ZRdb KZFP & Repeats
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LTR_LTR49-INT

  • Name
    LTR49-INT
  • Repbase
    HERV49I
  • Type
    LTR
  • Emergence
    74.0 Mya
  • Dfam Id
    DF0000539
Description :

Associated LTR is LTR49. It belongs to the MER4-int group of non-autonomous elements without apparent matches to ERV coding regions. Onecopy, present on chromosome 22, is flanked by LTRs (U62317, positions11281-10708 and 988-110) that are only 4% divergent from each other.Presumably, such a low divergence between two LTRs from the oldretrovirus (the expected divergence is >20%) is a consequence of geneconversion.
Consensus sequence The consensus sequences obtained from Dfam are derived from the seed alignment using a specialized caller. :
tttggcgctgtgagcaggatnaccaaagccgctctgctcttctggaagccgcagtnaagggaacccaggacctgacaagccggcagaagggtaagaatttcttaccagccaggctcccggcctctctctgtggaatccggtcgagcggacggtaaaaatcactgtctctttttcctctncaaaattttgattaatgggagaaaaggatttgtgtgactagtcttgggtgtagcgactctggtgtactttttggtactttgtggtatgaatattcatattgtttgatccctttcctcccagaaatagtttttccttgtctttgtctttctgtgttgttctgtcataaagaggggtaccggatgaggttccctctcgtcttgttttatgtccttgagagcttgacttgtgaccaagtgggagcactctctcttggtctccgccatccggggggcgtgattttcgggtcacgtcaggtggccagtctgaaaatggctgggaacccgagacacgtaagattttaagcagcactttttgttccgaatgtgtcaagctctcgggagagtttgtcttaagaagtcccatccataaggggcttttgtcgtctcaacccttgttgcctggttagtcctgggaaagtccaatcccaggagggcctacccggtgtcacagattaacgggtctgtgactggcggccccccacaaatttgtgggntaccggaggcaccgtacgcacaaacaccatccttaaccgtctgtggcaacaagagtcttttgctatcttagcctattcctgggagtgaattttttgggggatcntngggattgcctcttctatgccctctctaaacctggaaaattacntcctgggctttccatgaagaggcttattggattgagtcgctattggaataagtacaccattggaaattctaatcgtcagtggccaaaagatggatcctttaaattagaaagactcctaaatttnaaaaaaaaaaagattttagagatctcttattctaaacaattgccttatgtatttatgggaagatcaaatttnagaaagacacataatagtgtcatggctagccttagaaattctcttgacaaaattaaagagcaaaaatctgacctaaaacaaagttaaaatcctttgtacgctcaaactgcctgctttggatccctgcgggattnacaatgaaggccgctccaccttgtagtctagtagttaaaattccgcgctttcaccgccgtggcctgggttcgattcccggtcagggaaccagtcccttttggtttgatatttgtgtgacttttgacttttggggtacccatttgttattgatccttttcccttccatggacagcttttgatttcctttctttgagctgtctttggggatggttctggatcttgtgaggactgctttgcacctctttggagatgcctcgtgcgtccttggttaagtcataaccttggttaaggcttattggttttggtgagtcacttggaaggtacctttggtttaaaaaaaaagttcaaaagccaggaatatcggctgtttgtcccggctaaaatctgataataagagatttgaaaggatttttnaagagctctatggtcagaagtcagcttaattaaaancgctgatattcaggctatatntttacagccttttctcttttggatcctgtttctgggaatttttttcagtcgactgaaacccttttaaattatatgtttggtccctctgtttgcttcctttcttggcatgatttttgctgagaaaaatgtaaaacttcattggccttttagaagcttaaaatctccccaaattggctcctctaagacttgttcttccatttacttctactcctccctgctcctccttcctctttgccatcttcggtaccacatgaagagatctagaggggacttctaacgactctgagaccccttgaggaacacagaaaaaggcgccacncaccccctttttggggtcttctgtcttcctcgtggagtcccaagagtcatgggcaggttcctctcaggtctaaagctctgctctcttttgcattgcgttacctgatctctttggctttgggggtaccagggattactttgtactgtgagagagnacttgacctttgtgtgtgcgatggctggcgagtcactggcgagagctgncagttttggaggtggctgacagcggttgcagtgaatggttattactgcagggggctactcgtttctttgcgcgtttagataagaaaggcgcggtttgaacacttggaggctgtgggaacactcgccaccgagggataagactcctggggtgggctgatcgctgtgggtccccaccggcctcgggggaatgtctttgtagcgaggtgcactgtggaagcgttgcgcggcccggtcccgtgcgtttccctcttttgggggacccgggattcagtgtaaaagtgggatccttgatttttaaagatctagatgctctgccttccagctgcgcctgcttttccatatttaaatattaggccctaaactgcaaatgctttgttggcctgttcgttaatgggctccgccctgagctcagtggtccagttggaaaacggagactaaattagaagctacctatctaaataaaattggtctccttataaaatcctgtggtaaattcctatgattttgtgttaccttggcatccatttttaatcttcctnctaacacacccaaataaaagcttaaattctctctctgtgctttgagatgtaaatttgctaccctgttttctctaaaactcggtaagggcttcggccatgtgggacagataaacttaacttgttccatttacagaggcacagtttaatcaactgtccttttaaactagtgagttttaccngtctcatggctaaaattttaaaatcaaagctataaagtctttatttgtgtctgtatttttatgtgtacatgtctgtttgtatattgtctacatggtaccaaattgacttataaataaatgagtactcataaattaagtaaataagcccaaatgcttttcaagttcacgtgactttagtaatctttggtaaataaagctagtntttaaaattgttggtaaaataaaatacgtcttcagaatntaattcagacatttttgcctgggtctactggtcagacaggtttatgctgtctctgctagatgttttaaggtcataaaactgttgcttctgtgatatttttgaatacttgcttgatttgtctgtgagcttatgtctttggttttgagcctttagattctggggtctagacaagtggccatggtgaggcctggggacacncgtgngccncatcctccctggcccagctgtgcctcctggccatgctgggaggggtcggatcctccaggcattgtcttcacagctctgtcctttgtcctgggctctgcatctncggtacataattaaaattgcttacttcctaggtttttcactagaaaataagggttactaagagttaacattgtaattaatatatgtanattaaaactactagatataagagaaatctgtatgcaaagtgtataaaaaagtaggagtgtttttgtaaggaaggttataaaagtggtttttgttaaaaagtaattttgcctagtttagaggtttttaaagttgttttaaattaaaaataaaantaaatatagaaaanttaaaaattataagaggttataaaagagtttatgaaaatcttatgcgtgtggtcaaaactgattgagattagatttgtttataaggttttattaaaattagctttagcattaataatacactgatgcaaaggtaaaatttggttttctcttttgaacaagattttcgtgtagtattaataaaagatttttgtttacttttgagtaaactgcaaaaaaagagggagagagagacagattcngtttgcctcatgctgtctttattaggtcttttgattgtttgggaaacagtctcctctctatcaaagagtaaaggtttttgctttttgaaatctttgaattatcactttggctaaatgaatgactattattttacagtgacctgtgatcctattttgatcaagtgttttaaacctttgatatttgacaaacttcccaaaatcaaatttcaaattctaaattaagtcttttgacctcaaactaacttttggatattagggcccctggaagtccaagagagacatattaggcttatttggtatgttaaaatcatacgaaacattgtcaaataagaaatggtgtttaactttctttgagttatatttgtataaatgtgttattaatatgtgttccaaaattgtatgagattcctaaaantctgatatgtcttggtatatgttatcagtcataattatgattattatgttaaattgttgtatgccacagaaataaccaaatttccttgtcaattgcgtctttaaccatggctattctaagncttttgtcatccacagacaanttattgttttactttgattcttctcnaaaagcgntttacaatcagctacagtccaaaatttgctttttcttcaaggaaattcatggaaaggactctgacaagtactcttgaatacaggtttctgataactttggagatcataccattggactaggtaaaaacttccagaactctaatnaaaaagctgatgngttcatgaagattgctaacccaacatcaagcagaacaagaattaattacatgggactgaactgatagaggactgaaataattttttnatgacttttttgtttgaaacattgctgattctttttatgttttgttttccagagtcaagaaaacttttttcttttgagctatttatagcttacagcaattgggtaaagtatacttttgtgagcaaaattgaaacatttacctttctctctacctgatttctccagaatttggaaactattcgtgagtattcttantttatggcaatatagttatttgcataagttcaataagaatctgttttcttttgtaacaggacacaattggagacactggttattttaccaaggctttgactggaatggcatattttcagatatgaccagactgctttgaggaattgaggttgactttatagagccgataaaaagcccttggaaaagactggcctggtaccttgtctacgcggttcccttacaaggttcctgaccttgcggtaagtaaagaatgtcactttctgacaggcccaggaacctcaagatattttgggacctcgagaagagaggaattcacccaattcgtacaggtattacaggcacagtctgatggcgaatccttggcttggcttcctagcctcgagaggcttttaaaagtctaatctgagattccttatgaaaaagttccagcaaagccaacttnaaaagagcctatatggccaatcactattcttgctgcactttatgcaaataatcaggccaagtataataagactaaaacttattttgcaaataaattggtcctactatgatttatctttggtagaaatgggggactggagagagaaaaattatgtttcagaagaaaactatagtacacctgttattagattctagccctgtccattgtttttgagtttttattatttncctacaatttggactgaatcctgaattctttcctggctacaagtctccaaactaacgttttcaaatttttctcccatttttctgacttggaatcactagaaattaaaactgtgcttttcttaaagccctgcaagctgaagctagacaacttgaataaacttcgggagaaatcaccacagcaacttatatataaacagccttcgtgcctgctgatgtatggactactcagaaagttcacttgaacacctgattcgaactacaatccagaaaaatctgtcagattgccactgcaatctgaagatgcttcagagactctagaaaaactagtttatagactgctccagacattaacctttgttttcttctgtttccatagaaatgcctcttattaaagatctgtttgcctncatcatatatagaggcctagctttgnnagcccatctgcaacgccacctcctggaatgggacacagctgtttaactgaactgatctattctcaggactaagagactgattcaagaagatatgggacgatatatttaaatttgctcttttctgcttatcccaatttgttttctcccctcctttgcctatctctatctaacaacctctaacccaaatctctccaaagctatcaacttggctttaatatgtgaaactttttaaagtttcaaagtggggac
Repeats structure For certain families, there exists a curated collection of TE-derived proteins, which constitutes a non-redundant set. As a results, several families may lack an associated coding sequences directly linked to them. The annotation for these families is obtained from Dfam. :
...
Peak overlapping A ChIP-seq peak of KZFPs that intersects with a certain repeats sequence on the genome. :
# KZFP name Record number KZFP age(Mya) Time correlation with Repeats
1 ZNF382 68 99.0 Weakly correlated
2 ZNF766 40 43.0 Weakly correlated
3 ZNF486 31 8.6 Weakly correlated
4 ZNF263 28 180.0 Weakly correlated
5 ZNF43 25 43.0 Weakly correlated
6 ZNF589 23 28.9 Weakly correlated
7 ZNF175 22 94.0 Weakly correlated
8 ZIM3 19 87.0 Weakly correlated
9 ZNF394 19 99.0 Weakly correlated
10 ZKSCAN8 16 160.0 Weakly correlated
11 ZNF680 16 28.9 Weakly correlated
12 ZNF558 14 99.0 Weakly correlated
13 ZNF584 13 99.0 Weakly correlated
14 ZNF679 12 28.9 Weakly correlated
15 ZNF197 12 99.0 Weakly correlated
16 ZNF101 11 43.0 Weakly correlated
17 ZNF92 10 28.9 Weakly correlated
18 ZNF18 9 160.0 Weakly correlated
19 ZNF2 9 99.0 Weakly correlated
20 ZNF317 9 99.0 Weakly correlated
21 ZNF793 8 99.0 Weakly correlated
22 ZNF597 8 94.0 Weakly correlated
23 ZFP37 8 99.0 Weakly correlated
24 ZNF479 7 6.4 Weakly correlated
25 ZNF705B 7 28.9 Weakly correlated
26 ZNF429 6 28.9 Weakly correlated
27 ZNF257 5 0.0 Weakly correlated
28 ZNF350 5 99.0 Weakly correlated
29 ZNF723 5 15.2 Weakly correlated
30 ZNF519 5 19.6 Weakly correlated
31 ZNF534 5 19.6 Weakly correlated
32 ZNF554 5 99.0 Weakly correlated
33 ZNF701 5 28.9 Weakly correlated
34 ZNF682 5 28.9 Weakly correlated
35 ZNF528 4 43.0 Weakly correlated
36 ZNF490 4 43.0 Weakly correlated
37 ZNF547 4 74.0 Highly correlated
38 ZNF705D 4 28.9 Weakly correlated
39 ZNF735 4 28.9 Weakly correlated
40 ZNF610 4 28.9 Weakly correlated
41 ZNF441 4 43.0 Weakly correlated
42 ZNF485 4 94.0 Weakly correlated
43 ZNF274 4 99.0 Weakly correlated
44 ZNF28 4 28.9 Weakly correlated
45 ZNF320 4 28.9 Weakly correlated
46 ZNF251 4 94.0 Weakly correlated
47 ZNF324 4 99.0 Weakly correlated
48 ZNF182 4 99.0 Weakly correlated
49 ZNF284 3 43.0 Weakly correlated
50 ZNF595 3 43.0 Weakly correlated
51 ZNF140 3 99.0 Weakly correlated
52 ZNF778 3 74.0 Highly correlated
53 ZNF823 3 43.0 Weakly correlated
54 ZNF14 2 69.0 Moderately correlated
55 ZNF202 2 160.0 Weakly correlated
56 ZNF816 2 28.9 Weakly correlated
57 ZNF273 2 28.9 Weakly correlated
58 ZNF607 2 43.0 Weakly correlated
59 ZNF84 2 99.0 Weakly correlated
60 ZFP57 2 87.0 Weakly correlated
61 ZNF282 2 319.0 Weakly correlated
62 ZNF669 2 43.0 Weakly correlated
63 ZNF44 2 43.0 Weakly correlated
64 ZNF506 2 28.9 Weakly correlated
65 ZNF331 2 94.0 Weakly correlated
66 ZNF786 1 99.0 Weakly correlated
67 ZNF136 1 74.0 Highly correlated
68 ZNF135 1 94.0 Weakly correlated
69 ZNF75D 1 94.0 Weakly correlated
70 ZNF765 1 8.6 Weakly correlated
71 ZKSCAN1 1 160.0 Weakly correlated
72 ZNF347 1 43.0 Weakly correlated
73 ZNF705E 1 0.0 Weakly correlated
74 ZFP69B 1 99.0 Weakly correlated
75 ZNF480 1 43.0 Weakly correlated
76 ZNF354A 1 99.0 Weakly correlated
77 ZNF85 1 28.9 Weakly correlated
78 ZNF8 1 99.0 Weakly correlated
79 ZNF418 1 43.0 Weakly correlated
80 ZNF716 1 19.6 Weakly correlated
81 ZNF585A 1 99.0 Weakly correlated
82 ZNF337 1 43.0 Weakly correlated
83 ZNF334 1 99.0 Weakly correlated
84 ZNF17 1 69.0 Moderately correlated
85 ZNF700 1 28.9 Weakly correlated
86 ZNF530 1 28.9 Weakly correlated
87 ZNF674 1 99.0 Weakly correlated
88 ZNF671 1 94.0 Weakly correlated
89 ZNF440 1 28.9 Weakly correlated
90 ZNF30 1 94.0 Weakly correlated
91 ZNF549 1 87.0 Weakly correlated
92 ZNF287 1 99.0 Weakly correlated
93 ZNF560 1 43.0 Weakly correlated
94 ZNF563 1 28.9 Weakly correlated
KZFPs Motif in Repeats The motif of KZFPs found by the meme-chip appears in the repeats sequence. :
# KZFP name Record number KZFP age(Mya) Time correlation with Repeats
1 ZNF43 25 43.0 Weakly correlated
2 ZNF263 14 180.0 Weakly correlated
3 ZNF382 8 99.0 Weakly correlated
4 ZIM3 7 87.0 Weakly correlated
5 ZNF101 7 43.0 Weakly correlated
6 ZNF793 7 99.0 Weakly correlated
7 ZNF680 5 28.9 Weakly correlated
8 ZNF350 4 99.0 Weakly correlated
9 ZNF479 4 6.4 Weakly correlated
10 ZNF735 4 28.9 Weakly correlated
11 ZNF317 4 99.0 Weakly correlated
12 ZNF485 3 94.0 Weakly correlated
13 ZNF595 3 43.0 Weakly correlated
14 ZNF766 3 43.0 Weakly correlated
15 ZNF140 3 99.0 Weakly correlated
16 ZNF257 2 0.0 Weakly correlated
17 ZNF534 2 19.6 Weakly correlated
18 ZNF723 2 15.2 Weakly correlated
19 ZNF679 2 28.9 Weakly correlated
20 ZNF429 2 28.9 Weakly correlated
21 ZNF202 2 160.0 Weakly correlated
22 ZNF816 2 28.9 Weakly correlated
23 ZNF324 1 99.0 Weakly correlated
24 ZKSCAN1 1 160.0 Weakly correlated
25 ZNF597 1 94.0 Weakly correlated
26 ZNF584 1 99.0 Weakly correlated
27 ZNF558 1 99.0 Weakly correlated
28 ZNF610 1 28.9 Weakly correlated
29 ZFP57 1 87.0 Weakly correlated
30 ZNF589 1 28.9 Weakly correlated
31 ZNF287 1 99.0 Weakly correlated
32 ZNF440 1 28.9 Weakly correlated
33 ZNF85 1 28.9 Weakly correlated
34 ZNF674 1 99.0 Weakly correlated
35 ZNF585A 1 99.0 Weakly correlated
36 ZFP37 1 99.0 Weakly correlated
37 ZNF530 1 28.9 Weakly correlated
38 ZNF701 1 28.9 Weakly correlated
39 ZNF251 1 94.0 Weakly correlated
40 ZNF175 1 94.0 Weakly correlated
41 ZNF197 1 99.0 Weakly correlated
42 ZNF28 1 28.9 Weakly correlated
KZFPs Motif in Repeats Consensus The motif of KZFPs found by the meme-chip can find the corresponding region on the consensus sequence of repeats. :
# KZFP name KZFP age(Mya) Time correlation with Repeats
1 ZNF101 43.0 Weakly correlated
2 ZNF263 180.0 Weakly correlated
3 ZNF793 99.0 Weakly correlated