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Table 5 Summary of taurine haplotypes at aberrant sites for each amplicon determined from Hereford sequence and the species sharing the same haplotype (*).

From: Phylogenetic reconstruction and the identification of ancient polymorphism in the Bovini tribe (Bovidae, Bovinae)

Gene_Amplicon

(Taurine Haplotype)

Chromosome

Gaur

Mithan

Banteng

Bison

Yak

NRIP1_e1.2

(G)

bta01

*

*

*

 

*

NRIP1_e1.3

(T)

bta01

*

*

 

*

*

PIT1_e1

(T)

bta01

 

*

*

*

*

PIT1_e3

(T)

bta01

  

*

*

*

PIT1_e5

(C)

bta01

*

*

*

*

 

PIT1_e6

(ACAGTGAACTCCTAG)

bta01

    

*

ITGBP5_e3

(GG)

bta01

*

    

ITGBP5_e5

(ATAGAC)

bta01

    

*

ITGBP5_e6

(CGTG)

bta01

 

*

 

*

 

ITGBP5_e10

(CG)

bta01

   

*

*

5HT1F_e1

(T)

bta01

*

*

   

IGFBP2_e1

(AT)

bta02

 

*

   

IGFBP5_e2

(CGG)

bta02

 

*

   

IGFBP5_e3

(ACGGCC)

bta02

 

*

   

HFABP_e2

(GTTC)

bta02

 

*

   

HFABP_e3

(TGTA)

bta02

    

*

LACS3_e1

(T)

bta02

*

    

LACS3_e3

(T)

bta02

    

*

LACS3_e4

(C)

bta02

  

*

*

 

LACS3_e6

(CA)

bta02

   

*

 

5HT6_e1.2

(TGTGCA)

bta02

   

*

 

GMEB1_e1

(AC)

bta02

    

*

GMEB1_e3

(CCGG)

bta02

 

*

  

*

GMEB1_e4

(A)

bta02

    

*

GMEB1_e5

(AC)

bta02

   

*

 

GMEB1_e6

(G)

bta02

*

*

   

GMEB1_e7

(TA)

bta02

*

  

*

*

GMEB1_e8

(CT)

bta02

*

*

*

  

EGF_e1

(TTA)

bta06

  

*

  

ERa_e3

(A)

bta09

  

*

*

 

ERa_e4

(C)

bta09

    

*

ERa_e5

(AC)

bta09

    

*

ERa_e6

(T)

bta09

*

 

*

  

ERa_e7

(TGA)

bta09

    

*

PABPC1_e2

(AC)

bta14

  

*

  

PABPC1_e3

(TTTGCG)

bta14

    

*

PABPC1_e5

(GG)

bta14

  

*

  

PABPC1_e9

(CCCACGCACTAGACAGCG)

bta14

    

*

MFGE8_e2

(CCCTT)

bta21

    

*

MFGE8_e3

(ATC)

bta21

  

*

  

MFGE8_e5

(TCCA)

bta21

  

*

 

*

  1. *Number of exons represented as e(n) where e = exon and n = number, therefore, PIT1_e1 is exon 1 of PIT1. Exons that extend over the largest sequencing read, which is typically 800 bp are represented as e(n.j) where j equals order of read from 5-prime to 3-prime. Therefore NRIP_e1.1 and NRIP_e1.2 represent two subsequent reads of the l
  2. The number of aberrant alleles making each haplotype are given in brackets as the (taurine haplotype). Table displays haplotype blocks shared with Hereford and 5 members of the Bovinae for exons within the each gene and for genes on the same chromosome.
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BMC Genomics

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