Genome

Danio rerio (zebrafish) Danio rerio is a model organism for studies of vertebrate development, developmental biology, and some human genetic diseases. Lineage: Eukaryota[13363]; Metazoa[6241]; Chordata[2945]; Craniata[2917]; Vertebrata[2917]; Euteleostomi[2885]; Actinopterygii[1107]; Neopterygii[1099]; Teleostei[1096]; Ostariophysi[194]; Cypriniformes[99]; Danionidae[9]; Danioninae[9]; Danio[7]; Danio rerio[1]

Zebrafish (Danio rerio) is a small (4-5 cm in length) tropical fresh-water fish native to rivers of northern India, northern Pakistan, Nepal, and Bhutan in South Asia. This species has several advantages as a tool in research, including a short generation time, production of large clutches of eggs, external fertilization, and rapid embryogenesis, More...which is similar to that of higher vertebrates, that can be monitored through the transparent egg. Zebrafish is a widely used model organism for genetic studies in vertebrate development, developmental biology, and a variety of human congenital and genetic diseases. Less...

Summary Sequence data:  genome assemblies: 17; sequence reads: 14  (See  Genome Assembly and Annotation report) Statistics:  median total length (Mb): 1405.1  median protein count: 57100  median GC%: 36.9 NCBI Annotation Release:  106 Publications (limited to 20 most recent records) Population genetic diversity in zebrafish lines. Balik-Meisner M, et al. Mamm Genome 2018 Feb Structure, evolution and expression of collagen XXVIII: Lessons from the zebrafish. Gebauer JM, et al. Matrix Biol 2016 Jan Gene evolution and gene expression after whole genome duplication in fish: the PhyloFish database. Pasquier J, et al. BMC Genomics 2016 May 18 Alternative haplotypes of antigen processing genes in zebrafish diverged early in vertebrate evolution. McConnell SC, et al. Proc Natl Acad Sci U S A 2016 Aug 23 Bone morphogenetic protein/retinoic acid inducible neural-specific protein (brinp) expression during Danio rerio development. Giousoh A, et al. Gene Expr Patterns 2015 May-Jul The zebrafish reference genome sequence and its relationship to the human genome. Howe K, et al. Nature 2013 Apr 25 Tiling histone H3 lysine 4 and 27 methylation in zebrafish using high-density microarrays. Lindeman LC, et al. PLoS One 2010 Dec 20 A genomic view of the NOD-like receptor family in teleost fish: identification of a novel NLR subfamily in zebrafish. Laing KJ, et al. BMC Evol Biol 2008 Feb 6 Characterization of a binary tandem domain F-type lectin from striped bass (Morone saxatilis). Odom EW, et al. J Biol Chem 2006 Jan 20 The zebrafish gene map defines ancestral vertebrate chromosomes. Woods IG, et al. Genome Res 2005 Sep Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A 2002 Dec 24 The complete sequence of the zebrafish (Danio rerio) mitochondrial genome and evolutionary patterns in vertebrate mitochondrial DNA. Broughton RE, et al. Genome Res 2001 Nov More...  Representative (genome information for reference and representative genomes) Reference genome:   Danio rerio GRCz11 Submitter: Genome Reference Consortium Loc Type Name RefSeq INSDC Size (Mb) GC% Protein rRNA tRNA Other RNA Gene Pseudogene Chr 1 NC_007112.7 CM002885.2 59.58 36.4 2,176 - 31 326 1,444 22 Chr 2 NC_007113.7 CM002886.2 59.64 36.7 2,229 - 76 274 1,464 8 Chr 3 NC_007114.7 CM002887.2 62.63 36.9 2,436 - 346 362 1,992 23 Chr 4 NC_007115.7 CM002888.2 78.09 38.4 2,450 - 5,723 1,252 7,909 70 Chr 5 NC_007116.7 CM002889.2 72.5 36.4 2,713 1 140 395 1,679 6 Chr 6 NC_007117.7 CM002890.2 60.27 36.4 2,123 - 52 250 1,238 16 Chr 7 NC_007118.7 CM002891.2 74.28 36.7 2,531 - 72 322 1,641 14 Chr 8 NC_007119.7 CM002892.2 54.3 36.5 1,986 - 240 272 1,452 6 Chr 9 NC_007120.7 CM002893.2 56.46 36.5 1,832 - 60 226 1,060 9 Chr 10 NC_007121.7 CM002894.2 45.42 36.6 1,779 - 12 186 1,076 14 Chr 11 NC_007122.7 CM002895.2 45.48 36.4 1,596 - 13 166 952 4 Chr 12 NC_007123.7 CM002896.2 49.18 36.3 1,679 - 123 157 1,091 5 Chr 13 NC_007124.7 CM002897.2 52.19 36.5 1,805 - 46 230 1,046 6 Chr 14 NC_007125.7 CM002898.2 52.66 36.6 1,481 - 11 170 945 6 Chr 15 NC_007126.7 CM002899.2 48.04 36.8 1,814 - 135 193 1,229 14 Chr 16 NC_007127.7 CM002900.2 55.27 36.5 1,996 - 17 308 1,255 11 Chr 17 NC_007128.7 CM002901.2 53.46 36.6 1,703 - 109 190 1,111 9 Chr 18 NC_007129.7 CM002902.2 51.02 36.6 1,541 - 5 179 915 9 Chr 19 NC_007130.7 CM002903.2 48.45 36.4 1,762 - 7 185 1,038 7 Chr 20 NC_007131.7 CM002904.2 55.2 36.6 1,890 - 262 192 1,376 3 Chr 21 NC_007132.7 CM002905.2 45.93 36.6 1,948 - 253 237 1,374 8 Chr 22 NC_007133.7 CM002906.2 39.13 37.0 1,674 - 143 293 1,288 8 Chr 23 NC_007134.7 CM002907.2 46.22 36.7 1,755 - 11 204 1,015 5 Chr 24 NC_007135.7 CM002908.2 42.17 36.3 1,365 - 18 138 823 10 Chr 25 NC_007136.7 CM002909.2 37.5 36.6 1,453 - 72 129 978 4 MT NC_002333.2 - 0.02 39.9 13 2 22 - 37 - Un - . - 334.09 36.5 9,370 - 1,672 1,816 9,966 71 Chromosomes Click on chromosome name to open Genome Data Viewer External Resources Children's Hospital (Boston) Zebrafish Genome Project Ensembl Genome Browser Genetic and RH Maps (ZFIN) Other Fish - Cichlid Genome Consortium Other Fish - Fugu Other Fish - Medaka Other Fish - Stickleback Other fish - Salmon Other fish - Tetraodon The Danio rerio Sequencing Project The Gene Index Project (DFCI) Trans-NIH Zebrafish Initiative Tüebingen Zebrafish stock collection UCSC Genome Browser Washington University-Zebrafish Genome Resources ZFIN Zebrafish Gene Collection Zebrafish International Resource Center (ZIRC)