Table 1 |
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|
MHC genes identified in the survey of the zebra finch genome assembly. |
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|
Chicken |
Zebra Finch |
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|
Gene |
# loci |
Chr# |
Locus ID |
Chr# |
Coordinates and orientation (+/-) |
Ensembl ID |
|
|
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|
CD1 |
2 |
16 |
1 |
12 |
36510 -- 39728 (+) |
- |
|
2 |
12 |
31218 -- 32904 (+) |
ENSTGUG00000003538 |
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|
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 |
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|
ψ L |
Un |
Contig 43472 (-) |
- |
|||
|
ψ L |
Un |
Contig 237 (+) |
- |
|||
|
ψ L |
Un |
Contig 5814 (+) |
- |
|||
|
ψ L |
Un |
Contig 29268 (-) |
ENSTGUG00000014179 |
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|
ψ L |
Un |
Contig 24227 (-) |
ENSTGUG00000015460 |
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|
ψ L |
Un |
Contig 19531 (-) |
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|
ψ L |
Un |
Contig 1325 (-) |
ENSTGUG00000016290 |
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|
ψ C |
Un |
Contig 237 (+) |
ENSTGUG00000015195 |
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|
ψ O |
16_random |
79190 -- 79374 (+) |
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|
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 |
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|
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 |
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|
3 |
Un |
Contig 2943 (+) |
ENSTGUG00000014233 |
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|
4 |
Un |
Contig 11297 (-) |
ENSTGUG00000014649 |
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|
ψ L |
Un |
Contig 3510 (-) |
ENSTGUG00000015846 |
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|
ψ M |
22_random |
279244-283106(+) |
ENSTGUG00000017281 |
|||
|
ψ M |
Un |
Contig 3181 (-) |
- |
|||
|
ψ Q |
7_random |
92325-103474 (+) |
ENSTGUG00000016701 |
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|
ψ R |
Un |
- |
ENSTGUG00000017139 |
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|
ψ T |
22_random |
- |
ENSTGUG00000017280 |
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|
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 |
|
|
|
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|
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. |
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|
Balakrishnan et al. BMC Biology 2010 8:29 doi:10.1186/1741-7007-8-29 |
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