DataBase of Conserved Non-coding Sequences
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Instruction CNS DB Species tree

Status
Ready.

(A) Query search (< 10 sec for the example)
(A1) Keyword search against CNS DB
Example: PAX6b
Last common ancestor containing CNS:  
CNS distance from the gene of keyword:  
 
(A2) Sequence extraction (< 10 sec for the example)
Example: Flank lengths to SNPs:
Human (GRCh38/hg38) 11:31804100-31804215 or 11:31664397>A
Human (GRCh37/hg19) 11:31825648-31825763   11:31685945>A
Mouse (GRCm38/mm19) 2:105682368-105682481   2:3225781>C
Zebrafish (GRCz11/danRer11) 7:15881067-15881181   1:19548840>T
Stickleback (BROADS1/gasAcu1) groupII:12857766-12857880   groupXX:3156>T
To start your analysis, press SUBMIT with mode (A).
 

(B) BLAST & alignment (< 1 min as the default setting)
Example: fasta file
To start your analysis, press SUBMIT with mode (B).
 
BLAST options:  
-task: Search type BLASTN   MAGABLAST   DC-MAGABLAST  
-word_size: Length of initial exact match
-evalue: E-value threshold for reported sequences 1e-5   1e-4   1e-3   1e-2   1e-1   1  
-num_alignments: Number of hits to report per genome 1   2   3   5
-perc_identity: Percent identity cutoff
DC-MEGABLAST option:
-template_length: Discontiguous MegaBLAST template length
16   18   21  
BLASTDBCMD option: -range: 5'/3' flanking sequence lengths (bp) 0   500   1000   5000  
         
Genome taxon sampling Example: text file
  If the file is not uploaded, the following taxon sampling is applied.
         
Clear/select all         
Non vertebrates         
Protostomia        
 Ecdysozoa Caenorhabditis-elegans-N Nematode worm RefSeq
  Caenorhabditis-elegans Nematode worm Ens98
  Drosophila-melanogaster-N Fruit fly RefSeq
  Drosophila-melanogaster Fruit fly Ens98
Deuterostomia        
 Hemichordata Saccoglossus-kowalevskii-N Helical acorn worm RefSeq
 Echinodermata Strongylocentrotus-purpuratus Purple urchin EnsMet45
  Strongylocentrotus-purpuratus-N Purple urchin RefSeq
  Acanthaster-planci-N Crown-of-thorns starfish (Okinawa) RefSeq
 Cephalochordata Branchiostoma-floridae-N Florida lancelet RefSeq
  Branchiostoma-belcheri-N Belcher's lancelet RefSeq
 Urochordata Ciona-savignyi Pacific transparent sea squirt Ens98
  Ciona-intestinalis Transparent sea squirt Ens98
         
 Vertebrata         
  Myxiniformes Eptatretus-burgeri Inshore hagfish Ens98
  Petromyzontiformes Petromyzon-marinus Sea lamprey Ens98
  Chondrichthyes Callorhinchus-milii-N Elephant shark RefSeq
  Callorhinchus-milii Elephant shark Ens98
  Rhincodon-typus-N Whale shark RefSeq
  Bony vertebrates        
   Actinopterygii        
     Polypteriformes Erpetoichthys-calabaricus-N Reedfish RefSeq
  Erpetoichthys-calabaricus Reedfish Ens98
     Lepisosteidae Lepisosteus-oculatus-N Spotted gar RefSeq
  Lepisosteus-oculatus Spotted gar Ens98
     Teleostei        
       Osteoglossomorpha Scleropages-formosus Asian bonytongue Ens98
  Paramormyrops-kingsleyae P. kingsleyae Ens98
       Clupeocephala        
         Otocephala        
           Clupeiformes Denticeps-clupeoides Denticle herring Ens98
  Clupea-harengus Atlantic herring Ens98
           Otophysi Danio-rerio-N Zebrafish RefSeq
  Danio-rerio Zebrafish Ens98
  Electrophorus-electricus Electric eel Ens98
  Ictalurus-punctatus Channel catfish Ens98
  Astyanax-mexicanus Mexican tetra 2.0 in Ens98
  Pygocentrus-nattereri Red-bellied piranha Ens98
         Protacanthopterygii Esox-lucius Northern pike Ens98
  Hucho-hucho Huchen Ens98
         Gadiformes Gadus-morhua Atlantic cod Ens98
         Labridae Labrus-bergylta Ballan wrasse Ens98
         Perciformes Gasterosteus-aculeatus Three spined stickleback Ens98
  Cottoperca-gobio Channel bull blenny Ens98
         Sciaenidae Larimichthys-crocea Large yellow croaker Ens98
         Tetraodontiformes Mola-mola Ocean sunfish Ens98
  Tetraodon-nigroviridis Tetraodon Ens98
  Takifugu-rubripes Fugu Ens98
         Pleuronectiformes Cynoglossus-semilaevis Tongue sole Ens98
  Scophthalmus-maximus Turbot Ens98
         Centropomidae Lates-calcarifer Barramundi perch Ens98
         Carangiformes Seriola-lalandi-dorsalis Yellowtail amberjack Ens98
  Seriola-dumerili Greater amberjack Ens98
         Pomacentridae Stegastes-partitus Bicolor damselfish Ens98
  Amphiprion-ocellaris Clown anemonefish Ens98
  Acanthochromis-polyacanthus Spiny chromis Ens98
         Cichlidae Amphilophus-citrinellus Midas cichlid Ens98
  Oreochromis-niloticus Tilapia Ens98
  Neolamprologus-brichardi Lyretail cichlid Ens98
  Pundamilia-nyererei Makobe Island cichlid Ens98
  Maylandia-zebra Zebra mbuna Ens98
  Haplochromis-burtoni Burton's mouthbrooder Ens98
         Syngnathiformes Hippocampus-comes Tiger tail seahorse Ens98
  Mastacembelus-armatus Zig-zag eel Ens98
         Gobiiformes Periophthalmus-magnuspinnatus P. magnuspinnatus Ens98
         Synbranchiformes Monopterus-albus Swamp eel Ens98
         Atherinomorpha        
           Cyprinodontiformes Cyprinodon-variegatus Sheepshead minnow Ens98
  Fundulus-heteroclitus Mummichog Ens98
  Xiphophorus-maculatus Platyfish Ens98
  Poecilia-formosa Amazon molly Ens98
           Beloniformes Oryzias-melastigma Indian medaka Ens98
  Oryzias-latipes-N Japanese medaka HdrR RefSeq
  Oryzias-latipes Japanese medaka HdrR Ens98
   Sarcopterygii        
    Coelacanthiformes Latimeria-chalumnae-N Coelacanth RefSeq
  Latimeria-chalumnae Coelacanth Ens98
    Tetrapoda        
     Amphibia        
       Gymnophiona Rhinatrema-bivittatum-N Two-lined caecilian RefSeq
  Microcaecilia-unicolor-N Tiny Cayenne caecilian RefSeq
       Anura Nanorana-parkeri-N High Himalaya frog RefSeq
  Xenopus-tropicalis-N Western clawed frog RefSeq
  Xenopus-tropicalis Western clawed frog Ens97
  Xenopus-laevis-N Clawed frog RefSeq
     Sauria        
       Lepidosauria        
         Sphenodontia Sphenodon-punctatus Tuatara Ens98
         Squamata        
           Gekkota Gekko-japonicus-N Schlegel's Japanese Gecko RefSeq
           Unidentata        
             Laterata Salvator-merianae Argentine black and white tegu Ens98
  Podarcis-muralis-N Common wall lizard RefSeq
             Toxicofera        
               Iguania Pogona-vitticeps-N Central bearded dragon RefSeq
  Pogona-vitticeps Central bearded dragon Ens98
  Anolis-carolinensis-N Green anole RefSeq
  Anolis-carolinensis Green anole Ens98
               Serpentes        
                 Henophidia Python-bivittatus-N Burmese python RefSeq
                 Colubroidea        
                   Viperidae Protobothrops-mucrosquamatus-N Taiwan habu RefSeq
                   Colubridae Thamnophis-sirtalis-N Common garter snake RefSeq
                   Elapidae Pseudonaja-textilis-N Eastern brown snake RefSeq
  Notechis-scutatus Mainland tiger snake Ens98
  Notechis-scutatus-N Mainland tiger snake RefSeq
       Archelosauria             
         Testudines        
            Trionychidae Pelodiscus-sinensis Chinese softshell turtle Ens98
            Durocryptodira Chelonoidis-abingdonii Abingdon island giant tortoise Ens98
  Gopherus-agassizii Agassiz's desert tortoise Ens98
  Chrysemys-picta-bellii Painted turtle Ens98
         Crocodylia Crocodylus-porosus Australian saltwater crocodile Ens98
  Gavialis-gangeticus-N True gharial RefSeq
  Alligator-mississippiensis-N American alligator RefSeq
  Alligator-sinensis-N Chinese alligator RefSeq
         Aves        
            Palaeognathae        
               Tinamiformes Nothoprocta-perdicaria Chilean tinamou Ens98
               Apterygiformes Apteryx-rowi Okarito brown kiwi Ens98
               Casuariiformes Dromaius-novaehollandiae Emu Ens98
            Neognathae        
               Galloanseres        
                  Anseriformes Anas-platyrhynchos-platyrhynchos Mallard duck Ens98
                  Galliformes Meleagris-gallopavo Turkey Ens98
  Coturnix-japonica Japanese quail Ens98
  Gallus-gallus-N Chicken RefSeq
  Gallus-gallus Chicken Ens97
               Neoaves        
                  Charadriiformes Calidris-pugnax Ruff Ens98
                  Aequornithia        
                  Psittaciformes Melopsittacus-undulatus Budgerigar Ens98
                  Paridae Cyanistes-caeruleus Blue tit Ens98
  Parus-major Great tit Ens98
                  Muscicapidae Ficedula-albicollis Collared flycatcher Ens98
                  Passeroidea        
                     Fringillidae Serinus-canaria Common canary Ens98
                     Pipridae Manacus-vitellinus Golden-collared manakin Ens98
  Lepidothrix-coronata Blue-crowned manakin Ens98
                     Passerellidae Zonotrichia-albicollis White-throated sparrow Ens98
                     Estrildidae Taeniopygia-guttata Zebra finch Ens98
  Lonchura-striata-domestica White-rumped munia Ens98
     Mammalia        
       Monotremata Ornithorhynchus-anatinus Platypus Ens98
       Metatheria Monodelphis-domestica Gray short-tailed opossum Ens97
       Eutheria        
         Xenarthra Dasypus-novemcinctus Nine-banded armadillo Ens98
  Choloepus-hoffmanni Sloth Ens98
         Afrotheria        
            Afroinsectiphilia        
              Tubulidentata Orycteropus-afer-N Aardvark RefSeq
              Chrysochloridae Chrysochloris-asiatica-N Cape golden mole RefSeq
              Tenrecidae Echinops-telfairi Lesser hedgehog tenrec Ens98
            Paenungulata        
              Hyracoidea Procavia-capensis Hyrax Ens98
              Proboscidea Loxodonta-africana African elephant Ens98
              Sirenia Trichechus-manatus-N Florida manatee RefSeq
         Laurasiatheria        
           Eulipotyphla Condylura-cristata-N Star-nosed mole RefSeq
           Chiroptera Pteropus-vampyrus Megabat Ens98
  Myotis-lucifugus Microbat Ens98
           Perissodactyla Equus-caballus Horse Ens98
           Carnivora        
              Feliformia Felis-catus Cat Ens98
              Caniformia Canis-familiaris Dog Ens97
  Mustela-putorius-furo Ferret Ens98
  Ailuropoda-melanoleuca Giant panda Ens98
  Ursus-maritimus Polar bear Ens98
  Neomonachus-schauinslandi-N Hawaiian monk seal RefSeq
  Leptonychotes-weddellii-N Weddell seal RefSeq
  Odobenus-rosmarus-N Walrus RefSeq
           Cetartiodactyla        
             Camelidae Vicugna-pacos Alpaca Ens98
  Camelus-bactrianus-N Bactrian camel RefSeq
             Suidae Sus-scrofa Pig Ens98
             Ruminantia Ovis-aries Domestic sheep Ens98
  Bos-taurus Domestic cow Ens97
             Cetacea        
               Mysticeti Balaenoptera-acutorostrata-N Minke whale RefSeq
               Odontoceti Physeter-catodon-N Sperm whale RefSeq
  Lipotes-vexillifer-N Yangtze river dolphin RefSeq
  Orcinus-orca-N Killer whale RefSeq
  Tursiops-truncatus Dolphin Ens98
         Euarchontoglires        
            Scandentia        
            Glires        
               Lagomorpha Oryctolagus-cuniculus Domestic rabbit Ens98
               Rodentia        
                  Sciuridae        
                  Hystricomorpha Fukomys-damarensis Damara mole rat Ens98
  Heterocephalus-glaber-female-N Naked mole rat RefSeq
  Heterocephalus-glaber-female Naked mole rat Ens98
  Heterocephalus-glaber-male Naked mole rat Ens98
  Cavia-porcellus Guinea pig Ens98
                  Heteromyidae Dipodomys-ordii Kangaroo rat Ens98
                  Myomorpha Nannospalax-galili-N Upper Galilee mountains blind mole rat RefSeq
  Nannospalax-galili Upper Galilee mountains blind mole rat Ens98
  Cricetulus-griseus-crigri Chinese hamster Ens98
  Rattus-norvegicus-N Rat RefSeq
  Rattus-norvegicus Rat Ens97
  Mus-musculus-N House mouse RefSeq
  Mus-musculus House mouse Ens98
            Dermoptera        
            Primates        
               Strepsirrhini        
                  Galagidae Otolemur-garnettii Bushbaby Ens97
                  Lemuriformes Propithecus-coquereli Coquerel's sifaka Ens98
  Microcebus-murinus Gray mouse lemur Ens98
               Haplorrhini        
                  Tarsiiformes Carlito-syrichta Philippine tarsier Ens98
                  Simiiformes        
                     Platyrrhini Aotus-nancymaae Ma's night monkey Ens98
  Callithrix-jacchus Common marmoset Ens98
                     Catarrhini        
                        Cercopithecidae Colobus-angolensis-palliatus Angola colobus Ens98
  Chlorocebus-sabaeus Green monkey Ens98
  Papio-anubis Olive baboon Ens98
  Macaca-mulatta Rhesus macaque Ens98
                        Hominoidea        
                           Hylobatidae Nomascus-leucogenys Gibbon Ens98
                           Hominidae        
                              Ponginae Pongo-abelii Orangutan Ens98
                              Homininae Gorilla-gorilla Gorilla Ens98
  Pan-troglodytes Chimpanzee Ens98
  Pan-paniscus-N Bonobo RefSeq
  Pan-paniscus Bonobo Ens98
  Homo-sapiens-N Human RefSeq
  Homo-sapiens-hg19 Human Ens70
  Homo-sapiens Human Ens98

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