Novel LTR in MuERVC-C105 The novel LTR of MuERVC-C105 is shown in alignment with its only strong match in GenBank: a previously unrecognized LTR upstream of the fv1 gene. The mmfv1 LTR is in the wrong orientation to be an LTR of the putative retroviral-like sequence from which fv1 was derived. The mmfv1 LTR shows no similarity 5' of the inverted repeat (IR) and is presumably a 5' LTR or a solo LTR. The last 45 bases of mmfv1 stop matching. [ie. the 1st 45 bases of the GenBank entry; the sequence shown below is the complement of the GenBank entry]. The coordinates of the MuERVC-C105 element differ from GenBank entry MUSC105 by the excision of the 873 bp LINE-1 insert upstream of this position. Pcgtr is the most similar of the recognized LTRs to the MuERVC-C105 LTR. It is a version of LTR found on GALV. Similarity is confined to the R and U5 regions. A tandemly repeated element unique to MuERVC-C105 and mmfv1 is indicated. The likely position of the TATA box by comparison to MoLV LTRs is also indicated. 5930 5940 5950 5960 5970 5980 mmfv1 (-) TGAGACCCCGACTTAGAGCGTTTCTCCCTGGAAGGTAAAGCCCCTAGACGTTCCCCAAGC ||||||||| ||||||||||||||||||| |||||||||||||| || ||||||||||| MuERVC-C105 TGAGACCCCAACTTAGAGCGTTTCTCCCTAGAAGGTAAAGCCCC.GGATGTTCCCCAAGC 4850 4860 4870 4880 4890 4900 pcgtr >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> <---------- IR 5990 6000 6010 6020 6030 6040 mmfv1 (-) TTGTTTTCCCTGATCTTCAAAA.TGCAGCCAGAAAAAAGCTCTTTGTTCTCTATAGCCAC |||||||||||||||| |||| | |||| ||||| ||||||||||||||||||||||| MuERVC-C105 TTGTTTTCCCTGATCTCTAAAAATTCAGCTAGAAAGAAGCTCTTTGTTCTCTATAGCCAG 4910 4920 4930 4940 4950 4960 pcgtr >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 6050 6060 6070 6080 6090 6100 mmfv1 (-) AAAAAGCCTTTTGTTTT.CTATACTTTACAACCAGAGATGCCTACCTTCCTGTGCCAATG |||| | ||| | || ||||||||||||||||||||| ||| ||||||||||| | | MuERVC-C105 CAAAAAGCCTTTTTGTTTCTATACTTTACAACCAGAGATACCTGCCTTCCTGTGCTGAGG 4970 4980 4990 5000 5010 5020 pcgtr >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 6110 6120 6130 6140 6150 6160 mmfv1 (-) ACACGGAGATAAAAATTCAGAAAGAACTCACTCCCCACTCCTGCCTTGTAAATTTCACCA ||| |||||||||| ||||||||||||||||| ||||||||||||||||||||||||||| MuERVC-C105 ACATGGAGATAAAATTTCAGAAAGAACTCACTTCCCACTCCTGCCTTGTAAATTTCACCA 5030 5040 5050 5060 5070 5080 | || | | | | | pcgtr >>>>>>>>>> TGAAAGAAGTGTTTTTCAAGTTAGCTGCAGTAACGCCATTCATAAGG 1 10 20 30 40 6170 6180 6190 6200 6210 6220 mmfv1 (-) AGGACACCCGGAAGAGAA.....CTCCTCCCAACTCTTCCTAACTCCTCCCAATCTCCTC | ||||||| |||||||| ||||| | ||||| ||| ||||| |||||| |||||| MuERVC-C105 AAGACACCCAGAAGAGAAGAACTCTCCTTCTAACTCCTCCCAACTCTTCCCAA.CTCCTC 5090 5100 5110 5120 5130 5140 --------->--------->---------->-- | | | || | | || | |||| | || pcgtr CACGCCCAAAGCTAAAGGTTAAAGAAGAAAAAAACCGGGCCAAACAGGATATCTGTGGTC 50 60 70 80 90 100 6230 6240 6250 6260 6270 mmfv1 (-) CCAAGTCCTCCCAACTCTTCCTAACTCCTCCTAACTCT.CCTAACTC..CTCCCAACTCT |||| | |||||||||||||| ||||||||| |||||| || ||||| |||||||||| MuERVC-C105 CCAACTTCTCCCAACTCTTCCCAACTCCTCCCAACTCTTCCCAACTCTCCTCCCAACTC. 5150 5160 5170 5180 5190 5200 ------->--------->--------->--------->----------->-------->- | | | | | | |||||| | pcgtr ATACACCTGAACCCGGCCCAGGGCCAAACACAGATGGTTCCCAGAAATAAAATGGGTCAA 110 120 130 140 150 160 6280 6290 6300 6310 6320 6330 mmfv1 (-) CCTCCCAACTCCTCCCAACTCTTCCTAACTCCTCCCAACTCTCCTCCCAACTCTTCCTAA ||||||| ||||| MuERVC-C105 .CTCCCAATTCCTC.............................................. 5210 ----------->---------------->----------->----------->------- | | pcgtr CAGCAGTTTCAGGGTGCCCCTCAACTGTTTCAAGAAACTCCCATGACCGGAGCTCACCCC 170 180 190 200 210 220 6340 6350 6360 6370 6380 6390 mmfv1 (-) CTCCTATCAACTCTCCTCCCAACTCCTCCCAATTCCTCAGCTAGCTGTTAAAAGCCCCCT | ||| ||||||||| | ||| MuERVC-C105 ......................................ACCTAACTGTTAAAATCTGCCT 5220 5230 --->----------->--------->-----------> TATAA box | | | pcgtr TGACTCTATTTGAACTTAACCAATCACCTTGCTTCTCGCTTCTGTACCCGCGCTTTTTGC [1-459] 230 240 250 260 270 280 6400 6410 6420 6430 6440 6450 mmfv1 (-) AACTGTCACCACTCAG.GGTCGAACTCCCCTGCCCTGCACAATAGCACAAGTCATTAAGCT | |||||| |||||| || ||||||||||| | |||| | | | | | | MuERVC-C105 A.CTGTCAACACTCAC.AGTTGAACTCCCCTGGCATGCAAGGTGGAGGGACTTCATCCTCA 5240 5250 5260 5270 5280 5290 |||| | || | | || | | | |||| | | | | | pcgtr TATAAAAGGAGCTCAGAAATTCGGCGCGCCAGTCTTCCAAGAGACTGAGTCGCCCGGGTAC 290 300 310 320 330 340 <--- R region 6460 6470 6480 mmfv1 (-) TTAAATTAGCATGCTGCACTAGT<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< | | | || | MuERVC-C105 GCTAGCTGATAATAAAACCTCTTGGAGTTTGCATCAGGTGTGATTTTCTCTCGGGACATT 5300 5310 5320 5330 5340 5350 | | |||||||||||||| ||||||| | || | |||| | | | || pcgtr CCGTGTGATCAATAAAACCTCTTGCTACTTGCATCCGAAGTCGTGGTCTCGCTGTTCCTT 350 360 370 380 390 400 AATAAA poly(A) site R region -----> mmfv1 (-) <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< MuERVC-C105 GGGGTGTTGACCACCTCATCCCAGGACTTGAGTGGAGTCCCAGCATCAGGGGGGTCTTACA 5360 5370 5380 5390 5400 5410 ||| | | || | | |||| || ||| | | |||| ||| | pcgtr GGGAAGGTCTCCCC..........TAATTGATTGACCGCCCGG..ACTGGGGTCTCT..CA 410 420 430 440 450 IR ------------->