Multiple genome-alignment of 120 mammals using human as reference

This track hub contains a multiple genome alignment between 120 mammal genomes using human (hg38) as a reference genome, information about conservation and protein-coding gene annotations for 119 non-human mammals.

Downloads

• Multiple genome alignment per chromosome (MAF format)
• Conserved elements (BED format)
• Phylogenetic tree (NH and MOD format)
• Protein-coding gene annotation (GenePred format)
• Ultraconserved element alignments (FASTA format)
• Amino acid sequences of annotated genes (FASTA format)
• Coding DNA sequences of annotated genes (FASTA format)
• Genomes used in the 120 mammal alignment (2bit format)

Genome alignment track

Protein-coding gene annotation tracks

Protein-coding gene annotations can be accessed separately for each species through the links below:

Primatomorpha Chimp (Pan troglodytes): panTro5 Bonobo (Pan paniscus): panPan2 Gorilla (Gorilla gorilla gorilla): gorGor5 Orangutan (Pongo pygmaeus abelii): ponAbe2 Gibbon (Nomascus leucogenys): nomLeu3 Rhesus (Macaca mulatta): rheMac8 Crab-eating macaque (Macaca fascicularis): macFas5 Pig-tailed macaque (Macaca nemestrina): macNem1 Baboon (Papio anubis): papAnu3 Drill (Mandrillus leucophaeus): manLeu1 Sooty mangabey (Cercocebus atys): cerAty1 Green monkey (Chlorocebus sabaeus): chlSab2 Proboscis monkey (Nasalis larvatus): nasLar1 Golden snub-nosed monkey (Rhinopithecus roxellana): rhiRox1 Black snub-nosed monkey (Rhinopithecus bieti): rhiBie1 Angolan colobus (Colobus angolensis palliatus): colAng1 Ugandan red Colobus (Piliocolobus tephrosceles): HLpilTep1 Marmoset (Callithrix jacchus): calJac3 Mas night monkey (Aotus nancymaae): aotNan1 Squirrel monkey (Saimiri boliviensis): saiBol1 White-faced sapajou (Cebus capucinus imitator): cebCap1 Tarsier (Tarsius syrichta): tarSyr2 Bushbaby (Otolemur garnettii): otoGar3 Mouse lemur (Microcebus murinus): micMur3 Sifaka (Propithecus coquereli): proCoq1 Malayan flying lemur (Galeopterus variegatus): galVar1 Chinese tree shrew (Tupaia chinensis): tupChi1 Glires Lesser Egyptian jerboa (Jaculus jaculus): jacJac1 Prairie vole (Microtus ochrogaster): micOch1 Chinese hamster (Cricetulus griseus): criGri1 Golden hamster (Mesocricetus auratus): mesAur1 Prairie deer mouse (Peromyscus maniculatus bairdii): perManBai1 Mouse (Mus musculus): mm10 Ryukyu mouse (Mus caroli): HLmusCar1 Shrew mouse (Mus pahari): HLmusPah1 Rat (Rattus norvegicus): rn6 Mongolian gerbil (Meriones unguiculatus): HLmerUng1 Upper Galilee mountains blind mole rat (Nannospalax galili): nanGal1 American beaver (Castor canadensis): HLcasCan1 Ords kangaroo rat (Dipodomys ordii): HLdipOrd2 Naked mole-rat (Heterocephalus glaber): hetGla2 Damara mole-rat (Fukomys damarensis): HLfukDam1 Guinea pig (Cavia porcellus): cavPor3 Chinchilla (Chinchilla lanigera): chiLan1 Brush-tailed rat (Octodon degus): octDeg1 Squirrel (Spermophilus tridecemlineatus): speTri2 Alpine marmot (Marmota marmota marmota): HLmarMar1 Rabbit (Oryctolagus cuniculus): oryCun2 Pika (Ochotona princeps): ochPri3 Cetartiodactyla Alpaca (Vicugna pacos): vicPac2 Wild bactrian camel (Camelus ferus): HLcamFer2 Bactrian camel (Camelus bactrianus): HLcamBac1 Arabian camel (Camelus dromedarius): HLcamDro1 Bottlenose dolphin (Tursiops truncatus): HLturTru3 Killer whale (Orcinus orca): HLorcOrc1 Beluga whale (Delphinapterus leucas): HLdelLeu1 Yangtze river dolphin (Lipotes vexillifer): lipVex1 Sperm whale (Physeter catodon): phyCat1 Minke whale (Balaenoptera acutorostrata scammoni): balAcu1 Bowhead whale (Balaena mysticetus): HLbalMys1 Cow (Bos taurus): bosTau8 Zebu cattle (Bos indicus): HLbosInd1 Bison (Bison bison bison): bisBis1 Wild yak (Bos grunniens mutus): bosMut1 Water buffalo (Bubalus bubalis): bubBub1 Sheep (Ovis aries): HLoviAri4 Bighorn sheep (Ovis canadensis canadensis): HLoviCan1 Goat (Capra hircus): HLcapHir2 Tibetan antelope (Pantholops hodgsonii): panHod1 White-tailed deer (Odocoileus virginianus texanus): HLodoVir1 Red deer (Cervus elaphus hippelaphus): HLcerEla1 Pig (Sus scrofa): susScr11 Perissodactyla Horse (Equus caballus): HLequCab3 Przewalski horse (Equus przewalskii): equPrz1 Ass (Equus asinus): HLequAsi1 White rhinoceros (Ceratotherium simum): cerSim1 Ferae Cat (Felis catus): felCat8 Cheetah (Acinonyx jubatus): HLaciJub1 Amur tiger (Panthera tigris altaica): panTig1 Leopard (Panthera pardus): HLpanPar1 Dog (Canis lupus familiaris): canFam3 African hunting dog (Lycaon pictus): HLlycPic1 Ferret (Mustela putorius furo): musFur1 Sea otter (Enhydra lutris kenyoni): HLenhLut1 Lesser panda (Ailurus fulgens styani): HLailFul1 Panda (Ailuropoda melanoleuca): ailMel1 Polar bear (Ursus maritimus): ursMar1 Pacific walrus (Odobenus rosmarus divergens): odoRosDiv1 Weddell seal (Leptonychotes weddellii): lepWed1 Hawaiian monk seal (Neomonachus schauinslandi): neoSch1 Chinese pangolin (Manis pentadactyla): manPen1 Malayan pangolin (Manis javanica): HLmanJav1 Chiroptera Black flying-fox (Pteropus alecto): pteAle1 Large flying fox (Pteropus vampyrus): HLpteVam2 Egyptian rousette (Rousettus aegyptiacus): rouAeg1 Chinese rufous horseshoe bat (Rhinolophus sinicus): HLrhiSin1 Great roundleaf bat (Hipposideros armiger): HLhipArm1 Big brown bat (Eptesicus fuscus): eptFus1 David s myotis (bat) (Myotis davidii): myoDav1 Brandt s myotis (bat) (Myotis brandtii): myoBra1 Microbat (Myotis lucifugus): myoLuc2 Natal long-fingered bat (Miniopterus natalensis): HLminNat1 Common vampire bat (Desmodus rotundus): HLdesRot1 Eulipotyphla Hedgehog (Erinaceus europaeus): eriEur2 Shrew (Sorex araneus): sorAra2 Star-nosed mole (Condylura cristata): conCri1 Atlantogenata Elephant (Loxodonta africana): loxAfr3 Manatee (Trichechus manatus latirostris): triMan1 Cape rock hyrax (Procavia capensis): HLproCap2 Cape golden mole (Chrysochloris asiatica): chrAsi1 Tenrec (Echinops telfairi): echTel2 Cape elephant shrew (Elephantulus edwardii): eleEdw1 Aardvark (Orycteropus afer afer): oryAfe1 Armadillo (Dasypus novemcinctus): dasNov3 Hoffmanns two-fingered sloth (Choloepus hoffmanni): HLchoHof2 NonPlacental Opossum (Monodelphis domestica): monDom5 Tasmanian devil (Sarcophilus harrisii): sarHar1 Koala (Phascolarctos cinereus): HLphaCin1 Platypus (Ornithorhynchus anatinus): ornAna2

Credits

This track was produced by Nikolai Hecker, Hiller Lab at the Center for Systems Biology Dresden, Max-Planck Institute of Molecular Cell Biology and Genetics, and Max-Planck Institute for the Physics of Complex Systems. For questions regarding this hub, please contact Nikolai Hecker.

References