ZRdb KZFP & Repeats
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LTR_HERV1_I

  • Name
    HERV1_I
  • Repbase
    HERV15I
  • Type
    LTR
  • Emergence
    43.0 Mya
  • Dfam Id
    DF0000163
Description :

The associated LTRs are the HERV1_LTR variants. Target siteduplications are 4bp. The HERV1_I consensus encodes gag, protease,reverse transcriptase, RNase H, integrase and envelope proteins. HERV1elements in the genome are ~6% diverged from the HERV1_I consensus.
Consensus sequence The consensus sequences obtained from Dfam are derived from the seed alignment using a specialized caller. :
tttctgggggctcgtccgggattggagacggcaggtttctgtctcctttgcctgtgggctggagccccgggncgcgggagacccgggacccnaggcgccaccgggnaagacttagcccggaaggagancggctctcccgcgtcccggngccctcccccggcagcgcaaacggaaccganngaggggctgcaggacgatcncaggagcagcgcgcagncagnccgctgaaccgcggtaaggttgggcccnaggaaggcccgtcccataaggacggaaggggagcctgatcacctcccggggcgcgacnactagtccgacccagaggggctgggggcggcgggagtggcccgccgattcggatgaanctcacgcccccactacaagcgagagtggttcactgggtctggagacgggaactggaggtgtgtgggtgcgtgcgaaccnacccgggacacgagggaggctcgtttcatccgatgaggtggggnaggagtggtgtgtgtatgtgtgtgaatgtgggagcctaactaggctcacccgggacacgagagaggctcgtttcatccgatgaggagtcctggggcgggggaggtgtgtgaaagtgtgtgaaagagacggtctcgggagaggccaacgcggggagtgacgtggggaggcacagatctcttagcgcggactgtgtgctccgaggcgagtgtggganaaaccagacctaggncactgcatacggccgataggaccagctccacagctncacagcagcagttggctgtgacctggctaagcagcgtccgaacctcccgtaataggacccggtctggtggatccgagagtgaaagtgagagtgaaagcgcgccgcgagggaggaaatgggaggaaaagcatcgaagccnactccattggagtgcatgctgaagaactttaagaaaggttttaatggtgattatggggtnaagctaactccncagaagctgagaacnctttgtgagatagactggccntcttttaatgtagggtggccggccgagggnacnatagacagggaaataattggccgngtgtttcgggtggtcaccggggtcggagaacagccngggcacccggatcagtttccgtatatngactcctggctaagcgtaattcagacccgcccnaagtggctgcaggcctgctttgaggnntactgtaagactctagtggcccggacaaaacnaggaaccatagaaaagacccgcaaggcgcagncncaagagaaggagtcgcagggaaagcagaaaaaacctgtcctacaggccccgccngaagagttagaaantccacccccctatgcnccaatttatccatctctggcaaggcttaggcaggaggccgccccggcagctgcctccggaggntcagactcagaggagagcacccctcaggcnncaccacgcagggaggagccagagcccctgcctganaagccaagggaggaactccaggatgaggtcggccgcctcaggtcaggccgcgcccgagcnatgcagatgcccctccgagaaacnnggggacaaatttatttggatgcacagaatgaagtccaagggggagaacggctcttcgtttatcagcccttctctactactgatctcttaaattggagacagcatactccctcctatacggagaagccccaggctcttatagacctaatgcagtccatcttcctaactcacaaccctacctgggctgattgcaaacaacttcttctgtcattgtttaatacggaagagcgccgnagagttatacaagcggctcnccagtggctggagagcaatgcgcctgcaggcacaggagatgtcaggcagtatgcacaacaggcnctcccgatagaggctgacccaggctgggacccnaaccaggctcaagggctacaaagcttgcagnggtatcgagaggcactcctaaatggaataaaggctggagggaaaaaggcaacgaatatcggaaaggtctcagaggtccgccagaagccagatgaaagtcccagtgaattttatgagaggctctgcgaggcttaccggctttacacgccatttgacccagaggctgcaggnaatcagtgcatggttaatgcggcatttgtaagccaggcgcaaggngacatnaagcgaaagcttcagaagttggaaggntttgaaggtatgaatattacccagcttatccaggtggctactaaggtgtttgtaaatcgggatgaggaggccaagagagaagccaagcgcagagcnaaggaaaaggcaganttgctggcngcagccctggttggaagagaaactggntttgcgagaggacgtggacgtggtcgtggatgcggtcacggtagaggacaagctaggccaggccaggaggccaggncaggncaagagggccggcctaggctngagagagatcaatgtgcgagatgcaagcaganagggcactggaaggatgaatgtccagagagagaaaaggataaaggcaacaaccagggacagaatggctggccagggccccctncngccgccggncanggcgtagtaggatcngacgcggatctaatcgggctggcaggagtcgatgattattntgaggactgagacagaccgggctccatctcattaggccccgaggagcctatggtctcaatggaggtagggggccgaaaaatggactttatggtngatactggtgctgagcactcggtngtgactcaagcaattgggccgctgtctaaaaactatgccaatatnattggggctacaggngtcacagaaaagacgccttncttcaaatcnaagagatgtgtgattggaggncaagaagtccaacacgagtttttatatttgccaaattgtccggtgcccttgttaggaagagacttgctccagaaactgcaggcncaaatctcctttacaccgagaggggacatgaccctaaacctaggtcaaagaaaggccatggtantgacccttaccgtcccnanaacagaggaatggagactctatgagagnagttgcnaggaatntgnaaagangcacancgcagctgagaaagaggnantgtntacgganttacttctcaagctgccaggggtctgggcggaggacaatcccccggggctagccgtaaatcaggcacccgtagtggtggagctgctgcgaggnacctacccagtgcggatccgtcagtatcccattcccgtagaggccacccangggattacaaaacacttaaancggctccttgaatttgggataatagaaagatgtgcctcctcntggaacactccnctgctgccggtgttaaagccctctggngactaccggccngtacaggatttgcgggcngtaaacaaggtcgcggctacactgcatgccattgtgcccaacccgtacacnatgcttgggcgaatncctgctgatgctgcttggtttacatgcttggacatnaaggatgcgttcttctgcatccgactagcccctgnaagccagggcatctttgcctttgagtggggcccatcncagtatacctggaccagactcccccaaggatttaaaaactccccaaccatctttgaggaagcactagcctcagacctgaaggctttcacgccaccaagtgaccgctgtgtcctgttgcagtacatagatgatctattgttggccgcacccacaagagaagagtgcntccaaggnacagagagcctccttcgngtnctgtgggaggctggctataaggtgtctaaggaaaaggcacaaatctgtggccaaggagcncggtatcttggctttnacgtctcccaagggcagcgtgagcttggacgngagcgaaaagagactgtntgtagcattcctcggccngacacnaggcggcaagtgcgggagttcctaggggcagctggtttctgccgcatttggattccaaactactcgctcntggcaaagccnttgtatgaggctaccaaagngggggaaaaggaacccctcctgtggggaaaagagcaggacatggccttcaaggaaatcaagaaggctttgatccaggccccggcattaggactgccagacatgacaaagcctttttacctgtatgtccatgaaagaaaaggaatagctacaggagtcttggtacaaacgctagggtcatggtatcggcccgtggcatatttgtccaagcgactagacttggtggctatgggatggccaccctgtttcaaggcactggcngccactgccctgttagcngaagatgctaacaagctcacatttggacagaggttgataattcgggtgccccacacggtcgtcaccctgatggagcagagggggcatcgctggctctctaaccctaggatgttaagatatcaagggctcttgtgtgaaaacccntacataaccttggagactgtgaataccctaaatccggccacactgctgccaatagaatgggcggagcatggaaagcccccgttgtgtggcccagggtatcactgttgtgtggaaacagtggatgaagttttctcaagccggaaagacttaaaggaccagcccttaaaagacccagatgttgaatactttactgatggaagcagcttcatatctgagggtgtcagaaaggccggatatgcagtggtnacactgaactcagtagccgaagcccgccctctgccggtcggaacctcggcccaaagggcngagctaatagctctcacnagagcactgctcctggcgaaaggaaagtcagtaaacatctatactgactcaaggtatgcttttgccactttgcatgcccatggagccatatataaggaaagaggattattaactactgaaggaaaggaaatcaaaaataaaaaggaaatagagcagctcttagaagccgtatgggctccaaaagaagtagcagtcatccattgcaaagggcatcaaacaggaggaggtgatgaggctagaggaaacagaaaggcggacagagaagccaaaagagctgcaatgacagaggtaactaagaaggaagagacccntaccatgcccttactggagcttccccttacagaaccccctaactactcctctaatgaaaaggcntggttcgagcaggagagcggaagttaccagaaaggaggttggtggaagttctcagatgggaggcttgccatcccagaagcaatngccccccggttcataaagcagtttcatcaaggaacgcatatggggaaaacngcattagagactctcgtaggacggcatttctatgtgccgcgcctaactgccatcactcgagccgtttgtgagcaatgtttnacttgtgcccaaaacaatccanggcaggggccaacacggcccccagggattcaagaaactggagcnacgccntgtgaaaacctgcttgtggactttaccgagctgcctcgagccggaggctaccggtacatgctagtgtttgtctgcactttctcagggtgggtcgaggcatttcccaccaggacagagaaggctcgggaagtaaccaggatcttactaaaggacattattcctagatttggactgcctctaactttaggntcagacaacggcccagcatttgtggcagaagtagtacagcagctaacgcagatgttaaaaatcaaatggaaactgcatacagcctatcgcccacagagttctggaaaagttgaaagaatgaaccggacactnaaacagctgttaaagaagttttgccaagaaactcatctaaggtgggatcaggtgctgcccatggtccttctccgagtcaggtgcacccctactaaattaactgggtattcaccctatgagatagtgttcggccgaccacccccaatcataactcagataaaaggggatttaaaagaaattggggaattaaccttaagaaggcaaatgcaagccttaggtgaggccatgcaggaaatacaagggtgggtaagagaaagaatacctgttagcctcacagatgcagtacatcccttccaacctggagactctgtctgggtcaaacgatggaacccaaccaccttcgggcctttatgggatggcccccatattgtgatcntgtctacccccactgctgttaaagttgcaggtatcacaccttgggttcatcatagccggctgaaaccngcagccncagctcaggaccagtggaccagtcaacaagacccagaccacccgacncggctgatcctgcggngaaaccaagccgcngcnganaaggacgactgccctgctccgaccacaccggaggctggtcggtccacgcacggctgaagcttgaggaaacatcaagccctgctctagtcacacaactggaagctgactagtctacgcatggccgaagcttgaggaaacgtcaagccctgctctagtcacacaaccggaagctgactagtctacgcacggccgaagcctgaggaagtcaacgntagataagtaaatgtggattgaatttacaagcgtagttatactcttacttgtactgattgttttgctgtcatgttatctttgcaaatgctgccaagcttgttgcccagaagggtgcccgtgcatagtataagcttaatcatactagtaatactgangctaacaggcatgaaaggggaccaagatgactgtcatcactgtatgatagaagcctggtccggaaaaggtatgactaaaactctgttataccagacctactatgagtgtacagggactcatacgggaacttgtgtctataaccagactagttactcggtctgtgatccnggaaacgggcagccccaagtatgttatgacccagagttcttgccctatgacttctggtttgaagtccaaattggcgaacccctaatgccatcatatacaaaccccacagaaaccggggtcggtaaactcgtaaacaaaacagaggtattcccttactcgcataaagggcctgtctccatatattttgatgcctgccaagctgcacatctcagcaaactaaacaatattggggccgtctgtaaaaatctaggacaagaaagagtcagcagcagagccgccaaggccgtaacaggagaacccgaaaaggantgccctgattgtgacantcagtggaccacacatgagttcagccagcgcctntacgcaggaagagtngctctgcttgccagccaagaggcgaagatngggtgcgcgactggaacatgcaacccnctcaatctgacnatactaaagccaaatatgcctttctggactaaagggcataaaggagngctaanctttgatcgggaaggagcaaacctaggtattccnctagtcattacnaagaagacccaangggccnaagttcaagttagcccaatgcaacagttcaggttttntaaatccttcaatgaacactttaaccccgaggnaccaaaagttcaaattccnccnatatcagctgaaaacctgttcgctcagctagccgaaagtattgctantaatctnggagtcacctcatgttatgtatgtggaggtaccaatatgggagaccaatggccctgggaggctagagaattgatgccacaaganaattttaccntacctgaatttgttacaaagttcaatgcaaacccaagtgtttggctactaaggacccctatcattggaagatactgcatagcacgntggggaaaggnctttcaaacccaggtagggganacaacttgcctaggtcaacaatatttcgaagaatccgagaacaagacacagtggagaagctttatagacaattcctctgtgccagattttaatcccctcttncagtttccagcgctaaatcagtcatggtatcaactagatgctccaaatgtttggagagcaccngcaggactatattggatctgtgggacaaaggcctatcaactattgccnganaagtggacnggagcctgtgtgttaggaacaataaggccatccttcttcctactcccactgnagcaaggggaagatctaagttacccggtctatgacgaaganagaaaaagggccagaagaaacgtntttacncagataagtaccgtggaaaagataaacacaaacatnaagaaggacattgaaatagggagctggaaagacaatgaatggcctcctgaaagaattatcaaatactatgggccagctacntgggcncaagatgggtcatggggntaccgtactcctatttacatgttaaaccgaatcataagattgcaagcagtactagaaatcatagtcaatgaaacagcccgagccttggatttgctagccatacaggcnacccagatgagagatgccatatatcaaaataggctagcattagactatctcctagcctcagaaggaggagtttgtggnaaacttaatttgacnaactgctgcttacaaatcgatgacaatggaagagctgtcatggaaatcactgccaggatgcggaagttagcccatgtcccggtccagacctggtccggatggagcccaaattcactttttggaggatggttctcatggtttggaggctttaaaactttgataatcggttttatagccataataggnggatgcctaatnctnccttgtctcctgcctcttctcatcagaagcatccagtccaccatagaagcaatagtggaccggacaactaccacccgaataatggcnctgcaaaagtaccaaccggtnccccaagaagagtatgtacccacncaagaagaaatagataactgtggtgctctttattaatctacatttatgncgagcaccaaagggggggaa
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 ZNF766 22 43.0 Highly correlated
2 ZKSCAN8 7 160.0 Weakly correlated
3 ZNF723 6 15.2 Weakly correlated
4 ZNF589 6 28.9 Moderately correlated
5 ZNF75D 5 94.0 Weakly correlated
6 ZNF175 4 94.0 Weakly correlated
7 ZNF701 4 28.9 Moderately correlated
8 ZFP57 4 87.0 Weakly correlated
9 ZNF382 4 99.0 Weakly correlated
10 ZNF486 4 8.6 Weakly correlated
11 ZNF506 3 28.9 Moderately correlated
12 ZNF584 3 99.0 Weakly correlated
13 ZNF479 3 6.4 Weakly correlated
14 ZNF263 3 180.0 Weakly correlated
15 ZNF197 3 99.0 Weakly correlated
16 ZKSCAN1 3 160.0 Weakly correlated
17 ZNF597 2 94.0 Weakly correlated
18 ZNF679 2 28.9 Moderately correlated
19 ZNF18 2 160.0 Weakly correlated
20 ZNF274 1 99.0 Weakly correlated
21 ZNF528 1 43.0 Highly correlated
22 ZNF534 1 19.6 Weakly correlated
23 ZNF568 1 99.0 Weakly correlated
24 ZNF66 1 0.0 Weakly correlated
25 ZNF133 1 99.0 Weakly correlated
26 ZNF761 1 19.6 Weakly correlated
27 ZIM3 1 87.0 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 6 15.2 Weakly correlated
2 ZNF479 3 6.4 Weakly correlated
3 ZNF506 3 28.9 Moderately correlated
4 ZNF766 3 43.0 Highly correlated
5 ZFP57 2 87.0 Weakly correlated
6 ZNF589 2 28.9 Moderately correlated
7 ZNF75D 2 94.0 Weakly correlated
8 ZIM3 1 87.0 Weakly correlated
9 ZNF133 1 99.0 Weakly correlated
10 ZNF18 1 160.0 Weakly correlated
11 ZNF597 1 94.0 Weakly correlated
12 ZNF534 1 19.6 Weakly correlated
13 ZNF701 1 28.9 Moderately correlated
14 ZNF568 1 99.0 Weakly correlated
15 ZNF584 1 99.0 Weakly correlated
16 ZNF528 1 43.0 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
1 ZNF723 15.2 Weakly correlated