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Open Access Open Badges Research article

Genomic analysis reveals extensive gene duplication within the bovine TRB locus

Timothy Connelley1*, Jan Aerts2, Andy Law1 and W Ivan Morrison1

Author Affiliations

1 The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Roslin, EH25 9RG, UK

2 Genome Dynamics and Evolution Group, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK

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BMC Genomics 2009, 10:192  doi:10.1186/1471-2164-10-192

Published: 24 April 2009

Additional files

Additional file 1:

Table S1 – Location of bovine TRB genes in Btau_3.1. For each gene the start and stop positions on the scaffold as well as the orientation are shown.

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Additional file 2:

Table S2 – Summary of the analysis of non-functional TRBV gene segments identified in Btau_3.1. To be considered functional TRBV gene segment sequences were required to fulfil several conditions as described in the Methods. The table above summarises the lesions identified in the genomic sequences of TRBV genes that are considered to render them non-functional and therefore psuedogenes. TRBV6c, 6g, 6r, 6w and 6aa are open-reading frame (ORF) pseudogenes as their reading frame is maintained, the lesions causing their predicted loss of function resulting either in the loss of a conserved residue or loss of a consensus 23-RS.

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Additional file 3:

Figure S1 – Analysis of the repeat content in (A) Chr4.003.105, (B) Chr4.003.108_RC and (C) ChrUn.003.1717. The repeat content is calculated as the percentage (y-axis) of the sequence (x-axis) composed of repeat elements in 10 Kb windows using a rolling 1 Kb step. The positions of TRB genes and interposed/adjacent non-TRB genes, as well as regions of undetermined sequence are shown according to the legend. Abbreviations for gene names used in the figure have been described in Figure 9.

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