Genomic organization and recombinational unit duplication-driven evolution of ovine and bovine T cell receptor gamma loci

Table 2 Repeats shared by two or more conserved blocks corresponding to rows 1–14: V8-1, V2-1, V9-1, V1, V5-1 and V5-2 intergenic regions and rows 15–47: cassette-specific J-C intergenic regions

No	Type^a	Position^b	V8-1	V2-1	V9-1	V1	V5-1	V5-2
1	*Sine BovtA2*	5' V	X			X(A2)	X(tA3)	X
2	*Sine MIR*	5' V	X(b)	X		X(b)	X	X(3)
3	*LTR MLT1H (C)*	5' V	X			X
4	*LTR MLT1H (C)*	5' V	X			X
5	*Line L1MD2*	5' V	X			X
6	*Line L1MD2*	5' V		X		X	X	X
7	*Sine BovtA2*	5' V	X			X
8	*GA-rich*	5' V	X	X		X	X	X
9	*Line BovB*	5' V	X		X		X	X
10	*Line L1M2 (C)*	5' V	X(MA8)	X(MA9)	X(MA9)	X	X	X
11	*MER5A*	3' V	X	X	X		X	X
12	*Sine BovtA2 (C)*	3' V		X		X	X	X
13	*Line L1M2*	3' V				X	X	X
14	*Sine MIR*	3' V		X	X
			TRGC4	TRGC2	TRGC3	TRGC6	TRGC5	TRGC1
15	*Sine MIRb (C)*	5' Jd			X		X
16	*AT rich*	5' Jd		X			X	X
17	*Line L1M5 (C)*	5' Jd	X(MC)	X	X(MD)			X
18	*Sine BovtA3*	5' Jd		X			X(tA2)	X
19	*Line L2 (C)*	3'Jd	X	X	X	X	X	X
20	*Sine MIRb (C)*	3'Jd	X	X	X	X	X	X
21	*Sine BovtA2*	3'Jd	X		X
22	*Line L4 (C)*	3'Jd	X	X	X	X		X
23	*Sine BovA2*	3'Jd				X(tA3)	X
24	*AT rich*	3'Jd				X	X
25	*Sine MIRb*	3'Jp	X	X	X		X	X
26	*Sine BovtA2*	3'Jp		X				X
27	*CHR-L*	3'Jp	X(2B)	X				X
28	*Line L1 Art (C)*	3'Jp	X					X
29	*CHR-L*	5'C		X				X
30	*Sine BovtA3*	5'C		X			X	X
31	*Sine MIRb*	5'C	X	X(m)	X	X	X	X
32	*Sine BovtA2*	I intr. C				X	X
33	*Sine MIRb*	I intr. C	X	X	X	X	X	X
34	*Line L4 (C)*	I intr. C	X	X		X	X	X
35	*Sine BovtA2*	I intr. C		X	X	X		X
36	*Sine CHR-2 (C)*	I intr. C	X		X(B)	X(B)
37	*Sine BovA2*	I intr. C		X			X
38	*Sine MIRb*	I intr. C	X	X	X	X	X	X
39	*Line L2 (C)*	I intr. C	X				X
40	*Sine MIRm (C)*	I intr. C		X				X
41	*Sine BovtA1*	II intr.C			X	X
42	*Sine MIRb (C)*	ult.intr.C	X MARS	X		X(m)	X	X
43	*Sine MIR*	ult.intr.C	X	X			X(b)	X(b)
44	*Sine BovA2*	ult.intr.C		X	X(tA2)	X(tA2)		X
45	*Sine MIR*	ult.intr.C		X	X	X		X
46	*Sine MIR*	3'C	X	X	X	X	X(m)	X
47	*Sine MIR (C)*	3'C			X	X	X(b)

^a Type of repeat as reported in RepeatMasker output file. (C) indicates the opposite orientation of the repeat. ^b Repeat position. Jd e Jp signify respectively the distal or the proximal J segments with respect to the C gene of each cassette. The cassette-specific J-C intergenic regions include the sequence spanning from 5' of distal J segment and 3' of C gene (exon 3) for each TRGC cassette.

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