Draft tracks last updated 26 August 2001:The mammalian mitochondrial genome is a very natural extension of the nuclear genome that might simply be included as an "extra chromosome" to the existing human and mouse browsers. It is also a good choice for development of custom tracks, a proteome/mutational browser, and stand-alone web browser mirror issues because it factors out large file, assembly, draft, and recomputation issues, isolating core mirror/mysql database procedures. While the human and mouse mitochondrial genomes are finished, many dozen mammal and early eukaryote projects are underway. The mitochondrial genome was derived billions of years ago from an internalized alpha-proteobacteria, so the project also serves as a model for implementing the estimated 460 bacterial and archael genomes projects underway.
There already exist a number of superb mitochondrial sites furnishing well-maintained data of all types. Thus this project does not have to search the research literature for data but rather, since the data is not always in a format suitable for a custom track, develop automatic means of stripping out the content of these sites (and by implication, unattended maintainence of the mitochondrial genome browser).
Mito
Mitomap
MitoWu
MitoP
MitoDat
There are 72 principal features described in the mitochondrial genome literature; these are in a preliminary BED track that you can launch above. However, the bidirectional interaction of the mitochondrial genome with the rest of the genome requires three major integrative tracks to be recomputed with each new hg:
-- a track for the estimated 1,100 nuclear gene products targetted to the mitochondria (67 to respiratory chain alone) which is a fairly clean signal easily computable genomewide (part of the overal PSort track).
-- a track for past mitochondrial insertions into nuclear DNA (incorporating color chronology with Blat for recent and Blast/DBA/PipMaker etc for older events).
-- a track fo nuclear gene families that originated from horizontal transfer from the mitochondrial genome that are not necessarily targeted to it now.
Quickie Human Mitochondrial Genome BED Track: paste into text box launcher at UCSC
browser position chr22:1-17000 browser hide all track name=Mitochon.Coding description="Mitochrondrial Proteins" visibility=2 color=90,20,80 useScore=0 chr22 3307 4263 NADH.dehydrog.1. 1000 + chr22 4470 5512 NADH.dehydrog.2. 1000 + chr22 10059 10405 NADH.dehydrog.3. 1000 + chr22 10470 10767 NADH.dehydrog.4L 1000 + chr22 10760 12138 NADH.dehydrog.4. 1000 + chr22 12337 14149 NADH.dehydrog.5. 1000 + chr22 14149 14674 NADH.dehydrog.6. 1000 - chr22 5904 7446 CytC.oxidase.1 1000 + chr22 7586 8270 CytC.oxidase.2 1000 + chr22 9207 9991 CytC.oxidase.3 1000 + chr22 8366 8573 ATP.synthase.8 1000 + chr22 8527 9208 ATP.synthase.6 1000 + chr22 14747 15888 Cytochrome.b 1000 + track name=Neanderthal description="Neanderthal Polymorphisms" visibility=2 color=50,20,90 useScore=1 chr22 14 340 Neander_hyper2 1000 + 14 340 0 27 1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 14,55,70,84,85,88,89,106,116,125,131,146,160,166,186,200,207,211,221,233,235,247,255,276,288,297,339 chr22 16022 16398 Neander_hyper1 1000 + 16022 16398 0 11 1,1,1,1,1,1,1,1,1,1,1 73,146,150,152,189,243,245,247,262,263,391 track name=Lake_Mungo description="Ancient Australian Mitochondrial DNA" visibility=1 color=50,20,90 useScore=1 chr22 16046 16398 Lake_Mungo 1000 + 16223 16387 0 10 1,1,1,1,1,1,1,1,1,1 177,184,217,218,232,244,255,309,310,341 track name=Chrom_11_Insert description="Chromosome 11 Insert Related to Australian Mitochondrial DNA" visibility=1 color=50,20,90 useScore=1 chr22 16193 16284 Chr11 1000 + 16198 16273 0 13 1,1,1,1,1,1,1,1,1,1,1,1,1 5,7,17,23,26,31,33,50,60,61,74,79,81 track name=Diseases description="Mitochrondrial Mutation and Disease" visibility=1 color=80,90,20 useScore=0 chr22 583 583 MELAS 1000 + chr22 606 606 MYOGLO 1000 + chr22 618 618 MM 1000 + chr22 1310 1310 DM 1000 + chr22 1438 1438 DM 1000 + chr22 1555 1555 DEAF 1000 + chr22 1606 1606 AMDF 1000 + chr22 1642 1642 MELAS 1000 + chr22 2835 2835 RETT 1000 + chr22 3196 3196 ADPD 1000 + chr22 3243 3243 MELAS 1000 + chr22 3243 3243 DM.DMDF 1000 + chr22 3243 3243 MM 1000 + chr22 3243 3243 CPEO 1000 + chr22 3249 3249 KSS 1000 + chr22 3250 3250 MM.CPEO 1000 + chr22 3251 3251 MM 1000 + chr22 3252 3252 MELAS 1000 + chr22 3254 3254 MM 1000 + chr22 3256 3256 MELAS 1000 + chr22 3260 3260 MMC 1000 + chr22 3264 3264 DM 1000 + chr22 3271 3271 MELAS 1000 + chr22 3271 3271 PEM 1000 + chr22 3271 3271 DM 1000 + chr22 3288 3288 MYO 1000 + chr22 3291 3291 MELAS 1000 + chr22 3302 3302 MM 1000 + chr22 3303 3303 MMC 1000 + chr22 4269 4269 FICP 1000 + chr22 4274 4274 CPEO 1000 + chr22 4285 4285 CPEO 1000 + chr22 4295 4295 MHCM 1000 + chr22 4298 4298 CPEO.MS 1000 + chr22 4300 4300 MICM 1000 + chr22 4309 4309 CPEO 1000 + chr22 4317 4317 FICP 1000 + chr22 4320 4320 MECM 1000 + chr22 4336 4336 ADPD 1000 + chr22 4409 4409 MM 1000 + chr22 4450 4450 MYO 1000 + chr22 5521 5521 MM 1000 + chr22 5537 5537 MILS 1000 + chr22 5549 5549 DEMCHO 1000 + chr22 5692 5692 CPEO 1000 + chr22 5703 5703 CPEO,MM 1000 + chr22 5814 5814 ME 1000 + chr22 7445 7445 DEAF 1000 + chr22 7472 7472 PEM.AMDF 1000 + chr22 7497 7497 MM 1000 + chr22 7511 7511 SNHL 1000 + chr22 7512 7512 PEM.MERME 1000 + chr22 7543 7543 MEPR 1000 + chr22 8296 8296 DMDF.MERRF 1000 + chr22 8313 8313 MNGIE 1000 + chr22 8328 8328 ME 1000 + chr22 8342 8342 PEO.MYO 1000 + chr22 8344 8344 MERRF 1000 + chr22 8356 8356 MERRF 1000 + chr22 8363 8363 MICM.DEAF 1000 + chr22 9997 9997 MHCM 1000 + chr22 10006 10006 CIPO 1000 + chr22 10010 10010 PEM 1000 + chr22 10044 10044 GER.SIDS 1000 + chr22 12192 12192 MICM 1000 + chr22 12246 12246 CIPO 1000 + chr22 12258 12258 DMDF 1000 + chr22 12308 12308 CPEO 1000 + chr22 12311 12311 CPEO 1000 + chr22 12315 12315 CPEO 1000 + chr22 12320 12320 MM 1000 + chr22 14709 14709 MM.DM 1000 + chr22 15915 15915 MM 1000 + chr22 15923 15923 LIMM 1000 + chr22 15924 15924 LIMM 1000 + chr22 15940 15940 MM 1000 + chr22 15990 15990 MM 1000 + track name=Mitochondria.RNA description="Mitochondrial tRNAs and rRNAs" visibility=2 color=20,90,80 useScore=0 chr22 648 1602 12S.rRNA 1000 + chr22 1671 3230 16S.rRNA 1000 + chr22 3206 3230 5S.RNA 1000 + chr22 16106 16569 7S.DNA 1000 + chr22 0 192 7S.DNA 1000 + chr22 577 648 tRNA.Phenylalan 1000 + chr22 1602 1671 tRNA.Valine 1000 + chr22 3230 3305 tRNA.Leucine.1 1000 + chr22 4263 4332 tRNA.Isoleucine 1000 + chr22 4329 4401 tRNA.Glutamine 1000 - chr22 4402 4470 tRNA.Methionine 1000 + chr22 5512 5577 tRNA.Tryptophan 1000 + chr22 5587 5656 tRNA.Alanine 1000 - chr22 5657 5730 tRNA.Asparagine 1000 - chr22 5761 5827 tRNA.Cysteine 1000 - chr22 5826 5892 tRNA.Tyrosine 1000 - chr22 7445 7517 tRNA.Serine.1 1000 - chr22 7518 7586 tRNA.Aspartate 1000 + chr22 8295 8365 tRNA.Lysine 1000 + chr22 9991 10059 tRNA.Glycine 1000 + chr22 10405 10470 tRNA.Arginine 1000 + chr22 12138 12207 tRNA.Histidine 1000 + chr22 12207 12266 tRNA.Serine2 1000 + chr22 12266 12337 tRNA.Leucine2 1000 + chr22 14674 14743 tRNA.Glutamate 1000 - chr22 15888 15954 tRNA.Threonine 1000 + chr22 15955 16024 tRNA.Proline 1000 - track name=Intergenic.Space description="Intergenic Spacers between Mitochondrial Genes" visibility=1 color=90,20,80 useScore=0 chr22 3305 3307 intergenic 1000 + chr22 4401 4402 intergenic 1000 + chr22 5577 5587 intergenic 1000 + chr22 5656 5657 intergenic 1000 + chr22 5892 5904 intergenic 1000 + chr22 7517 7518 intergenic 1000 + chr22 8270 8295 intergenic 1000 + chr22 8365 8366 intergenic 1000 + chr22 14743 14747 intergenic 1000 + chr22 15954 15955 intergenic 1000 + track name=Control.Elements description="Mitochondrial Promoters and Control Elements" visibility=1 color=90,20,80 useScore=0 chr22 233 261 mtTF1.binding 1000 + chr22 276 304 mtTF1.binding 1000 + chr22 418 446 mtTF1.binding 1000 + chr22 523 551 mtTF1.binding 1000 + chr22 110 442 H-strand.origin 1000 + chr22 317 322 Repl.primer 1000 + chr22 371 380 strand.controlH4 1000 + chr22 384 392 strand.controlH3 1000 + chr22 392 446 promoter.L 1000 + chr22 545 568 Major.promoter 1000 + chr22 645 646 Minor.promoter 1000 + chr22 3229 3257 Transcript.term 1000 + chr22 5721 5799 L-strand.origin 1000 + chr22 15925 16569 membrane.attach 1000 + chr22 0 500 membrane.attach 1000 + chr22 16024 16569 D.loop 1000 - chr22 0 577 D.loop 1000 - chr22 16157 16173 termination 1000 + chr22 16194 16209 control.element. 1000 + chr22 16499 16507 control.elementL 1000 + chr22 299 316 conserved.block1 1000 + chr22 346 364 conserved.block2 1000 + chr22 213 236 conserved.block3 1000 + chr22 57 373 hypervariable2 500 + chr22 16024 16384 hypervariable1 500 + track name=Nuclear.Inserts description="Nuclear Mitochrondrial Inserts: Best Matches" visibility=2 color=90,20,80 useScore=1 chr22 5433 9754 chr5..105430960 961 + chr22 6969 8552 chr17..20396229 914 - chr22 420 2697 chr5..144381696 820 - chr22 1339 2718 chr9....5594806 820 - chr22 10267 15486 chr1......31379 772 - chr22 520 2972 chr4..165089771 772 - chr22 6551 11158 chr2..133550840 678 - chr22 6115 15244 chr1..275544825 537 + chr22 12660 16077 chrX...54045145 490 + chr22 0 1914 chr5...99707971 490 + chr22 573 3093 chr7...63493454 396 + chr22 573 3093 chr2..118578365 396 + chr22 2086 4590 chr2..142216783 396 - chr22 1323 3628 chr11...9897737 396 - chr22 2138 10569 chr5...85383840 348 - chr22 574 5890 chr8...35035672 348 - chr22 573 3628 chr7..146946828 348 - chr22 345 3160 chr4..165146803 348 + chr22 655 3451 chr7..146079189 348 + chr22 280 5956 chr9...36419318 301 + chr22 666 3748 chr20..57635602 301 - chr22 575 6347 chr8...65820500 254 - chr22 695 4887 chr4..124629171 254 + chr22 5215 7913 chr17..22747035 254 - chr22 1545 12704 chr8...49532974 207 + chr22 345 6188 chr4...69219704 207 - chr22 3115 10472 chr3..102763339 207 + chr22 2792 6612 chr17..20334764 207 - chr22 1834 12614 chr14..83213694 207 + chr22 3762 12826 chrX..127211269 113 + chr22 3725 10495 chr11.113878202 113 - chr22 13044 15614 chr7...63679489 113 -Details, detailsMitochondrial disorders
Leber hereditary optic neuropathy Leigh syndrome MNGIE mitochondrial neurogastrointestinal encephalomyopathy Mohr-Tranebjaerg syndrome iron-storage disorders related to Friedreich ataxia hereditary spastic paraplegia Kearns-Sayre Ocular Myopathy (sporadic) Pearson syndrome Pigmentary retinopathy Cardiomyopathy NARP/MILS Kearns-Sayre Wolfram External ophthalmoplegia (PEO) Rhabdomyolysis Disease data taken from Emory site: LHON Leber Hereditary Optic Neuropathy CIPO Chronic Intestinal Pseudoobstruction with myopathy and Ophthalmoplegia AD Alzeimer's Disease CPEO Chronic Progressive External Ophthalmoplegia ADPD Alzeimer's Disease and Parkinsons's Disease MMC Maternal Myopathy and Cardiomyopathy NARP Neurogenic muscle weakness, Ataxia, and Retinitis Pigmentosa; alternate Leigh Disease FICP Fatal Infantile Cardiomyopathy Plus a MELAS-associated cardiomyopathy MM Mitochondrial Myopathy LIMM Lethal Infantile Mitochondrial Myopathy DMDF Diabetes Mellitus + DeaFness MHCM Maternally inherited Hypertrophic CardioMyopathy MELAS Mitochondrial Encephalomyopathy, Lactic Acidosis, and Stroke-like episodes LDYT Leber's hereditary optic neuropathy and DYsTonia MERRF Myoclonic Epilepsy and Ragged Red Muscle Fibers DEAF Maternally inherited DEAFness or aminoglycoside-induced DEAFness PEM Progressive encephalopathy Cons = interspecies conservation of the substituted nucleotide or amino acid, H = high, M = medium, L = low "<" indicates that none of the controls tested was positive for the mutation (e.g. < 2% is equivalent to 0 out of 50 controls). Homoplasmy = pure mutant mtDNAs. Heteroplasmy = mixture of mutant and normal mtDNAs. nd = not determined. "Prov" (provisional) status indicates that only one group has reported the mutation as pathologic. "Cfrm"(confirmed) status indicates that more than one independent group has published a report on the pathogenicity of a specific mutation (although clinical phenotypes may be different) or independent occurences of the mutation have resulted in a similar phenotype. Additional data will be necessary to confirm the pathological significance of some of these mutations. "P.M." (polymorphism) status indicates that some published reports have dete ... Human mitochondrial DNA encodes 37 gene products (13 proteins, 2 rRNAs and 22 tRNAs) over 16,569 base pairs. All its encoded proteins are directly involved in oxidative phosphorylation and include components of: -- complex I (NADH dehydrogenase subunits ND1, ND2, ND3, ND4, ND4L, ND5, ND6), -- complex III (cytochrome b), -- complex IV (cytochrome oxidase subunits I, II and III) -- complex V (mitochondrial ATPase subunits 6 and 8) [4]. Genes on Strands: Heavy (H) strand: Rich in guanines; 28 genes Light (L) strand: Rich in cytosines; 9 genes NC_001807 16568 bp Aug 24 1999 Cambridge Reference Sequence All other human genes encoding mitochondrial proteins (total estimated at around 1,100) are transcribed in the nucleus, translated in the cytoplasm and their products imported into mitochondria. MITOMAP: Mitochondrial DNA Function Locations (Last edited Aug 22, 2001) "D-Loop" in this database refers to the non-coding region between Proline and Phenylalanine (np 16024-576) Locus names are the official designations delineated by the given numbers. The map positions correspond to the pair(np) numbers determined from the DNA sequence. The map symbols are used to indicate the position of the locus on the map. Notes further define each locus: TAS=termination associated sequence, CSB=conserved sequence block, mtTF1=mitochondrial transcription factor, Y=either pyrimidine, N=any base H-strand replication origin positions have been identified at np 110, 147, 169, 191, 219, 310, 441 L-strand promoter positions have been identified at np 407, 392-435. H-strand promoter positions have been identified at np 559 1, 561. L-strand replication origin positions have been identified at np 5721-5781, 5761, 5799. Note RepeatMasker run today at slow mode primates does *not* report back any tRNAs, even though there are 22 of them in the mitochondrial genome. Arian Smit's manual states the list of tRNAs used for masking is "complete", evidently meaning for nuclear tRNAs. However, mitochondrial tRNA inserts into the genome can still be masked in the RM track in the genome browser. Some also appear in the RNA gene and mouse Blat tracks.