Question: Where can I find the coordinates of mitochondrial DNA on the human genome on UCSC Genome Browser?
2
gravatar for quachtina96
4.5 years ago by
quachtina9640
United States
quachtina9640 wrote:

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?

ADD COMMENTlink modified 4.5 years ago by Jeremy Leipzig18k • written 4.5 years ago by quachtina9640
1

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

ADD REPLYlink written 4.5 years ago by Pierre Lindenbaum124k

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 REPLYlink written 4.5 years ago by quachtina9640

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

ADD REPLYlink written 4.5 years ago by Devon Ryan93k

chrM:1-16569 ?

ADD REPLYlink modified 4.5 years ago • written 4.5 years ago by Jeremy Leipzig18k

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

ADD REPLYlink written 4.5 years ago by h.mon28k

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 REPLYlink written 4.5 years ago by quachtina9640

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 REPLYlink written 4.5 years ago by Devon Ryan93k

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

ADD REPLYlink written 4.5 years ago by quachtina9640

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 REPLYlink written 4.5 years ago by Devon Ryan93k

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 REPLYlink written 4.5 years ago by quachtina9640
3
gravatar for h.mon
4.5 years ago by
h.mon28k
Brazil
h.mon28k wrote:

Download the appropriate annotation and look How to remove Mitochondrial genes from Human annotation file (.GTF)?for a tip on how to get chrM. For the nuclear gene which code proteins localized on the mitochondria, see MitoCarta.
 

ADD COMMENTlink written 4.5 years ago by h.mon28k
3
gravatar for Jeremy Leipzig
4.5 years ago by
Philadelphia, PA
Jeremy Leipzig18k wrote:
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
ADD COMMENTlink written 4.5 years ago by Jeremy Leipzig18k

how to extract this can u please elaborate

ADD REPLYlink written 3.5 years ago by kapil.joshi03680
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