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Overview

StatusReference proteome
Proteinsi46,929
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_manual">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 modifiedOctober 26, 2018
Genome assembly and annotationi GCA_000002035.4 from Ensembl

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)
Proteins
Unplaced
5976
Mitochondrion13
Chromosome 11883
Chromosome 22049
Chromosome 32026
Chromosome 42499
Chromosome 52056
Chromosome 61634
Chromosome 72184
Chromosome 81721
Chromosome 91527
Chromosome 101526
Chromosome 111463
Chromosome 121336
Chromosome 131522
Chromosome 141393
Chromosome 151530
Chromosome 161628
Chromosome 171501
Chromosome 181308
Chromosome 191550
Chromosome 201628
Chromosome 211559
Chromosome 221595
Chromosome 231461
Chromosome 241150
Chromosome 251222

Publications

  1. "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]
  2. "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 2013:498-503(2013) [PubMed] [Europe PMC] [Abstract]
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