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Overview

StatusReference proteome
Proteinsi <p>Number of protein entries associated with this proteome: UniProtKB entries for regular proteomes or UniParc entries for redundant proteomes (<a href="/help/proteome%5Fredundancy">more...</a>)</p> 46,848
Gene counti <p>This is the total number of unique genes found in the proteome set, algorithmically computed. For each gene, a single representative protein sequence is chosen from the proteome. Where possible, reviewed (Swiss-Prot) protein sequences are chosen as the representatives.</p> - Download one protein sequence per gene (FASTA)
Proteome IDi <p>The proteome identifier (UPID) is the unique identifier assigned to the set of proteins that constitute the <a href="http://www.uniprot.org/manual/proteomes%5Fmanual">proteome</a>. It consists of the characters 'UP' followed by 9 digits, is stable across releases and can therefore be used to cite a UniProt proteome.<p><a href='/help/proteome_id' target='_top'>More...</a></p>UP000000437
Taxonomy7955 - Danio rerio
StrainTuebingen
Last modifiedMay 10, 2020
Genome assembly and annotationi <p>Identifier for the genome assembly (<a href="https://www.ensembl.org/Help/Faq?id=216">more...</a>)</p> GCA_000002035.4 from Ensembl full
BuscoC:95.5%[S:53%,D:42.5%],F:1.7%,M:2.8%,n:3640
CompletenessClose to Standard

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 <p>Genomic components encoding the proteome</p>

Component nameGenome Accession(s)
Component representationProteins
Unplaced
5960
Mitochondrion13
Chromosome 11881
Chromosome 22044
Chromosome 32024
Chromosome 42496
Chromosome 52057
Chromosome 61632
Chromosome 72173
Chromosome 81718
Chromosome 91524
Chromosome 101528
Chromosome 111465
Chromosome 121331
Chromosome 131521
Chromosome 141392
Chromosome 151536
Chromosome 161615
Chromosome 171497
Chromosome 181306
Chromosome 191548
Chromosome 201619
Chromosome 211553
Chromosome 221591
Chromosome 231459
Chromosome 241154
Chromosome 251222

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.
    Stemple D.L.
    Nature 496:498-503(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. 11:1958-1967(2001) [PubMed] [Europe PMC] [Abstract]
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