To localize a gene in the genomic sequence

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yangp
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To localize a gene in the genomic sequence

Post by yangp » Thu Jul 19, 2007 12:59 am

Dear all:

I intend to localize a gene (NM_178759) in its genomic sequence (NM_178759, or AC_000033), can you tell me how? Thanks. Parker.

blcr11
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Post by blcr11 » Thu Jul 19, 2007 1:04 pm

What do you mean by "localize?" If you go to the ExPASY Proteomics server and search for Timd4 you will pull out links for the mouse or the human gene. Open whichever you want and look at the Sequence databases annotation for links to either the mRNA sequence, which will have 5' and 3' untranslated sequences, or for just the CoDingSequence. If you want the genomic sequence you can follow the links under Genome annotation databases where -- eventually (after several links) -- you can look at the sequence of the contig containing the entire gene, introns and all. To use this information most easily, it helps to know the boundaries fairly precisely, or else align the mRNA with the contig sequence and get your intron/exon boundaries that way.

yangp
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Post by yangp » Fri Jul 20, 2007 1:04 am

Dear Sir or Madam:

Thanks for your direction. I'm still a little unclear. What I want to know is where is the start point of TIM4 in the genomic sequence, because the mouse chromosome 11 is too long to find this point by net eye. Parker.

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Post by blcr11 » Fri Jul 20, 2007 2:31 pm

But you don’t have to do it by eye. From the MGI database, the mouse Timd4 gene covers 33,533 bases and is located on chromosome 11 from positions 46,654,223 to 46,687,755. That includes introns (there are 9 exons for the gene) and it apparently has some alternate forms that differ in their 3’ ends. You can download the gene sequence in fasta format including as much or as little of the flanking sequence as you want. You can also look at the transcript itself.

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