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Statistics on ncRNA trees

Since release 58, Compara computes phylogenetic trees for the non-coding RNAs annotating by RFAM. The manuscript is in preparation. More information can be obtained here

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Gene-tree coverage (per species)

Laurasiatheria

Species# Genes# Sequences# Genes in a tree# Orphaned genes# Genes in a single-species tree# Genes in a multi-species treeCoverage# species-specific duplicationsGene events
Panda (Ailuropoda melanoleuca)3141314132328180323
5
Cow (Bos taurus)38253825312270303122
182
Dog (Canis lupus familiaris)37743774338239203382
344
Horse (Equus caballus)21422142188725501887
74
Hedgehog (Erinaceus europaeus)6456645622462320224
4
Cat (Felis catus)185518551370485416954
677
Ferret (Mustela putorius furo)3614361431532990315
2
Microbat (Myotis lucifugus)4408440831740910317
16
Sheep (Ovis aries)39853985307391203073
144
Megabat (Pteropus vampyrus)4171417128038910280
3
Shrew (Sorex araneus)4558455820443540204
6
Pig (Sus scrofa)30243036256046402560
378
Dolphin (Tursiops truncatus)3790379031334770313
10
Alpaca (Vicugna pacos)2532253221623160216
4

Primates

Species# Genes# Sequences# Genes in a tree# Orphaned genes# Genes in a single-species tree# Genes in a multi-species treeCoverage# species-specific duplicationsGene events
Marmoset (Callithrix jacchus)90009000842257808422
1628
Gorilla (Gorilla gorilla gorilla)67016701603067106030
251
Human (Homo sapiens)16218201357278894037275
215
Macaque (Macaca mulatta)65796579608949006089
361
Mouse Lemur (Microcebus murinus)7111711128068310280
8
Gibbon (Nomascus leucogenys)7172717257665960576
5
Bushbaby (Otolemur garnettii)7276727635369230353
11
Chimpanzee (Pan troglodytes)868186817195148607195
273
Orangutan (Pongo abelii)69966996638760906387
505
Tarsier (Tarsius syrichta)5386538625051360250
15

Glires

Species# Genes# Sequences# Genes in a tree# Orphaned genes# Genes in a single-species tree# Genes in a multi-species treeCoverage# species-specific duplicationsGene events
Guinea Pig (Cavia porcellus)5963596331556480315
11
Kangaroo rat (Dipodomys ordii)3036303625127850251
6
Squirrel (Ictidomys tridecemlineatus)3166316631228540312
2
Mouse (Mus musculus)76538278421334403523861
1399
Pika (Ochotona princeps)5732573215955730159
10
Rabbit (Oryctolagus cuniculus)33753375312325203123
542
Rat (Rattus norvegicus)1713171365210610652
52

Other mammals

Species# Genes# Sequences# Genes in a tree# Orphaned genes# Genes in a single-species tree# Genes in a multi-species treeCoverage# species-specific duplicationsGene events
Sloth (Choloepus hoffmanni)2030203017518550175
8
Armadillo (Dasypus novemcinctus)5984598442555590425
8
Tenrec (Echinops telfairi)5680568023654440236
3
Elephant (Loxodonta africana)2644264432423200324
11
Wallaby (Macropus eugenii)14721472115232001152
53
Opossum (Monodelphis domestica)18501850165319721651
130
Platypus (Ornithorhynchus anatinus)38713871328658518171469
2326
Hyrax (Procavia capensis)1720172023014900230
0
Tasmanian devil (Sarcophilus harrisii)14901490120328701203
84
Tree Shrew (Tupaia belangeri)3073307322528480225
7

Fish

Species# Genes# Sequences# Genes in a tree# Orphaned genes# Genes in a single-species tree# Genes in a multi-species treeCoverage# species-specific duplicationsGene events
Cave fish (Astyanax mexicanus)70970915694015
1
Zebrafish (Danio rerio)513753593963117425611402
3406
Cod (Gadus morhua)15411541131528013
2
Stickleback (Gasterosteus aculeatus)1617161713532641961157
887
Spotted gar (Lepisosteus oculatus)261926197261207
1
Tilapia (Oreochromis niloticus)82182118803018
2
Medaka (Oryzias latipes)7597596091500609
125
Fugu (Takifugu rubripes)7037036031000603
103
Tetraodon (Tetraodon nigroviridis)8138136391740639
158
Platyfish (Xiphophorus maculatus)372372536705
0

Sauropsids

Species# Genes# Sequences# Genes in a tree# Orphaned genes# Genes in a single-species tree# Genes in a multi-species treeCoverage# species-specific duplicationsGene events
Duck (Anas platyrhynchos)56756713554013
0
Anole Lizard (Anolis carolinensis)31603160290225862896
2075
Flycatcher (Ficedula albicollis)89789720877020
0
Chicken (Gallus gallus)155815586678910667
71
Turkey (Meleagris gallopavo)7567564712850471
6
Chinese softshell turtle (Pelodiscus sinensis)10421042121030012
0
Zebra Finch (Taeniopygia guttata)7247245871370587
148

Other vertebrates

Species# Genes# Sequences# Genes in a tree# Orphaned genes# Genes in a single-species tree# Genes in a multi-species treeCoverage# species-specific duplicationsGene events
Coelacanth (Latimeria chalumnae)2918291826202989031717
2007
Lamprey (Petromyzon marinus)2652265223762761400976
2035
X.tropicalis (Xenopus tropicalis)13061306114116501141
664

Others

Species# Genes# Sequences# Genes in a tree# Orphaned genes# Genes in a single-species tree# Genes in a multi-species treeCoverage# species-specific duplicationsGene events
C.elegans (Caenorhabditis elegans)246632483402466300
0
C.intestinalis (Ciona intestinalis)4294291682610168
50
C.savignyi (Ciona savignyi)340340277630277
135
Fruitfly (Drosophila melanogaster)157020310157000
0
S.cerevisiae (Saccharomyces cerevisiae)413413041300
0