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Zebrafish Assembly and Annotation Information

Danio rerio

This site presents data from the manual annotation of the Tuebingen strain by the Havana group at the Welcome Trust Sanger Institute. Grey shading is used to distinguish between annotated and non annotated regions.

The AB chromosome, containing PAC clones from the AB strain and sorted out to avoid problems arising from high variations between the AB and the Tuebingen strain, was manually annotated by Zebrafish Group at the Wellcome Trust Sanger Institute.

External database identifiers

  • Gene structures from Vega are incorporated into the Zfin database and genome browser, and reciprocal links to Zfin added to Vega genes. Links are also added to Zfin Expression patterns.
  • Uniprot records, Gene Ontology (GO) terms and Gene Ontology Annotation (GOA) records are imported into Vega. These are generated by the EBI Uniprot and GOA teams.

Relevant Publications:

  • Howe (née Jekosch), K.
    The Zebrafish Genome project: sequence analysis and annotation.
    Methods in Cell Biology (2004) Volume 77 pp. 225-239. Elsevier
  • Howe K, Clark MD, Torroja CF, Torrance J, Berthelot C, Muffato M, Collins JE, Humphray S, McLaren K, Matthews L, McLaren S, Sealy I, Caccamo M, Churcher C, Scott C, Barrett JC, Koch R, Rauch GJ, White S, Chow W, Kilian B, Quintais LT, Guerra-Assunção JA, Zhou Y, Gu Y, Yen J, Vogel JH, Eyre T, Redmond S, Banerjee R, Chi J, Fu B, Langley E, Maguire SF, Laird GK, 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, Eliott D, Threadgold G, Harden G, Ware D, Mortimer 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, 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 CM, Ersan-Ürün Z, Eser C, Geiger H, Geisler M, Karotki L, Kirn A, Konantz J, Konantz M, Oberländer M, Rudolph-Geiger S, Teucke M, Osoegawa K, Zhu B, Rapp A, Widaa S, Langford C, Yang F, Carter NP, Harrow J, Ning Z, Herrero J, Searle SM, Enright A, Geisler R, Plasterk RH, Lee C, Westerfield M, de Jong PJ, Zon LI, Postlethwait JH, Nüsslein-Volhard C, Hubbard TJ, Roest Crollius H, Rogers J, Stemple DL.
    The zebrafish reference genome sequence and its relationship to the human genome.
    Nature. 2013 Apr 25;496(7446):498-503. doi: 10.1038/nature12111. Epub 2013 Apr 17. PUBMED: 23594743

Genome Summary

Last Full Update 16 November 2016
Datafreeze Date 2 August 2016
Total Bases 1,447,077,140
Golden Path Length 1,340,430,591
Annotated bases 1,019,982,382
Clones 30,685
Annotated clones 9,587

GRCz10 assembly genes

Havana: 24,853
Protein coding 21,558
lncRNAs: 1,682
lincRNA 914
antisense 696
sense intronic 65
sense overlapping 7
ncRNAs: 16
rRNA 12
miRNA 4
Unclassified processed transcripts 1,106
Pseudogenes: 325
unprocessed pseudogene 228
processed pseudogene 32
transcribed unprocessed pseudogene 29
IG pseudogene 26
polymorphic pseudogene 10
IG 150
Other: 16
TEC 16
Readthrough genes 47

Chromosome AB genes

Havana: 592
Protein coding 525
Unclassified processed transcripts 20
Pseudogenes 47

About this species