Zoonomia 241 Placent Track Settings
Assembly: Human Dec. 2013 (GRCh38/hg38)
Downloads for data in this track are available:
Cactus alignments (MAF format), and phylogenetic trees, and PhyloP conservation (WIG and bigWig format)
Description
Warning: Unlike other alignment tracks on the genome browser, this one does not show
insertions in the query genomes. Also, all other alignment tracks show one query
genome sequence for each target genome sequence, but in this track, each
target genome sequence can be aligned to multiple query genome sequences.
Only the first sequence is shown on the genome browser itself, the others are shown on the details page,
when one clicks on the alignment. If you are interested in this track and want
these shortcomings to be fixed, please contact us.
This track shows multiple alignments of 241 vertebrate
species and measurements of evolutionary conservation
from the Zoonomia Project .
The multiple alignments were generated using the
Cactus comparative genomics alignment system.
Cactus produces reference-free, whole-genome multiple alignments.
The base-wise conservation scores are computed using phyloP from the
PHAST package , for all species.
This version was prepared by Michael Dong (Uppsala U) with an improved neutral
model incorporating better versions of ancestral repeats.
For genome assemblies not available in the genome browser, there are
alternative assembly hub genome browsers. Missing sequence in any assembly is
highlighted in the track display by regions of yellow when zoomed out and by
Ns when displayed at base level (see Gap Annotation , below).
count
common
CLADE
group
scientific
sequencing
NCBI
species
1
Cape golden mole
AFROSORICIDA
Chrysochloridae
Chrysochloris asiatica
1. Zoonomia
GCA_004027935.1 LC
2
Small madagascar hedgehog
AFROSORICIDA
Tenrecidae
Echinops telfairi
2. Existing assembly
GCF_000313985.1 LC
3
Talazac's shrew tenrec
AFROSORICIDA
Tenrecidae
Microgale talazaci
1. Zoonomia
GCA_004026705.1 LC
4
Cheetah
CARNIVORA
Felidae
Acinonyx jubatus
2. Existing assembly
GCF_001443585.1 CR
5
Giant panda
CARNIVORA
Ursidae
Ailuropoda melanoleuca
2. Existing assembly
GCA_002007445.1 VU
6
Lesser panda
CARNIVORA
Ailuridae
Ailurus fulgens
2. Existing assembly
GCA_002007465.1 EN
7
Domestic dog
CARNIVORA
Canidae
Canis lupus familiaris
2. Existing assembly
GCF_000002285.3 LC
8
Domestic dog (village dog)
CARNIVORA
Canidae
Canis lupus familiaris
1. Zoonomia
GCA_004027395.1 LC
9
Fossa
CARNIVORA
Eupleridae
Cryptoprocta ferox
1. Zoonomia
GCA_004023885.1 VU
10
Sea otter
CARNIVORA
Mustelidae
Enhydra lutris
2. Existing assembly
GCF_002288905.1 EN
11
Domestic cat
CARNIVORA
Felidae
Felis catus
2. Existing assembly
GCF_000181335.2 LC
12
Black-footed cat
CARNIVORA
Felidae
Felis nigripes
1. Zoonomia
GCA_004023925.1 VU
13
Dwarf mongoose
CARNIVORA
Herpestidae
Helogale parvula
1. Zoonomia
GCA_004023845.1 LC
14
Striped hyena
CARNIVORA
Hyaenidae
Hyaena hyaena
1. Zoonomia
GCA_004023945.1 NT
15
Weddell seal
CARNIVORA
Phocidae
Leptonychotes weddellii
2. Existing assembly
GCF_000349705.1 LC
16
African hunting dog
CARNIVORA
Canidae
Lycaon pictus
2. Existing assembly
GCA_001887905.1 EN
17
Honey badger
CARNIVORA
Mustelidae
Mellivora capensis
1. Zoonomia
GCA_004024625.1 LC
18
Northern elephant seal
CARNIVORA
Phocidae
Mirounga angustirostris
1. Zoonomia
GCA_004023865.1 LC
19
South African banded mongoose
CARNIVORA
Herpestidae
Mungos mungo
1. Zoonomia
GCA_004023785.1 LC
20
Domestic ferret
CARNIVORA
Mustelidae
Mustela putorius
2. Existing assembly
GCF_000239315.1 LC
21
Hawaiian monk seal
CARNIVORA
Phocidae
Neomonachus schauinslandi
2. Existing assembly
GCA_002201575.1 EN
22
Pacific walrus
CARNIVORA
Odobenidae
Odobenus rosmarus
2. Existing assembly
GCF_000321225.1 DD
23
Jaguar
CARNIVORA
Felidae
Panthera onca
1. Zoonomia
GCA_004023805.1 NT
24
Leopard
CARNIVORA
Felidae
Panthera pardus
2. Existing assembly
GCA_001857705.1 VU
25
Amur tiger
CARNIVORA
Felidae
Panthera tigris
2. Existing assembly
GCF_000464555.1 EN
26
Asian palm civet
CARNIVORA
Viverridae
Paradoxurus hermaphroditus
1. Zoonomia
GCA_004024585.1 LC
27
Giant otter
CARNIVORA
Mustelidae
Pteronura brasiliensis
1. Zoonomia
GCA_004024605.1 EN
28
Puma
CARNIVORA
Felidae
Puma concolor
2. Existing assembly
GCF_003327715.1 LC
29
Western spotted skunk
CARNIVORA
Mephitidae
Spilogale gracilis
1. Zoonomia
GCA_004023965.1 LC
30
Meerkat
CARNIVORA
Herpestidae
Suricata suricatta
1. Zoonomia
GCA_004023905.1 LC
31
Polar bear
CARNIVORA
Ursidae
Ursus maritimus
2. Existing assembly
GCF_000687225.1 VU
32
Arctic fox
CARNIVORA
Canidae
Vulpes lagopus
1. Zoonomia
GCA_004023825.1 LC
33
California sea lion
CARNIVORA
Otariidae
Zalophus californianus
1. Zoonomia
GCA_004024565.1 LC
34
Aoudad
CETARTIODACTYLA
Bovidae
Ammotragus lervia
2. Existing assembly
GCA_002201775.1 VU
35
Pronghorn
CETARTIODACTYLA
Antilocapridae
Antilocapra americana
1. Zoonomia
GCA_004027515.1 LC
36
Minke whale
CETARTIODACTYLA
Balaenopteridae
Balaenoptera acutorostrata
2. Existing assembly
GCF_000493695.1 LC
37
Antarctic minke whale
CETARTIODACTYLA
Balaenopteridae
Balaenoptera bonaerensis
2. Existing assembly
GCA_000978805.1 DD
38
Hirola
CETARTIODACTYLA
Bovidae
Beatragus hunteri
1. Zoonomia
GCA_004027495.1 CR
39
American bison
CETARTIODACTYLA
Bovidae
Bison bison
2. Existing assembly
GCF_000754665.1 NT
40
Zebu cattle
CETARTIODACTYLA
Bovidae
Bos indicus
2. Existing assembly
GCA_000247795.2 LC
41
Wild yak
CETARTIODACTYLA
Bovidae
Bos mutus
2. Existing assembly
GCF_000298355.1 VU
42
Cattle
CETARTIODACTYLA
Bovidae
Bos taurus
2. Existing assembly
GCF_000003205.7 LC
43
Water buffalo
CETARTIODACTYLA
Bovidae
Bubalus bubalis
2. Existing assembly
GCF_000471725.1 LC
44
Bactrian camel
CETARTIODACTYLA
Camelidae
Camelus bactrianus
2. Existing assembly
GCF_000767855.1 LC
45
Arabian camel
CETARTIODACTYLA
Camelidae
Camelus dromedarius
2. Existing assembly
GCF_000767585.1 LC
46
Wild bactrian camel
CETARTIODACTYLA
Camelidae
Camelus ferus
2. Existing assembly
GCF_000311805.1 CR
47
Wild goat
CETARTIODACTYLA
Bovidae
Capra aegagrus
2. Existing assembly
GCA_000978405.1 VU
48
Goat
CETARTIODACTYLA
Bovidae
Capra hircus
2. Existing assembly
GCF_001704415.1 LC
49
Chacoan peccary
CETARTIODACTYLA
Tayassuidae
Catagonus wagneri
1. Zoonomia
GCA_004024745.1 EN
50
Beluga whale
CETARTIODACTYLA
Monodontidae
Delphinapterus leucas
2. Existing assembly
GCF_002288925.1 LC
51
Pere david's deer
CETARTIODACTYLA
Cervidae
Elaphurus davidianus
2. Existing assembly
GCA_002443075.1 CR
52
Grey whale
CETARTIODACTYLA
Eschrichtiidae
Eschrichtius robustus
1. Zoonomia
GCA_004363415.1 LC
53
North Pacific right whale
CETARTIODACTYLA
Balaenidae
Eubalaena japonica
1. Zoonomia
GCA_004363455.1 EN
54
Giraffe
CETARTIODACTYLA
Giraffidae
Giraffa tippelskirchi
2. Existing assembly
GCA_001651235.1 VU
55
Nilgiri tahr
CETARTIODACTYLA
Bovidae
Hemitragus hylocrius
1. Zoonomia
GCA_004026825.1 EN
56
Hippopotamus
CETARTIODACTYLA
Hippopotamidae
Hippopotamus amphibius
1. Zoonomia
GCA_004027065.1 VU
57
Amazon river dolphin
CETARTIODACTYLA
Iniidae
Inia geoffrensis
1. Zoonomia
GCA_004363515.1 DD
58
Pygmy sperm whale
CETARTIODACTYLA
Physeteridae
Kogia breviceps
1. Zoonomia
GCA_004363705.1 DD
59
Yangtze river dolphin
CETARTIODACTYLA
Iniidae
Lipotes vexillifer
2. Existing assembly
GCF_000442215.1 CR
60
Sowerby's beaked whale
CETARTIODACTYLA
Ziphiidae
Mesoplodon bidens
1. Zoonomia
GCA_004027085.1 DD
61
Narwhal
CETARTIODACTYLA
Monodontidae
Monodon monoceros
1. Zoonomia
GCA_004026685.1 LC
62
Siberian musk deer
CETARTIODACTYLA
Moschidae
Moschus moschiferus
1. Zoonomia
GCA_004024705.1 VU
63
Yangtze finless porpoise
CETARTIODACTYLA
Phocoenidae
Neophocaena asiaeorientalis
2. Existing assembly
GCA_003031525.1 EN
64
White-tailed deer
CETARTIODACTYLA
Cervidae
Odocoileus virginianus
2. Existing assembly
GCA_002102435.1 LC
65
Okapi
CETARTIODACTYLA
Giraffidae
Okapia johnstoni
2. Existing assembly
GCA_001660835.1 EN
66
Killer whale
CETARTIODACTYLA
Delphinidae
Orcinus orca
2. Existing assembly
GCF_000331955.2 DD
67
Sheep
CETARTIODACTYLA
Bovidae
Ovis aries
2. Existing assembly
GCF_000298735.2 LC
68
Peninsular bighorn sheep
CETARTIODACTYLA
Bovidae
Ovis canadensis cremnobates
1. Zoonomia
GCA_004026945.1 EN
69
Chiru
CETARTIODACTYLA
Bovidae
Pantholops hodgsonii
2. Existing assembly
GCF_000400835.1 NT
70
Harbor porpoise
CETARTIODACTYLA
Phocoenidae
Phocoena phocoena
1. Zoonomia
GCA_004363495.1 LC
71
Indus river dolphin
CETARTIODACTYLA
Platanistidae
Platanista gangetica minor
1. Zoonomia
GCA_004363435.1 EN
72
Siberian reindeer
CETARTIODACTYLA
Cervidae
Rangifer tarandus
1. Zoonomia
GCA_004026565.1 VU
73
Russian saiga
CETARTIODACTYLA
Bovidae
Saiga tatarica tatarica
1. Zoonomia
GCA_004024985.1 CR
74
Pig
CETARTIODACTYLA
Suidae
Sus scrofa
2. Existing assembly
GCF_000003025.5 LC
75
Java lesser chevrotain
CETARTIODACTYLA
Tragulidae
Tragulus javanicus
1. Zoonomia
GCA_004024965.1 DD
76
Bottlenose dolphin
CETARTIODACTYLA
Delphinidae
Tursiops truncatus
2. Existing assembly
GCA_001922835.1 LC
77
Alpaca
CETARTIODACTYLA
Camelidae
Vicugna pacos
2. Existing assembly
GCA_000767525.1 LC
78
Cuvier's beaked whale
CETARTIODACTYLA
Ziphiidae
Ziphius cavirostris
1. Zoonomia
GCA_004364475.1 LC
79
Tailed tailless bat
CHIROPTERA
Phyllostomidae
Anoura caudifer
1. Zoonomia
GCA_004027475.1 LC
80
Jamacian fruit-eating bat
CHIROPTERA
Phyllostomidae
Artibeus jamaicensis
1. Zoonomia
GCA_004027435.1 LC
81
Seba's short-tailed bat
CHIROPTERA
Phyllostomidae
Carollia perspicillata
1. Zoonomia
GCA_004027735.1 LC
82
Bumblebee bat
CHIROPTERA
Craseonycteridae
Craseonycteris thonglongyai
1. Zoonomia
GCA_004027555.1 VU
83
Common vampire bat
CHIROPTERA
Phyllostomidae
Desmodus rotundus
2. Existing assembly
GCA_002940915.2 LC
84
Straw-colored fruit bat
CHIROPTERA
Pteropodidae
Eidolon helvum
2. Existing assembly
GCA_000465285.1 NT
85
Big brown bat
CHIROPTERA
Vespertilionidae
Eptesicus fuscus
2. Existing assembly
GCF_000308155.1 LC
86
Great roundleaf bat
CHIROPTERA
Hipposideridae
Hipposideros armiger
2. Existing assembly
GCA_001890085.1 LC
87
Cantor's leaf-nosed bat
CHIROPTERA
Hipposideridae
Hipposideros galeritus
1. Zoonomia
GCA_004027415.1 LC
88
Eastern red bat
CHIROPTERA
Vespertilionidae
Lasiurus borealis
1. Zoonomia
GCA_004026805.1 LC
89
Long-tongued fruit bat
CHIROPTERA
Pteropodidae
Macroglossus sobrinus
1. Zoonomia
GCA_004027375.1 LC
90
Greater false vampire bat
CHIROPTERA
Megadermatidae
Megaderma lyra
1. Zoonomia
GCA_004026885.1 LC
91
Hairy big-eared bat
CHIROPTERA
Phyllostomidae
Micronycteris hirsuta
1. Zoonomia
GCA_004026765.1 LC
92
Natal long-fingered bat
CHIROPTERA
Vespertilionidae
Miniopterus natalensis
2. Existing assembly
GCF_001595765.1 LC
93
Common bent-wing bat
CHIROPTERA
Vespertilionidae
Miniopterus schreibersii
1. Zoonomia
GCA_004026525.1 NT
94
Ghost-faced bat
CHIROPTERA
Mormoopidae
Mormoops blainvillei
1. Zoonomia
GCA_004026545.1 LC
95
Ashy-gray tube-nosed bat
CHIROPTERA
Vespertilionidae
Murina feae
1. Zoonomia
GCA_004026665.1 LC
96
Brandt's bat
CHIROPTERA
Vespertilionidae
Myotis brandtii
2. Existing assembly
GCF_000412655.1 LC
97
David's myotis bat
CHIROPTERA
Vespertilionidae
Myotis davidii
2. Existing assembly
GCF_000327345.1 LC
98
Little brown bat
CHIROPTERA
Vespertilionidae
Myotis lucifugus
2. Existing assembly
GCF_000147115.1 LC
99
Greater mouse-eared bat
CHIROPTERA
Vespertilionidae
Myotis myotis
1. Zoonomia
GCA_004026985.1 LC
100
Greater bulldog bat
CHIROPTERA
Noctilionidae
Noctilio leporinus
1. Zoonomia
GCA_004026585.1 LC
101
Common pipistrelle
CHIROPTERA
Vespertilionidae
Pipistrellus pipistrellus
1. Zoonomia
GCA_004026625.1 LC
102
Parnell's mustached bat
CHIROPTERA
Mormoopidae
Pteronotus parnellii
2. Existing assembly
GCA_000465405.1 LC
103
Black flying fox
CHIROPTERA
Pteropodidae
Pteropus alecto
2. Existing assembly
GCF_000325575.1 LC
104
Large flying fox
CHIROPTERA
Pteropodidae
Pteropus vampyrus
2. Existing assembly
GCF_000151845.1 NT
105
Chinese rufous horseshoe bat
CHIROPTERA
Rhinolophidae
Rhinolophus sinicus
2. Existing assembly
GCA_001888835.1 LC
106
Egyptian fruit bat
CHIROPTERA
Pteropodidae
Rousettus aegyptiacus
1. Zoonomia
GCA_004024865.1 LC
107
Mexican free-tailed bat
CHIROPTERA
Molossidae
Tadarida brasiliensis
1. Zoonomia
GCA_004025005.1 LC
108
Stripe-headed round-eared bat
CHIROPTERA
Phyllostomidae
Tonatia saurophila
1. Zoonomia
GCA_004024845.1 LC
109
Screaming hairy armadillo
CINGULATA
Dasypodidae
Chaetophractus vellerosus
1. Zoonomia
GCA_004027955.1 LC
110
Nine-banded armadillo
CINGULATA
Dasypodidae
Dasypus novemcinctus
2. Existing assembly
GCF_000208655.1 LC
111
Southern three-banded armadillo
CINGULATA
Dasypodidae
Tolypeutes matacus
1. Zoonomia
GCA_004025125.1 NT
112
Sunda flying lemur
DERMOPTERA
Cynocephalidae
Galeopterus variegatus
1. Zoonomia
GCA_004027255.1 LC
113
Star-nosed mole
EULIPOTYPHLA
Talpidae
Condylura cristata
2. Existing assembly
GCF_000260355.1 LC
114
Indochinese shrew
EULIPOTYPHLA
Soricidae
Crocidura indochinensis
1. Zoonomia
GCA_004027635.1 LC
115
Western european hedgehog
EULIPOTYPHLA
Erinaceidae
Erinaceus europaeus
2. Existing assembly
GCF_000296755.1 LC
116
Eastern mole
EULIPOTYPHLA
Talpidae
Scalopus aquaticus
1. Zoonomia
GCA_004024925.1 LC
117
Hispaniolan solenodon
EULIPOTYPHLA
Solenodontidae
Solenodon paradoxus
1. Zoonomia
GCA_004363575.1 EN
118
European shrew
EULIPOTYPHLA
Soricidae
Sorex araneus
2. Existing assembly
GCF_000181275.1 LC
119
Gracile shrew-like mole
EULIPOTYPHLA
Talpidae
Uropsilus gracilis
1. Zoonomia
GCA_004024945.1 LC
120
African yellow-spotted rock hyrax
HYRACOIDEA
Procaviidae
Heterohyrax brucei
1. Zoonomia
GCA_004026845.1 LC
121
South African rock hyrax
HYRACOIDEA
Procaviidae
Procavia capensis
1. Zoonomia
GCA_004026925.1 LC
122
Snowshoe hare
LAGOMORPHA
Leporidae
Lepus americanus
1. Zoonomia
GCA_004026855.1 LC
123
American pika
LAGOMORPHA
Ochotonidae
Ochotona princeps
2. Existing assembly
GCF_000292845.1 LC
124
Rabbit
LAGOMORPHA
Leporidae
Oryctolagus cuniculus
2. Existing assembly
GCF_000003625.3 NT
125
Cape elephant shrew
MACROSCELIDEA
Macroscelididae
Elephantulus edwardii
1. Zoonomia
GCA_004027355.1 LC
126
Southern white rhinoceros
PERISSODACTYLA
Rhinocerotidae
Ceratotherium simum
2. Existing assembly
GCF_000283155.1 NT
127
Northern white rhino
PERISSODACTYLA
Rhinocerotidae
Ceratotherium simum cottoni
1. Zoonomia
GCA_004027795.1 CR
128
Sumatran rhinoceros
PERISSODACTYLA
Rhinocerotidae
Dicerorhinus sumatrensis
2. Existing assembly
GCA_002844835.1 CR
129
Black rhinocerous
PERISSODACTYLA
Rhinocerotidae
Diceros bicornis
1. Zoonomia
GCA_004027315.1 CR
130
Ass
PERISSODACTYLA
Equidae
Equus asinus
2. Existing assembly
GCF_001305755.1 LC
131
Horse
PERISSODACTYLA
Equidae
Equus caballus
2. Existing assembly
GCF_000002305.2 LC
132
Przewalski's horse
PERISSODACTYLA
Equidae
Equus przewalskii
2. Existing assembly
GCF_000696695.1 EN
133
Malayan tapir
PERISSODACTYLA
Tapiridae
Tapirus indicus
1. Zoonomia
GCA_004024905.1 EN
134
South American tapir
PERISSODACTYLA
Tapiridae
Tapirus terrestris
1. Zoonomia
GCA_004025025.1 VU
135
Malayan pangolin
PHOLIDOTA
Manidae
Manis javanica
2. Existing assembly
GCF_001685135.1 CR
136
Chinese pangolin
PHOLIDOTA
Manidae
Manis pentadactyla
2. Existing assembly
GCA_000738955.1 CR
137
Linnaeus's two toed sloth
PILOSA
Megalonychidae
Choloepus didactylus
1. Zoonomia
GCA_004027855.1 LC
138
Hoffmann's two-fingered sloth
PILOSA
Megalonychidae
Choloepus hoffmanni
2. Existing assembly
GCA_000164785.2 LC
139
Giant anteater
PILOSA
Myrmecophagidae
Myrmecophaga tridactyla
1. Zoonomia
GCA_004026745.1 VU
140
Southern tamandua
PILOSA
Myrmecophagidae
Tamandua tetradactyla
1. Zoonomia
GCA_004025105.1 LC
141
Mexican howler monkey
PRIMATES
Atelidae
Alouatta palliata mexicana
1. Zoonomia
GCA_004027835.1 CR
142
Ma's night monkey
PRIMATES
Aotidae
Aotus nancymaae
2. Existing assembly
GCA_000952055.2 VU
143
Geoffroy's spider monkey
PRIMATES
Atelidae
Ateles geoffroyi
1. Zoonomia
GCA_004024785.1 EN
144
White-eared titi
PRIMATES
Pitheciidae
Callicebus donacophilus
1. Zoonomia
GCA_004027715.1 LC
145
White-tufted-ear marmoset
PRIMATES
Cebidae
Callithrix jacchus
2. Existing assembly
GCA_002754865.1 LC
146
White-fronted capuchin
PRIMATES
Cebidae
Cebus albifrons
1. Zoonomia
GCA_004027755.1 LC
147
White-faced sapajou
PRIMATES
Cebidae
Cebus capucinus
2. Existing assembly
GCF_001604975.1 LC
148
Sooty mangabey
PRIMATES
Cercopithecidae
Cercocebus atys
2. Existing assembly
GCF_000955945.1 NT
149
De brazza's monkey
PRIMATES
Cercopithecidae
Cercopithecus neglectus
1. Zoonomia
GCA_004027615.1 LC
150
Fat-tailed dwarf lemur
PRIMATES
Cheirogaleidae
Cheirogaleus medius
1. Zoonomia
GCA_004024725.1 LC
151
Green monkey
PRIMATES
Cercopithecidae
Chlorocebus sabaeus
2. Existing assembly
GCF_000409795.2 LC
152
Angolan colobus
PRIMATES
Cercopithecidae
Colobus angolensis
2. Existing assembly
GCF_000951035.1 VU
153
Aye-aye
PRIMATES
Daubentoniidae
Daubentonia madagascariensis
1. Zoonomia
GCA_004027145.1 EN
154
Patas monkey
PRIMATES
Cercopithecidae
Erythrocebus patas
1. Zoonomia
GCA_004027335.1 LC
155
Sclater's lemur
PRIMATES
Lemuridae
Eulemur flavifrons
2. Existing assembly
GCA_001262665.1 CR
156
Common brown lemur
PRIMATES
Lemuridae
Eulemur fulvus
1. Zoonomia
GCA_004027275.1 NT
157
Western lowland gorilla
PRIMATES
Hominidae
Gorilla gorilla
2. Existing assembly
GCA_900006655.3 CR
158
Human
PRIMATES
Hominidae
Homo sapiens
2. Existing assembly
GCA_000001405.27 LC
159
Indri
PRIMATES
Indridae
Indri indri
1. Zoonomia
GCA_004363605.1 CR
160
Ring tailed lemur
PRIMATES
Lemuridae
Lemur catta
1. Zoonomia
GCA_004024665.1 EN
161
Crab-eating macaque
PRIMATES
Cercopithecidae
Macaca fascicularis
2. Existing assembly
GCF_000364345.1 DD
162
Rhesus monkey
PRIMATES
Cercopithecidae
Macaca mulatta
2. Existing assembly
GCF_000772875.2 LC
163
Pig-tailed macaque
PRIMATES
Cercopithecidae
Macaca nemestrina
2. Existing assembly
GCF_000956065.1 VU
164
Drill
PRIMATES
Cercopithecidae
Mandrillus leucophaeus
2. Existing assembly
GCF_000951045.1 EN
165
Gray mouse lemur
PRIMATES
Cheirogaleidae
Microcebus murinus
2. Existing assembly
GCA_000165445.3 LC
166
Coquerel's giant mouse lemur
PRIMATES
Cheirogaleidae
Mirza coquereli
1. Zoonomia
GCA_004024645.1 EN
167
Proboscis monkey
PRIMATES
Cercopithecidae
Nasalis larvatus
1. Zoonomia
GCA_004027105.1 EN
168
Northern white-cheeked gibbon
PRIMATES
Hylobatidae
Nomascus leucogenys
2. Existing assembly
GCF_000146795.2 CR
169
Sunda slow loris
PRIMATES
Lorisidae
Nycticebus coucang
1. Zoonomia
GCA_004027815.1 VU
170
Small-eared galago
PRIMATES
Galagidae
Otolemur garnettii
2. Existing assembly
GCF_000181295.1 LC
171
Pygmy chimpanzee
PRIMATES
Hominidae
Pan paniscus
2. Existing assembly
GCF_000258655.2 EN
172
Chimpanzee
PRIMATES
Hominidae
Pan troglodytes
2. Existing assembly
GCA_002880755.3 EN
173
Olive baboon
PRIMATES
Cercopithecidae
Papio anubis
2. Existing assembly
GCA_000264685.2 LC
174
Ugandan red colobus
PRIMATES
Cercopithecidae
Piliocolobus tephrosceles
2. Existing assembly
GCA_002776525.1 EN
175
White-faced saki
PRIMATES
Pitheciidae
Pithecia pithecia
1. Zoonomia
GCA_004026645.1 LC
176
Sumatran orangutan
PRIMATES
Hominidae
Pongo abelii
2. Existing assembly
GCA_002880775.3 CR
177
Coquerel's sifaka
PRIMATES
Indridae
Propithecus coquereli
2. Existing assembly
GCF_000956105.1 EN
178
Red-shanked douc
PRIMATES
Cercopithecidae
Pygathrix nemaeus
1. Zoonomia
GCA_004024825.1 EN
179
Black snub-nosed monkey
PRIMATES
Cercopithecidae
Rhinopithecus bieti
2. Existing assembly
GCF_001698545.1 EN
180
Golden snub-nosed monkey
PRIMATES
Cercopithecidae
Rhinopithecus roxellana
2. Existing assembly
GCF_000769185.1 EN
181
Emperor tamarin
PRIMATES
Cebidae
Saguinus imperator
1. Zoonomia
GCA_004024885.1 LC
182
Bolivian squirrel monkey
PRIMATES
Cebidae
Saimiri boliviensis
2. Existing assembly
GCF_000235385.1 LC
183
Northern Plains gray langur
PRIMATES
Cercopithecidae
Semnopithecus entellus
1. Zoonomia
GCA_004025065.1 LC
184
African savanna elephant
PROBOSCIDEA
Elephantidae
Loxodonta Africana
2. Existing assembly
GCF_000001905.1 VU
185
Cairo spiny mouse
RODENTIA
Muridae
Acomys cahirinus
1. Zoonomia
GCA_004027535.1 LC
186
Gobi jerboa
RODENTIA
Dipodidae
Allactaga bullata
1. Zoonomia
GCA_004027895.1 LC
187
Mountain beaver
RODENTIA
Aplodontiidae
Aplodontia rufa
1. Zoonomia
GCA_004027875.1 LC
188
Desmarest's hutia
RODENTIA
Capromyidae
Capromys pilorides
1. Zoonomia
GCA_004027915.1 LC
189
North American beaver
RODENTIA
Castoridae
Castor canadensis
1. Zoonomia
GCA_004027675.1 LC
190
Brazilian guinea pig
RODENTIA
Caviidae
Cavia aperea
2. Existing assembly
GCA_000688575.1 LC
191
Domestic guinea pig
RODENTIA
Caviidae
Cavia porcellus
2. Existing assembly
GCF_000151735.1 LC
192
Montane guinea pig
RODENTIA
Caviidae
Cavia tschudii
1. Zoonomia
GCA_004027695.1 LC
193
Long-tailed chinchilla
RODENTIA
Chinchillidae
Chinchilla lanigera
2. Existing assembly
GCF_000276665.1 EN
194
Gambian pouched rat
RODENTIA
Nesomyidae
Cricetomys gambianus
1. Zoonomia
GCA_004027575.1 LC
195
Chinese hamster
RODENTIA
Nesomyidae
Cricetulus griseus
2. Existing assembly
GCA_900186095.1 LC
196
Common gundi
RODENTIA
Ctenodactylidae
Ctenodactylus gundi
1. Zoonomia
GCA_004027205.1 LC
197
Social tuco-tuco
RODENTIA
Ctenomyidae
Ctenomys sociabilis
1. Zoonomia
GCA_004027165.1 CR
198
Lowland paca
RODENTIA
Cuniculidae
Cuniculus paca
1. Zoonomia
GCA_004365215.1 LC
199
Central American agouti
RODENTIA
Dasyproctidae
Dasyprocta punctata
1. Zoonomia
GCA_004363535.1 LC
200
Pacarana
RODENTIA
Dinomyidae
Dinomys branickii
1. Zoonomia
GCA_004027595.1 LC
201
Ord's kangaroo rat
RODENTIA
Heteromyidae
Dipodomys ordii
2. Existing assembly
GCF_000151885.1 LC
202
Stephen's kangaroo rat
RODENTIA
Heteromyidae
Dipodomys stephensi
1. Zoonomia
GCA_004024685.1 VU
203
Patagonian mara
RODENTIA
Caviidae
Dolichotis patagonum
1. Zoonomia
GCA_004027295.1 NT
204
Transcaucasian mole vole
RODENTIA
Cricetidae
Ellobius lutescens
2. Existing assembly
GCA_001685075.1 LC
205
Northern mole vole
RODENTIA
Cricetidae
Ellobius talpinus
2. Existing assembly
GCA_001685095.1 LC
206
Damara mole-rat
RODENTIA
Bathyergidae
Fukomys damarensis
2. Existing assembly
GCF_000743615.1 LC
207
Edible dormouse
RODENTIA
Gliridae
Glis glis
1. Zoonomia
GCA_004027185.1 LC
208
Woodland doormouse
RODENTIA
Gliridae
Graphiurus murinus
1. Zoonomia
GCA_004027655.1 LC
209
Naked mole-rat
RODENTIA
Bathyergidae
Heterocephalus glaber
2. Existing assembly
GCF_000247695.1 LC
210
Capybara
RODENTIA
Caviidae
Hydrochoerus hydrochaeris
1. Zoonomia
GCA_004027455.1 LC
211
Northern crested porcupine
RODENTIA
Hystricidae
Hystrix cristata
1. Zoonomia
GCA_004026905.1 LC
212
Thirteen-lined ground squirrel
RODENTIA
Sciuridae
Ictidomys tridecemlineatus
2. Existing assembly
GCF_000236235.1 LC
213
Lesser egyptian jerboa
RODENTIA
Dipodidae
Jaculus jaculus
2. Existing assembly
GCF_000280705.1 LC
214
Alpine marmot
RODENTIA
Sciuridae
Marmota marmota
2. Existing assembly
GCF_001458135.1 LC
215
Mongolian jird
RODENTIA
Muridae
Meriones unguiculatus
1. Zoonomia
GCA_004026785.1 LC
216
Golden hamster
RODENTIA
Cricetidae
Mesocricetus auratus
2. Existing assembly
GCF_000349665.1 VU
217
Prairie vole
RODENTIA
Cricetidae
Microtus ochrogaster
2. Existing assembly
GCF_000317375.1 LC
218
Ryukyu mouse
RODENTIA
Muridae
Mus caroli
2. Existing assembly
GCA_900094665.2 LC
219
House mouse
RODENTIA
Muridae
Mus musculus
2. Existing assembly
GCF_000001635.26 LC
220
Shrew mouse
RODENTIA
Muridae
Mus pahari
2. Existing assembly
GCA_900095145.2 LC
221
Western wild mouse
RODENTIA
Muridae
Mus spretus
2. Existing assembly
GCA_001624865.1 LC
222
Hazel dormouse
RODENTIA
Gliridae
Muscardinus avellanarius
1. Zoonomia
GCA_004027005.1 LC
223
Coypu
RODENTIA
Myocastoridae
Myocastor coypus
1. Zoonomia
GCA_004027025.1 LC
224
Upper galilee mountains blind mole rat
RODENTIA
Spalacidae
Nannospalax galili
2. Existing assembly
GCF_000622305.1 DD
225
Degu
RODENTIA
Octodontidae
Octodon degus
2. Existing assembly
GCF_000260255.1 LC
226
Muskrat
RODENTIA
Cricetidae
Ondatra zibethicus
1. Zoonomia
GCA_004026605.1 LC
227
Scorpion mouse
RODENTIA
Cricetidae
Onychomys torridus
1. Zoonomia
GCA_004026725.1 LC
228
Pacific pocket mouse
RODENTIA
Heteromyidae
Perognathus longimembris pacificus
1. Zoonomia
GCA_004363475.1 LC
229
Prairie deer mouse
RODENTIA
Cricetidae
Peromyscus maniculatus
2. Existing assembly
GCF_000500345.1 LC
230
Dassie rat
RODENTIA
Petromuridae
Petromus typicus
1. Zoonomia
GCA_004026965.1 LC
231
Fat sand rat
RODENTIA
Muridae
Psammomys obesus
2. Existing assembly
GCA_002215935.1 LC
232
Norway rat
RODENTIA
Muridae
Rattus norvegicus
2. Existing assembly
GCF_000001895.5 LC
233
Hispid cotton rat
RODENTIA
Cricetidae
Sigmodon hispidus
1. Zoonomia
GCA_004025045.1 LC
234
Daurian ground squirrel
RODENTIA
Sciuridae
Spermophilus dauricus
2. Existing assembly
GCA_002406435.1 LC
235
Greater cane rat
RODENTIA
Thryonomyidae
Thryonomys swinderianus
1. Zoonomia
GCA_004025085.1 LC
236
Cape ground squirrel
RODENTIA
Sciuridae
Xerus inauris
1. Zoonomia
GCA_004024805.1 LC
237
Meadow jumping mouse
RODENTIA
Dipodidae
Zapus hudsonius
1. Zoonomia
GCA_004024765.1 LC
238
Northern tree shrew
SCANDENTIA
Tupaiidae
Tupaia belangeri chinensis
2. Existing assembly
GCF_000334495.1 LC
239
Large treeshrew
SCANDENTIA
Tupaiidae
Tupaia tana
1. Zoonomia
GCA_004365275.1 LC
240
Florida manatee
SIRENIA
Trichechidae
Trichechus manatus
2. Existing assembly
GCF_000243295.1 EN
241
Aardvark
TUBULIDENTATA
Orycteropodidae
Orycteropus afer
1. Zoonomia
GCA_004365145.1 LC
Table 1. Genome assemblies included in the 241-way Conservation track. Species status: LC = Least Concern; NT = Near threatened; VU = Vulnerable; EN = Endangered; CR = Critically endangered
Display Conventions and Configuration
In full and pack display modes, conservation scores are displayed as a
wiggle track (histogram) in which the height reflects the
size of the score.
The conservation wiggles can be configured in a variety of ways to
highlight different aspects of the displayed information.
Click the Graph configuration help link for an explanation
of the configuration options.
Pairwise alignments of each species to the human genome are
displayed below the conservation histogram as a grayscale density plot (in
pack mode) or as a wiggle (in full mode) that indicates alignment quality.
In dense display mode, conservation is shown in grayscale using
darker values to indicate higher levels of overall conservation
as scored by phastCons.
Checkboxes on the track configuration page allow selection of the
species to include in the pairwise display.
The names of selected species are colored according to their clade,
alternating between blue and green.
Note that excluding species from the pairwise display does not alter the
the conservation score display.
To view detailed information about the alignments at a specific
position, zoom the display in to 30,000 or fewer bases, then click on
the alignment.
Gap Annotation
The Display chains between alignments configuration option
enables display of gaps between alignment blocks in the pairwise alignments in
a manner similar to the Chain track display. The following
conventions are used:
Single line: No bases in the aligned species. Possibly due to a
lineage-specific insertion between the aligned blocks in the human genome
or a lineage-specific deletion between the aligned blocks in the aligning
species.
Double line: Aligning species has one or more unalignable bases in
the gap region. Possibly due to excessive evolutionary distance between
species or independent indels in the region between the aligned blocks in both
species.
Pale yellow coloring: Aligning species has Ns in the gap region.
Reflects uncertainty in the relationship between the DNA of both species, due
to lack of sequence in relevant portions of the aligning species.
Genomic Breaks
Discontinuities in the genomic context (chromosome, scaffold or region) of the
aligned DNA in the aligning species are shown as follows:
Vertical blue bar: Represents a discontinuity that persists indefinitely
on either side, e.g. a large region of DNA on either side of the bar
comes from a different chromosome in the aligned species due to a large scale
rearrangement.
Green square brackets: Enclose shorter alignments consisting of DNA from
one genomic context in the aligned species nested inside a larger chain of
alignments from a different genomic context. The alignment within the
brackets may represent a short misalignment, a lineage-specific insertion of a
transposon in the human genome that aligns to a paralogous copy somewhere
else in the aligned species, or other similar occurrence.
Base Level
When zoomed-in to the base-level display, the track shows the base
composition of each alignment. The numbers and symbols on the Gaps
line indicate the lengths of gaps in the human sequence at those
alignment positions relative to the longest non-human sequence.
If there is sufficient space in the display, the size of the gap is shown.
If the space is insufficient and the gap size is a multiple of 3, a
"*" is displayed; other gap sizes are indicated by "+".
Codon translation is available in base-level display mode if the
displayed region is identified as a coding segment. To display this annotation,
select the species for translation from the pull-down menu in the Codon
Translation configuration section at the top of the page. Then, select one of
the following modes:
No codon translation: The gene annotation is not used; the bases are
displayed without translation.
Use default species reading frames for translation: The annotations from
the genome displayed in the Default species to establish reading frame
pull-down menu are used to translate all the aligned species present in the
alignment.
Use reading frames for species if available, otherwise no translation:
Codon translation is performed only for those species where the region is
annotated as protein coding.
Use reading frames for species if available, otherwise use default species:
Codon translation is done on those species that are annotated as being protein
coding over the aligned region using species-specific annotation; the remaining
species are translated using the default species annotation.
Codon translation uses the following gene tracks as the basis for translation:
Gene Track Species UCSC Genes Human Ensembl Genes v104 Brazilian guinea pig, gibbon RefSeq Genes Angolan colobus, Balaenoptera acutorostrata, Bison bison, Black flying-fox, Brandt's myotis (bat), Bushbaby, Camelus bactrianus, Camelus ferus, Canis lupus familiaris, Cape elephant shrew, Capra hircus, Cavia porcellus, Ceratotherium simum, Cercocebus atys, Chinchilla, Chinese tree shrew, Chlorocebus sabaeus, Condylura cristata, Damara mole rat, Dasypus novemcinctus, David's myotis (bat), Delphinapterus leucas, Echinops telfairi, Enhydra lutris, Eptesicus fuscus, Equus asinus, Equus przewalskii, Erinaceus europaeus, Felis catus, Heterocephalus glaber, Jaculus jaculus, Kangaroo rat, Killer whale, Leptonychotes weddellii, Lipotes vexillifer, Little brown bat, Loxodonta africana, Macaca fascicularis, Macaca nemestrina, Mandrillus leucophaeus, Manis javanica, Marmota marmota, Mesocricetus auratus, Miniopterus natalensis, Mus musculus, Nannospalax galili, Ochotona princeps, Octodon degus, Oryctolagus cuniculus, Pacific walrus, Pan paniscus, Panthera tigris, Peromyscus maniculatus, Prairie vole, Propithecus coquereli, Pteropus vampyrus, Puma concolor, Rattus norvegicus, Rhinopithecus bieti, Shrew, Squirrel monkey, Squirrel, Sus scrofa, Trichechus manatus, Ursus maritimus, White-faced sapajou, Wild yak no annotation Acinonyx jubatus, Acomys cahirinus, Ailuropoda melanoleuca, Ailurus fulgens, Allactaga bullata, Alouatta palliata, Ammotragus lervia, Anoura caudifer, Antilocapra americana, Aotus nancymaae, Aplodontia rufa, Artibeus jamaicensis, Ateles geoffroyi, Balaenoptera bonaerensis, Beatragus hunteri, Bos indicus, Bos taurus, Bubalus bubalis, Callicebus donacophilus, Callithrix jacchus, Camelus dromedarius, Canis lupus, Capra aegagrus, Capromys pilorides, Carollia perspicillata, Castor canadensis, Catagonus wagneri, Cavia tschudii, Cebus albifrons, Ceratotherium simum cottoni, Cercopithecus neglectus, Chaetophractus vellerosus, Cheirogaleus medius, Choloepus didactylus, Choloepus hoffmanni, Chrysochloris asiatica, Craseonycteris thonglongyai, Cricetomys gambianus, Cricetulus griseus, Crocidura indochinensis, Cryptoprocta ferox, Ctenodactylus gundi, Ctenomys sociabilis, Cuniculus paca, Dasyprocta punctata, Daubentonia madagascariensis, Desmodus rotundus, Dicerorhinus sumatrensis, Diceros bicornis, Dinomys branickii, Dipodomys stephensi, Dolichotis patagonum, Elaphurus davidianus, Ellobius lutescens, Ellobius talpinus, Equus caballus, Erythrocebus patas, Eschrichtius robustus, Eubalaena japonica, Eulemur flavifrons, Eulemur fulvus, Felis nigripes, Galeopterus variegatus, Giraffa tippelskirchi, Glis glis, Gorilla gorilla, Graphiurus murinus, Helogale parvula, Hemitragus hylocrius, Heterohyrax brucei, Hippopotamus amphibius, Hipposideros armiger, Hipposideros galeritus, Hyaena hyaena, Hydrochoerus hydrochaeris, Hystrix cristata, Indri indri, Inia geoffrensis, Kogia breviceps, Lasiurus borealis, Lemur catta, Lepus americanus, Lycaon pictus, Macaca mulatta, Macroglossus sobrinus, Manis pentadactyla, Megaderma lyra, Mellivora capensis, Meriones unguiculatus, Mesoplodon bidens, Microcebus murinus, Microgale talazaci, Micronycteris hirsuta, Miniopterus schreibersii, Mirounga angustirostris, Mirza coquereli, Monodon monoceros, Mormoops blainvillei, Moschus moschiferus, Mungos mungo, Murina feae, Mus caroli, Mus pahari, Mus spretus, Muscardinus avellanarius, Mustela putorius, Myocastor coypus, Myotis myotis, Myrmecophaga tridactyla, Nasalis larvatus, Neomonachus schauinslandi, Neophocaena asiaeorientalis, Noctilio leporinus, Nycticebus coucang, Odocoileus virginianus, Okapia johnstoni, Ondatra zibethicus, Onychomys torridus, Orycteropus afer, Ovis aries, Ovis canadensis, Pan troglodytes, Panthera onca, Panthera pardus, Pantholops hodgsonii, Papio anubis, Paradoxurus hermaphroditus
Table 2. Gene tracks used for codon translation.
Methods
The Zoonomia alignment was composed of two sets of mammalian genomes: newly
assembled DISCOVAR assemblies and GenBank assemblies. The DISCOVAR genomes
were masked with RepeatMasker (commit 2d947604), using Repbase version
20170127 as the repeat library and CrossMatch as the alignment engine. The
pipeline used is available at
repeatMaskerPipeline
(commit a6ad966). The
guide-tree topology was taken from the TimeTree database (using release
current in October 2018), and the branch lengths were estimated using the
least-squares-fit mode of PHYLIP , version
3.695. The distance matrix used was largely based on distances from the 4d
site trees from the UCSC browser. To add those species not present in the
UCSC tree, approximate distances estimated by Mash (commit 541971b)
to the closest UCSC species
were added to the distance between the two closest UCSC species. We used the
HAL package (commit 68db41d)
produce the HAL file.
Phylogenetic Tree Model
The phyloP are phylogenetic methods that rely
on a tree model containing the tree topology, branch lengths representing
evolutionary distance at neutrally evolving sites, the background distribution
of nucleotides, and a substitution rate matrix.
The
all-species tree model for this track was
generated using the phyloFit program from the PHAST package
(REV model, EM algorithm, medium precision) using multiple alignments of
4-fold degenerate sites extracted from the 241-way alignment
(msa_view). The 4d sites were derived from the RefSeq (Reviewed+Coding) gene
set, filtered to select single-coverage long transcripts.
This same tree model was used in the phyloP calculations; however, the
background frequencies were modified to maintain reversibility.
The resulting tree model:
all species .
PhyloP Conservation
The phyloP program supports several different methods for computing
p-values of conservation or acceleration, for individual nucleotides or
larger elements (
http://compgen.cshl.edu/phast/ ). Here it was used
to produce separate scores at each base (--wig-scores option), considering
all branches of the phylogeny rather than a particular subtree or lineage
(i.e., the --subtree option was not used). The scores were computed by
performing a likelihood ratio test at each alignment column (--method LRT),
and scores for both conservation and acceleration were produced (--mode
CONACC).
References
Zoonomia:
Zoonomia Consortium..
A comparative genomics multitool for scientific discovery and conservation .
Nature . 2020 Nov;587(7833):240-245.
PMID: 33177664 ;
PMC: PMC7759459 ;
DOI: 10.1038/s41586-020-2876-6
Cactus:
Armstrong J, Hickey G, Diekhans M, Fiddes IT, Novak AM, Deran A, Fang Q, Xie D, Feng S, Stiller J
et al .
Progressive Cactus is a multiple-genome aligner for the thousand-genome era .
Nature . 2020 Nov;587(7833):246-251.
PMID: 33177663 ;
PMC: PMC7673649 ;
DOI: 10.1038/s41586-020-2871-y
Paten B, Earl D, Nguyen N, Diekhans M, Zerbino D, Haussler D.
Cactus: Algorithms for genome multiple sequence alignment .
Genome Res . 2011 Sep;21(9):1512-28.
PMID: 21665927 ;
PMC: PMC3166836 ;
DOI: 10.1101/gr.123356.111
Harris RS.
Improved pairwise alignment of genomic DNA .
Ph.D. Thesis . Pennsylvania State University, USA. 2007.
PhyloP:
Cooper GM, Stone EA, Asimenos G, NISC Comparative Sequencing Program., Green ED, Batzoglou S, Sidow
A.
Distribution and intensity of constraint in mammalian genomic sequence .
Genome Res . 2005 Jul;15(7):901-13.
PMID: 15965027 ;
PMC: PMC1172034 ;
DOI: 10.1101/gr.3577405
Pollard KS, Hubisz MJ, Rosenbloom KR, Siepel A.
Detection of nonneutral substitution rates on mammalian phylogenies .
Genome Res . 2010 Jan;20(1):110-21.
PMID: 19858363 ;
PMC: PMC2798823
Siepel A, Haussler D.
Phylogenetic Hidden Markov Models .
In: Nielsen R, editor. Statistical Methods in Molecular Evolution.
New York: Springer; 2005. pp. 325-351.
DOI: 10.1007/0-387-27733-1_12
Siepel A, Pollard KS, and Haussler D. New methods for detecting
lineage-specific selection. In Proceedings of the 10th International
Conference on Research in Computational Molecular Biology (RECOMB 2006), pp. 190-205.
DOI: 10.1007/11732990_17
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