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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 modifiedFebruary 26, 2021
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
Buscoi <p>The Benchmarking Universal Single-Copy Ortholog (BUSCO) assessment tool is used, for eukaryotic and bacterial proteomes, to provide quantitative measures of UniProt proteome data completeness in terms of expected gene content. BUSCO scores include percentages of complete (C) single-copy (S) genes, complete (C) duplicated (D) genes, fragmented (F) and missing (F) genes, as well as the total number of orthologous clusters (n) used in the BUSCO assessment.</p> C:95.5%[S:52.9%,D:42.6%],F:1.7%,M:2.8%,n:3640 actinopterygii_odb10
Completenessi <p>Complete Proteome Detector (CPD) is an algorithm which employs statistical evaluation of the completeness and quality of proteomes in UniProt, by looking at the sizes of taxonomically close proteomes. Possible values are 'Standard', 'Close to Standard' and 'Outlier'.</p> Close to standard (high value)

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
5728
Mitochondrion13
Chromosome 11891
Chromosome 22051
Chromosome 32040
Chromosome 42500
Chromosome 52071
Chromosome 61650
Chromosome 72200
Chromosome 81727
Chromosome 91529
Chromosome 101536
Chromosome 111476
Chromosome 121347
Chromosome 131537
Chromosome 141406
Chromosome 151544
Chromosome 161626
Chromosome 171504
Chromosome 181317
Chromosome 191555
Chromosome 201628
Chromosome 211565
Chromosome 221593
Chromosome 231471
Chromosome 241154
Chromosome 251227

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. 11:1958-1967(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 496:498-503(2013) [PubMed] [Europe PMC] [Abstract]
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