ZRdb KZFP & Repeats
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LTR_HERVE

  • Name
    HERVE
  • Repbase
    HERVE
  • Type
    LTR
  • Emergence
    19.6 Mya
  • Dfam Id
    DF0000174
Description :

Associated long terminal repeat is LTR2. The gag and pol genes are ~40%similar to Moloney murine leukemia virus (MoMuLV). Some uniquecharacteristics of the endogenous human retroviral DNA included a tRNAGlu primer binding site separated from the 5' LTR by a pentanucleotideand a putative env sequence which does not appear to overlap the Cterminus of pol and has virtually no homology with the env gene of knowninfectious retroviruses. The reconstructed (though still pseudogenic)gene boundaries are: Gag: 571-2094, Pol: 2095-5655, Env: 5678-7750.
Consensus sequence The consensus sequences obtained from Dfam are derived from the seed alignment using a specialized caller. :
tttcttggttccctgaccgggaagcgaggtaattgacggacggtcgaggcagccccttaggcggcttaggcctgccctgtggagcatccctgcgggggactccggccagcttgagcgacgcggatcctgagagcgctcccgggtaggcaattgccccggtggaacgcctcgtcagagagtgcgtggcaggcccccgtggaggatcaacgcagtggctgaacaccgggaaggaacgggcacttggagtccggacatttgaaacttggtaagactggtctttggaacttgcccactccatttgagtggaagcgtggcctgatcacccacggcgtgcctgtaccggcactttggtttttgtttttgacttgacttgaattgcttgatactttggttttggtttgacctggcttggatttctggatactctgattttggttttgattctggtttggtgaaaactgaaaaagtgtgtgtgtgccctttttacccattctttgttctgtggtgtgcgtgtggtgtgagcttggtgttttgtctcgaggaaacgtgggtcagacacaaagtaagcctactccgctaggaactatgttgaaaaattttaagaaaggatttaatggagactatggggttactatgacaccagggaaacttagaactttgtgtgaaatagattggccaacattagaagtgggttggccatcagaaggaagcctggacaggtcccttgtttctaaggtatggcacaaggtaactggtaagtcaggacacccagaccagttcccatacatagacacttggttacagctggtgctagaccccccacagtggctaagagggcaggcagcagcagtgctagtagcaaagggacagatagccaaggaaggatcccgctccacccgccgagggaaatcaactcctgaagttctgttcgacccaacatcagaagatccattgcaggagatggcaccagtgatcccagtggtgccctccccttaccagggagagaggctccccactcttgagcccacagtgcttgcgcctccgcaagacaaacatatccctaggccacccagagtagacaagagaggaggtgaagactcgggagaaacccctccctcggcagctcgtttacgacccaaaacggggatacaaatgcccctgagagagcagcggtatactgggatagatgaggatggtcacgtggtggagaggcgtgtttttgggtaccagcccttcacctccgccgaccttctcaactggaaaaacaataccccgtcctataccgaaaagccacaagccctaattgatttgctccaaactgttatccagacccacaaccccacctgggctgattgccaccagttgctcatgttcctctttaacagagatgaaaggcggagagtgctccaagcagcaactaagtggctagaggaacatgcaccagctgattatcaaaacccccaagagtatggaaggacccagttaccaggaaccgacccccagttggacccacatgaaagagaggatatgcaaaggctaaaccgagacagggaagctctcttggaaggattaangaggggagctcagaaggccacaaacgttaacaaggtctctgaggtcattcagggaaaagaagaaagtccagcacaattctacgagagactgtgtgaggcctatcgtatgtatactccctttgatcccgatagccctgaaaatcagcgcatgattcacatggctttagtccgtcaaagcgcagaagacatgagaagaaaactgcagaaacaggctgggcttgcagggatgaatacatcacaattactagaaatagctagccaggtgtttgtaaacagggatgcagtaagccgtaaggaaancgcaaagagaatggaggtcaggcccggcgaaacgcgcctgttagctgcagcaatcagaggggcccccccaaangaggcaaggnngaaggggggccctgggaaagaaactcagcttggctgtcagagtttgcagcgtaaccagtgtgcttattgtaaagaaataggacagtggaagaacaaatgccctcagctcaaaagaaaacaaggtgactcagagcaggaggccccggacaaggaggaaggggccctgctcaacctggcagaagggttattggactgagggagaccgggctcaagcgtccccaaagagcctctggtcagaatgacagtcgggggtagagacattgattttcttgtagatagcggtgctgaacattcgctagtaaccgccccggtcgcccccttatccaaaaagactattgacgtcatcggagccacgggggtttcagcaaagcaagctttctgcttgcctcggacttgtactgtaggaggacataaagtcattcatcagttttngtacatgcctgactgtcccttgcccttnttgggaagggacttgctcagcaagctgagagccactatctctttgacagagcacggctctttgctgctaaagttacccggaacgggagtcattatgacccttacggtcccccgagaggaggaatggagacttttcttaactgagccgggccaagagagaagaccagctctggctaagcggtggccaagagtacgggcggaagacaaccctccggggttggcagtcaaccgagcccncgtactcgtngaagttaagactggggcccagccggttaggcaaaaacaggacccggtccccagagaagctcttcaaggtatccaggtccgtctcaagcacctaagaacttttggaattatngttccttgtcagtctccatggaacactcccctcctgcctgttcccaagccacggaccaaggactacnggccggtacaggatttgcgcttgcttnatcaagctacactgactttacatccaacagtacctaacccgtccacattgttggggttgctgccagctgaggacagctggttcacctgcttggacctgaaagacgctttctttcctatcagattagcccctgagaggcagaagctgtttgcctttcagtgggaagatccggagtcaggtgtcactactcagtacacttggaccgggcttccccaagggttcaagaactcccccaccatcttcggggaggcgttggctcgagacctccagaagtttcccaccagagacctaggctgcgtgttgctccagtaggttgatgaccttctgctgggacaccccacggcagtcgggtggccaagggaacggatgccctacnccggcacctggaggactgtgggtataaggtgtccaagaagaaangctcagatctgccgacggcaggtacgttacttgggatttactatccgacagggggaacgcagcccgggatcagaaagaaagcaggtcatttgcaatctaccggagcctaagagcagaaggcaggtgagagaattcttaggagctgtggggttttgtagactgtggatcccaaactttgcagtattagccaagcctttgtatgaggtcacaaaggggggggaccgggaacctttggaatggggatcccaacaacagcaagtctttcatgagttaaaggaaaaacttctggcagccccagccctggggctacccgatctgacaaagccttttccattgtatgcgtcagagagagaaaagatggcagctggacttttaacccaaactgtggggccctggccgaggccggtggcctacctctctaaacaactagacggggtttctaaaggatggcccccctgtttgagggccttggcagcaactgccctgctagtacaagaagcaaataagctgactcttgggcaaaacctgaacataaaggccccccatgctgtggtgactttaatgaatactaaaggacatcattggctaacgaatgccagactcaccaagtaccaaactttgctctgtgaaaatccccgtataaccattgaagtttgtaacaccctacaccccgccaccttgctcccggtatcagagagccctgtcgagcntgattgtgtagaagtgttggactcagttgactctgggcatcagtagactgggaactatacgtggatgggagcagcttcntcaacccccaaggagagagaggtgcagggtatgcggtggtaaccctggacactgttgttgaagccagatcgttgccccaggccacttcagcccagaaagctgaactcattgctttcattcgggccttagaactcagtgagggtgagactgtcaacatttacactgattctcggtatgcctttttaacccttcaagtgcatggagcgtgatagaaagaaaagggcctattgaactctgggggaaaagacagaaaatatcaacaagaaatcttgcaattattagaagcagtatggaaaccccacaaggtggcagttatgcattgcagaggacaccagcgagcttccaccttgctgggtttggggaattcccgcgctgactcagaggctcgaaaagcagcatctgcccttccgggcatcagtgacagcccccctgctccctcaagcacctgatcttggacctacttnttctaaagaagaaaaggactttctccaggtagagggaggacaagtgatggaggaaggatggattcggttaccagatgggagagtagctgtgccacagctgctaggagctgcagttgtactggctgtgcangaaaccacccatcgaggtcaggagtcactggaaaagttgttaggccggtatttctacatctcgcntttgtcagcccttgccaaaacggtgaggcagcggtgtgttacctgccgacagcatgatgcgaggcaaggtccagccgttccgcccggcatacgagcttatggagcagccccctttgaagatctccaggtggacttcacagagatgccaaagtgtggaggtaacaagtatttactagttcttgggcgtacctactctgggtgggtggaggcctatccaacacgaactgagaaagctcgtgaagtaacccgtgtgcttcttcgagatctgattcctagatttggactgcccttacggatcggctcagataacgggcctgcgtttntggctgncttggtacagaagacggcaaaggtattggggatcacacggaaactgcatgccgcctcccggcctcagagttccggaaaggtggagcggatgaatcggactatcaaaaatagtttagggaaagtatgtcaggaaacaggattaaaatggatacaggctctccctatggtattatttaaaattagatgtaccccttctaaaagaacaggatattccccttatgaaatattatatcataggccccctcccatattgcggggacttccaggcactccccgagagttaggtgaaattgagttacagcgacagctacaggctttaggaaaaattacacaaacaatctcagcctgggtaaatgagagatgccctgttagcttattctccccagttcaccctttctccccaggtgatcgagtgtggatcaaggactggaacgtagcctctttgtgcccacggtggaaaggaccccagactgtcgtcctgancactcccaccgctgtgaaggtagaaggaatcccagcctggatccaccacagccgtgtaaaacctgcagcgcctgaaacctgggaggcaagaccaagcccggacaacccttgcagagtgaccctgaagaagacgacaagccctgctccagtcacacccggaagctgactggtccacgcacggccgaagcatgaggaagctcatcgtgggattcatttttcttaaattttggacttatacagtaagggcttcaactgaccttactcaaactggggactgttcccagtgtattcatcaggtcaccgaggtaggacagcaaattaaaacaatctttctgttctatagttattatgaatgtatgggaacattaaaagaaacttgtttgtataatgccactcagtacaaggtatgtagcccgggaaatgaccgacctgatgtgtgttataacccatctgagccccctgcaaccaccgtttttgaaataagaataagaactggccttttcctaggtgatacaagtaaaataataactagaacagaagaaaaagaaatccccaagcaaataactttaagatttgatgcttgtgcagccattaatagtaaaaagctagaaataggatgtggttctcttaactgagaaaggagctanagagtagaaaataaatatgtttgtcatgagtcaggggtttgtgaaaattgtgcctattggccatgtgttatttaggctacttagaaaaagaacaaaaaggacccggttcatcttcagaagggggaagccaacccctcctgtgctgccggtcactgtaacccactagaactaataattaccaatcccctagatccccgttggaaaaagggagaacgtgtaaccctggggatcgatgggacagggttaaacccccaagttgccattttaattagaggggaggtccacaagcgctctcccaaaccagtatttcaaaccttttatgaggagctgaatctgccagcaccagaacttccgaaaaagacaaaaaatttgtttctccaattagcagaaaatgtagctcattcccttaatgttacttcttgttatgtacgcgggggaaccactatcggagacngatggccttgggaagcccgagagttggtgcctactgatccagctcctgatataattccagttcagaaggcccaagctagcaacttctaggtcctaaaaacctcaattattagacaatactgtatagctagagaagggaaagactttatcatccctgtaggaaagcttaattgtataggacagaagttgtataacagcacaacaaagacaattacttggtggggcctaaaccacactgaaaagaatccatttagtaaattttctaaattaaaaactgcttgggctcatccagaatctcatcaggactggacggctcccgctggactatactagatatgtaggcacagagcctacattcggttacctaataaatgggcaggcagttgtgttattggcactattaagccgtcctttttcttattacccataaaaacgggtgagctcctaggtttccctgtctacgcctcccgagaaaagaaaggcatagttataggaaactggaaagataatgagtggccccctgaaaggatcatncagtattatgggcctgccacatgggcacaagacggctcatggggataccgaacccccatctacatgctcaatcggatcatacggttgcaggccgtcttagaaataattactaatgaaactggcagagctttgactgttttagcttggcaagaaacccaaatgaggaatgctatctatcagaatagactggccttagactacttgctagtagctgaaggaggagtttgtggaaaatttaacttaaccaattgctgcctacaaataaatgatcaaggacaggtggttaaaaacatagtcagggacatgacaaaggtggcacatgtgcctgtacaggtttggcacgagtttaatcctgagtctttatttggaaaatggtttccagctataggaggatttaaaaccctcattgtaggtgtattgctagtgataggaacttgcttgctgctcccctgtgtattacccttgctttttcaaatgataaaaggttttgttgctactttggttcatcagaaaacttcagcacacgtgtattatataaatcactatcgctctatctcacaaagagactcaaaaagtaaagatgagagtgagaactcccactaaaagtgaaaatnctcaaaggggggaaaa
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 ZNF723 44 15.2 Moderately correlated
2 ZNF766 33 43.0 Weakly correlated
3 ZNF257 31 0.0 Weakly correlated
4 ZNF701 28 28.9 Weakly correlated
5 ZNF100 28 28.9 Weakly correlated
6 ZNF479 25 6.4 Moderately correlated
7 ZIM3 23 87.0 Weakly correlated
8 ZNF597 17 94.0 Weakly correlated
9 ZNF589 17 28.9 Weakly correlated
10 ZNF528 17 43.0 Weakly correlated
11 ZNF274 17 99.0 Weakly correlated
12 ZKSCAN1 16 160.0 Weakly correlated
13 ZFP57 15 87.0 Weakly correlated
14 ZNF382 15 99.0 Weakly correlated
15 ZNF175 13 94.0 Weakly correlated
16 ZNF263 10 180.0 Weakly correlated
17 ZNF18 10 160.0 Weakly correlated
18 ZNF584 10 99.0 Weakly correlated
19 ZNF251 8 94.0 Weakly correlated
20 ZNF486 8 8.6 Moderately correlated
21 ZNF534 7 19.6 Highly correlated
22 ZKSCAN8 7 160.0 Weakly correlated
23 ZFP37 6 99.0 Weakly correlated
24 ZNF707 6 74.0 Weakly correlated
25 ZNF394 6 99.0 Weakly correlated
26 ZNF468 6 28.9 Weakly correlated
27 ZNF28 6 28.9 Weakly correlated
28 ZNF324 5 99.0 Weakly correlated
29 ZFP69B 5 99.0 Weakly correlated
30 ZNF680 5 28.9 Weakly correlated
31 ZNF679 5 28.9 Weakly correlated
32 ZNF197 5 99.0 Weakly correlated
33 ZNF101 5 43.0 Weakly correlated
34 ZNF558 4 99.0 Weakly correlated
35 ZNF93 4 8.6 Moderately correlated
36 ZNF506 4 28.9 Weakly correlated
37 ZNF141 4 43.0 Weakly correlated
38 ZNF671 3 94.0 Weakly correlated
39 ZNF320 3 28.9 Weakly correlated
40 ZNF793 3 99.0 Weakly correlated
41 ZNF2 3 99.0 Weakly correlated
42 ZNF445 3 99.0 Weakly correlated
43 ZNF610 3 28.9 Weakly correlated
44 ZNF334 2 99.0 Weakly correlated
45 ZNF75D 2 94.0 Weakly correlated
46 ZNF485 2 94.0 Weakly correlated
47 ZNF222 2 43.0 Weakly correlated
48 ZNF735 2 28.9 Weakly correlated
49 ZNF350 2 99.0 Weakly correlated
50 ZNF554 2 99.0 Weakly correlated
51 ZFP69 2 99.0 Weakly correlated
52 ZNF695 1 28.9 Weakly correlated
53 ZNF510 1 99.0 Weakly correlated
54 ZNF813 1 28.9 Weakly correlated
55 ZNF519 1 19.6 Highly correlated
56 ZNF792 1 94.0 Weakly correlated
57 ZNF786 1 99.0 Weakly correlated
58 ZNF133 1 99.0 Weakly correlated
59 ZNF682 1 28.9 Weakly correlated
60 ZNF425 1 94.0 Weakly correlated
61 ZNF611 1 19.6 Highly correlated
62 ZNF547 1 74.0 Weakly correlated
63 ZNF44 1 43.0 Weakly correlated
64 ZNF549 1 87.0 Weakly correlated
65 ZNF585B 1 99.0 Weakly correlated
66 ZNF284 1 43.0 Weakly correlated
67 ZNF317 1 99.0 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 ZNF723 45 15.2 Moderately correlated
2 ZNF257 29 0.0 Weakly correlated
3 ZNF597 16 94.0 Weakly correlated
4 ZIM3 14 87.0 Weakly correlated
5 ZNF100 9 28.9 Weakly correlated
6 ZNF479 6 6.4 Moderately correlated
7 ZNF707 5 74.0 Weakly correlated
8 ZNF468 5 28.9 Weakly correlated
9 ZNF263 4 180.0 Weakly correlated
10 ZNF506 3 28.9 Weakly correlated
11 ZNF485 3 94.0 Weakly correlated
12 ZNF679 3 28.9 Weakly correlated
13 ZNF175 2 94.0 Weakly correlated
14 ZNF589 2 28.9 Weakly correlated
15 ZNF197 2 99.0 Weakly correlated
16 ZNF793 2 99.0 Weakly correlated
17 ZKSCAN1 2 160.0 Weakly correlated
18 ZNF584 2 99.0 Weakly correlated
19 ZNF44 1 43.0 Weakly correlated
20 ZFP69B 1 99.0 Weakly correlated
21 ZNF701 1 28.9 Weakly correlated
22 ZNF682 1 28.9 Weakly correlated
23 ZNF680 1 28.9 Weakly correlated
24 ZNF534 1 19.6 Highly correlated
25 ZKSCAN8 1 160.0 Weakly correlated
26 ZNF558 1 99.0 Weakly correlated
27 ZNF75D 1 94.0 Weakly correlated
28 ZNF350 1 99.0 Weakly correlated
29 ZNF425 1 94.0 Weakly correlated
30 ZNF320 1 28.9 Weakly correlated
31 ZNF554 1 99.0 Weakly correlated
32 ZNF766 1 43.0 Weakly correlated
33 ZNF735 1 28.9 Weakly correlated
34 ZFP37 1 99.0 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 ZIM3 87.0 Weakly correlated
2 ZNF100 28.9 Weakly correlated
3 ZNF257 0.0 Weakly correlated
4 ZNF479 6.4 Moderately correlated
5 ZNF597 94.0 Weakly correlated
6 ZNF723 15.2 Moderately correlated