  C10orf26  C10orf27  C10orf28  C10orf30  C10orf32
> C10orf33  C10orf35  C10orf38  C10orf4  C10orf46  C10orf47  C10orf49
> C10orf53  C10orf54  C10orf55  C10orf56  C10orf57  C10orf58  C10orf59
> C10orf6  C10orf61  C10orf62  C10orf63  C10orf64  C10orf65  C10orf67
> C10orf68  C10orf71  C10orf72  C10orf73  C10orf76  C10orf78
> which I guess are junk entries. Thus I would require HGNC symbols from some
> other table so that I can compare these values and get only the proper gene
> symbols and hence proper genes.
> 
> Please let me know which table has the HGNC symbols.
> 
> Please help me in this.
> 
> Thanks
> siddarth
> 
> On 08/01/2008, Ann Zweig <ann at soe.ucsc.edu> wrote:
>> Hello Siddarth,
>>
>>         If you have successfully extracted the sequence for all Known
>> Genes, but you
>> only want the sequence for the canonical gene in each gene cluster, then
>> my
>> suggestion would be to use the output from the knownCanonical table to
>> filter
>> out those genes from your list that you are not interested in.
>>
>>         If this does not address your issue, please feel free to write
>> back to the
>> genome list.
>>
>>
>> Regards,
>>
>> ----------
>> Ann Zweig
>> UCSC Genome Bioinformatics Group
>> http://genome.ucsc.edu
>>
>> Please feel free to search the Genome mailing list archives by visiting
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>> list.
>>
>>
>>
>>
>> SiddarthGautham Selvaraj wrote:
>>> Hi:
>>>
>>> I am siddarth, a graduate student in Arizona State University. I have
>> been
>>> trying to get the coding exon sequences of all genes in the human
>> genome.
>>> I define genes as an unit of the genome which codes for something. I do
>> not
>>> need gene variants. That is a gene may get alternatively spliced to
>> produce
>>> different products. I am not bothered on the variants a gene can produce
>>> through alternate splicing.
>>>
>>> I tried KnownCanonical Table but I guess it does not focus on all exons.
>>>
>>> Thus where can I get information on coding exons of all genes in the
>> human
>>> genome.
>>>
>>> Awaiting Your reply
>>>
>>> Thanks
>>> siddarth
>>> _______________________________________________
>>> Genome maillist  -  Genome at soe.ucsc.edu
>>> http://www.soe.ucsc.edu/mailman/listinfo/genome
> _______________________________________________
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