ZRdb KZFP & Repeats
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LTR_LTR39-INT

  • Name
    LTR39-INT
  • Repbase
    HERV39
  • Type
    LTR
  • Emergence
    43.0 Mya
  • Dfam Id
    DF0000508
Description :

While originally named HERV39, this is clearly non-autonomous.
Consensus sequence The consensus sequences obtained from Dfam are derived from the seed alignment using a specialized caller. :
attagttggcaaccanaaagggacaaaagtcccgagcggnngcctcgcccgtggcacatnagcccctggctgcggccacccttggaccccgtccagcagctgcctgaattattttattcagggacggatccgtgtatttngtgccnaaccaggcgtcgtggnccgtggcgcttttactttcgcagcattagaaataaggcaccgggctgggaagacgtcttttgtaagtggngagttcgtgggcaacagccccaaggtattttttnctttagacgctgggttctgctttggcaggacatctggccttgcttcggcaaggcactgggctctgcttcatcagagtatttggtttggtnggggatactccntagagagctgaagggatcgagaccttgagaaatcatatttgattttgatttgctnnnnnccgacttgcttgaaantctgtctaaagcccggccgaggcattaagggtttcgtcacctaaggttttgtcatctaaaatgggaaacacgagctctattccnccttgtagcccattagggtgcattctgcagaattgggccatttttagctttgagcccatgaaaaagaaaaagttttttttttttttaattgtagcactgcttggccgcaatattccttagactccgggggaaaatggcctgaaaangggtcctttaaattggactcctaaatttaaaaaaaaattttagagatctcttattctaaacaattgatgggaagatcaaattttaaaaaggacacataatagtgtcatggctagccttaaaaattctcttgactaaattaaagagcaaaaatctgacctaaaacaaagttaaaatccnttgcaagctcaaanctgcctgctttggatcccctncgggantaacagcgaaggccgctccacnctgtagtctagtagctaaaattccgccntttcaccgcggcggcctgggttcggtcagggaaccagtccttttggtttgatatttgtgtgacttttgccatttattgatccttttcccttccatggacagcttttgatttcctgtcttcttccatcttnggggcacacgggctttngggnccttcgtgtgtagacggtcagctgagaccctagagaatatggccggacagaaatgtgggttgtaccccatttgcggctagcgaaactttcctttctttgagctgtctttggggtggttctggatcttgtgaggactgctttgcacctctttggagacctcgtgcgtctcttggttaagtcataactaatccagggttctaactgaatagatggcaattgattgattttgcaaatagtgggccctaacataacattgtgaacacgacccatgtttacttatttcataaaccaggtgtaaacctgttttaaccaatcctgagtgcaatccaagtattgtaattgttctgctgctttgttagttaacaaagcaggagaacagttgttctaataagtggatctcttttaattcccaggacttggggatcttttgttctgttgagatttttgcagggctggtatttgttgtaacaattcggctgaaagataagaacatggatgtatgtagccgtgtgaagtgctttgctgagagcaaggaagattattttgagtcactgcacctgcctgcctccctggctataatacaaaaacataatcctttcaaataaaggagtgtaggaagtgaccgtccctcagcctcaccaatcaattcaaatcagttccaagaaaacagattcaaatcagtaacccaaaccctacccagagccaattctttctgaacaatagctgttaccaaggtctcaggagcattaggcgctcaattctattttaagtagcatggttggagcttaaccccaagtcaggtttaagtgattaaaccagttaagtaattaattttattctgcctctttatttaaaaaggacatgaggggttttacaacttaaaatacggtgaccatgaagcatttaaaaagagactggaagcctcataatggcaaagtgggaaatattctatcaggaatgtggacaaatagtttgagcatgaaattcgactctgagcttcctagcactcaaggcaatnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnttcaaggaagagtaagaacaaaaccaagaagtagcagcatcagcattttgtttgtttgcttgttgacaagcagcatttttgtttggagaagcaaacattcacttggcattacatttctggaaaattagatttcgtagatcctcatgtaagagacttggggtaacttgttcgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntttaggtctcaccatgaaatcatgaaagctcgaatcagtgacgtttcttctcgggagagcagtcaatttataattaagctcccgcgtccacgcctgatcccatgtcacntttatttttgactttggttcagggatgagaggtggttgctcacaatgacttgagtttcagaaagatggatttgagagtcacggctgatacaggtaacacaaacaagccagcttgagtcagccaccagaaaacccccatgccttctatttccactagttgctcaatactgtatttacctctatgtgctgctctcaagagagaaagtaaaaaaaccagggtgatcttggctagagttgccacaaggactagcactgacttcacggcctgaagaggagcttcagctgttggaaattctcagtgtgcacattttggcaatttccacctggaatgtggtcctgctgggatggtggcaaacagccagacctgtacaagtggcctgtgctcaaaggcaaatgtcctggccctgggcttgccctcctgaaccagctgacaagctggcccagttccagtgtttaaccttgtatacaaaggcaacttttcttaantcacatttgccggggaattcaattaccttgttttcttgccttctctcttctggtacttttgcaaccagctgtgagaactgcattgcaaatgcctgtagggagtgtttagaatcacagtgacccctatcactcttgtcggcgattcccagggaagattccagcttctctggattgacaaccaatgcttcccacaaggaaagggtacagaattaaatgcagacactccatctcctgcttccagccttcttaatgagaaagtttccacttgtggggacagctcagtgattgattctttttagctgtgtgtcttttggaaggcacagattccttcttagggtgccaggtgaatggcagcggtggtgagtaacagtcttgtctctaggacagtgtgctcttttgtggtcaatggaagggcatgagttggctttgggaagcaagggctggggctgtccccttgctgccaaagtcaagtcaaaggacaggaaacaagctccccaatttccccagtttattaaactggtgcattctgcggcaccctgtgcaggtctgagcatagcagatgtggggctttccctgtccaggtgagtcaagtgattcagccctctggctaattttctttcttggcacttggctctaagtcttgacttgactctagaaaaaatatgcttctcagaaatgggtaccacttggctaaaccacctacaagggagccagatatctctgcagaaattctctaggctcccccagccatccaggnagtaacgttaatgtcataaccttggttaaggcttattgctttcacctgggaggatacctttggaaagaagntcaaaagccagaaatatcagctgttcgtcccgctaaaatctggtaacaagagatttnaaatttttttaaaagagctctatagtcaaaagttgacttaattaaaactgaatatnnnntttaggctatntatgtatacattttaaggcctctgttctctctctgtaaaaacttctcagtcaactgaattcctctcttcttaaacccctgctagccatatgcgctccctctgtctgtctctccatttacttctgtctgtccctccttcctcttgccaccctcgatgccacatgaggggaccaaaaaaanannttctaacagcctgggatcccttaaggaaaacagaaaaggcgccacggactcctcttttgggaggaacctctgtttttcctcacggaaccccaagagttgtaagcggacagannnnttncctctcaggtctaaaactctgctctcttttgcattgcattacctgatctcttggcttttggggtaccagaaattactttgtattgtgaaaaaantttccttataaaatncnatggcannttcctgtnattttgtgttacttggcatccattttnaatcttcctccaacacancccaaactccttcttgaaagggaataaattctttctctctctctnctttgagatataaattgctacaccntgttttctctaaaactcggtgagggcttgagccatgtgggacagatgaactttaaccttttccatttacagaggcacaacttgaatccaaccgtccttttaacttttgccagtctcatggctagagttttaaaatcaaagctatagagtctttgtttatgcctgtctggatntttattatgtncatgtgtatgnctttgtatattgtctatgataccaaattgacttataaataaangagtactcataaattaaataaataagcccaaatgcttttcaggttcacgtgactttagtaatctttggtaaataaagatagttttaaaattattggtaaaataaaatagaaacgtcttcagaatttaatttagacatttttgcccgggtctactggtcagatactgtctctgctagatgttttaaggtcataaaactattgcttctgtaatatttttgatacttgcttgacttgtctataaacttatgtacgnctttagatttgagcctttaggccatgntgaggcctagntccaggnanngtcctttgtcctgggctctgcatctggtacattaaaattgcttacctcctaggtttttcactaaaaataagagttactaagagttaacattgtaattaatatatgtaattaaaactactagatataagagaaacaattctatatgcaaagnatnttttntaaaaaaggatatnaggagtnnangnncgtttttnatnnggttataaaaggcatgggaatgtggtttttgttaaagggaaagtaagatgnaaagaaagttnaaaaganagagtaatttttcttttacatgagagagaactttgtgtggtcaaaatgatgatagggaaaagaaagtaaatttttgtcctaaggtaaaatgataggacaaaactgaaggtttaagcaagttgtagaannnggtttgtggaagattgatcttgtgaaaggaattttgtgtgtgatcaagttggctaaaattnaaaggggattatttagtttttctaaaaattgagcattaatatnaaaagcacactgatgcagggccagagtctgggcccctgtgtcggaataacagggttttcttggagcattgatctgctctttaatagaaaattgtaaaaggttataaaaggtttacggaaatcttaccttgtgtggtcaaaactgattgagattggatggatttgtttataagattttattaaaattagctttagcattaataatacgctaatgcaaaggtaaaatttggttttctcttttaacaagattttcgtgtaatattaataagagatagtaaaagattttgtttaccttttgagtaaactgcaaaaanaaaagaggggaaagagaaagagacagattcagttggcctcacgctgtctttattaggtcttatgnttgtttgggaaactgagtctcctctctatcaaagagtaaattttgctttttaaaatctttgagttatcactttggctaaatgaatgactattattttacggtgacctgtgatcctattttgtgatatcaagtgttttaaacctttgatatttgacaaactttccaaaatcaaatttcaaattctaaattcagtctttttgacctcaaactaactttttnatattaggncccctgaaagtccaagagagacatattnggcttatttggtatgttaaaatcatacaggaagcattgtcaaatatgaaatggtgtttaactttctttgggttatatttatataaatgtgttattagtatgtgttccaaaattgtatgagattcctataattctgatgtctcaatatgttatcagtaataattatgattattacgttaaattgttgtatgccacagatccttgtcaattgcgtctttaaccatggctnttcnaagacttgtcgtctataatttctcaaaaagcggtttcttctttaaggaagttcatggaaaggactctgacaagtgctcttgaatacaggtttctgataactttggagatcgtgccattgactagnnnaaannnnnnnnnnnnnccgagaaaaaacttccaggactctnattggagagctgatgcgttcatgaggattgctgacccaatatcaagcagaacaggagttaattgcatgggactaaactaanagangactgaaanaattttttnacttttttgtttgaaacattgctgttctttttgttttgttttccagagtcaagaaaactttttcttttgagctatttatagcttttaacaattgngtaaagtatactcttgtgagcaaaatttgaagcatntttctctctacctgatttctccagaattcggaaactatttgtgagtattcttantttatggcaatatagttatttgcataagttcaataagaatctgttttcttttgtaacaggacacaattggagacactggttattttaccaaggctttgactggaatggcatattttcagatatgaccagactgctttgaggaattgagattgactttatagagccgataaaaagcccctgggaaaaactgtctacacggttcctttacagggtttctgaccttgtggtaagtaaagaatgtcactttctgacagcccaggaacctcaagntattttgggacctcgagaagagaggaattcacccaattcatacaggtatctgcaggcacagataaatccttggctnggcttnagaggcttttaaaaagtctaatctganattccttatgaaaaaatgttccagcaaagccaactttaaaagagcctatatggccaatgactattcttgctgcactttatgcaaataatcaggccaagtataataagactaaaacttattttgcaaataaattggtcctactatgatttgtctttggtaaaaatgggggatggagagagaaaaatttcttccatttttctgacttggactcaatgaaattgctactacctttttctcgagctgaagctcatgccntgtgatgcttcgagtctaacatctagacgcctcgactgactgccctccggactntaaggagactggtttnnggncngcttcattcttcttggatgggaccatatgaggtgctgctgatgactcattcctcagtaaaattaannagagtcaaactgnnnnnnnnnnattcctgggtaaagctggtttccnaagagtcatttgaccccaactctcgaaatgcaacagaaaatgggaagcacatcataacaacatcacagtcctgaccatccaagcctgaggtggaggcnnncccccaaggctgacttctctaattggaccagcaaaccctgatagatcccaagttgccactcagaagacagactcctaaatataagtaataagagatacagacntacgnngttntttgccatcntttattttntncgtctactactggctaagcagattctgtgtgctgccctggggtcttaattacttcaggtgctcacgttgaactatnaatatgattgcctttttgttatgcttccttgtggactntnatccccccaaatcaaaagggnaactctatgnttaggatttctnanncgttggcaaaganaggtaacctgtagatatgtcatctgacccagctaatagaacaacggtgcncnagttcnttnaaccgtcatancctgacaatccattattttagaagtcccctctgttggttgcctcnntataangncttnctcgattttncctcttnagangagcaaggcccccaaatatncctccttagaggcctgctccctaaacatgtcagaaatcnctatcnnnnnnnnnnnnnnnnnttagctcccnacaaattaancgncttgntaaaactaaacggtccacanactctngggatccacaaatccatacttgcccgggtaccaaaaagatggagctgggtacttcttcgggcgaactttgttaccttggtggggagtggcgtcccatgagcgcataattagaaatctctccctaactttangaattcttgccgangaaactgcatgcaatagccgcccagcagaaaggaattaattcattggctcaggttgtcttagataataggatagccttagattacatcttagccgancagggagaagtgtgtatggttgcaaatnccacatgctatacttacataaacgaatctgcggaggtaaaaactcattaaaaaaaattagagaacaagccacttggttacaacaggtctccccgactgtccccaaggactggttttctttnttttcttggattcctcatggaatacagtccatgttttctggattgctaaagttaggcatatcaatcttgctaattttgcttatgctttatattataaccaaattaaaatgttgtaataaagcagtgactaaagcaactaatataatgatagttcagcaccatggtgccatgcctgggactcatgaatatctcgagctccatgctagaaatttctctcctcatatcctagtccccaatctttgccccaattcagcagnaagtagccagagcggtctgcatccctatacccttcaggattgaggagtgacgaaagacagggggaa
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 6 99.0 Weakly correlated
2 ZNF766 3 43.0 Highly correlated
3 ZNF30 3 94.0 Weakly correlated
4 ZNF2 2 99.0 Weakly correlated
5 ZIM3 2 87.0 Weakly correlated
6 ZNF479 1 6.4 Weakly correlated
7 ZNF8 1 99.0 Weakly correlated
8 ZNF850 1 28.9 Moderately correlated
9 ZNF723 1 15.2 Weakly correlated
10 ZNF680 1 28.9 Moderately correlated
11 ZNF679 1 28.9 Moderately correlated
12 ZNF585A 1 99.0 Weakly correlated
13 ZNF486 1 8.6 Weakly correlated
14 ZNF317 1 99.0 Weakly correlated
15 ZNF28 1 28.9 Moderately correlated
16 ZNF263 1 180.0 Weakly correlated
17 ZNF222 1 43.0 Highly correlated
18 ZNF133 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 ZIM3 1 87.0 Weakly correlated
2 ZNF382 1 99.0 Weakly correlated
3 ZNF680 1 28.9 Moderately correlated
4 ZNF585A 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