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The IMGT reference sequences for the polymorphism in the HLA-A introns 4, 5, 6 and 7 are selected from [1].

Polymorphisms in the introns 4, 5, 6 and 7 of the HLA-A gene, are presented in relation with the HLA-A alleles and with the HLA-A serological families.

Based on phylogenetic relationship of exons, HLA-A serological families can be grouped into two major lineages: the HLA-A2 lineage which comprises the A2/A28, A10 and A19 families and the HLA-A3 lineage which consists of the A1/A36, A3, A9, A80, A11, A30 and A80 families.

Polymorphisms in the HLA-A introns 4, 5, 6 and 7

HLA-A
lineages		 HLA-A
serological families		 HLA-A alleles (1)
Introns 4, 5, 6 and 7 (2) IMGT reference
sequences (3)		 Sequences from the literature
(3)
HLA-A2 A2/A28 A*02 HLA-A*02011 (4)
HLA-A *0202
*0203
*0205
*0206
*0207
*0211
*02172
*0225
*0227 (nd)
*68011
*6802
*6813 (nd)
*6901
HLA-A*68012 (4)
A10 A*25 HLA-A*2501 (5)
HLA-A *2601
*2603
*4301
*6601
HLA-A*3402 (5) HLA-A*6602
A19 A*29 HLA-A*2901 (6) HLA-A*2902
HLA-A*31012 (6)
HLA-A *3108 (nd) (1)
*3301
*3303
*3305
HLA-A*3201 (6)
HLA-A*7401
*7402
*7403
HLA-A3 A1/A36 A*01 HLA-A*01011 HLA-A*3601
A3 A*03 HLA-A*03011
A9 A*23 HLA-A*2301
HLA-A *2402101
*24031
*2405
*2407
*2410
*2417 (nd)
*2418 (nd)
A11 A*11 HLA-A*1101 (7) HLA-A*1102 (7)
A30 A*30 HLA-A*3001 (8)
HLA-A*3002 (8)
HLA-A*3004 (8)
A80 A*80 HLA-A*8001

(nd): not defined serology.

EMBL/GenBank/DDBJ accession numbers of the IMGT reference sequences for the HLA-A introns 4, 5, 6 and 7 [1]

IMGT reference sequences Intron 4 Intron 5 Intron 6 Intron 7
HLA-A*02011 AJ458204 AJ491722 AJ490827 AJ490942
HLA-A*2501 AJ458226 AJ491744 AJ490849 AJ490964
HLA-A*2901 AJ458228 AJ491746 AJ490851 AJ490966
HLA-A*01011 AJ458203 AJ491721 AJ490826 AJ490941
HLA-A*03011 AJ458214 AJ491732 AJ490837 AJ490952
HLA-A*2301 AJ458217 AJ491735 AJ490840 AJ490955
HLA-A*1101 AJ458215 AJ491733 AJ490838 AJ490953
HLA-A*3001 AJ458230 AJ491748 AJ490853 AJ490968
HLA-A*8001 AJ458250 AJ491767 AJ490873 AJ490988
IMGT notes:
(1) Alleles designations are those used in [1], except for HLA-A*2416, which is now designated as HLA-A*3108 [3].
(2) The nine polymorphisms of the introns 4, 5, 6 and 7 are designated by the two first numbers of the IMGT reference sequence "first" HLA-A allele in each serological family. These "first" alleles correspond in the table, to the first line of each serological family.
(3) EMBL/GenBank/DDBJ accession numbers from [1] are given for the IMGT reference sequences. Accession numbers of the other sequences are available in [1]. Nucleotide differences between the IMGT reference sequences "first" HLA-A alleles and the other IMGT reference sequences are shown in notes (4), (5), (6) and (8). Sequences from the literature refer to alleles whose sequences of the introns 4, 5, 6 and 7 are identical to those of the IMGT reference sequences.
(4)
Intron 7
A*02011 g41
A*68012 a41

(5)
Intron 6
A*2501 g100
A*3402 c100

(6)
Intron 4 Intron 5 Intron 6
A*2901 g34 a14, c203 c17, g22, c24, t25, g28, g29, c32, t33
A*31012 g34 g14, t203 a17, c22, a24, a25, a28, a29, a32, c33
A*3201 c34 a14, c203 c17, g22, c24, t25, g28, g29, c32, t33
(7) Both A*1101 and A*1102 alleles have a nucleotide change in intron 5 (g19>a) which creates a second DONOR-SPLICE and results in a transcript with an elongated cytoplasmic region [2].
(8)
Intron 5 Intron 7
A*3001 g207, t222 g41
A*3002 a207, t222 a41
A*3004 a207, a222 g41
References:
[1] Elsner, H-A. et al., Immunogenetics, 54, 447-462 (2002).
[2] Tijssen, H.J. et al., Tissue Antigens, 55, 422-428 (2000).
[3] Marsh S.G.E et al. Tissue Antigens, 60, 407-464 (2002).