UTGB/medaka: genomic resource database for medaka biology

Medaka (Oryzias latipes) is a small egg-laying freshwater teleost native to East Asia that has become an excellent model system for developmental genetics and evolutionary biology. The draft medaka genome sequence (700 Mb) was reported in June 2007, and its substantial genomic resources have been op...

Full description

Saved in:
Bibliographic Details
Published in:Nucleic acids research 2008-01, Vol.36 (suppl-1), p.D747-D752
Main Authors: Ahsan, Budrul, Kobayashi, Daisuke, Yamada, Tomoyuki, Kasahara, Masahiro, Sasaki, Shin, Saito, Taro L, Nagayasu, Yukinobu, Doi, Koichiro, Nakatani, Yoichiro, Qu, Wei, Jindo, Tomoko, Shimada, Atsuko, Naruse, Kiyoshi, Toyoda, Atsushi, Kuroki, Yoko, Fujiyama, Asao, Sasaki, Takashi, Shimizu, Atsushi, Asakawa, Shuichi, Shimizu, Nobuyoshi, Hashimoto, Shin-ichi, Yang, Jun, Lee, Yongjun, Matsushima, Kouji, Sugano, Sumio, Sakaizumi, Mitsuru, Narita, Takanori, Ohishi, Kazuko, Haga, Shinobu, Ohta, Fumiko, Nomoto, Hisayo, Nogata, Keiko, Morishita, Tomomi, Endo, Tomoko, Shin-I, Tadasu, Takeda, Hiroyuki, Kohara, Yuji, Morishita, Shinichi
Format: Article
Language:English
Subjects:
Animals
Chromosomes, Artificial, Bacterial
Databases, Genetic
Freshwater
Gene Expression
Genetic Markers
Genetic Variation
Genomics
Internet
Oryzias - genetics
Oryzias latipes
Plasmids - genetics
Polymorphism, Single Nucleotide
Teleostei
Transcription Initiation Site
User-Computer Interface
Citations: Items that this one cites
Items that cite this one
Online Access:Request full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary:Medaka (Oryzias latipes) is a small egg-laying freshwater teleost native to East Asia that has become an excellent model system for developmental genetics and evolutionary biology. The draft medaka genome sequence (700 Mb) was reported in June 2007, and its substantial genomic resources have been opened to the public through the University of Tokyo Genome Browser Medaka (UTGB/medaka) database. This database provides basic genomic information, such as predicted genes, expressed sequence tags (ESTs), guanine/cytosine (GC) content, repeats and comparative genomics, as well as unique data resources including (i) 2473 genetic markers and experimentally confirmed PCR primers that amplify these markers, (ii) 142 414 bacterial artificial chromosome (BAC) and 217 344 fosmid end sequences that amount to 15.0- and 11.1-fold clone coverage of the entire genome, respectively, and were used for draft genome assembly, (iii) 16 519 460 single nucleotide polymorphisms (SNPs), and 2 859 905 insertions/deletions detected between two medaka inbred strain genomes and (iv) 841 235 5′-end serial analyses of gene-expression (SAGE) tags that identified 344 266 transcription start sites on the genome. UTGB/medaka is available at: http://medaka.utgenome.org/
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gkm765