ZRdb KZFP & Repeats
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LTR_LTR52-INT

  • Name
    LTR52-INT
  • Repbase
    HERV52I
  • Type
    LTR
  • Emergence
    99.0 Mya
  • Dfam Id
    DF0000544
Description :

Internal sequence of retrovirus-like element with LTR52 LTRs. Theelement appears to have been non-autonomous, as part of the pol gene ismissing.
Consensus sequence The consensus sequences obtained from Dfam are derived from the seed alignment using a specialized caller. :
attggcgcngtgagcaggatgtctaggcgatgaccaccaccacctgggggtctttcttctcttgctttggcttgctaactggctctgctgcctgctggcnagcatgcactttgagctgctgcctgctggcnagcttgcgctttgagctgtgctgctttgtgctgcatttgctgagtcctaccgagcctctgttatagatttaaccgacctaagtcggaagtttcgataattggcatttagggacaggagtatgggattggggccctccttaaagtggccctgggtcgtgtgtctcggcccggacctatctgtgtgtcttagattgaatcgtgtgtctcgattccagcataagccgtgactgacgctaggctcaggggaacgactcttatnccctgtgaccgttggttgtcgtgtctcaaccaggcgttggcccccattctatagagcgctcaggggaaagactgataccctgtgcaatatatgggcccatcgggtggtcgctcgtgtggaggaagagcagtcactatgtggcatgctgaggtccacactcctaaaagcagatggctcactaggaccctacaaaatgcctttgctgctgctgctgctatgcctctgtcacanaaaaagatcctgatcctcagggtttagggaaaaacactccatggcacacccttatgaaacagncccaaatgcttacccnacccttaaaggccagaggacaccatcgccctatggaaactgtaaaggaccacgaagacgggtctaattgagtgccgcgacttgcaacatgccaaggggttaattcaaacccgactntaagcccggggtccttaaacccaataaagcaaccattgccatgggggaggcccctaaccctgatgatactgatttgaggctctctggaggaagaaacttataaatatgagcagggtagagaggaccccctccccctaaagtatatccagtaactcaccnaaaaacaaaacgaaaacttgaanaagaggnaaaggaaacaaaaaccanaatttgaccaattggaatccaaatttactaaaanantntaaaaaaaaagataaaaagggtgctgattggcttttgcgcctctacaacataggttctaaattaactttaacactgctgaaatgcaccaattggcaaaccttcatgnccttaatcaatactggggctcaaattacagttatacctggggatcactgaaatttaaacaaggtacccctnatantctagggaggttanctcgaannncataaaatagaggacaaacaggtatgcctcaccttaaccaccggaactnttgccttgcctaaattccccatggtcatagcgcccgttgccctaaaataccccanagtgggcatggatactctgacctaacgagtaataaatnaaaataaaattaagtctttggcacttanaatcggcttganaaaatgggaccccatggaccttnctctcccggttaaaatagtnaanatgncccaatataaattaaaacagggcctncaaganttaagacccattatacaagacctattnagggaagaagcgattatccccnctgcttctccttttaanancccgntttggccgntnntcaaacttgangaaaatgaatggcacctaacgntgantnaccgtaacctnaatgccgtggtcccaccgattaagnccccnatacctaatatattactaaaattactgactccatccaatcagcaactggnaaatattttgctntcgtagatttggctaatatgttctnttnagtgcctatttcaacagcctctcancncagtttgccttcaccttcgaaggaacacaatatacccttacctgnctacccatggganaccccaacggcnctgccatcgnanacaatctttgcnatnnaagatcttaacnacatccaactttctccaggagcacaggtatgacatnacatgnacgacatcctcctcaaaggagattnatttancnnntcnntncaganncnnagannaccnnnaaaagggnccncganaaaaggggnnggncnntnnnccnnnncgannnncagaatttggacagctgagtaaannattccaactaattattggtcaccccntgacatgctccatgttctatccctaacactgctnaagaagcannnnnnnnnnnnnnnnnntaatattgaattaattaaaattaaacaaagaggaaattcttgtccctcccagcatttcaataaacaggcccaacgtcttttagncntttncgggttttggaggcaacgtatttctcatttacaaattttacttaagcccatttatgctgttacttacaaatcggcccactttgaatggggtcccctacaacaaaaggctctagaatctgtccaaattgcaatnnataggcactcccgttagtgccccccagagactccttcactgtagaggctttagcaacctcctctcgngcctcctggagtctctggaccacccgtgatggccataagttgcccgcgggcttctgacgcaagaaactgccctcctcagccccatgctacacaccattggagcggcaactgctggccgcatactgggcncttctggagatggaggctctcacgggccctgagcccgtgactctccgcacccagctgcctattatgccttgggtcgtggaggcagcaccctgaaagctcggcatggctacagaggcctccttactaaaatggaaacggtacttacagaatagagccaaacctgggccctctggcatatcccgcctgcaggaggngatggcttcccctgtcctcagtcccttgccagatgcnatggcgccggaggaggtcacccctctcccggacccattggctacctggggagccccttgggatcaactgagtgancagcaaaggganttcatacactttatggatggcagcgccaccatcacatgtgatgaagcctctagtggagagctgctgctntccatcccctaaccgggacatccctgatnaaggacgggacccaagggtcagcacaattggccgaacttcaggcagtcatcttagcactaaggatgccctggccaacaancggccccatctgcacatttttacagactcttgggccattgccaatgatctggccgtctggtccggccaatggcagcaacaattccttatccaaggttccccctttggggtaaagaannnctctgggaatttcttgcctcacagatacccaaaatataaatcaaggtcacacatgtctctgcacatactaaagccacaatacaaggcctcaccaagacactccttatccccttcagagttccagacattattgatagtgaccaaggcactcatttcacttctcaaaatacacaacgctgggctcttgaanaaggcattcaacggaactttcacctcccttaccggcctcaggctgcaggcctcatagagcgccataatggcttacttaaacaagttcaaattcaattaaatgaaacatggcacatttcagtcatcagtcaaacatcaggggtgaat
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 ZIM3 3 87.0 Moderately correlated
2 ZNF486 3 8.6 Weakly correlated
3 ZNF479 3 6.4 Weakly correlated
4 ZNF382 3 99.0 Highly correlated
5 ZFP57 3 87.0 Moderately correlated
6 ZNF222 2 43.0 Weakly correlated
7 ZNF2 2 99.0 Highly correlated
8 ZNF705D 2 28.9 Weakly correlated
9 ZNF701 2 28.9 Weakly correlated
10 ZNF490 2 43.0 Weakly correlated
11 ZNF519 2 19.6 Weakly correlated
12 ZNF93 1 8.6 Weakly correlated
13 ZNF878 1 43.0 Weakly correlated
14 ZNF723 1 15.2 Weakly correlated
15 ZNF705B 1 28.9 Weakly correlated
16 ZNF679 1 28.9 Weakly correlated
17 ZNF563 1 28.9 Weakly correlated
18 ZNF133 1 99.0 Highly correlated
19 ZNF425 1 94.0 Moderately correlated
20 ZNF157 1 99.0 Highly correlated
21 ZNF317 1 99.0 Highly correlated
22 ZNF263 1 180.0 Weakly correlated
23 ZNF251 1 94.0 Moderately 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 ZNF133 1 99.0 Highly correlated
2 ZNF157 1 99.0 Highly correlated
3 ZNF723 1 15.2 Weakly correlated
4 ZNF2 1 99.0 Highly correlated
5 ZNF490 1 43.0 Weakly correlated
6 ZNF701 1 28.9 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