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Open Access Research article

Bos taurus genome sequence reveals the assortment of immunoglobulin and surrogate light chain genes in domestic cattle

Anna Ekman1, Mikael Niku2, Jenni Liljavirta1 and Antti Iivanainen1*

Author Affiliations

1 Department of Basic Veterinary Sciences, University of Helsinki, Helsinki, Finland

2 Department of Applied Chemistry and Microbiology, University of Helsinki, Helsinki, Finland

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BMC Immunology 2009, 10:22  doi:10.1186/1471-2172-10-22

Published: 30 April 2009

Additional files

Additional file 1:

Table S1 – Immunoglobulin λ genes in Btau_3.1. F = functional, FL = fragmented locus, ORF = open reading frame, P = pseudogene, T = truncated pseudogene. Variations in the RSS heptamer motif and spacer length that likely prevent recombination are in bold and underlined. Scaffold coordinates are used.

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Additional file 2:

Table S2- Sequence identity matrix of ruminant immunoglobulin λ variable genes. Sequences corresponding to the V region but excluding CRD3 were aligned and a sequence identity matrix was calculated as described in the methods. Ovine genomic sequences 1.2, 1.3, 2.1, 2.2, 3, 3.1, 4.1, 4.2, 5.1, 5.2, 5.3, 5.4, 6.1, 6.2, 8.0, 9, 10, 12.1, 12.2, 16.1, 16.2, 17, 18, 26.1, 26.2, 26.3 (AF040900–AF040924, M60441) are from Reynaud et al. [13]. Ovine sequences 6a, 6b, 6c and 6d (AF038145–AF038148) are derived from cDNA [14]. Identities ≥ 80% are in bold. Subgroups are bounded and colored light green. Diagonal cells are marked as ID.

Format: XLS Size: 150KB Download file

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Additional file 3:

Table S3 – Immunoglobulin κ genes in Btau_3.1. F = functional, FL = fragmented locus, ORF = open reading frame, P = pseudogene. Variations in the RSS heptamer motif that likely prevent recombination are in bold and underlined. Scaffold coordinates are used.

Format: XLS Size: 23KB Download file

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Additional file 4:

Table S4 – Sequence identity matrix of ruminant immunoglobulin κ variable genes. Sequences corresponding to the V region but excluding CRD3 were aligned and a sequence identity matrix was calculated as described in the methods. The ovine sequences 1, 2.1, 2.2, 2.3, 3 and 4 (AF038133–AF038138) are derived from cDNA [14]. Identities ≥ 80% are in bold. Subgroups are bounded and colored light green. Diagonal cells are marked as ID.

Format: XLS Size: 28KB Download file

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Additional file 5:

Table S5 – Single nucleotide differences in VPREB1, VPREB3 and IGLL1. cDNA clones or PCR products from genomic DNA were sequenced. The sequences were compared against the Btau_3.1 minus strand of Chr17.003.88 scaffold reference sequence. Both alleles are indicated whenever possible.

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Additional file 6:

Table S6 – V and J region amino acid sequences of the apparently functional bovine immunoglogulin light chains. Dots indicate gaps that were introduced during the alignment. White spaces separate consecutive FRs and CDRs.

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