ZRdb KZFP & Repeats
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LTR_HARLEQUIN

  • Name
    HARLEQUIN
  • Repbase
    HARLEQUIN
  • Type
    LTR
  • Emergence
    74.0 Mya
  • Dfam Id
    DF0000017
Description :

Harlequin is an internal part of an endogenous retrovirus-like elementflanked by LTR2s. Its consensus sequence has been reconstructed based oneight full-length copies; they are ~92% similar to the consensussequence. One copy has been inserted into Alu-Y repeat. Harlequin wasbuilt up from several different retroviruses including HERVE, HERVI,HERV17 and MER4I-group sequences. We suggest that shuffling of non-homologous endogenous retroviral sequences may generate mosaicretrovirus-like elements. Presumably, the shuffling occurs in virionswhere RNA genomes of different retroviruses could be packed in together.Self-catalytic RNA recombinations or jumping of reverse transcriptasebetween non-homologous RNA molecules may induce the shuffling.
Consensus sequence The consensus sequences obtained from Dfam are derived from the seed alignment using a specialized caller. :
tttcttggttccctgaccgggaagcgaggtgattaacggacggtcgaggcagccccttaggcggcttaggcctgccctgtggagcatccctgcgggggactccggccagcctgagcgacgcggatcctgagagcgctcccgggtaggcaattgccccggtggaacgcctcgccagagcagcgcgtggcaggcccccgcggaggatcaacgcagtggctgaacaccgggaaggaactggcacttggagtccggacatctgaaacttggtaagactggtctttggaacttgccccactccatttgagtggaagcgtggcctgatcacccacggcgtgcctgtaccggcactttggtttttgtttttgacttgacttggattgcttgatactttggttttggttttgacctggcttggatttctggatactctgattttggttttgattttggtttggtgtaaactgcaaaagtgtgtgtgtgccctttttacccgttctttgttttgtggtgtgcgtgtggtgtgagcgtggtgttttgtctcgaagaagcatgggtcaggcacaaagtaagcccaccccactaggaactatgttgaaaaatttcaagaaaggatttaagggagactacggngttactatgacaccaggaaaacttagaactttgtgtgaaatagactggccagcattagaggtgggttggccatcagaaggaagcctggacaggtcccttgtttcaaaggtatggcacaaggtaacctgtaagccagggcacccagaccagttcccgtacatagacacttggttacagctggttttagaccccccgcccccacagtggttgagagaacagcagcataagcggctggcagaggcaaggaaagaccagcagagaganngagagaggaaagagacagagaggaaaagaggcaaagagagagaggaagagacagagaggaagagacagagagacaaagagggagtcaaggagagagaaagagagaggcagagagagaggaagagacagaggcaaaaggaaagtcaaagagaganagaaagtcaaagagagaaagaaagagagagatatacaagtagttaagaaaaaaaacagtgtaccctattcctttaaaagccaaggtaaatttaaaacctataattgataattgaaggtattctccgtaaccctataacactccaataccactttgttgtcagtgtaaacaagggcgtatcccgaaagcactgaggccttcctatcaaaaatccttaacccagtaacccgcggatggcccaaatgcattcaatctgtagcggcaactgctttgctaacagaaaaaagtaaaaaaaataacttttagaggaaacctcattgtgagcacacctcaccagttcagaagtatcctaaggaaaaaaaaaaaaaaaaggatgatttaacattaaccactgaaaattcccttaacccagcaggtttcctaacaggggatctaaatcttaattaccatacaaaggtccgaccagacctaggaggaactcccttcaggacaggacgatagatggttcctcccgggtaattgaagaaagaaaaaaagccatctataccaattctaagttaatttggactaaacaaggtcttattaatagcaaaggataattgaaatcccaaacttacaaggttttcaacaaaagtaaagtttgctaaaagttaacagtgtaacatgtattatagtaacttctaatcttgtggccttagacagtctagtccacagacataaaggaagttcgctttggaaaagaatggttatcatcttcgaaaaaaaaagagaggaaagggggggcagaatttatgtaaaaagagtgttatatggtaaattcttgtcctgaaataaattaactggttgtttaaagaaagaaatgtttgtaataagtcagaaagttgaggcatgtcgaagaattgtctgcgaaagtcgtgaaagaaaaaaatgttataaaaaaagaatttatgcaagaaatgttgtataatttaaaagtaattaggcctcctgaatgtaaaactattgaaaaaacagtttatgtgcaaggtgtataaggaaagtaaaatatacctttggtaaaaggattataaggaggcataagaatgtggatttttacctacattaaaaggttaaaaaaattattgttttgaaggtttaagcaagttttaaaacgttaattgtaaagaaaattctgtgtgtaaacatattagctaaagttaaagaggtatcatccagtttttctgtgaactggacattaaagtaaaaacgcaacgggtttttcttaaagcaccaacctgctctttaacaaaaattataaaaggttaaaaagagtctataaaaatcttaccttatggtcaaacattaaaaattggataaatatgtctacaaggttttattaaaattaagtttaacattaataacacactaatataaaggtgaaatttagcttatctggtataaaaatcatacaagaagcattgttaaatataaaatggtgtttggctttctttggtctaaaaactaataaaaataggtgctaaaggaaatttctcagtaaaaaggcaccaaggactataaagtccactgccgatgtccccacatttaaaacaaaaggtcaatttcttagaaattatatacttggtttatcttccactttcctttccctcaaaactaaaagtcttttagcacatgtaccacccctagaatttccggtaaaccagcaccagcctgaagatcacgttctcatcaaagggtggaaagaaggaaaactcgagccagcctgggaaggaccctaccttgtgctgctaaccaccgagactgctgttcgtacagcgaaaaagggatggactcatcacacccgagtcaagaaagcgccaccccctccagagtcgtgggccatagtcccaggggaaaaccctaccaaactaaagctaagaaaaatttaactctttcatctattctattactctttcttctttcctcgctctattgctgaccatctagttattaacataaccaagtcaatttcgcctcaaactattgcatttaatgcttgccttgttataccctgtggggacttgccaagtcaaagacagctctctacttcagaaaagtacctctgtccctcctgactctcctcagactgggcattagtaaattaggaccatttaatccggggagatttcgataaagaccccagtgtcaaccaggagtcttgccccccgatgtagagcttttatgccgtagttggtccaacgttctgtggaccactaaagagcaaggatggactgccccaaccggtttttgtaatttcctaaaaccatacattcattttactagaggatcatagaagttaaagacttaaaacaaactttggcaattaagacaggataccaagatgcaaatgcctggttggaatggatcaaatattccatccgcacgttaaacaaaagcaattgttatgcttgtgcacatggcaggccagaggcccagattgtcccctttccactaaggtggtcctccagtcgaccaggcgtgggctgcatggtagctcttttccaggattctacagcctggagtaataagtcgtgccaagctctctctgctatatcccgaagtccggcaccctgcgggtcagcccccgagggccatccagcttccgtctcccaacactaagttcacttcgtgtctctcacgacagggaggaaacttagcgttccttggagacctgaagggatgcagtgagcttaagaattttcaagagcttatcaatcagtcagcccttgttcatccccgagcggatgtgtggtggtattgtggtggacctttactgggcactctgccgaataactggagtggcacttgtgctttagtccaattggctatccctttcaccctggcatttcatcaaccagagggaggaaaaataagacatcgtaaagcgagagaagccccttatgggtctttcgactctcacgtctatttagacgcaattggagtcccacggggaataccagatcaatttaaagcttgaaatcaaatagctgcaggatttgagtcaatattttggtgggtgacagttaataaaaatgtagattggataaactacatctattacaaccaacagcaacgagcttttcatgagttaaaagaaaaactcatgtcggccccagccctggggctacctgacctgacaaaaccctttacactctatgtgtcagaaagagaaaaaatggcagttggagttttaacccagactgtggggccctggccaaggccagtggcctatctctcaaaacaactagacggggtttccaaaggctggcccccatgtctaagggccctggcagcaacggccctgttagcacaagaagcagataaactaacccttgggcaaaacctgaatataaaggccccccatgctgtggtaactttaatgaataccaaaggacatcattggctaacgaatgctagattaaccaagtaccaaagcttgctatgtgaaaatccccgcataaccattgaagtttgcaacaccctaaaccccgccaccttgctcccggtatcagagagcccagttgaacataactgtgtagaggtgttggactcagtttattctagcgggcccaacctccgagaccatccttgaacatcagtagactgtgagctgtacgtggacgggagcagcttcgccaacccctgcaaagtgactctgaagaagacgacaagccctgctccagtcacacccggaagctgactggtccacgcacggccgaagcatgagaaaactcatcgcgggactcattttccttaaaatttggacttgtacagtaaggacttcaactgaccttcctcagactgaggactgttcccagtgtatacatcaagtcactgaggtaggacaaaaggttgctacggtcctattattttatggttattataagtgtaccggaactctaaaaagaacttgtttgtataatgttattctatacaaggtatgtagcccaggaaatgaccaacctgatgtgtgttatgacccatctgagcctcccatgaccacagtttttaaaataagattaaggactgaggactggtgggggctcataaacgatacgagtaaagtgttagccaaaacagaagaaaaaggggtgcccaaacaagtcaccttgaaatttgatgcctgtgctgtcattaatagtaataagtntaggaataggatgtggttctcttaattnnaggaaagaggctatatggcagaaaataagtacatttgtcatgaattaggactgtgtggaaataaatgtggatactggtcttgtgtcatttaggctacttggataaaaaatgaaaaggatcctgtccaccttcagaaagggaaaagtggcccttcctgtaccagtggtcagtgtaaccccttagaactagtaataaccaacccccttgatcctcgctggaaaaaaggggagcgtgtaaccctaggaatcgatggggccggactggatcctcgagtaaatatcgtggttcgaggagaagtttataaacgctctcctgagccagtatttcaaaccttctatgatgaactgaatgtgccagtaccagaaattccaggaaaaacaagaaatttgtttttgcaattagccgagcatgtagcccagtctctcaatgtcacttcatgttatgtatgtggaggaactgtaatgggagatcaatggccatgggaagcccgagaattagtacctacagacccagttcctgatgaattcccggctcaaaagaatcaccctgataacttctgggtcctaaaagcctcaatcattagacaatactgtatagcaagagtggggaaggacttcacccttcccgtgggaagactcagctgccttgggcaaaaactgtataatagtactacaaaaacagccacctggtggagttcaaaccacactaagaaaaatccatttagtaaattcccaaagttgcaaaccgtgtggacccacccggagtcccaccgggactggacagcccccactggattatactggatatgtgggcatagagcttacgccaaattacccgaccagtgggcaggtagttgtgttattggcactattaaaccatctttcttcctactgcccataaagacaggcgaactcctgggcttccctgtctatgcttcccgcgaaaagagaagcatagctataggaaattggaaagatgataaatggccccctgagagaatcatacaatattatgggcctgctacttgggcacaagacggctcgtggggataccggacccccatttacatgctcaaccgaatcatacggttacaagctgtcttagaaataatcactaataagaccggcagagccttgactattctggcccggcaagaaactcagatgagaaatgctatctatcaaaatagattggctctcgactacttgctagcagctgaaggaggggtctgtaggaaatttaaccttactaattgctgcctacacatagatgatcaagggcaagtagttgaagacatagttagagatatgacaaaactggcacatgtgcccgtgcaagtgtggcatggatttgatcctggggccatgtttggaaaatggttcccagcgctaggaggatttaaaactcttataataggagttataatagtaataggaacctgcttactgctcccttgtttgctacctgtacttcttcaaatgataaaaagcttcatcgctaccttagttcaccaaaatgcttcagcacaagtgtactatatgaatcactatcgatctgtcttgcaagaagacatgggtagtgagaatgaaagtgagaactcccactantgagtgagattctcaaagggggggaa
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. :
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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 ZNF534 66 19.6 Weakly correlated
2 ZNF274 28 99.0 Weakly correlated
3 ZNF479 22 6.4 Weakly correlated
4 ZNF793 20 99.0 Weakly correlated
5 ZNF382 17 99.0 Weakly correlated
6 ZNF766 15 43.0 Weakly correlated
7 ZNF506 15 28.9 Weakly correlated
8 ZNF723 12 15.2 Weakly correlated
9 ZNF169 12 94.0 Weakly correlated
10 ZNF707 11 74.0 Highly correlated
11 ZNF263 10 180.0 Weakly correlated
12 ZNF680 9 28.9 Weakly correlated
13 ZNF705B 9 28.9 Weakly correlated
14 ZNF823 8 43.0 Weakly correlated
15 ZNF528 7 43.0 Weakly correlated
16 ZIM3 7 87.0 Weakly correlated
17 ZNF182 6 99.0 Weakly correlated
18 ZNF257 6 0.0 Weakly correlated
19 ZNF671 5 94.0 Weakly correlated
20 ZNF679 5 28.9 Weakly correlated
21 ZFP69B 5 99.0 Weakly correlated
22 ZNF133 5 99.0 Weakly correlated
23 ZNF677 4 99.0 Weakly correlated
24 ZNF28 4 28.9 Weakly correlated
25 ZNF224 4 69.0 Moderately correlated
26 ZNF202 4 160.0 Weakly correlated
27 ZNF251 3 94.0 Weakly correlated
28 ZNF597 3 94.0 Weakly correlated
29 ZNF585A 3 99.0 Weakly correlated
30 ZNF558 3 99.0 Weakly correlated
31 ZNF175 3 94.0 Weakly correlated
32 ZNF813 3 28.9 Weakly correlated
33 ZNF486 3 8.6 Weakly correlated
34 ZNF485 3 94.0 Weakly correlated
35 ZNF441 3 43.0 Weakly correlated
36 ZNF197 3 99.0 Weakly correlated
37 ZNF777 3 319.0 Weakly correlated
38 ZNF778 2 74.0 Highly correlated
39 ZKSCAN1 2 160.0 Weakly correlated
40 ZNF101 2 43.0 Weakly correlated
41 ZNF705D 2 28.9 Weakly correlated
42 ZNF589 2 28.9 Weakly correlated
43 ZNF585B 2 99.0 Weakly correlated
44 ZNF320 2 28.9 Weakly correlated
45 ZNF554 2 99.0 Weakly correlated
46 ZNF136 2 74.0 Highly correlated
47 ZNF324 2 99.0 Weakly correlated
48 ZNF350 2 99.0 Weakly correlated
49 ZNF716 1 19.6 Weakly correlated
50 ZNF780A 1 43.0 Weakly correlated
51 ZNF8 1 99.0 Weakly correlated
52 ZNF735 1 28.9 Weakly correlated
53 ZNF786 1 99.0 Weakly correlated
54 ZFP57 1 87.0 Weakly correlated
55 ZNF75D 1 94.0 Weakly correlated
56 ZNF93 1 8.6 Weakly correlated
57 ZNF2 1 99.0 Weakly correlated
58 ZKSCAN5 1 160.0 Weakly correlated
59 ZNF124 1 43.0 Weakly correlated
60 ZNF135 1 94.0 Weakly correlated
61 ZNF17 1 69.0 Moderately correlated
62 ZNF205 1 180.0 Weakly correlated
63 ZNF268 1 94.0 Weakly correlated
64 ZNF284 1 43.0 Weakly correlated
65 ZNF287 1 99.0 Weakly correlated
66 ZNF701 1 28.9 Weakly correlated
67 ZNF317 1 99.0 Weakly correlated
68 ZNF440 1 28.9 Weakly correlated
69 ZNF490 1 43.0 Weakly correlated
70 ZNF563 1 28.9 Weakly correlated
71 ZNF584 1 99.0 Weakly correlated
72 ZNF611 1 19.6 Weakly correlated
73 ZNF616 1 43.0 Weakly correlated
74 ZNF682 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 ZNF534 64 19.6 Weakly correlated
2 ZNF793 12 99.0 Weakly correlated
3 ZNF707 11 74.0 Highly correlated
4 ZNF723 9 15.2 Weakly correlated
5 ZNF506 9 28.9 Weakly correlated
6 ZNF823 8 43.0 Weakly correlated
7 ZNF479 6 6.4 Weakly correlated
8 ZNF169 6 94.0 Weakly correlated
9 ZNF263 6 180.0 Weakly correlated
10 ZNF133 5 99.0 Weakly correlated
11 ZIM3 4 87.0 Weakly correlated
12 ZNF671 4 94.0 Weakly correlated
13 ZNF257 4 0.0 Weakly correlated
14 ZNF677 3 99.0 Weakly correlated
15 ZNF485 3 94.0 Weakly correlated
16 ZNF680 2 28.9 Weakly correlated
17 ZFP69B 1 99.0 Weakly correlated
18 ZNF440 1 28.9 Weakly correlated
19 ZNF324 1 99.0 Weakly correlated
20 ZKSCAN1 1 160.0 Weakly correlated
21 ZKSCAN5 1 160.0 Weakly correlated
22 ZNF251 1 94.0 Weakly correlated
23 ZNF735 1 28.9 Weakly correlated
24 ZNF28 1 28.9 Weakly correlated
25 ZNF382 1 99.0 Weakly correlated
26 ZNF780A 1 43.0 Weakly correlated
27 ZNF705B 1 28.9 Weakly correlated
28 ZNF597 1 94.0 Weakly correlated
29 ZNF679 1 28.9 Weakly correlated
30 ZNF75D 1 94.0 Weakly correlated
31 ZNF766 1 43.0 Weakly correlated
32 ZNF705D 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 ZNF169 94.0 Weakly correlated
2 ZNF263 180.0 Weakly correlated
3 ZNF479 6.4 Weakly correlated
4 ZNF506 28.9 Weakly correlated
5 ZNF534 19.6 Weakly correlated
6 ZNF707 74.0 Highly correlated
7 ZNF793 99.0 Weakly correlated
8 ZNF823 43.0 Weakly correlated