ZRdb KZFP & Repeats
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LTR_HERV9NC

  • Name
    HERV9NC
  • Repbase
    No find
  • Type
    LTR
  • Emergence
    19.6 Mya
  • Dfam Id
    DF0001278
Description :

Non-autonomous. Flanked by LTR12C LTRs. Like HERV9, but an internaldeletion (replaced with a GA-rich sequence at 5000-5222) has halved thepol and envelope genes. Intact gag: 1336-2796.
Consensus sequence The consensus sequences obtained from Dfam are derived from the seed alignment using a specialized caller. :
ttttggcgaccacgaagggactntcgcctatcgccaagcggtgagactatcgccgagcggtgagaccatcgcctatcgccgagcggtgagactatcgcctatcgccaagcagtgagtaccatcggacccctttcgcttgctattctgtcctatttttccttagaattcgggggctaaataccgggcacctgtcggccagttaaaagcgactagcgcggccgccggactaaagacacgggtgtcaggctttctgggaaagggctctctaacaacccccgactcttcggagttgggagcgttggtttgcctggaaccagcttccgcttttcctgtacttctgggctgagccgagggtcgacagagaggaaagccatncagctccggggtcccgacaacaagttggttgaccctgcggccatgagcggaactctcaaaggcatgtcgcccaagcgagactcgcccatctatcctatctatcctgacccttgccccctgggtcctaatgcctgccagacaaacttcctctcgcctctcttctccgaggctagtcccgcttctaaaaatcgctncctgtctctggtgcttttctagtttctcctataagaatgatttctagtataaactccaggactctgttaccttctttaggcacccgggctcaccaatcagaaagacataatttttgcccaaagccccgtcgtagtggggactacctggaattttaggatccctcctcagactaacaggcctaacaaaagctattcctgaagctaggatatggggagcctcagaaattgtatccttcctattcatataagtgaggacaaaaggcgtcactcttccaaccctggagatcccttccctccctcagggtatggccctccacttcatttttggggcataacatctttataggacaggggtaaagtcccaatactaacaggagaatgcttaggactctaacaggttttcgagaatgcgtcggtaagggccactaaatccgatttttctcggtcggtcctccttgtggtctaggaggacaggcaagggtgcaggttttcgagaatgcgtcggtaagggccactaaatccgaccttcctcggtcctccntgtggtctgggaggaaaactagtgtttctgctgctgcgtcggtgagcgcaactattccgatcagcagggtccagggaccgttgcgggttcttgggcaggggttgtttctgctgctgcgtcggtgagcgcaactattccgatcagcagggtccagggaccgttgcgggttcttgggcagggggagaaacaaaacaaaccaaaaccgcgggcggttttgtctttcagatgggaaacactcaggcatcaacaggctcacccttgaaatgcatcctaagccattgggaccaatttgacccacaaaccctgaaaaagaggcggctcatttttttctgcactacggcctggccccaatattctctctctgatggggaaaaatggccacctgagggaagtacaaattacaatactatcctgcagcttgaccttttctgtaagagggaaggcaaatggagtgaaataccttatgtccaagctttcttttcattgagggagaatacacaactatgcaaagcttgcaatttacatcccacaggaggacctctcagcttacccccatatcctagcctccctatagctccccttcctattaatgataatcctcctctaatctcccctgcccagaaggaaataagcaaagaaatctccaaaggaccacaaaaacccccgggctatcggttatgtccccttcaagctgtagggggaggggaatttggcccaacccgggtacatgtccccttctccctctctgatttaaagcagatcaaggcagacctggggaagttttcagatgatcctgataggtacatagatgtcctacagggtctagggcaaaccttcgacctcgcttggagagatgtcatgctactgttagatcaaaccctggcctttaatgaaaagaatgcggctttagctgcagcccgagagtttggagatacctggtatcttagtcaagtaaatgatagaatgacagccgaagaaagggacaaattccctaccggtcagcaagccatccccagtatggatccccactgggaccttgactcagatcatggggactggagtcgtaaacatctgttgacctgtgttctagaaggactaaggagaattaggaaaaagcccatgaattattcaatgatgtccaccataactcagggaaaggaagaaaatccttctgccttcctcgagcggctacgggaggccttaagaaaatatactcccctgtcacccgaatcactcgagggtcaattgattctaaaagataagtttattacccaatcagccgcagatatcaggagaaagctccaaaagcaagccctgggccctgaacaaaatctggaggcattattaaacctggcaacctcggtgttctataatagggaccaagaggaacaggcccaaaaggaaaagcgagatcagagaaaggccgcagccttagtcatggccctcagacaaacaaaccttggtggttcagagaggacagaaaatggagcaggccaatcacccggtagggcttgttatcagtgtggtttacnaggacactttaaaaaagattgtccaatgagaaacaagctgccccctcgtccatgtccactatgccgaggcaatcactggaaggtgcactgccccagaggacgaaggttctctgggtcagaagcccccaaccagatgatccaacaacaggactgagggtgcccggggcaagcgccagctcatgtcatcaccctcactgagccccgggtacgtttaaccattgagggccaggaaattgacttcctcctggacactggcgcggccttctcagtgttaatctcctgtcctggacgactgtcctcaaggtccgttaccatccgaggaatcctgggacagcctgtaaccaggtatttctcccacctcctcagttgtaattgggagactttgctcttttcacatgcctttcttgttatgcctgaaagtcccacacccttattagggagggatatattagccaaggctggagctattatctacatgaatatggggaacaagttacccatttgttgtcccctacttgaggagggaatcaaccctgaagtctgggcattggaaggacaatttggaagggcaaaaaatgcccgcccagtccaaatcaggctaaaagatcccaccacttttccttatcaaaggcaatatcccttaaggcctgaagctcataaaggattacaggatattgttaaacatttaaaagctcaaggcttagtaaggaaatgcagcagtccctgcaacaccccaattctaggagtacaaaaaccgaacggtcagtggagactagtgcaagatcttagactcatcaatgaggcagtaattcctctatatccagttgtacccaacccctataccctgctctctcaaataccagaggaagcagaatggttcacggttctggacctcaaggatgccttcttctgtattcccctgcactctgactcccagtttctctttgcctttgaggatcccacagaccacacgtcccaacttacgtggacggtcttgccccaagggtttagggatagccctcatctgtttggtcaggcactggcccaagatctaggccacttctcaagtccaggcactctggtccttcagtatgtggatgatttacttttggctaccagttcggaagcctcgtgccagcaggctactctagatctcttgaactttctagctaatcaagggtacaaggcgtctaggtcgaaggcccagctttgcctacagcaggtcaaatatctaggcctaatcttagccagagggaccagggccctcagcaaggaacgaatacagcctatactggcttatcctcgccctaagacattaaaacagttgcgggggttccttggaatcaccggcttttgccgactatggatccccggatacagcgagatagccaggcccctctatactctaatcaaggagacccagagggcaaatactcatctagtagaatgggaaccagaggcagaaacagccttcaaaaccttaaagcaggccctagtacaagctccagctttaagccttcccacaggacaaaacttctctttatacgtcacagagagagcagggatagctcttggagtccttactcagactcgtgggacaaccccacaaccagtggcatacctaagtaaggaaattgatgtagtagcaaaaggctggcctcactgtttangggtagttgcggcggtggccgtcttagtgtcagaggctatcaaaataatacaaggaaaggatctcactgtctggactactcatgatgtaaatggcatactaggtgccaaaggaagtttatggctatcagacaaccgcctacttagataccaggcgctactccttgagggaccggtgcttcaaatacgcacgtgcgtggccctcaaccctgccacttttctcccagaggatggggaaccaatcgagcatgactgccaacaaattatagtccagacttatgccgcccgagatgatctcttagaagtccccttagctaatcctgaccttaacctatataccgatggaagttcatttgtggagaatgggatacgaagggcaggttatgccatagttagtgatgtaaccgtacttgaaagtaagcctcttcccccagggaccagcgcccagttagcagaactagtggcacttacccgagccttagaactgggaaagggaaaaagaataaatgtgtatacagatagcaagtatgcttatctaatcctacatgcccatgctgcaatatggaaagaaagggagttcctaacctctgggggaacccccattaaataccacaaggaaatcatggagttattgcacgcagtgcaaaaacccaaggaggtggcagtcttacactgccgaagccatcaaaaggggaaggagaggggagaacagcagcataagcggctggcagaggcagnnggaaagaccagcaagaaggaaagagagaaagagaaagagagagagagagagaaagagncaaagagggagtcagagagaaagagaaagagacaaagaagaagtcaaagagaaagagagatggaagtagtaaagaaaaaacagtgtaccctattcctttaaaagccagggtaaatttctgtctacccagccaaggcatattcttcttatgtggaacntcgacctatatctgcctccccactaactggacaggcacctgcaccttagtctttctaagtcccaacattaacattgccccaggaaatcagaccctatcagtacccctcaaagctcaagtccgtcagcgcagagccatacaactaatacccctacttatagggttaggaatggctactgctacaggaaccggaatagccggtttatctacttcattatcctactaccacacactctcaaaggatttctcagacagtttgcaagaaataacgaaatctatccttactttacaatcccaaatagactctttggcagcagtgactctccaaaaccgccgaggcctagacctcctcactgctgagaaaggaggactctgcaccttcttaggggaagagtgttgtttttacactaaccagtcggggatagtacgagatgccgcccggcgtttacaggaaaaggcttctgaaatcagacaacgcctttcaaactcttataccaacctctggagttgggcaacatggcttctcccctttctaggtcccgtggcagccatcttgctgttactcgcctttgggccctgtatttttaaccttcttgtcaaatttgtttcctctagaatcgaggccatcaagctacagatggtcttacaaatggaaccccaaatgagttcaactaacaacttctaccgaggacccctggaccgacccgctggcacttccnctggcctagagagttcccctctggaggacactacaactgcagggccccttcttcgcccctatccagcaggaagtagctagagcggtcatcggccaaattcccaacagcagttggggtgtcctgtttagagggggga
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 82 15.2 Moderately correlated
2 ZNF669 66 43.0 Weakly correlated
3 ZNF257 53 0.0 Weakly correlated
4 ZNF728 50 19.6 Highly correlated
5 ZNF793 32 99.0 Weakly correlated
6 ZNF680 24 28.9 Weakly correlated
7 ZNF101 10 43.0 Weakly correlated
8 ZNF28 10 28.9 Weakly correlated
9 ZNF506 9 28.9 Weakly correlated
10 ZFP57 9 87.0 Weakly correlated
11 ZNF589 9 28.9 Weakly correlated
12 ZNF382 9 99.0 Weakly correlated
13 ZNF766 9 43.0 Weakly correlated
14 ZNF479 8 6.4 Moderately correlated
15 ZNF616 8 43.0 Weakly correlated
16 ZNF175 8 94.0 Weakly correlated
17 ZKSCAN8 8 160.0 Weakly correlated
18 ZNF679 7 28.9 Weakly correlated
19 ZNF705B 6 28.9 Weakly correlated
20 ZNF394 6 99.0 Weakly correlated
21 ZNF320 5 28.9 Weakly correlated
22 ZNF534 5 19.6 Highly correlated
23 ZNF584 5 99.0 Weakly correlated
24 ZKSCAN1 5 160.0 Weakly correlated
25 ZFP69B 4 99.0 Weakly correlated
26 ZNF850 3 28.9 Weakly correlated
27 ZNF597 3 94.0 Weakly correlated
28 ZIM3 3 87.0 Weakly correlated
29 ZNF169 3 94.0 Weakly correlated
30 ZFP37 2 99.0 Weakly correlated
31 ZNF92 2 28.9 Weakly correlated
32 ZNF75D 2 94.0 Weakly correlated
33 ZNF786 2 99.0 Weakly correlated
34 ZNF765 2 8.6 Moderately correlated
35 ZNF445 2 99.0 Weakly correlated
36 ZNF441 2 43.0 Weakly correlated
37 ZNF263 2 180.0 Weakly correlated
38 ZNF2 2 99.0 Weakly correlated
39 ZNF317 2 99.0 Weakly correlated
40 ZNF133 2 99.0 Weakly correlated
41 ZNF140 2 99.0 Weakly correlated
42 ZNF347 2 43.0 Weakly correlated
43 ZNF197 2 99.0 Weakly correlated
44 ZNF324 2 99.0 Weakly correlated
45 ZNF264 1 99.0 Weakly correlated
46 ZNF695 1 28.9 Weakly correlated
47 ZNF735 1 28.9 Weakly correlated
48 ZNF251 1 94.0 Weakly correlated
49 ZNF17 1 69.0 Weakly correlated
50 ZNF780A 1 43.0 Weakly correlated
51 ZNF823 1 43.0 Weakly correlated
52 ZNF845 1 28.9 Weakly correlated
53 ZNF84 1 99.0 Weakly correlated
54 ZKSCAN5 1 160.0 Weakly correlated
55 ZNF85 1 28.9 Weakly correlated
56 ZFP28 1 99.0 Weakly correlated
57 ZNF705D 1 28.9 Weakly correlated
58 ZNF282 1 319.0 Weakly correlated
59 ZNF701 1 28.9 Weakly correlated
60 ZNF471 1 94.0 Weakly correlated
61 ZNF674 1 99.0 Weakly correlated
62 ZNF641 1 99.0 Weakly correlated
63 ZNF334 1 99.0 Weakly correlated
64 ZNF417 1 28.9 Weakly correlated
65 ZNF587 1 28.9 Weakly correlated
66 ZNF440 1 28.9 Weakly correlated
67 ZNF558 1 99.0 Weakly correlated
68 ZNF555 1 94.0 Weakly correlated
69 ZNF554 1 99.0 Weakly correlated
70 ZNF547 1 74.0 Weakly correlated
71 ZNF485 1 94.0 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 80 15.2 Moderately correlated
2 ZNF669 43 43.0 Weakly correlated
3 ZNF793 19 99.0 Weakly correlated
4 ZNF680 11 28.9 Weakly correlated
5 ZNF28 8 28.9 Weakly correlated
6 ZNF506 7 28.9 Weakly correlated
7 ZNF534 4 19.6 Highly correlated
8 ZNF257 3 0.0 Weakly correlated
9 ZNF597 3 94.0 Weakly correlated
10 ZNF320 3 28.9 Weakly correlated
11 ZKSCAN1 2 160.0 Weakly correlated
12 ZNF479 2 6.4 Moderately correlated
13 ZIM3 2 87.0 Weakly correlated
14 ZNF169 2 94.0 Weakly correlated
15 ZNF735 1 28.9 Weakly correlated
16 ZNF75D 1 94.0 Weakly correlated
17 ZKSCAN8 1 160.0 Weakly correlated
18 ZFP28 1 99.0 Weakly correlated
19 ZNF85 1 28.9 Weakly correlated
20 ZNF197 1 99.0 Weakly correlated
21 ZNF766 1 43.0 Weakly correlated
22 ZNF589 1 28.9 Weakly correlated
23 ZNF133 1 99.0 Weakly correlated
24 ZNF263 1 180.0 Weakly correlated
25 ZNF823 1 43.0 Weakly correlated
26 ZNF728 1 19.6 Highly correlated
27 ZNF674 1 99.0 Weakly correlated
28 ZNF616 1 43.0 Weakly correlated
29 ZNF347 1 43.0 Weakly correlated
30 ZNF394 1 99.0 Weakly correlated
31 ZNF17 1 69.0 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 ZNF28 28.9 Weakly correlated
2 ZNF680 28.9 Weakly correlated
3 ZNF723 15.2 Moderately correlated
4 ZNF793 99.0 Weakly correlated