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posted on 30.12.2011, 14:36 authored by T. Hubbard, D. Andrews, M. Caccamo, G. Cameron, Y. Chen, M. Clamp, L. Clarke, G. Coates, T. Cox, F. Cunningham, V. Curwen, T. Cutts, T. Down, R. Durbin, X. M. Fernandez-Suarez, J. Gilbert, M. Hammond, J. Herrero, H. Hotz, K. Howe, V. Iyer, K. Jekosch, A. Kahari, A. Kasprzyk, D. Keefe, S. Keenan, F. Kokocinsci, D. London, I. Longden, G. McVicker, C. Melsopp, P. Meidl, S. Potter, G. Proctor, M. Rae, D. Rios, M. Schuster, S. Searle, J. Severin, G. Slater, D. Smedley, J. Smith, W. Spooner, A. Stabenau, J. Stalker, R. Storey, S. Trevanion, A. Ureta-Vidal, J. Vogel, S. White, C. Woodwark, E. Birney

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Taken from "Ensembl 2005"

Nucleic Acids Research 2004 ;33(Database Issue):D447-D453.

Published online 17 Dec 2004

PMCID:PMC540092.

Copyright © 2005 Oxford University Press

The view shows genome sequence with annotation from human, mouse and chicken, aligned according to DNA–DNA similarity, shown in green. Pairwise similarity is shown between the ‘primary’ genome (human in this case) and each of the other genomes. Menus allow additional genomes to be added to the display. The ‘P’ button allows a different genome to be selected as the primary one. Genes automatically identified as putative orthologues are linked by blue lines. The region shown is centred around the gene in the HOX cluster on human chromosome 17 and is shown to be syntenic with a region on mouse chromosome 11. All Ensembl known gene structures are conserved and have been correctly identified as orthologues. Two novel Ensembl gene structures predicted in mouse are not seen in human. It would be interesting to investigate the corresponding region in human to understand why they were not predicted there. Features such as alignments to cDNAs and proteins can be turned on using the menus to facilitate such a comparison. Putative orthologue prediction and DNA similarity show a much weaker and incomplete link to a region in the chicken genome; however this is on chromosome Un, which is a fake chromosome composed of fragments that could not be mapped onto chromosomes in the current assembly. Whereas the chicken fragment contains and , and others are absent. The putative chicken orthologue for human is found in another chicken fragment in the fake Un chromosome (data not shown), suggesting that the chicken equivalent of the human chromosome 17 HOX cluster is fragmented in the current chicken assembly.

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