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Searle S, Frankish A, Bignell A, Aken B, Derrien T, Diekhans M, Harte R, Howald C, Kokocinski F, Lin M, Tress M, Van Baren M, Barnes I, Hunt T, Carvalho-Silva D, Davidson C, Donaldson S, Gilbert J, Kay M, Lloyd D, Loveland J, Mudge J, Snow C, Vamathevan J, Wilming L, Brent M, Gerstein M, Guigó R, Kellis M, Reymond A, Zadissa A, Valencia A, Harrow J, Hubbard T. The GENCODE human gene set. Genome Biol 2010. [PMCID: PMC3026266 DOI: 10.1186/gb-2010-11-s1-p36] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Hubbard TJP, Aken BL, Ayling S, Ballester B, Beal K, Bragin E, Brent S, Chen Y, Clapham P, Clarke L, Coates G, Fairley S, Fitzgerald S, Fernandez-Banet J, Gordon L, Graf S, Haider S, Hammond M, Holland R, Howe K, Jenkinson A, Johnson N, Kahari A, Keefe D, Keenan S, Kinsella R, Kokocinski F, Kulesha E, Lawson D, Longden I, Megy K, Meidl P, Overduin B, Parker A, Pritchard B, Rios D, Schuster M, Slater G, Smedley D, Spooner W, Spudich G, Trevanion S, Vilella A, Vogel J, White S, Wilder S, Zadissa A, Birney E, Cunningham F, Curwen V, Durbin R, Fernandez-Suarez XM, Herrero J, Kasprzyk A, Proctor G, Smith J, Searle S, Flicek P. Ensembl 2009. Nucleic Acids Res 2008; 37:D690-7. [PMID: 19033362 PMCID: PMC2686571 DOI: 10.1093/nar/gkn828] [Citation(s) in RCA: 683] [Impact Index Per Article: 42.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The Ensembl project (http://www.ensembl.org) is a comprehensive genome information system featuring an integrated set of genome annotation, databases, and other information for chordate, selected model organism and disease vector genomes. As of release 51 (November 2008), Ensembl fully supports 45 species, and three additional species have preliminary support. New species in the past year include orangutan and six additional low coverage mammalian genomes. Major additions and improvements to Ensembl since our previous report include a major redesign of our website; generation of multiple genome alignments and ancestral sequences using the new Enredo-Pecan-Ortheus pipeline and development of our software infrastructure, particularly to support the Ensembl Genomes project (http://www.ensemblgenomes.org/).
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Affiliation(s)
- T J P Hubbard
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
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Hagen IJ, Zadissa A, McEwan JC, Veenvliet BA, Hickey SM, Cullen NG, Morris CA, Wilson T. Molecular and bioinformatic strategies for gene discovery for meat traits: a reverse genetics approach. ACTA ACUST UNITED AC 2005. [DOI: 10.1071/ea05044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The identification of genes that influence meat quality and meat yield has relevance for several livestock species. Candidate genes include those involved in the biochemical pathways controlling muscle differentiation, growth and development. Mutations in one such gene, myostatin, have previously been reported to have dramatic effects on muscle phenotype in cattle. Here we report a screening strategy for the discovery of novel mutations in 10 genes involved in muscle development using single-stand conformation polymorphism gels and DNA sequencing. Several novel mutations, both non-synonymous and synonymous were discovered, and some of these may alter gene function. In addition, we also conducted a meta-analysis of published quantitative trait loci from cattle, sheep, pigs and mice, identifying those muscle development genes most likely to contribute to variation in muscle traits within species. From this strategy we found several genes that map into regions that are part of the extended muscle development pathway.
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Affiliation(s)
- C Diez-Tascón
- Ag Research Molecular Biology Unit, Department of Biochemistry, University of Otago, PO Box 56, Dunedin, New Zealand.
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