Is There A Webpage Or Server That Contains Data On Mouse Mitchondrial Genes With Coordinates And Gene Annotations

Question

[Honey]

I am trying to find web page or server/ database which will allow me to download the txt/ bed file for mouse mitchondrial genes with coordinates and gene annotations. I have tried google NCBI, EBI and could not find the same.

Thanks

[Rm]

Download from UCSC table browser:

#mm10.knownGene.name    mm10.knownGene.chrom    mm10.knownGene.strand    mm10.knownGene.txStart    mm10.knownGene.txEnd    mm10.knownGene.proteinID    mm10.kgXref.kgID    mm10.kgXref.mRNA    mm10.kgXref.geneSymbol    mm10.kgXref.refseq    mm10.kgXref.description
uc009vev.1    chrM    +    69    852        uc009vev.1    AK140265    AK140265        Mus musculus adult male corpora quadrigemina cDNA, RIKEN full-length enriched library, clone:B230350D20 product:unclassifiable, full insert sequence.
uc012hdk.1    chrM    -    1093    2681        uc012hdk.1    GU332589    GU332589        Mus musculus strain BALB/c clone 3 antisense RNA, complete sequence; mitochondrial.
uc009vew.1    chrM    +    1148    3703        uc009vew.1    AK018753    AK018753        Mus musculus adult male kidney cDNA, RIKEN full-length enriched library, clone:0610040O15 product:NADH dehydrogenase 1, mitochondrial, full insert sequence.
uc009vex.2    chrM    +    3844    4925        uc009vex.2    AK163440    AK163440        Mus musculus adult male aorta and vein cDNA, RIKEN full-length enriched library, clone:A530057D15 product:NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) homolog [Mus musculus], full insert sequence.
uc009vey.1    chrM    +    5326    6938        uc009vey.1    DQ539915    DQ539915        Mus musculus clone MBI-45 miscellaneous RNA, partial sequence.
uc009vez.1    chrM    +    7009    7699        uc009vez.1    AK131586    Cox2        Mus musculus cytochrome c oxidase subunit II (Cox2) mRNA, complete cds; mitochondrial gene for mitochondrial product.
uc009vfa.1    chrM    +    7765    8607        uc009vfa.1    AK131579    Atpase6        Mus musculus ATPase subunit 6 (Atpase6) mRNA, mitochondrial gene encoding mitochondrial protein, complete cds.
uc009vfb.1    chrM    +    9875    11542    D3Z738    uc009vfb.1    AK142750    Gm10222        SubName: Full=Uncharacterized protein;
uc012hdm.1    chrM    -    11719    14070        uc012hdm.1    BC071253    BC071253        Mus musculus adult male hypothalamus cDNA, RIKEN full-length enriched library, clone:A230051L08 product:NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) homolog [Mus musculus], full insert sequence.
uc009vfc.1    chrM    +    12405    15288        uc009vfc.1    X57780    Cytb        Mus musculus adult male kidney cDNA, RIKEN full-length enriched library, clone:0610008A24 product:cytochrome b, mitochondrial, full insert sequence.

Answer 1

[Mitch Bekritsky]

I don't do mouse research, so if there's someone who has more knowledge than I do on where to get this information from, listen to them. But this looks like it might be what you're looking for: MGI Genes and Markers Query Form. Select MT under chromosomes in the Map Position box and specify an output type (didn't see BED, but I did see tab-delimited, which should be easy to make into a BED format file).

Answer 2

[Richard Smith]

As Mitch says MGI (the mouse model organism database) looks like the best place to get this. Their genome downloads page has files of gene coordinates in tab delimited formats and GFF which include mitochondrial genes.

Answer 3

[Assa Yeroslaviz]

the ensembl FTP Server is a very good option. here you can download the wanted annotations

Answer 4

[macmath]

http://mitominer.mrc-mbu.cam.ac.uk/release-4.0/begin.do MitoMiner, an integrated web resource of mitochondrial localisation evidence and phenotype data for mammals, zebrafish and yeasts. MitoMiner is now gene centric, with all data attached to gene objects

Answer 5

[pschnepp]

There's a website MitoCarta that seems to have a list of mitochondrial genes for both human and mouse. https://www.broadinstitute.org/scientific-community/science/programs/metabolic-disease-program/publications/mitocarta/mitocarta-in-0 This could be what you're looking for.