how to extract this can u please elaborate
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Where can I find the coordinates of mitochondrial DNA on the human genome on UCSC Genome Browser?
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?
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quachtina96 •
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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
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uh ? http://genome.ucsc.edu/cgi-bin/hgTracks?org=Human&db=hg38&position=chrM
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?)
What do you mean on the human genome? mtDNA is chrM, it's not like that's somewhere on chr1 or something.
chrM:1-16569 ?
Are you looking for coordinates for the whole chromosome, or sets of intervals spanning genes?
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?
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?
Isn't the chrM part of the entire human genome? I'm looking for the mitochondrial genes
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).
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?