Genomic mapping

Species with genomic mapping

Genomic mapping is available for the following 369 species:

Species Assembly
Bombyx mori silkworm ASM15162v1
Daucus carota carrots ASM162521v1
Kryptolebias marmoratus mangrove rivulus ASM164957v1
Mola mola ocean sunfish ASM169857v1
Plasmodium falciparum ASM276v2
Schizosaccharomyces pombe ASM294v2
Chenopodium quinoa ASM168347v1
Rhinopithecus bieti Black snub-nosed monkey ASM169854v1
Manacus vitellinus golden-collared manakin ASM171598v2
Ailuropoda melanoleuca giant panda ASM200744v2
Acanthochromis polyacanthus spiny chromis ASM210954v1
Malus domestica golden ASM211411v1
Anas zonorhyncha Eastern spot-billed duck ASM222487v1
Oryzias latipes Japanese medaka HdrR ASM223467v1
Delphinapterus leucas beluga whale ASM228892v3
Dictyostelium discoideum dicty_2.7
Monodelphis domestica gray short-tailed opossum ASM229v1
Spermophilus dauricus Daurian ground squirrel ASM240643v1
Anser brachyrhynchus pink-footed goose ASM259213v1
Ananas comosus F153
Callithrix jacchus white-tufted-ear marmoset ASM275486v1
Piliocolobus tephrosceles Ugandan red Colobus ASM277652v2
Physeter catodon sperm whale ASM283717v2
Gopherus agassizii Agassiz's desert tortoise ASM289641v1
Accipiter nisus Eurasian sparrowhawk Accipiter_nisus_ver1.0
Ovis aries sheep Oar_v3.1
Pavo cristatus Indian peafowl AIIM_Pcri_1.0
Aegilops tauschii Tausch's goatgrass ASM34733v1
Prunus dulcis ALMONDv2
Brassica rapa field mustard IVFCAASv1
Saccharomyces cerevisiae baker's yeast R64-1-1
Amphiprion ocellaris clown anemonefish AmpOce1.0
Anolis carolinensis green anole AnoCar2.0v2
Apteryx owenii little spotted kiwi aptOwe1
Bos taurus cattle ARS-UCD1.2
Hucho hucho huchen ASM331708v1
Ursus americanus American black bear ASM334442v1
Carassius auratus goldfish ASM336829v1
Galdieria sulphuraria red algae ASM34128v1
Triticum urartu red wild einkorn wheat ASM34745v1
Chondrus crispus Irish moss ASM35022v2
Papaver somniferum ASM357369v1
Ipomoea triloba ASM357664v1
Chelonoidis abingdonii Abingdon island giant tortoise ASM359739v1
Calidris pygmaea Spoon-billed sandpiper ASM369795v1
Junco hyemalis dark-eyed junco ASM382977v1
Phasianus colchicus Ring-necked pheasant ASM414374v1
Oryza indica Indian rice ASM465v1
Varanus komodoensis Komodo dragon ASM479886v1
Capsicum annuum ASM51225v2
Oreochromis aureus blue tilapia ASM587006v1
Struthio camelus australis African ostrich ASM69896v1
Oryzias sinensis Chinese medaka ASM858656v1
Stachyris ruficeps rufous-capped babbler ASM869450v1
Anas platyrhynchos mallard ASM874695v1
Vitis vinifera wine grape 12X
Nymphaea colorata ASM883128v1
Cyanidioschyzon merolae haploid red algae ASM9120v1
Ostreococcus lucimarinus green algae ASM9206v1
Ursus thibetanus thibetanus Asiatic black bear ASM966005v1
Leptobrachium leishanense Leishan spiny toad ASM966780v1
Eragrostis tef ASM97063v1
Asparagus officinalis Aspof.V1
Haplochromis burtoni Burton's mouthbrooder AstBur1.0
Brassica napus oilseed rape AST_PRJEB5043_v1
Astyanax mexicanus Mexican tetra Astyanax_mexicanus-2.0
Athene cunicularia burrowing owl athCun1
Coffea canephora AUK_PRJEB4211_v1
Labrus bergylta ballan wrasse BallGen_V1
Aquila chrysaetos chrysaetos golden eagle bAquChr1.2
Vombatus ursinus common wombat bare-nosed_wombat_genome_assembly
Catharus ustulatus Swainson's thrush bCatUst1.pri
Drosophila melanogaster fruit fly BDGP6.32
Bison bison bison American bison Bison_UMD1.0
Brassica oleracea wild cabbage BOL
Bos mutus wild yak BosGru_v2.0
Brachypodium distachyon false brome Brachypodium_distachyon_v3.0
Brassica rapa bai cai Brapa_1.0
Strigops habroptila Kakapo bStrHab1_v1.p
Cairina moschata domestica muscovy Duck (domestic type) CaiMos1.0
Camelus dromedarius Arabian camel CamDro2
Canis lupus familiaris dog CanFam3.1
Colobus angolensis palliatus Angola colobus Cang.pa_1.0
Mus caroli Ryukyu mouse CAROLI_EIJ_v1.1
Catagonus wagneri Chacoan peccary CatWag_v2_BIUU_UCD
Cercocebus atys Sooty mangabey Caty_1.0
Anas platyrhynchos platyrhynchos common mallard CAU_duck1.0
Cavia aperea Brazilian guinea pig CavAp1.0
Cavia porcellus domestic guinea pig Cavpor3.0
Chara braunii Cbr_1.0
Aegilops tauschii Tausch's goatgrass Aet v4.0
Corchorus capsularis jute CCACVL1_1.0
Castor canadensis American beaver C.can_genome_v1.0
Cynara cardunculus CcrdV1
Cebus capucinus White-headed capuchin Cebus_imitator-1.0
Eragrostis curvula CERZOS_E.curvula1.0
Cervus hanglu yarkandensis Yarkand deer CEY_v1
Chelydra serpentina Common snapping turtle Chelydra_serpentina-1.0
Chinchilla lanigera Long-tailed chinchilla ChiLan1.0
Chlamydomonas reinhardtii chlamy Chlamydomonas_reinhardtii_v5.5
Choloepus hoffmanni Hoffmann's two-fingered sloth choHof1
Chrysemys picta bellii Western painted turtle Chrysemys_picta_bellii-3.0.3
Chrysolophus pictus golden pheasant Chrysolophus_pictus_GenomeV1.0
Clupea harengus Atlantic herring Ch_v2.0.2
Citrus clementina Citrus_clementina_v1.0
Sorex araneus European shrew sorAra1
Coturnix japonica Japanese quail Coturnix_japonica_2.0
Cricetulus griseus crigri Chinese hamster CriGri_1.0
Crocodylus porosus Australian saltwater crocodile CroPor_comp1
Camelina sativa Cs
Ciona savignyi Sea squirt Ciona savignyi CSAV 2.0
Cyprinodon variegatus sheepshead minnow C_variegatus-1.0
Capra hircus blackbengal goat CVASU_BBG_1.0
Cyanistes caeruleus blue tit cyaCae2
Dasypus novemcinctus nine-banded armadillo Dasnov3.0
Fukomys damarensis Damara mole rat DMR_v1.0
Dipodomys ordii Ord's kangaroo rat Dord_2.0
Dromaius novaehollandiae emu droNov1
Pseudonaja textilis eastern brown snake EBS10Xv2-PRI
Eptatretus burgeri Inshore hagfish Eburgeri_3.2
Electrophorus electricus electric eel Ee_SOAP_WITH_SSPACE
Eucalyptus grandis Egrandis1_0
Esox lucius northern pike Eluc_v4
Equus caballus horse EquCab3.0
Eutrema salsugineum Eutsalg1_0
Falco tinnunculus common kestrel FalTin1.0
Anabas testudineus climbing perch fAnaTes1.2
Astatotilapia calliptera eastern happy fAstCal1.2
Betta splendens Siamese fighting fish fBetSpl5.2
Cottoperca gobio channel bull blenny fCotGob3.1
Cyclopterus lumpus lumpfish fCycLum1.pri
Denticeps clupeoides denticle herring fDenClu1.1
Echeneis naucrates live sharksucker fEcheNa1.1
Felis catus domestic cat Felis_catus_9.0
Erpetoichthys calabaricus reedfish fErpCal1.1
Gouania willdenowi blunt-snouted clingfish fGouWil2.1
Ficedula albicollis Collared flycatcher FicAlb1.5
Mastacembelus armatus zig-zag eel fMasArm1.2
Myripristis murdjan pinecone soldierfish fMyrMur1.1
Parambassis ranga Indian glassy fish fParRan2.1
Salarias fasciatus jewelled blenny fSalaFa1.1
Salmo trutta brown trout fSalTru1.1
Scleropages formosus Asian bonytongue fSclFor1.1
Sparus aurata gilthead seabream fSpaAur1.1
Sphaeramia orbicularis orbiculate cardinalfish fSphaOr1.1
Takifugu rubripes fugu fTakRub1.2
Fundulus heteroclitus mummichog Fundulus_heteroclitus-3.0.2
Gadus morhua Atlantic cod gadMor3.0
Arabis alpina A_alpina_V4
Geospiza fortis medium ground-finch GeoFor_1.0
Glycine max soybeans Glycine_max_v2.1
Anser cygnoides swan goose GooseV1.0
Gorilla gorilla Western Lowland Gorilla gorGor4
Erythrura gouldiae Gouldian finch GouldianFinch
Gossypium raimondii Graimondii2_0_v6
Gallus gallus chicken GRCg6a
Homo sapiens human GRCh38.p13
Mus musculus mouse GRCm39
Danio rerio zebrafish GRCz11
Poecilia reticulata guppy Guppy_female_1.0_MT
Helianthus annuus common sunflower HanXRQr1.0
Hippocampus comes tiger tail seahorse H_comes_QL1_v1
Erinaceus europaeus western European hedgehog eriEur1
Heterocephalus glaber male naked mole-rat HetGla_1.0
Salvator merianae Argentine black and white tegu HLtupMer3
Peromyscus maniculatus bairdii Northern American deer mouse HU_Pman_2.1
Hordeum vulgare two-rowed barley IBSC v2
Salmo salar Atlantic salmon ICSASG_v2
Ictalurus punctatus channel catfish IpCoco_1.2
Oryza sativa Japanese rice IRGSP-1.0
Kalanchoe fedtschenkoi K_fedtschenkoi_M2_v1
Ciona intestinalis Sea squirt Ciona intestinalis KH
Latimeria chalumnae coelacanth LatCha1
Laticauda laticaudata blue-ringed sea krait latLat_1.0
Larimichthys crocea large yellow croaker L_crocea_2.0
Lepidothrix coronata blue-crowned manakin Lepidothrix_coronata-1.0
Lepisosteus oculatus Spotted gar LepOcu1
Lonchura striata domestica Bengalese finch LonStrDom1
Loxodonta africana African savanna elephant Loxafr3.0
Bos grunniens domestic yak LU_Bosgru_v3.0
Lupinus angustifolius blue lupin LupAngTanjil_v1.0
Macaca fascicularis Crab-eating macaque Macaca_fascicularis_6.0
Monopterus albus swamp eel M_albus_1.0
Manihot esculenta cassava Manihot esculenta v6
Marchantia polymorpha Marchanta_polymorpha_v1
Marmota marmota marmota Alpine marmot marMar2.1
Balaenoptera musculus Blue whale mBalMus1.v2
Malurus cyaneus samueli superb fairywren mCya_1.0
Medicago truncatula barrel medic MedtrA17_4.0
Suricata suricatta meerkat meerkat_22Aug2017_6uvM2_HiC
Cucumis melo Melonv4
Melopsittacus undulatus Budgie Melopsittacus_undulatus_6.3
Mesocricetus auratus Golden Hamster MesAur1.0
Notamacropus eugenii tammar wallaby Meug_1.0
Amphilophus citrinellus Midas cichlid Midas_v5
Mandrillus leucophaeus Drill Mleu.le_1.0
Lynx canadensis Canada lynx mLynCan4_v1.p
Macaca mulatta Macaque Mmul_10
Microcebus murinus gray mouse lemur Mmur_3.0
Macaca nemestrina Pig-tailed macaque Mnem_1.0
Ornithorhynchus anatinus platypus mOrnAna1.p.v1
Moschus moschiferus Siberian musk deer MosMos_v2_BIUU_UCD
Phocoena sinus vaquita mPhoSin1.pri
Rhinolophus ferrumequinum greater horseshoe bat mRhiFer1_v1.p
Sarcophilus harrisii Tasmanian devil mSarHar1.11
Lates calcarifer barramundi perch ASB_HGAPassembly_v1
Sciurus vulgaris Eurasian red squirrel mSciVul1.1
Meriones unguiculatus Mongolian gerbil MunDraft-v1.0
Musa acuminata wild Malaysian banana Musa_acuminata_v2
Mus spicilegus steppe mouse MUSP714
Mustela putorius furo Domestic ferret MusPutFur1.0
Myotis lucifugus little brown bat Myoluc2.0
Zalophus californianus california sea lion mZalCal1.pri
Maylandia zebra zebra mbuna M_zebra_UMD2a
Naja naja Indian cobra Nana_v5
Amphiprion percula orange clownfish Nemo_v1
Neolamprologus brichardi lyretail cichlid NeoBri1.0
Nothobranchius furzeri turquoise killifish Nfu_20140520
Monodon monoceros narwhal NGI_Narwhal_1
Nicotiana attenuata coyote tobacco NIATTr2
Nomascus leucogenys Northern white-cheeked gibbon Nleu_3.0
Neovison vison American mink NNQGG.v01
Nothoprocta perdicaria Chilean tinamou notPer1
Numida meleagris helmeted guineafowl NumMel1.0
Oryza barthii African wild rice O.barthii_v1
Ochotona princeps American pika OchPri2.0-Ens
Octodon degus Degu OctDeg1.0
Olea europaea sylvestris O_europaea_v1
Oryzias javanicus javanese ricefish OJAV_1.1
Oryza longistaminata long-staminate rice O_longistaminata_v1.0
Oryzias melastigma Indian medaka Om_v0.7.RACA
Oncorhynchus mykiss rainbow trout Omyk_1.0
Oreochromis niloticus Nile tilapia O_niloticus_UMD_NMBU
Oryza rufipogon common wild rice OR_W1943
Oryctolagus cuniculus rabbit OryCun2.0
Oryza brachyantha malo sina Oryza_brachyantha.v1.4b
Oryza glaberrima African rice Oryza_glaberrima_V1
Oryza glumipatula South American wild rice Oryza_glumaepatula_v1.5
Oryza meridionalis Australian wild rice Oryza_meridionalis_v1.3
Oryza nivara weedy rice Oryza_nivara_v1.0
Oryza punctata red rice Oryza_punctata_v1.2
Otolemur garnettii small-eared galago OtoGar3
Oncorhynchus tshawytscha Chinook salmon Otsh_v1.0
Otus sunia Oriental scops-owl OtuSun1.0
Mus pahari Shrew mouse PAHARI_EIJ_v1.1
Panthera leo lion PanLeo1.0
Pan paniscus bonobo panpan1.1
Arabidopsis halleri Ahal2.2
Amborella trichopoda Amborella AMTR1.0
Aotus nancymaae Ma's night monkey Anan_2.0
Panthera pardus leopard PanPar1.0
Panthera tigris altaica Tiger PanTig1.0
Pan troglodytes chimpanzee Pan_tro_3.0
Papio anubis Olive baboon Panu_3.0
Parus major Great Tit Parus_major1.1
Prunus avium PAV_r1.0
Propithecus coquereli Coquerel's sifaka Pcoq_1.0
Pelodiscus sinensis Chinese softshell turtle PelSin_1.0
Pelusios castaneus West African mud turtle Pelusios_castaneus-1.0
Triticum aestivum arinalrfor PGSBv2.0_Arinalrfor
Phascolarctos cinereus koala phaCin_unsw_v4.1
Panicum hallii PhalliiHAL_v2.1
Panicum hallii fil2 PHallii_v3.1
Phaseolus vulgaris French bean PhaVulg1_0
Physcomitrium patens moss Phypa V3
Pistacia vera PisVer_v2
Paramormyrops kingsleyae Paramormyrops kingsleyae PKINGS_0.1
Poecilia latipinna sailfin molly P_latipinna-1.0
Petromyzon marinus sea lamprey Pmarinus_7.0
Poecilia mexicana shortfin molly P_mexicana-1.0
Periophthalmus magnuspinnatus Periophthalmus magnuspinnatus PM.fa
Podarcis muralis common wall lizard PodMur_1.0
Poecilia formosa Amazon molly Poecilia_formosa-5.1.2
Populus trichocarpa poplar Pop_tri_v3
Pongo abelii Bornean orangutan PPYG2
Procavia capensis cape rock hyrax proCap1
Prolemur simus greater bamboo lemur Prosim_1.0
Prunus persica peach Prunus_persica_NCBIv2
Pteropus vampyrus large flying fox pteVam1
Pundamilia nyererei Makobe Island cichlid PunNye1.0
Pygocentrus nattereri red-bellied piranha Pygocentrus_nattereri-1.0.2
Rosa chinensis RchiOBHm-V2
Actinidia chinensis Red5_PS1_1.69.0
Beta vulgaris sugar beet RefBeet-1.2.2
Neogobius melanostomus round goby RGoby_Basel_V2
Gopherus evgoodei Goodes thornscrub tortoise rGopEvg1_v1.p
Rattus norvegicus Norway rat Rnor_6.0
Rhinopithecus roxellana Golden snub-nosed monkey Rrox_v1
Saimiri boliviensis boliviensis Bolivian squirrel monkey SaiBol1.0
Sinocyclocheilus grahami golden-line barbel SAMN03320097.WGS_v1.1
Sinocyclocheilus rhinocerous horned golden-line barbel SAMN03320098_v1.1
Sinocyclocheilus anshuiensis blind barbel SAMN03320099.WGS_v1.1
Serinus canaria common canary SCA1
Seriola dumerili greater amberjack Sdu_1.0
Seriola lalandi dorsalis yellowtail amberjack Sedor1
Setaria italica foxtail millet Setaria_italica_v2.0
Setaria viridis Setaria_viridis_v2.0
Sesamum indicum S_indicum_v1.0
Solanum lycopersicum tomato SL3.0
Sander lucioperca pike-perch SLUC_FBN_1
Strix occidentalis caurina northern spotted owl Soccid_v01
Solanum tuberosum potato SolTub_3.0
Sorghum bicolor sorghum Sorghum_bicolor_NCBIv3
Ictidomys tridecemlineatus thirteen-lined ground squirrel SpeTri2.0
Mus spretus algerian mouse SPRET_EiJ_v1
Sus scrofa pig Sscrofa11.1
Saccharum spontaneum Sspon.HiC_chr_asm
Stegastes partitus bicolor damselfish Stegastes_partitus-1.0.2
Camarhynchus parvulus small tree finch STF_HiC
Triticum turgidum durum wheat svevo
Scophthalmus maximus turbot ASM1334776v1
Arabidopsis thaliana thale-cress TAIR10
Carlito syrichta Philippine tarsier Tarsius_syrichta-2.0.1
Dioscorea rotundata TDr96_F1_v2_PseudoChromosome
Echinops telfairi small Madagascar hedgehog TENREC
Tetraodon nigroviridis spotted green pufferfish TETRAODON 8.0
Theropithecus gelada gelada Tgel_1.0
Terrapene carolina triunguis Three-toed box turtle T_m_triunguis-2.0
Tupaia belangeri northern tree shrew tupBel1
Trifolium pratense purple clover Trpr
Meleagris gallopavo turkey Turkey_5.1
Tursiops truncatus bottlenosed dolphin turTru1
Bos indicus hybrid hybrid cattle UOA_Brahman_1
Corvus moneduloides New Caledonian crow UO_Cmon_1.0
Apteryx haastii Great spotted kiwi aptHaa1
Calidris pugnax ruff ASM143184v1
Zosterops lateralis melanops silver-eye ASM128173v1
Gambusia affinis western mosquitofish ASM309773v1
Canis lupus dingo dingo ASM325472v1
Citrullus lanatus Cla97_v1
Cyprinus carpio common carp common_carp_genome
Apteryx rowi Okarito brown kiwi aptRow1
Equus asinus asinus donkey ASM303372v1
Anopheles gambiae African malaria mosquito AgamP4
Taeniopygia guttata zebra finch bTaeGut1_v1.p
Callorhinchus milii elephant shark Callorhinchus_milii-6.1.3
Nannospalax galili Upper Galilee mountains blind mole rat S.galili_v1.0
Sphenodon punctatus tuatara ASM311381v1
Urocitellus parryii Arctic ground squirrel ASM342692v1
Amazona collaria yellow-billed parrot ASM394721v1
Cucumis sativus cucumbers ASM407v2
Gasterosteus aculeatus three-spined stickleback BROAD S1
Bubo bubo Eurasian eagle-owl BubBub1.0
Buteo japonicus eastern buzzard ButJap1.0
Chlorocebus sabaeus African green monkey ChlSab1.1
Cynoglossus semilaevis tongue sole Cse_v1.0
Jaculus jaculus Lesser Egyptian jerboa JacJac1.0
Leersia perrieri Leersia Lperr_V1.4
Microtus ochrogaster vole MicOch1.0
Oncorhynchus kisutch coho salmon Okis_V2
Pogona vitticeps central bearded dragon pvi1.1
Dicentrarchus labrax European seabass seabass_V1.0
Notechis scutatus mainland tiger snake TS10Xv2-PRI
Ursus maritimus Polar bear UrsMar_1.0
Arabidopsis lyrata lyrate rockcress v.1.0
Selaginella moellendorffii spikemoss v1.0
Quercus lobata ValleyOak3.0
Vicugna pacos alpaca vicPac1
Vigna angularis adzuki bean Vigan1.1
Vigna radiata mung bean Vradiata_ver6
Vulpes vulpes red fox VulVul2.2
Juglans regia English walnut Walnut_2.0
Caenorhabditis elegans C.elegans WBcel235
Triticum dicoccoides wild emmer wheat WEWSeq v.1.0
Xenopus tropicalis tropical clawed frog Xenopus_tropicalis_v9.1
Xiphophorus couchianus Monterrey platyfish Xiphophorus_couchianus-4.0.1
Xiphophorus maculatus southern platyfish X_maculatus-5.0-male
Zea mays maize Zm-B73-REFERENCE-NAM-5.0
Zonotrichia albicollis white-throated sparrow Zonotrichia_albicollis-1.0.1

About genomic mapping

RNAcentral imports genome locations from Ensembl, LNCipedia, miRBase, and other Expert Databases. In addition, sequences are mapped to the reference genomes downloaded from Ensembl and Ensembl Genomes using blat.

Data access

RNAcentral sequences can be viewed in their genomic context using a light-weight genome browser powered by Genoverse. External links are provided to the fully-featured genome browsers such as Ensembl, Ensembl Genomes, and UCSC genome browser.

The genomic coordinates of the RNAcentral entries can be downloaded in BED format from the FTP site or through the REST API.

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