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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)3141314131528260315
4
Cow (Bos taurus)38253825312270303122
197
Dog (Canis lupus familiaris)37743774338339103383
354
Horse (Equus caballus)21422142188725501887
87
Hedgehog (Erinaceus europaeus)6456645621462420214
5
Cat (Felis catus)185518551370485566804
673
Ferret (Mustela putorius furo)3614361430633080306
1
Microbat (Myotis lucifugus)4408440830341050303
15
Sheep (Ovis aries)39853985308490103084
136
Megabat (Pteropus vampyrus)4171417127338980273
3
Shrew (Sorex araneus)4558455819743610197
6
Pig (Sus scrofa)30243036256046402560
380
Dolphin (Tursiops truncatus)3790379030134890301
8
Alpaca (Vicugna pacos)2532253220823240208
2

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
1834
Gorilla (Gorilla gorilla gorilla)67016701603067106030
215
Human (Homo sapiens)17071211177158991367152
278
Macaque (Macaca mulatta)65796579608949006089
237
Mouse Lemur (Microcebus murinus)7111711127168400271
8
Gibbon (Nomascus leucogenys)7172717254666260546
4
Bushbaby (Otolemur garnettii)7276727633969370339
12
Chimpanzee (Pan troglodytes)868186817195148607195
274
Olive baboon (Papio anubis)760376035845175805845
196
Orangutan (Pongo abelii)69966996638760906387
494
Tarsier (Tarsius syrichta)5386538624351430243
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)5963596330456590304
10
Kangaroo rat (Dipodomys ordii)3036303624527910245
7
Squirrel (Ictidomys tridecemlineatus)3166316630328630303
2
Mouse (Mus musculus)86319812421644154923724
1443
Pika (Ochotona princeps)5732573216955630169
4
Rabbit (Oryctolagus cuniculus)33753375312325203123
618
Rat (Rattus norvegicus)1713171365210610652
53

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)2030203017118590171
7
Armadillo (Dasypus novemcinctus)5984598441555690415
8
Tenrec (Echinops telfairi)5680568023154490231
3
Elephant (Loxodonta africana)2644264431523290315
12
Wallaby (Macropus eugenii)14721472115132101151
53
Opossum (Monodelphis domestica)18501850165319721651
140
Platypus (Ornithorhynchus anatinus)38713871328658516121674
2365
Hyrax (Procavia capensis)1720172022414960224
1
Tasmanian devil (Sarcophilus harrisii)14901490120328701203
90
Tree Shrew (Tupaia belangeri)3073307321928540219
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)70970916693016
1
Zebrafish (Danio rerio)513753593964117326431321
3441
Cod (Gadus morhua)15411541141527014
2
Stickleback (Gasterosteus aculeatus)1617161713532642911062
874
Spotted gar (Lepisosteus oculatus)261926198261108
1
Tilapia (Oreochromis niloticus)82182119802019
1
Medaka (Oryzias latipes)7597596091500609
118
Amazon molly (Poecilia formosa)6796794532260453
58
Fugu (Takifugu rubripes)7037036031000603
108
Tetraodon (Tetraodon nigroviridis)8138136391740639
161
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)56756715552015
1
Anole Lizard (Anolis carolinensis)3160316029022584782424
2052
Flycatcher (Ficedula albicollis)89789719878019
0
Chicken (Gallus gallus)155815586678910667
71
Turkey (Meleagris gallopavo)7557554702850470
9
Chinese softshell turtle (Pelodiscus sinensis)10421042161026016
3
Zebra Finch (Taeniopygia guttata)7247245871370587
161

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)2918291826202989391681
2097
Lamprey (Petromyzon marinus)2652265223762769181458
2055
X.tropicalis (Xenopus tropicalis)13061306114116501141
733

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)4554551682870168
54
C.savignyi (Ciona savignyi)340340277630277
160
Fruitfly (Drosophila melanogaster)157020310157000
0
S.cerevisiae (Saccharomyces cerevisiae)413413041300
0