mitochondria genes from RefSeq

[Wang, Xiaojing]

 

Hello,

 

I found there is no mitochondria genes information from the table or GTF files downloaded from table browser.

I used hg19 and chose refGene table.

Is there any reason for this?

 

Thanks,

Xiaojing

 

 

[Luvina Guruvadoo]

Hi  Xiaojing,

We have mitochondrial chromosome data included in our UCSC Genes track, which we refer to as "chrM", for most assemblies in the Genome Browser. To get gene information for a section of DNA (including the mitochondrial chromosome) use our Table Browser at http://genome.ucsc.edu/cgi-bin/hgTables. After selecting your organism and assembly of interest, select the UCSC Genes track. For region, select the "position" button and type in "chrM". Finally, select your output format and file if desired and click "get output".

If you have further questions please feel free to contact the mailing list again at gen...@soe.ucsc.edu.

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Luvina Guruvadoo
UCSC Genome Bioinformatics Group

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[Wang, Xiaojing]

Hi,

Thanks for your quick response.

 

Actually we have to use RefSeq annotation for a specific project.

So is there a reason why RefSeq GTF downloaded from Table Browser didn't contain any genes in mitochondrial?

And do you have any idea where can I download the complete GTF file?

 

Thanks,

Xiaojing

[Luvina Guruvadoo]

Hi Xiaojing,

RefSeq does not annotate human mitochondrial RNAs/mRNAs. You may want to contact NCBI for more information: http://www.ncbi.nlm.nih.gov/RefSeq/update.cgi.

If you have further questions please feel free to contact the mailing list again at gen...@soe.ucsc.edu.

---
Luvina Guruvadoo
UCSC Genome Bioinformatics Group

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