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Table 4 Percent frequency of cloned cDNA, distribution and classification of the transcribed CojaIIB allele as five distinct Coja haplotypes

From: The major histocompatibility complex (Mhc) class IIB region has greater genomic structural flexibility and diversity in the quail than the chicken

HT number

Locus

Allele

PM2 alleles

Nt. Acc, No.

Nucleotide similarity to HT1 (%)

% frequency of cDNA clones per individual quail (% frequency of cDNA clones per haplotype)

      

quail individual number

      

302*

311

312

321

322

323

HT1

Coja-DAB1

Coja-DAB1*01

 

AB181861

100

46.9** (46.9)***

-

17.1 (37.1)

5.9 (19.0)

-

-

 

Coja-DBB1

Coja-DBB1*01

Coja-DBB1*01

AB181862

100

35.9 (35.9)

-

22.4 (48.6)

16.2 (52.4)

-

-

 

Coja-DCB1

Coja-DCB1*01

 

AB181863

100

6.3 (6.3)

-

1.3 (2.9)

2.9 (9.5)

-

-

 

Coja-DDB1

-

 

-

-

-

-

-

-

-

-

 

Coja-DEB1

Coja-DEB1*01

 

AB181865

100

4.7 (4.7)

-

2.6 (5.6)

-

-

-

 

Coja-DFB1

Coja-DFB1*01

 

AB181866

100

-

-

1.3 (2.9)

1.5 (4.8)

-

-

 

Coja-DGB1

Coja-DGB1*01

 

AB181868

100.0

6.3 (6.3)

-

-

4.4 (14.3)

-

-

 

Coja-DGB1

Coja-DGB1*02

 

AB181869

98.9 (DGB1)

-

-

1.3 (2.9)

-

-

-

HT2

CojaII-13

CojaII-13*01

Coja-DBB1*02

AB181874

76.3 (DCB1) ~ 87.4 (DAB1)

-

62.9 (100)

53.9 (100)

-

-

67.2 (100)

HT3

CojaII-16

CojaII-16*01

Coja-DBB1*03

AB264281

78.9 (DCB1) ~ 85.2 (DBB1)

-

12.9(34.8)

-

-

-

-

 

CojaII-17

CojaII-17*01

 

AB264282

77.5 (DCB1) ~ 83.3 (DGB1)

-

24.2 (65.2)

-

-

-

-

HT4

CojaII-02

CojaII-02*01

Coja-DBB1*04

AB181871

78.1 (DCB1) ~ 88.9 (DBB1)

-

-

-

13.2 (19.1)

14.5 (29.4)

-

 

CojaII-01

CojaII-01*01

 

AB181870

78.9 (DCB1) ~ 87.8 (DBB1)

-

-

-

36.8 (53.2)

21.7 (44.1)

-

 

CojaII-04

CojaII-04*01

 

AB181872

77.8 (DCB1) ~ 84.4 (DBB1)

-

-

-

19.1 (27.7)

13.0 (26.5)

-

HT5

CojaII-14

CojaII-14*01

Coja-DBB1*05

AB181876

77.4 (DCB1) ~ 87.4 (DAB1)

-

-

-

-

47.8 (94.3)

28.1 (85.7)

 

Coja-DFB1

Coja-DFB1*02

 

AB181867

99.3 (DFB1)

-

-

-

-

2.9 (5.7)

4.7 (14.3)

 

cDNA sub-clone

    

64

62

76

68

69

64

 

Presumptive HT

    

1/1

2/3

1/2

1/4

4/5

2/5

  1. Bold letter indicates sub-clone frequency over 30%. (-) means not transcribed. Coja-DFB1*02 was categorized to "HT5" because this allele sequence was observed in only HT5.
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BMC Genomics

ISSN: 1471-2164

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