ZRdb KZFP & Repeats
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LTR_HERV30

  • Name
    HERV30
  • Repbase
    HERV30I
  • Type
    LTR
  • Emergence
    28.9 Mya
  • Dfam Id
    DF0000170
Description :

Associated Long Terminal Repeat is LTR30. Contains Gag (pos 1367-2445)and Pol (2827-6400), though the latter is not an open reading frame.
Consensus sequence The consensus sequences obtained from Dfam are derived from the seed alignment using a specialized caller. :
ttttggcgagccagccaggaggctccaggaaaggcatctagatcgtcacgtggtgagtacgatcggacctctttcgcttgctattctgtcctgtccttccttagaattcggaggctaaaccgggcacctgtcggccacttaaaggcgattagcgcggccgccggactaaagacacgggtgtcaggctgtctggaaaagggctctctaacaacccccgacccttcggggttgggagcgttggttngcctggaccagttcnaactctttcgctttccgtggtggtcccgaagtacacccgggagtgctcagcggacgtcctagtctcccagatatcctggttgagaccatggccccgccagaggctccccctgcangggttactgagcgtgagacagccacatcttctgactcctgcctcctgggtcctaatgtccgccggctagacttctttcctcatctcgcaagcaaggttattcccgctaggcaggatcaagattccctatttagaagtcttaaattcttggggtggtgcccagaagatccctgttcatggtgccctccagggtttaggcaggtgtcgccattcgatggctattttgaagggccagttccccaccatagtgtatggtcccccacatcaggacaatttaaagacaggtctgtaattttcatgtggatagtagaagccttagggcatttcctccattgctccccagatagactttccccttccttggggcctctcaagtacaatctgtggtgcatgggcacagctcttagagccgttgaattgtttttcaaccattcaataattggtattggaaggaagaaaatatagtcagttgggacacaggatactggtaccgccttgagagaggggcttactcctttgatggcaagtggggacagaaggctagagtacagcagctgttctctcggccctggcctagaggacatccaccaccccctttaagcttactaagcctcctgtcgctaattcagagatttctccttgaaggacagttttnatggccaggcccacgtaaattgggccttagcatgcaagcatcagtggtgcccccgacccaggccttgccaccctggaacaggtaggacgcgttggcagaaggaccacaataaatccaacagtccttgtgccccatttagtggtcaatgggcgcacggcaggggcaagggaagtttccatcccgccggtaagcatggttaaatccggtagatggagggctcaggaaaagcggccatgagctttgagcacaattggacctgacccttgggggacgccctaagggaagacgagtcccaggactaaccaggggtgcgggcatccctgtgtttaaaattccagatgggcaccacaccttcaaaaccggacactcccttaagatgtatcctgaataactgggacaaattcgaccctgaaaccttaaaaaagaagcggctgattttcttctgtaccactgcctggccacagtattccttacaaaatggagaaacttggccccctgagggaagtattaattataacacccttctacaactagatcttttctgtaaacaggaaggtaaatggagtgaagtcccttatgtacaggctttctttgcccttcgtgacaatactgccctgtgccaagcctgcaagctttgcccaaatgacagaggcccacaattgcctccatactcagggcctcttccctcagccccactctcctcccccactgactctcctccatccggccccaccgaagtgttaaaggcacaccggaaagagaacgtaaactccgcgagccaggcacccaaactatgtcccttacaagcagtaggaggagaatttgggcccattcacgtgcatgccccttctcactctcagatttaaaacaaataaaggcagatttagggaaattctcggatgatcctgataactatatagatgtcctgcaaggattggggcagtcctttgatctaacatggagagatatcatgttgcttcttgatcagaccttaagtcctactgaaaaagaagcagctttagcagcagcccggcaatttggggatctgtggtaccttagccaggtaaacgatcgaatggccctggaggagagggaaaaattccccacagggcaacaggcagtccccactgtagaccctcattgggatactgactcagatcatggagattggagccgcaggcatttgctaacttgcattttagaagggttgaggaagactaggaaaaagcctatgaactactcaatgctatccacaattacgcagggaaaagaggaaaacccctccgcttttctagaaaggctaagggaggccctaagaaagcacacctccctaactccggattccgtggaaggccaacttattttaaaggataaatttatcacccaatcagcggctgacattaggagaaaactccaaaagtctgccttaggcccagaacaaaatttggagacattattaaacctggcaacctcggtgttctataacagggaccaagaggaacaggccaaaagggaaaagcgagataagagaaaggctgcagccttagtcatggccctcagacaggcagaccttggtggctcagagggaaccaagagaggagcaggccaattgcctagtagggcttgttatcagtgcggtttgcaaggacactttaagaaagattgtccaacnagaaacaaaccgccccctcgcccatgtccaatatgccaaggcaatcactggaaggcgcactgccccagaggacgaaggccctctgggccagaagcacccaaccagatgattcagcaacaggactgagggtgcccggggcaagcgccagctcatgccatcaccctcacagagccccgggtaagtttgaccattgagggccaggaagtggacttcctcctggacactggcgcggccttctcagttttaatctcctgccccggacgactgtcctcaaagtccgttactatccgaggaatcttaggacagcctgtaaccaggtatttctctcgcctcctcagctgcaattgggagactttgctcttttcacatgcctttcttgttatgcccgaaagtcccacacccttattagggagggacatattagccaaagctggggctattatctacatgaatatggggaacaaattacccatttgttgtcccctacttgaagaaggaatcaactctgaagtctgggccttggaaggacaattcggaagggcaaagaatgcccatccagttcaaatcaggctaaaagaccccaccacttttccttatcaaaggcaatatcccttaaggcctgaagctcacaaaggattacaggatattgttagacatttaaaagctcaaggcttagtaagaaaatgtaagcagtccttgcaacaccccaatcctaggaatacaaaaaccaaatggtcagtggagactagtgcaagacctcagaatcatcaatgaggcagtaattcctttatatcctgctgtacccaacccctatacactgctctctcagataccagaggaagcagaatggttcactgttctggacctcaaagatgccttcttctgcattcccctgcactctgactcccagttcctctttgcctttgaggatcctacagaccacacgtcccagcttacgtggacggtcttgccccaagggtttagagatagccctcatctgtttggtcaggcactggcccgagacctaggccaattctcaagtccaggcactctggtcctccaatacgtggatgacgtacttctggctatcagtttggaagcctcatgtcagcaggctactctagatctcttaaactttctagctaatcgagggtacaaagcgtctaggacaaaggcccagctctgtctacaacaagttaaatatctaggcctaatcctagccaaaggaactagagccctcagcaaagagcgtattcagcctatactggcctatcctcaccctaagacgttgaaacagttgngggggttccttggaatcaccggcttttgccaactgtggattcccggatanagtgaaatggccaggccactctataccctgataaaggagantcagaaggcaaatacccatctagtagaatgggaaccggaggcggaaacagccttcaaaactttaaagcaggccctggtacaagctccagccctgagcctccccacaggacaaaatttatctttatatgtcaccgagagagcaggaatagctcttggagttcttactcagactcgtgggacagccccacaaccagtggcatacctaagtaaggaaattgatgtagtagccaaaggctggcctcactgtttatnggtggttgcagcagtagccatcttagtgtcagaggctattaaaataatacaaggaaaggatctcactgtctggaccactcatgatgtaagtggcatattaaatgctaaaggaagtttgtggctntcagataaccgcctacttaaataccaggcgccactccttgagggaccagtatttcaaatacgcacgtgtgcggccctcaaccctgccacttttctcccagagggtggggaaccaattgagcatgactgccaacaaattntagcccagacttntgccgcccgagaagatctcttagaagtccccttaactaaccctgaccttaacctgtactccgatggaagttcatttgtagaaaatngggtacgaaaggcaggctatgccatagttagtgatgcagcagtacttgaaagtaagcctcttcccccagggaccagtgctcagttagcagaactcgtggcgcttacccgagccttagaactgggagaaggaaaaagaataaatgtgtacacagatagcaagtatgcttatctagtcctacatgcacatgctgcaatatggaaagaaagggagttcctaacctccggaggaacacccattaagtaccacagagaaatcatggagttantgcacgcagtgcaaaaacctaaggaggtggcagtcttacactgccggggccatcagaaaggtgaaggagaagaagcagaaggaaaccgccgagcagacgctgaggccaaaattgctgccaggcaggactttccttcagaaatgcccatggaaggacccctggtatggagcaaccccctccaggaggttaagccccagtattccccaactgaaacagaatggggactttcacgaggacatagttttctcccctcggggtggctaacaacagaggaaggaaaggtgctcatacctgaagccagccagtggaaaatacttaaaaccctccaccaaacttttcatacgggtattgaaagtacccataanatggccacgtccctatttacagggccaaacctcctcaaaaccatccggcaagtagtcaaagcctgtgaagtgtgccaaaagaataaccccttggcccaccgtaaggcctctccgggaggacaaagaacaggacattatcccggagaggactggcagttagattttacccatatgccaaagtcaagaggatttcaatacttattggtctgtgttgatacctttacaaattgggtggaagccttcccttgtagaatagagaaggcccaagaagtggttaaagtcttagttcatgaaataattcctagatttggacttccccaaagcttacagagcgacaatggtccagcttttaaagctacaataactcaaggaatttccaaggcactaggaatacaatatcaccttcactgtgcctggaggccacaatcctcagggaaagtcgaaaaggcaaatgaaacactcaagaggcatttgagaaagctagcaaaaactcatctcccacggcccactctcttgcccatggccttattaagaatccgaaactcccctcacagaatggggctcagtccatatgaaatgctgtatggatggccttttctcacaaatgacctcctgctcaatcaggaaacggccaatttagtcaaagatataacttctctggcaaaatatcaacaaaaccttaaaactttacccgaaaggtgtgacagggaaaaaggaatagagntgtttcaaccaggagatctagtattggtcaagtctctcccctctacctctccatctatggatcccttatgggagggaccatactcggtaatcctctctacccccactgcagttaaagtggcgggagtggaatcctggattcaccacacccgagttaaaccttggacacctcctgaggaacttacaggatcatcanctcaggagtcacaaggtcagccagaccagcctcgatacacctgtcagccacnagaggacctgcatctcctatttcggaaggaaacacctcagaccagaaaaactcctgcagttaatcctgaagaggaacttctccctacctaaangaggataagtggnnnnnnnnnnnnnaaaaaaaacctacatgatctttgacatctctccttgctctctttaatggaatccttctactgtttcgttacattattaagcacctttcttctatcgtccttccttctaacagcaatttactcctttttccctcctctttcctacgaccgttccacctacaacacgtcatgactcctcttaggcttcctgncatcctcttcgtactcgtgtccctttctccaactacaacacacnccccgtgtcagtgtgcctcccctggaggagncaactggcattctctcagaaactcttggggattaggtagccccttccaagcacccacatcttttgccacncatacttacatgagaaaagaatgttataaaactgcttctctctgctctcacaatggccgtacatatcaccaaggaaaaatgannnaatccgagctgactgccctgagaaatggggggccaacgcttgttggacatattatacccatataggtatgtctgacggaggaggcgtccaagatgaggctaaagaatggcatatccaacaagtaattaaaaacttagtccagctctccagtactcccagtccatacaagaaattagacctttccaggctacaagaaacccttaactctcattctcgtctctggagcctgtttaacaccacccttacaggaatacaagaggcctctcctagtaatccaaccaactgttggatgtgtctccccttgcgttttcaaccatatgtcccagtccctgtccccggacagtggaacttatccaccccagtcctaaacaccaccaaattaatcggtcccatagtcaccaatttaccagccacacaggcctcaaatctcacatgcataaacttcagcatgactctcaataagaacgcctcccgatgtcagtcctggatatcagtaacctcaggtttcacctgtctaacttcaggcatcttttttcatctgtgataacacagcctatcgatgcctaaatggcactccgaaagaactatgctttctctcctttctagcacctcccatgtccatatatactgaacaagagttacaaagtctccttataccccaatctcgccacacgcgagcccttattgtcccttttattgtaggagccggaatactgggcgggcttgggactnncggaattggaggcataacctcctccacccaattctattataaattatcacgagaattaaatgatgacatggaacgagttgccgactccctagtgaccctacaaagccagcttaattctctagctgcggtagtccttcaaaaccggagagccctagacttattaacagctgaaagaggaggaacctgcctcttcttnnnnnnnnnaggagaagaatgttgctatttcgttaaccagtcaggaatcattactgaaaaggtcaaagaaataagagaacggaagaaagtagaaaaaaggagcttgaacactcagggccctggaatatgtttaaccaatggataccttggctcctcccctttctaggccctgcgacagccatcctactttactcgcctttgggccttgcatttttaacctccttgtcaaatttgtttcctccaggatcgaggccatcaagctacaaatggtcttacaaatggaacctcaaatgagctcaactcacggcttctaccgaggacccctggatcgacccgctggtccctcactagcctaaaaagttcccctctggaggacaccacaactgcaggccccttcttcgcccctaaccagcaggaagtagccagaacgaccgccgcccagttcccaacagcagttggggtgtcctgtctagaggggggac
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 ZNF680 7 28.9 Highly correlated
2 ZNF723 5 15.2 Moderately correlated
3 ZNF2 5 99.0 Weakly correlated
4 ZNF766 4 43.0 Weakly correlated
5 ZKSCAN1 4 160.0 Weakly correlated
6 ZNF28 4 28.9 Highly correlated
7 ZNF320 4 28.9 Highly correlated
8 ZNF669 4 43.0 Weakly correlated
9 ZFP57 3 87.0 Weakly correlated
10 ZNF382 3 99.0 Weakly correlated
11 ZNF394 2 99.0 Weakly correlated
12 ZNF75D 2 94.0 Weakly correlated
13 ZNF679 2 28.9 Highly correlated
14 ZFP69B 2 99.0 Weakly correlated
15 ZFP37 1 99.0 Weakly correlated
16 ZNF584 1 99.0 Weakly correlated
17 ZNF597 1 94.0 Weakly correlated
18 ZNF324 1 99.0 Weakly correlated
19 ZNF263 1 180.0 Weakly correlated
20 ZNF251 1 94.0 Weakly correlated
21 ZNF701 1 28.9 Highly correlated
22 ZNF141 1 43.0 Weakly correlated
23 ZNF728 1 19.6 Moderately correlated
24 ZNF133 1 99.0 Weakly correlated
25 ZNF792 1 94.0 Weakly correlated
26 ZNF793 1 99.0 Weakly correlated
27 ZNF92 1 28.9 Highly 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 5 15.2 Moderately correlated
2 ZNF28 3 28.9 Highly correlated
3 ZNF680 3 28.9 Highly correlated
4 ZNF320 2 28.9 Highly correlated
5 ZNF669 2 43.0 Weakly correlated
6 ZFP57 1 87.0 Weakly correlated
7 ZFP69B 1 99.0 Weakly correlated
8 ZNF133 1 99.0 Weakly correlated
9 ZNF141 1 43.0 Weakly correlated
10 ZNF382 1 99.0 Weakly correlated
11 ZNF597 1 94.0 Weakly correlated
12 ZNF263 1 180.0 Weakly correlated
13 ZNF2 1 99.0 Weakly correlated
14 ZNF793 1 99.0 Weakly correlated
15 ZNF75D 1 94.0 Weakly correlated
16 ZNF92 1 28.9 Highly 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