Question

Where can I find the coordinates of mitochondrial DNA on the human genome on UCSC Genome Browser?

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8.8 years ago

quachtina96 ▴ 40

Hi! I am trying to find the coordinates for the mitochondrial DNA in the human genome so that I can calculate the depth of coverage on just those portions of the genome.

I believe it should look something like the following except with chrM:

chr1:2121092-2121243 chr1:2124337-2124458 chr1:2125002-2125624 chr1:2129392-2129633 chr1:2130128-2130489

Where on the UCSC Genome Browser can I find this? What kind of file name should I look for?

mtDNA DNA-Seq coordinates ucsc genome browser • 8.2k views

ADD COMMENT • link updated 16 months ago by Ram 43k • written 8.8 years ago by quachtina96 ▴ 40

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uh ? http://genome.ucsc.edu/cgi-bin/hgTracks?org=Human&db=hg38&position=chrM

ADD REPLY • link 8.8 years ago by Pierre Lindenbaum 161k

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is there anything where I find where the mtDNA is on the human genome rather than looking specifically at chrM (which is all of those regions put together?)

ADD REPLY • link 8.8 years ago by quachtina96 ▴ 40

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What do you mean on the human genome? mtDNA is chrM, it's not like that's somewhere on chr1 or something.

ADD REPLY • link 8.8 years ago by Devon Ryan 104k

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chrM:1-16569 ?

ADD REPLY • link 8.8 years ago by Jeremy Leipzig 22k

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Are you looking for coordinates for the whole chromosome, or sets of intervals spanning genes?

ADD REPLY • link updated 16 months ago by Ram 43k • written 8.8 years ago by h.mon 35k

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I'm looking for sets of intervals spanning genes. I was under the impression that there would be mtDNA in segments integrated into the entire human genome. Am I wrong?

ADD REPLY • link 8.8 years ago by quachtina96 ▴ 40

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Perhaps you're actually after something else. mtDNA is only on chrM, by definition...however there are non-mitochondrial genes expressed in the mitochondria. Are you instead looking for those?

ADD REPLY • link 8.8 years ago by Devon Ryan 104k

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Isn't the chrM part of the entire human genome? I'm looking for the mitochondrial genes

ADD REPLY • link 8.8 years ago by quachtina96 ▴ 40

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Yes, chrM, like every other chromosome, is part of the genome. The question becomes whether you're looking for genes expressed in the mitochondria or genes on DNA in the mitochondria (these are a subset of all genes actually expressed in the mitochondria).

ADD REPLY • link 8.8 years ago by Devon Ryan 104k

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I'm looking for genes on DNA in the mitochondria, but now that you've mentioned that this is a just a subset, I would also like to know how to find the non-mitochondrial genes expressed in the mitochondria. How can I find these two things?

ADD REPLY • link 8.8 years ago by quachtina96 ▴ 40

Ram · Answer 1 · 2015-06-25

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8.8 years ago

h.mon 35k

Download the appropriate annotation and look here for a tip on how to get chrM. For the nuclear gene which code proteins localized on the mitochondria, see MitoCarta.

ADD COMMENT • link updated 16 months ago by Ram 43k • written 8.8 years ago by h.mon 35k

score 3 · Answer 2 · 2015-06-26

these are the genes on chrM
##gff-version 3
##sequence-region chrM 1 16569
chrM    Mitomap    coding    14149    14673    .    -    .    Name=ND6;ID=33
chrM    Mitomap    coding    12337    14148    .    +    .    Name=ND5;ID=32
chrM    Mitomap    coding    8366    8572    .    +    .    Name=ATPase8;ID=21
chrM    Mitomap    tRNA    4263    4331    .    +    .    Name=I;ID=7
chrM    Mitomap    tRNA    10405    10469    .    +    .    Name=R;ID=26
chrM    Mitomap    tRNA    7518    7585    .    +    .    Name=D;ID=18
chrM    Mitomap    coding    5904    7445    .    +    .    Name=COI;ID=16
chrM    Mitomap    coding    10470    10766    .    +    .    Name=ND4L;ID=27
chrM    Mitomap    tRNA    8295    8364    .    +    .    Name=K;ID=20
chrM    Mitomap    coding    4470    5511    .    +    .    Name=ND2;ID=10
chrM    Mitomap    tRNA    12266    12336    .    +    .    Name=L(CUN);ID=31
chrM    Mitomap    coding    14747    15887    .    +    .    Name=Cytb;ID=35
chrM    Mitomap    tRNA    5512    5579    .    +    .    Name=W;ID=11
chrM    Mitomap    tRNA    12138    12206    .    +    .    Name=H;ID=29
chrM    Mitomap    tRNA    5587    5655    .    -    .    Name=A;ID=12
chrM    Mitomap    tRNA    5826    5891    .    -    .    Name=Y;ID=15
chrM    Mitomap    coding    7586    8269    .    +    .    Name=COII;ID=19
chrM    Mitomap    rRNA    648    1601    .    +    .    Name=12S;ID=2
chrM    Mitomap    tRNA    7446    7516    .    -    .    Name=S(UCN);ID=17
chrM    Mitomap    tRNA    577    647    .    +    .    Name=F;ID=1
chrM    Mitomap    tRNA    12207    12265    .    +    .    Name=S(AGY);ID=30
chrM    Mitomap    coding    10059    10404    .    +    .    Name=ND3;ID=25
chrM    Mitomap    coding    10760    12137    .    +    .    Name=ND4;ID=28
chrM    Mitomap    tRNA    5761    5826    .    -    .    Name=C;ID=14
chrM    Mitomap    tRNA    9991    10058    .    +    .    Name=G;ID=24
chrM    Mitomap    coding    8527    9207    .    +    .    Name=ATPase6;ID=22
chrM    Mitomap    tRNA    5657    5729    .    -    .    Name=N;ID=13
chrM    Mitomap    coding    9207    9990    .    +    .    Name=COIII;ID=23
chrM    Mitomap    coding    3307    4262    .    +    .    Name=ND1;ID=6
chrM    Mitomap    tRNA    1602    1670    .    +    .    Name=V;ID=3
chrM    Mitomap    tRNA    15888    15953    .    +    .    Name=T;ID=36
chrM    Mitomap    tRNA    4402    4469    .    +    .    Name=M;ID=9
chrM    Mitomap    tRNA    4329    4400    .    -    .    Name=Q;ID=8
chrM    Mitomap    rRNA    1671    3230    .    +    .    Name=16S;ID=4
chrM    Mitomap    tRNA    14674    14742    .    -    .    Name=E;ID=34
chrM    Mitomap    tRNA    15955    16023    .    -    .    Name=P;ID=37
chrM    Mitomap    tRNA    3230    3304    .    +    .    Name=L(UUA/G);ID=5