Table 5.
Species-specific interspersed elements found by the comparative genomic analysis of the casein cluster in camelids (A, alpaca; B, Bactrian; D, dromedary; F, feral camel) and listed in order 5’ > 3’ as they appear in the cluster. Repbase was used as repeat database. Positions are indicated according to the corresponding GenBank sequence (wild feral: AGVR01039100.1; Bactrian: NW_011517196.1; dromedary: NW_011591251; alpaca: KN269544). The direction of the repeat fragment is indicated as d = direct or c = complementary; Sim, similarity with repeat element in the database; and Pos/Mm, Ts column is a ratio of mismatches to transitions in nucleotide alignments. The closer Pos/Mm, Ts number is to 1 the more likely is that mutations are evolutionary.
| Species | Position | Name | Class | Dir | Sim | Pos/Mm : Ts | Size (bp) | |
|---|---|---|---|---|---|---|---|---|
| A | 345745-345817 | ERV3-1_SSc-I | ERV | c | 0.785 | 2.00 | 72 | |
| 352418-352502 | ERV44_MD_I | ERV | c | 0.712 | 1.47 | 84 | ||
| D | Compl. to | 485496-485356 | CHARLIE8 | DNA/hAT | c | 0.647 | 1.59 | 140 |
| Compl. to | 478096-478030 | miR | SINE | c | 0.806 | 1.22 | 66 | |
| F | 268407-268493 | THER2 | SINE | c | 0.755 | 2.00 | 86 | |
| A | 369205-369268 | MER4BI | ERV | c | 0.822 | 2.00 | 63 | |
| 372430-372493 | L1-2B_EC | LINE | d | 0.790 | 1.50 | 63 | ||
| 381127-381183 | MARINER4_MD | Mariner | d | 0.836 | 1.00 | 56 | ||
| B | Compl. to | 7053559-7053474 | MER35 | MER | d | 0.717 | 1.58 | 85 |
| A | 391846-391888 | L1A-2_MD | LINE | d | 0.809 | 1.17 | 42 | |
| 395574-395643 | Zaphod3 | DNA/hAT | d | 0.760 | 1.18 | 69 | ||
| 408816-408940 | ERV3-5-EC_LTR | ERV | c | 0.830 | 2.11 | 124 | ||
| F | 310230-310295 | L1-2_Vpa | LINE | d | 0.750 | 1.67 | 65 | |
| A | 413499-413572 | HAL1-3_ML | LINE | c | 0.783 | 1.50 | 73 | |
| 417674-417832 | L2 | CR1 | d | 0.652 | 1.47 | 158 | ||
| 417888-418114 | L2 | CR1 | d | 0.654 | 1.83 | 226 | ||
| D | Compl. to | 426349-425998 | LTR2_Vpa | ERV | d | 0.758 | 4.61 | 351 |
| A | 422684-422764 | LTR28_OC | ERV | c | 0.707 | 1.62 | 80 | |
| 426397-426425 | SQR2_MM | Sat | d | 0.931 | 2.00 | 28 | ||
| 427755-427846 | L1-2_Vpa | LINE | d | 0.768 | 1.80 | 91 | ||
| 451056-451088 | HERVK3I | ERV | d | 0.882 | 1.50 | 32 | ||
| D | Compl. to | 383725-383659 | SloEFV-I | ERV | d | 0.776 | 1.83 | 66 |
| A | 465703-465770 | MER104B | DNA | c | 0.753 | 1.78 | 67 | |
| 468337-468372 | ERV2-1-I_Opr | ERV | c | 0.865 | 1.00 | 35 | ||
| 471920-471998 | RMER3D-int | ERV | d | 0.782 | 1.83 | 78 | ||
| 478503-478578 | LTR16 | ERV | c | 0.701 | 1.69 | 75 | ||
| 480865-480899 | SINE_VV | SINE | c | 0.888 | 1.50 | 34 | ||
| F | 393221-393292 | L1-1H_Cpo | LINE | d | 0.833 | 2.00 | 71 | |
| A | 493574-493639 | MER28 | Mariner | d | 0.791 | 1.44 | 65 | |
| 502950-503003 | RLTR17B_Mm | ERV | c | 0.763 | 1.33 | 53 | ||
| 505352-505434 | RLTR17_MM | ERV | d | 0.765 | 1.56 | 82 | ||
| B | Compl. to | 6936860-6936781 | ERV36_MD_I | ERV | d | 0.779 | 1.71 | 79 |
| A | 509996-510114 | PRIMA4_I | ERV | d | 0.736 | 1.85 | 118 | |
| B | Compl. to | 6933341-6933305 | RLTR25_MM | LTR | c | 0.8611 | 2.00 | 36 |
| F | 412370-412416 | L1-3_TS | LINE | c | 0.847 | 9.90 | 46 | |
| A | 519191-519256 | L1MdV_II | LINE | c | 0.761 | 1.44 | 65 | |
| D | Compl. to | 328118-328009 | L1MAB2_ML | LINE | d | 0.684 | 1.48 | 109 |
| A | 519318-519379 | ERV2-3_STr-I | ERV | d | 0.796 | 1.50 | 61 | |
| 524222-524291 | UCON28c | Int. Rep. | c | 0.843 | 2.50 | 69 |