Citing these figures: Spiesser T. and Lefranc M.-P., Polymorphism by insertion/deletion between human TRBV4-2 and TRBV7-2. IMGT Repertoire on-line, IMGT the international ImMunoGeneTics information system® http://www.imgt.org

Haplotype representation

Most 3' (first line) and most 5' (second line) limits of the extent of the insertion (haplotype A)/deletion (haplotype B)
Recombination breakpoint areas (rectangles, third line)		 Schema L36
Haplotype with insertion (L36092)
Haplotype A: TRB LocusRepL36092
Haplotype with deletion (L36190)
Haplotype B: TRB LocusRepL36190

Extent of the insertion/deletion: 21 kb (21,659 bp)

The deletion in haplotype B probably results from an homologous recombination event which occurred between the two duplicated regions of haplotype A (shown by rectangles, on the third line, and in yellow in the map). The precise positions of the homologous recombination breakpoints cannot be determined inside these areas owing to the high similarity between the duplicated sequences.
Genes are represented by the V-EXON (L-PART1 not shown).

Haplotype description

A polymorphism by insertion/deletion of 3 genes between the TRBV4-2 and TRBV7-2 genes has been described in the human TRB locus [1,2]. It corresponds to haplotype A (21 kb insertion, L36092) and haplotype B (21 kb deletion, L36190). These haplotypes A and B correspond to the insertion/deletion of the pseudogene TRBV3-2, the functional TRBV4-3 gene and one gene belonging to the TRBV6 subgroup.

Arbitrarily as the two genes are highly homologous, the TRBV6-3 gene is described as the result of the duplication of the TRBV6-2 gene, and present in haplotype A (with insertion) or absent in haplotype B (with deletion). The 6kb duplicated and highly homologous regions encompassing the TRBV6-2 and TRBV6-3 genes in haplotype A and the TRBV6-2 gene in haplotype B are shown in yellow.

If haplotype B indeed results from a deletion which occurred after the TRBV6-2 gene duplication, the recombination can have occurred at any homologous position of the 6kb duplicated regions, either upstream or downstream of the V-EXON, or within the V-EXON. Assignment of the gene name TRBV6-2 to the TRBV6 subgroup gene in haplotype B follows the rules of the nomenclature based on positions in the locus [3,4]. It does not mean that the recombination occurred necessarily downstream of the TRBV6-2 gene.

TRBV gene positions

IMGT/LIGM-DB
accession numbers		 IMGT Gene name Positions of the V-EXON V-EXON length
(bp)		 Distance between the V-EXONs
(bp)
L36092 TRBV4-2
TRBV6-2
TRBV3-2
TRBV4-3
TRBV6-3
TRBV7-2		 138078..138531
141898..142330
151879..152044
155338..155791
163579..164011
167212..167708 		453
433
165
453
433
496 		3367
9549
3294
7788
3201
L36190 TRBV4-2
TRBV6-2
TRBV7-2 		1725..2178
5412..5843
9043..9525
 453
431
482 		3234
3200

Restriction sites in L36092 (red) and L36190 (blue)

Upstream of TRBV6-2 (138078..142330)

L36092_138078_142330

Upstream of TRBV6-3 (159758..164011)

L36092_159758_164011

Upstream of TRBV6-2 (1725..5843)

L36190_1725_5843

Downstream of TRBV6-2 (142328..145528)

L36092_142328_145528

Downstream of TRBV6-3 (164009..167214)

L36092_164009_167214

Downstream of TRBV6-2 (5841..9045)

L36190_5841_9045

Legend:
AT-Ins: Insertion of a region rich in AT from 140525 to 140664 in L36092 (length 139 bp).
B: BamHI G∧GATCC
R: EcoRI G∧AATTC
H: HindIII A∧AGCTT
K: KpnI GGTAC∧C
P: PstI CTGCA∧G Pv: PvuII CAG∧CTG
S: SacI (SstI) GAGCT∧C
T: TaqI T∧CGA
Xb: XbaI T∧CTAGA
X: XhoI C∧TCGAG

Notes:
Genes are represented by the V-EXON (in green) (L-PART1 not shown). TRBV6-2 and TRBV6-3 V-EXON are split on two lines.
Numbers above the restriction sites indicate the position of the nucleotide preceding the enzyme cuts in the restriction enzyme sites (for example position of G in an EcoRI site). No BamHI and XhoI sites were found in the areas shown in the maps.
Numbers below the map indicate positions in L36092 and L36190. L36092 is only available in IMGT/LIGM-DB (Germline gene table: Human TRBV).

References:
[1] Zhao, T.M. et al., J. Exp. Med., 180, 1405-1414 (1994) PMID: 7931073
[2] Rowen, L. et al., Science, 272, 1755-1762 (1996) PMID: 8650574
[3] Lefranc, M.-P., Nomenclature of the human T cell receptor genes, Current Protocols in Immunology, A.1O.1-A.1O.23 (2000).
[4] Lefranc, M.-P. and Lefranc, G., The T cell receptor FactsBook, Academic Press, London, 398 pages (2001) ISBN:0124413528.