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Overview

Proteome nameDanio rerio Tuebingen - Reference proteome
Proteins43,541
Proteome IDiUP000000437
StrainTuebingen
Taxonomy7955 - Danio rerio
Last modifiedJuly 18, 2017
Genome assembly and annotationi GCA_000002035.3 from Ensembl
© fishbase.org.cn

Danio rerio commonly known as zebrafish is a tropical fish belonging to the minnow family (Cyprinidae). It is a major model for studying developmental biology; aided by the transparency of the embryo and adult body, researchers can modify the fish's genotype at the egg stage and see resulting changes as little as three days later.

Zebrafish have the ability to regenerate many of their tissues including fins, skin, heart and, in larval stages, brain. Zebrafish have been used to study cancers, including melanoma, leukemia, pancreatic cancer and hepatocellular carcinoma.

The Tubingen strain was used as the the reference strain for the genome sequencing project as it had been used extensively to identify mutations affecting embryogenesis. Sequencing revealed that 71.4% of human genes have at least one zebrafish ortholog. Currently the zebrafish genome is thought to have more than 26,000 protein-coding genes.

Componentsi

DownloadView all proteins
Component nameGenome Accession(s)
Proteins
Unplaced
1789
Mitochondrion13
Chromosome 11999
Chromosome 22143
Chromosome 32078
Chromosome 42533
Chromosome 52107
Chromosome 61697
Chromosome 72284
Chromosome 81739
Chromosome 91586
Chromosome 101535
Chromosome 111438
Chromosome 121337
Chromosome 131551
Chromosome 141402
Chromosome 151547
Chromosome 161668
Chromosome 171451
Chromosome 181327
Chromosome 191665
Chromosome 201707
Chromosome 211569
Chromosome 221591
Chromosome 231486
Chromosome 241134
Chromosome 251240

Publications

  1. "The zebrafish reference genome sequence and its relationship to the human genome."
    Howe K., Clark M.D., Torroja C.F., Torrance J., Berthelot C., Muffato M., Collins J.E., Humphray S., McLaren K., Matthews L., McLaren S., Sealy I., Caccamo M., Churcher C., Scott C., Barrett J.C., Koch R., Rauch G.J.
    , White S., Chow W., Kilian B., Quintais L.T., Guerra-Assuncao J.A., Zhou Y., Gu Y., Yen J., Vogel J.H., Eyre T., Redmond S., Banerjee R., Chi J., Fu B., Langley E., Maguire S.F., Laird G.K., Lloyd D., Kenyon E., Donaldson S., Sehra H., Almeida-King J., Loveland J., Trevanion S., Jones M., Quail M., Willey D., Hunt A., Burton J., Sims S., McLay K., Plumb B., Davis J., Clee C., Oliver K., Clark R., Riddle C., Elliot D., Threadgold G., Harden G., Ware D., Begum S., Mortimore B., Kerry G., Heath P., Phillimore B., Tracey A., Corby N., Dunn M., Johnson C., Wood J., Clark S., Pelan S., Griffiths G., Smith M., Glithero R., Howden P., Barker N., Lloyd C., Stevens C., Harley J., Holt K., Panagiotidis G., Lovell J., Beasley H., Henderson C., Gordon D., Auger K., Wright D., Collins J., Raisen C., Dyer L., Leung K., Robertson L., Ambridge K., Leongamornlert D., McGuire S., Gilderthorp R., Griffiths C., Manthravadi D., Nichol S., Barker G., Whitehead S., Kay M., Brown J., Murnane C., Gray E., Humphries M., Sycamore N., Barker D., Saunders D., Wallis J., Babbage A., Hammond S., Mashreghi-Mohammadi M., Barr L., Martin S., Wray P., Ellington A., Matthews N., Ellwood M., Woodmansey R., Clark G., Cooper J., Tromans A., Grafham D., Skuce C., Pandian R., Andrews R., Harrison E., Kimberley A., Garnett J., Fosker N., Hall R., Garner P., Kelly D., Bird C., Palmer S., Gehring I., Berger A., Dooley C.M., Ersan-Urun Z., Eser C., Geiger H., Geisler M., Karotki L., Kirn A., Konantz J., Konantz M., Oberlander M., Rudolph-Geiger S., Teucke M., Lanz C., Raddatz G., Osoegawa K., Zhu B., Rapp A., Widaa S., Langford C., Yang F., Schuster S.C., Carter N.P., Harrow J., Ning Z., Herrero J., Searle S.M., Enright A., Geisler R., Plasterk R.H., Lee C., Westerfield M., de Jong P.J., Zon L.I., Postlethwait J.H., Nusslein-Volhard C., Hubbard T.J., Roest Crollius H., Rogers J., Stemple D.L.
    Nature 2013:498-503(2013) [PubMed] [Europe PMC] [Abstract]
  2. "The complete sequence of the zebrafish (Danio rerio) mitochondrial genome and evolutionary patterns in vertebrate mitochondrial DNA."
    Broughton R.E., Milam J.E., Roe B.A.
    Genome Res. 2001:1958-1967(2001) [PubMed] [Europe PMC] [Abstract]