Table 1.
Summary of rice LTR retrotransposons characterized in this study
| 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.