Long terminal repeat retrotransposons of Oryza sativa

McCarthy, Eugene M; Liu, Jingdong; Lizhi, Gao; McDonald, John F

doi:10.1186/gb-2002-3-10-research0053

Table 1 Summary of rice LTR retrotransposons characterized in this study

From: Long terminal repeat retrotransposons of Oryza sativa

Family	Pre-existing name(s)	Accession number of exemplar	Location	Chromosome number	LTR length (bp)	Inserted element length	TSR	%LNI (mean for family)	Approximate copy number (haploid genome)^‡
Osr1	Tos14/Rire15	AC023240	100410-106807	10	965	6,398	AGTCC	98.1	250
Osr2		AL442110	95121-100070	4	267	4,950	ATATT	98.5	<50
Osr3		AF458765	51-5250	?	146	5,200	CATTC	99.3	50-100
Osr4		AB026295	160208-165872	6	350	5,665	GTTAC	98.9	<50
Osr5		AC021891	56044-62135	X	477	6,092	TACAG	96.2	<50
Osr6		AP001366	57569-62773	1	440	5,205	ACCTG	99.8	<50
Osr7		AP002538	44996-53915	1	1608	8,920	AGTTT	98.8	<50
Osr8		AC021891	65191-74406	X	1220	9,216	TAAAT	97.2	1100
Osr9 ^*		AP000969	25869-28634	1	ND	ND	ND	ND	50-100
Osr10 ^*		AC069324	137920-139740	10	ND	ND	ND	ND	400
Osr11 ^*	Rire1	AP003853	96975-98088	1	ND	ND	ND	ND	<50
Osr12		AC073166	104289-109024	10	221	4,736	AGAAG	99.7	<50
Osr13	Tos5	AC073405	72924-79364	5	968	6,441	TATGT	99.6	650
Osr14	Tos1/Tos4	AC069324	8821-17191	10	319	8,371	CTCCC	97.6	350
Osr15	Tos12	AP002867	127118-132180	1	262	5,062	GCTTC	94.5	250
Osr16	Tos6	AP002845	42644-49551	1	300	6,908	TGCTT	97.9	<50
Osr17		AC018727	102539-96583	10	501	5,957	TCATC	99.6	50-100
Osr18		AC068654	23423-25036	X	ND	ND	ND	ND	<50
Osr19		AC069300	73013-77731	10	205	4,719	GGGAC	99.5	50-100
Osr20		AC084406	8749-14200	3	286	5,452	TTATA	97.9	50-100
Osr21 ^*	Tos17	AC087545	81711-84269	10	ND	ND	ND	ND	50-100
Osr22		AC074283	24546-19810	10	191	4,647	GAACC	97.9	50-100
Osr23		AP002843	144255-139782	1	209	4,774	AGGAT	99.5	50-100
Osr24		AC016781	25997-30858	ND	221	4,852	CCGAG	98.6	<50
Osr25		AP001278	28729 35569	1	417	6,841	TCGAG	98.9	500^§
Osr26	Rire2	AP001111	59274-70587	5	440	11,314	GATAT	97.9	500
Osr27	Rire9	AP000399	75139-88038	6	1087	12,900	AATAT	99.0	900
Osr28		AP002539	139654-121650	1	2195	18,005	GTTAT	99.0	<50
Osr29		AP002747	78609-87615	1	656	9,007	GGAAC	96.0	550
Osr30		AC078891	52683-65684	10	1507	13,002	ACTTT	97.2	1500
Osr31	Rire7	AP003054	102778-110180	1	787	7,403	AAACC	99.9	<50
Osr32 ^*		AP002820	111559-12278	1	ND	ND	ND	ND	50-100
Osr33	Rire8	AP002864	35539-47557	6	3009	12,009	CACAC	99.1	550
Osr34		AF111709	25889-38685	5	3292	12,797	AGAAA	99.4	450
Osr35		AC068924	94924-100611	10	423	5,688	CTAAT	98.3	<50
Osr36		AP001551	59722-64876	1	319	5,155	GGTCA	98.4	<50
Osr37	Rire4?	AC068654	2534-6969	X	794	4,436	CTTGA	98.9	600
Osr38 ^†		AF458766	31-5535	?	332	5,525	TGAGG	96.2	<50
Osr39		AF458767	51-5267	?	368	5,217	CAAAG	97.6	<50
Osr40		AC020666	65731-77151	10	564	11,421	ACATG	98.3	600
Osr41		AP003631	27347-43001	1	518	15,655	GGTTC	97.7	300
Osr42		AF458768	51-5655	?	358	5,605	ATGTC	99.9	<50
Osr43		AP000815	77117-78910	1	291	1,794	CTGAT	98.6	<50
Osr44		AP000364	41541-42747	8	148	1,207	AACAA	99.9	<50

^*Location given is for an example RT in the GBRD (no full-length element was identified for this family). ^†As a full-length element is known in the MRD, the TSR and lengths of the LTR and element (columns 5-7) are taken from an element in the MRD while the location (if given) in columns 2-4 refers to an RT in the GBRD. ^‡Percentages based on number of hits using a sample LTR from each family as query to search the MRD. ^§N. Jiang and S.R. Wessler (unpublished work) suggest that if pericentric DNA (which is largely heterochromatic) is taken into account, Osr25 elementsexist at a higher copy number (~1,000 copies in the entire genome) than our survey, based largely on euchromatic sequences, would suggest. ND, not determined.

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