Table 1 |
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Haplotypic organization of VCBP genes and alleles based on BAC and PAC assisted reassembly efforts. |
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Haplotype genes |
Genomic scaffold BAC/PAC support |
Alleles |
|
|
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Haplotype A |
Scaffold_82; _869 |
|
|
VCBP 5a |
BAC 63n5-43b24 contig |
VCBP5S2*01 |
|
VCBP 2b |
BAC 63n5-43b24 contig |
VCBP2S1*02 |
|
VCBP 5b |
BAC 63n5-43b24 contig |
VCBP5S1*02 |
|
VCBP 4a |
BAC 100j9 |
VCBP4S1*02 |
|
VCPB 1a |
BAC 100j9 |
VCBP1S1*02 |
|
VCBP 1b |
Note1 |
VCBP1S3*01 |
|
VCBP 1c |
VCBP1S2*01 |
|
|
Haplotype B |
Scaffold_295 |
|
|
VCBP 5a |
BAC 62d19 |
VCBP5S2*02 |
|
VCBP 2b |
BAC 62d19 |
VCBP2S1*03 |
|
VCBP 5b |
BAC 62d19 |
VCBP5S1*03 |
|
VCBP 4a |
BAC 5h9 |
VCBP4S1*04 |
|
VCBP 1a |
BAC 5h9 |
VCBP1S1*03 |
|
VCBP 1d |
Note2 |
VCBP1S4*01 |
|
Haplotype C |
Independent animal |
|
|
VCBP 5a |
PAC 37d15 |
VCBP5S2*03 |
|
VCBP 2b |
PAC 37d15 |
VCBP2S1*04 |
|
VCBP 5b |
PAC 37d15 |
VCBP5S1*04 |
|
VCBP 2a |
PAC 37d15 |
VCBP2S2*01 |
|
Haplotype A/B: VCBP3 |
Scaffold_1 |
|
|
VCBP3 |
BAC 90F15 |
VCBP3S1*02 |
|
VCBP3 |
BAC 54h3 |
VCBP3S1*03 |
|
Haplotype X |
Independent animal |
|
|
VCBP3 |
PAC 30b18 |
VCBP3S1*04 |
|
|
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Haplotypes and gene naming are consistent with Figure 1, where a, b, c, etc. are paralogous VCBP genes. In the absence of known genetic linkage, haplotypic assignment of VCBP3 alleles is not clear, relative to the other VCBPs, see Figure 1. Haplotype X is an independent animal from the same multi-animal library from which haplotype C was acquired, yet no relationship between the haplotypes is discernable. Accession numbers and downloadable sequences are available in Additional file 1. Note1 BAC support was not pursued for VCBP1b and VCBP1c. Note2 VCBP1d is a five exon pseudogene. BAC support was not pursued; a VCBP5-like pseudogene consisting of only the CBD exon is also present on haplotype A and B but not listed here, see Additional file 1. |
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Dishaw et al. BMC Genetics 2008 9:78 doi:10.1186/1471-2156-9-78 |
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