ZRdb KZFP & Repeats
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LTR_HERV-FC2

  • Name
    HERV-FC2
  • Repbase
    HERV-Fc2
  • Type
    LTR
  • Emergence
    15.2 Mya
  • Dfam Id
    DF0000179
Description :

HERV-Fc2 may be single-copy in human (hg18) and chimp (panTro2), andappears to be hominidae specific . Curiously, LTR divergence (~5%)suggests an older insertion event.
Consensus sequence The consensus sequences obtained from Dfam are derived from the seed alignment using a specialized caller. :
ttggtgccaaaacccgggaggagacccctctctgacccagggtcggggagcatctcctctccctacctgccaggaaccagactcgggccagcgcattcggcctttgctattgggtaagtctcccctccgtcctgtaggccccgggaacctctgtctgtaatcgcggccacntcagagtcttccccccatcagtttccgactacgggaccgaggacgcggagacgtccgtcctcctcggcctccgccatccgcgcttcaaggaaggttgggggacgcccctccccggcctccgncnncccgcctcagggnagtggggggtgcccaatccaaaanctccctgaccttgaatcgcccgcctcaggacnatgggagcctcccagtccaaaatcgatcctaagacacccctcgggtgtctcctccgcaaccttaacgctctcggcctccgttcggacctaaaacctaaacgncttattttcttctgcaacaccgcttggccccaatacaaactngacaatggctctaaatggccannngaaggcactttcgatttctccatcctacaagacctagataatttttgccgaaaanngggcaaatggtctgaggtgccttacgtccaggcntttttanacttncgctccctccctagcctctgttcccaatgctccctnnnncagatcttnctnnctnnnncntccccctctnncnnngcgcctgactcctcccctctccccgagccttctgaagccctcncttttccaccancgccgnctgncctccctcctccccgtccaggntcctccggccccaccccaacggctcctccgctncctcctncnccaccttcctcccccnctaaccctcccgcttctgctctgccaccgccttcccccgtacccgcccacactcgnccnaagacagccctcttatttcctcttngagaggtggctggagctgaaggcatagtcagggtacatgtgcctttttctctatcagacctttcccaaatcggncagcgtttngggtctttctcatcagaccccactaaatatatacaggaattccgatatctaactcagtcctacgatctaacctggagtgacttaaatgtcatcctgacttctaccctctccccagatgaacgggaaagagtttnttctntagccaggcaacacgccgaccancttcatccaactgaccccgccaggcctncaggaacnntagcagttccccgagngganccccantgggactaccaggcngatcaggctagccgncgncggcgagattacatggtttcctgcctnntngaaggcanaaaggcagcttncaataaggctgttaattatgacaagctnaaagaaactacccaaggtaaagacgaaaacccagcagtttncntngcccgcctngcagcgacccttagacgctntaccgncctagaccccgnctccccggnaggggccaccgtcttnnntacgcattttatcacccagtcngctcctgacattagaaaaaagcttcaaaaattggaatccggccctcaaaccccacaacaggacttaatcaacctcgccttcaaggtgtacaataacagagaggaggcggccgagncgcaaagacaggcaacgctannncngangntacagctncntgcccnngccgtggnagccgccccgcggccggccggctccaggagccaaccgaaagggggttccggccaccgagcnccncctggancttgcttcaagtgccggaaatctggccactgggccaaggaatgcccgcacccgnaggattcctcctaaccgtgccccgtctgtcancgggcgggacactggaagtcggactgtccnagcgtcggagcgnccacagagcccctangctgcgaaaactccgaggcgnccggtgactccttcccactcctcggcgcggctgaagactgacgctgcccggactcggaagcccccttcaccgncgccgagcttcgggtaactcttacagtggagggtaagtccgtcccctttttaatcgatacgggggctacccactccacattaccttcttttcaagggcctngtttcccttcccccataactgttgtgggtattgacggcgncccttcnacccctcttaaaactccccnactctggtgccaactggacaacattcttttntgccactcttttttagttatccccacctgcccagttcccttattaggccgagacattttaaccaaattatctgcttccattcgnctgggctacagccacacctcnattgcnacctctttgcttcccccgccaacncnnagccgcgncnctccttcgccnntcctntcgctccctncgcccnttaacccacaagtatgggacacctctactccctccctggcccgacancatgcccccattaccatccnactnaannacccnaccanncttccctcgcggccncaatatcccatcccacccgaacancnctaagggttaaagcctgttatcactcgnctcctgcnacagcgcgttctaaaacctacaaactctccttacaattcccccattctacctgtccaaaaaaccgctggcangtacaggttagttcaggatctgcgccttatcaaccaaattgtcttgcctatccaccccgtggtgccnaacccgtacactctcctgtcctcaatacctccctccacaacccactattccgttcttgatctcaaagatgctttcttcactattcccctgcaccctnnntcccancccctcttcgctttcacctggactgaccctgacacccatnnctcncagcaacttacctgggctgtactgccgcaaggcttcagggacagccctcattacttcggccaagctctttctcatgacctcnntactttcnctccgcccctcngcncccttattcaatatattgatgaccttctnctttgcagcccctccttatctnnctcccaacaagacaccctcctgctccttaacttcttnncaaaanaagggtatcgggttccccctcncaaagctcaaatttcttccccatccgttacctacctcggcatttctctcatcgaaaccaccaagngcctccccgccgaccgngtcngcctcatcaaanacctccaacttctncaaaacgnanacaacatcctttccttcctaggcatggttggatactttcgcctttggatacccggttttgccatcctaacnaaaccactatataaactcgcaaaaggaanacctaccgaccccntanccgatcctaccctanttccccnccgtttccgncagctnnagcagcgcttncncacagctcccgcnctanccctncctnaccccncncaaccttttcatttctacacagccgaagtgcagggctgtgcggtcggcttaccagggcaaccggnaggacccgcctnncgnntngtagcctttctgtccaaacaacttgacctcaccgttctaggctggccatcatgtctccgtgcgntggcggccgccgcnatncttactnnagaggccctcaaaatcacgctcnatcacccactcacngtctacngctctcataacttccaaaatctactttctcncanacgcctgncccatctgnctccctccagnntccagctgtctcacgcnctctttgttgagnccccanatatcaccctgaccgcctcaccacctctcaacccngccacacttnttcccatagaagcccctgacccccctcctgncctgtcncattcttgtcccgaactcctnacnttcatccccatttccccactttccttcttcgnncgncctgttcctcaccctgatcacacttggtttattgatggcagttcaggcctcgccactcaccaccggcaanaggcaggctatgctatagtcttccacanctnntcattggaggctaccgctctgcccccctccactacctctcagcaagccgaactcgttgccttaactcgagccctactcttgncaaagggactacgcgtcaatatttatactgactctaaatatgcctntccatattgcacgcacncatgctgttatatggccggaaagaggtttcctcactacgcaagggtcctccatcattaatgnncctcttnnntaaaaactcttcaaggccttacgnnnnttccaagaggtggagntcattcactgcaagggccatcaaaaggcatcagatcccatcgctcagggcaacgcttatgctgataaggtagctaagcagctagctccnacttctgtccctnncccagcttccgcgnttttcccctccgnttcagncactcccacctactccccaccgaaaaccttccacctcacttcccacnnacaaggaatggtcgaccaagacggntgaacntngancaataannaaattctccttccagcctcacaggcccattctattgtcgtcgatttncataacctcttccacgtaggttacaagccgctagcccgcctcttagaacctcttttcctntnttccatcntggaanccntcatcctcnaggganatcacttctgtgttatctgttctacnntcacccctcagggattgttcaggcccccncgtccccatcaccagctcngngggnatctgcccgcccaggactggcaaattgactttactcacatgccccganncaggaactacnaatacctncttggtctggtagacactttcactggatgggtagaggcctttcccacagggtctgaganaggccacgccgcggtctcttccctnccggnagacataattcctcggtttggccttcccacctctatacagtccgataacggaccggcctttatttcaaaaatcacccaagcagtttctcaggctcttggtattcagtggaaccttcataccccttaccgtcctcaatcttcaggaaaggtagaacggactaatggtcttttaaaagcacacctcaccaagctcagcctccaaaaaaagnngacgtggacaatacttttaccacttgcccttctcagaattcgggcctgtcctcgggatgctacagggtacagcccatttgagctcctgtatggacgcnccttcttacttcccggtctnncccccactgnttcgccccctcccctcgcggnntatcttccnnntctntccctcntccgcgatcttctccgcgaacaagccgacgcaggccctcccgaanctaccccctcctccccggacgcccctgctncgctccctccaggagannatgtcttccttaaaaacccttantccaagaccttgancccgcggtggtaaggccctttccaagtcatcctcacnacccccaccgcagccaaactnccaggacnaccatcttggtaccatctttcnaggttaaaaaaggcnccnactcagcacgactggtcctcaaaactcaccccaacccggcttcgtatcacccatggccagaccttccccactatgcctcctactcctcctgaccctcctaacccccatagtgcccagtaactccctcctaactgaacccccgttccgatggaggttctacctgcatgagacttggacccaaggcaaccggctctccactgtcacactggcaacggtggactgccaacctcacggttgtcaggcccaagtaacttttaacttcacttcctttaaaagtgttctgcggggctggtccaatcccaccatctgctttgtctatgatcaaacacacagcaactgccgcgactattgggtggacacaaacggaggatgcccctatgcctattgtcgtatgcatgtgacccagctccataccgccaagaaactccaacacacctatcgcctgacatctgatggaaggacaacttacttcctgaccatcccagacccatgggattctcggtgggtcagtggagtcactggtcgactgtaccggtggcccaccgactcctacccagttggcaaactccggatattcctgacttatatacgagttatcccccaggttttgtctaatttaaaggaccaagcagacaacattaagcatcaggaagaggtcatcaatactttggtgcagtcccatccgaaggctgacatggtcacctatgatgacaaggctgaggcaggaccgttttcatggataaccctagtccgccacggggctcgccttgttaatatggcaggcctagttaatctctcccactgtttcctttgcaccgccctcagccaaccaccactagtagctgtacccctaccccaggcttttaacacctctggtaaccacactgcccacccttccggcgtcttctctgagcaggtccctcttttccgagaccccctccagccccagttccccttctgctacaccactcctaactcatcctggtgcaaccagacctattctggctccctatctaacctctctgcaccggcaggtggctacttctggtgtaacttcacccttacaaaacatcttaatatttcctctaacaataccctttctagaaacttatgcctccccatctctctggtgcctcgactcactctgtacagcgaggctgaactctcttcccttgtcaacccgcctatgcgtcagaagcgggccgttttcccaccgctggtaataggtgtctccttgacctcctcacttgttgcctccgggctgggcacaggtgctattgtacatttcataagctcttcccaagatctctctattaagctccagatggccatcgaagcctcagccgaatccttagcctctctacagagacagattacgtctgtggccaaggtggccntgcagaaccgnagagnnctagatctcctcacagccgacnaaggnggaacntgcgtntttctcggggaagagcgctgttnttgcatcaatgaatcaggcttagtagaaaccagcctcctcacccttgataaaatccgggacggtctccatcgaccctcctcaactcccaactatggaggagggtggtggcaatcccctttaaccacttggattatccctttcataagccccatcctaatcatttgccttttacttctcatagccccctgtgtcctcaagttcatcaaaaaccgcatcagcgaagtctcccgggtgacggtcaaccaaatgttactacacccttactcccgtcttccgacctccgaagaccactatgacgacgccctcactcagcaggaagcagccagatgattacgtcgcccctttttcttacagtatgaggtcggaa
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 2 15.2 Highly correlated
2 ZFP57 1 87.0 Weakly correlated
3 ZNF425 1 94.0 Weakly correlated
4 ZNF479 1 6.4 Moderately correlated
5 ZNF8 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 2 15.2 Highly correlated
2 ZFP57 1 87.0 Weakly correlated
3 ZNF479 1 6.4 Moderately 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