Table 1

MHC genes identified in the survey of the zebra finch genome assembly.

Chicken

Zebra Finch

Gene

# loci

Chr#

Locus ID

Chr#

Coordinates and orientation (+/-)

Ensembl ID


CD1

2

16

1

12

36510 -- 39728 (+)

-

2

12

31218 -- 32904 (+)

ENSTGUG00000003538

TNXB

1

16

-

-

-

CYP21

1

16

22_random

5,200 - 8,483

ENSTGUG00000003380

CENP-A

1

16

Un

Contig 19574 (-)

ENSTGUG00000016809

C4

1

16

-

-

-

TAP1

1

16

14_random

8635 -- 8114 (-)

ENSTGUG00000015337

TAP2

1

16

-

-

Class I

2

(+MHC-Y)

16

1

22_random

954 -- 3750 (+)

ENSTGUG00000017273

ψ L

Un

Contig 5002 (-)

-

ψ L

Un

Contig 19247 (+)

ENSTGUG00000016646

ψ L

Un

Contig 43472 (-)

-

ψ L

Un

Contig 237 (+)

-

ψ L

Un

Contig 5814 (+)

-

ψ L

Un

Contig 29268 (-)

ENSTGUG00000014179

ψ L

Un

Contig 24227 (-)

ENSTGUG00000015460

ψ L

Un

Contig 19531 (-)

ψ L

Un

Contig 1325 (-)

ENSTGUG00000016290

ψ C

Un

Contig 237 (+)

ENSTGUG00000015195

ψ O

16_random

79190 -- 79374 (+)

DMA

1

16

-

-

-

DMB

2

16

-

-

-

BRD2

1

16

Un

Contig 10922

Class IIB

2

(+MHC-Y)

16

1

Un

Contig 1486 (-)

ENSTGUG00000013745

1

Un

Contig 3597 (-)

ENSTGUG00000016075

1

Un

Contig 12575 (-)

ENSTGUG00000015634

1

Un

Contig 648 (+)

ENSTGUG00000014620

1

Un

Contig 926 (+)

ENSTGUG00000017149

1

Un

Contig 3052 (-)

ENSTGUG00000014503

1

Un

Contig 11727 (+)

ENSTGUG00000015020

2

Un

Contig 395 (+)

ENSTGUG00000016844

2

Un

Contig 4424 (-)

ENSTGUG00000014905

3

Un

Contig 2943 (+)

ENSTGUG00000014233

4

Un

Contig 11297 (-)

ENSTGUG00000014649

ψ L

Un

Contig 3510 (-)

ENSTGUG00000015846

ψ M

22_random

279244-283106(+)

ENSTGUG00000017281

ψ M

Un

Contig 3181 (-)

-

ψ Q

7_random

92325-103474 (+)

ENSTGUG00000016701

ψ R

Un

-

ENSTGUG00000017139

ψ T

22_random

-

ENSTGUG00000017280

TAPBP

1

16

-

-

-

Blec1

1

16

Z

64162080 -- 64162784 (+)

ENSTGUG00000005208

NKr

1

16

Z

64155557 -- 64154733 (-)

-

BG

3

16

-

-

-

TRIM41

1

16

-

-

-

TRIM27

1

16

Z

64166328 -- 64164434 (-)

ENSTGUG00000005203

TRIM39

1

16

Un

Contig 15508 (+)

ENSTGUG00000014157

TRIM27.2

1

16

-

-

-

TRIM7

1

16

16_random

756 -- 1262 (+)

ENSTGUG00000015652

LAO

1

16

16_random

127,342-132,827 (+)

ENSTGUG00000016298

TRIM7.2

1

16

16_random

147414 -- 164815 (+)

ENSTGUG00000015672

KIFC1

1

16

22_random

7,798-8,481 (+)

-

Class IIA

1

16 Un

Un

Contig 28013 (+)

-

CIITA

1

14

14

6294135 -- 6303566 (+)

ENSTGUG00000004838

Ii

1

13

13

6774603 -- 6780145 (+)

ENSTGUG00000000882

B2M

1

10

10

-

ENSTGUG00000004607


Genes are listed in order according to their organisation on chicken chromosome 16. Duplicated genes are given a numbered Locus ID if they appear functional. Putative pseudogenes are marked with a ψ and given a lettered locus ID. Loci are classified based on sequence similarity such that identical sequences found in multiple places in the genome assembly are given the same Locus ID. Where Ensembl IDs have been assigned these are also given. Three genes outside of the MHC region but with a related function (CIITA, Ii, and B2M) are also included.

Balakrishnan et al. BMC Biology 2010 8:29   doi:10.1186/1741-7007-8-29

Open Data