ZRdb KZFP & Repeats
...

LTR_MER83A-INT

  • Name
    MER83A-INT
  • Repbase
    MER83AI
  • Type
    LTR
  • Emergence
    99.0 Mya
  • Dfam Id
    DF0000938
Description :

MER38A-int is flanked by MER83 LTRs. Note that MER stands for MEdiumReiteration frequency interspersed repeat. As such, MERs as a group area grab bag of DNA transposons and retrotransposons.
Consensus sequence The consensus sequences obtained from Dfam are derived from the seed alignment using a specialized caller. :
acattttggtggcccgtacggggactctctctccttacggggaaccctctcccctnctctcttttctctttcccaacttgggaccctcggtggacagcgtctaagcacggagacaactgcaggtctctggctggagctacactccggtgggactgaaaggtgtccgtgtggaagcgtctgaccgccacgcccgttcgggtgagggacctgagtttattttctcttttcagtctttcagcagccggcttctagtatccctctggcaattgacggtaactggccggggccactctccggtgttgcctgaaggccaaagggtgaacagggctggccgccctgcccggaagggggaaggctctctcctntcttttctggtcgnaagtccctaatccctacgtgtgacgcaactgacagcggaagctcgttcagggcaaattcacacacgtttcgggtgactcagaccctctctttctcactctaaattctcctgtggagtcagccagccatcctgttccggacgttgctaaatcaggtgatctcggacagcctcagaacggtgagtctcccctncccgccccctctcctgggccggcaccaggcggagntcttcctttaccctttttcctcgtacctgggctgatcacccagcgtnagtgagtacctggactggccatccagcgtaaggcccccgagcggccgagnggtcttttctaataggtgggacgcccctttagaaagtgcacccgagtccctcagcagacataagtggaacccttttcatcttggcgggacgccccgagagaaagtgcggttcgantagccccgagcggcgcgttttccagtcccaccatgggacaaaccccgtctattccttcagactcacctctaggctgcattctaaaacattgggacaaatttaaccctcagactctcaaaaagaaacgtctaattttcttgtgtaacacagcatggcccctatgcaggaaatcctcaaattagcctcctcagtcttttataaccgagagcagaataaggaggacagggctaagaagagagaaaaacgcagggacaagaggcaggctcaactgttggctgctttacaagcccccagccccctccaggtttccctaaggacactcctccagataactgccatcggtgcagaaggccaggccactanaaaggcaaantgccccaatgggataaatgggaaaaagccccgcatggcttgccccctctgccacaagctcggccactggaaacgggactgccctgagaaccgaagggcccccgggacagaatcccaacccctgatggccttaagctgaaggggctctctgctccggctggaaacagctcaccttaactggtgacttgcggaggtgggaggaattcgtcccacaccgtgtaggtctggggtgctaaggctctccctgacgggagataaacgagggtggtaggggtgctggccccgcaccgtgcagtggctggaaggctcacaagccctcctgtaaagcttaacctttccctctccattcctttctttttttctctttttctgttcaatccaggggtccagccttaaaagggaaaaacagtttccaacatcctagcccctgattttgtcgttctctttgggactccagctggttacatattatggcccgtttttgtgcacattttaaactgatgggcaaattacaacaagaaaaattcagagctcaaatggttaacctgcactatagagttaagtagagtcttctaaagctctctatcttcctctctttttttctgcctgctttaaatctgctgttactaagctgctggtgctgagactcattatttatggtctaactagaatgtaaacattggaaactcgtttgaaactgaaaaaaagggtaaaagaggttttgttaaaccaaacaacctagaatttttaacctcccttaaagttgatggaaataagtccagcgcctcttttaaaccttattcttagagctgactctttttattcaattctactacaggctctcagtaattatccaactgcctcacttaagcagcttcaccctcttgatattaatgcttttataagggaggtagtatacgattgctatttgcagggggacttccaagattaccgcccagatgaaatttctttatatttgtcctagtaatgtcatntacccccacgccacaacancgatgtgctaaggtactaggtgttttttaacgtttngttttcttatactctttacagcccttcttctttcctgtctccctgagttcactacatattgtcattttccttaaatatggctctgtttttatnntgtctgtcatggctaactattgcctcnatggctgcanccaggcacccactctanccagtaatatctcaggttgctaacataacacacagcactaactgctggatatgcccacgcgggcaggcactcgagaatgacattacactcctagcagtcccactatctatagaagaaattgctaacacgcaagcccgatgntctggattcgactacaccatntacacgcacaccaaaaacacaggtttaggaggggaacctaggccaatcgatccctcatggcaatcatccactgtgaccgagcggatngggaaggcaccagagaatggcctgtaaggctgcatcagaaactccgaggggtctggccctttcctaggggctttaacacaagcccattgcaattacaccctcaactataatcaaacacaccaggaatgggagccatacgacgactgtgacgagttcactgtgtacctccgcaggttttctctatggtggggaaacaacaaagttaatgccagcaaaatttatagtgattcctttatgcctataaatagttcagcaaccgggatggaatatataggaataggggtcgaaactggacaacttctcaacctcactaatacatctacancttttcctcgattttcccttatcccattaatatttaaaaatcttatctgtcaggccccacattcacataacacaacaagtnaaacttttacccccttatgcgtggatgactactttttgggtcaccgcccatccacatttgatccccggggaccatgggatccctctatttatgcaaattatactggaatccaaactaaccacacctatgcctggttacgaggtccctcctcgggagtttcattaaaaggaactgggttcttctttttatgcggatccaacatgtttctagccttgcctattaagtggagaggcacntgcactacagttgcagcnatacctggagtgcatatatataactcctcagacttcataacctctggccaagttccaaatttgggatccttcctaagtcgggccctccaaaggccatcagaagaaaacagaaacgggacttaacctcccatcatttggcatcctcgccactgataatcccgttatagagaggaatggtctaggacattctgtagccngtgcaatcttttggtttgcaggtatacccatgcttaagcgcagcattcgtaatctcaccatcctagtccggcaatcttgagaagctacagtcacggccatcgagggccaataacgggccctaaattcgttggcaggggttgtcttgcagaaccgacgcgctttggatgtgcttaccgctgaggcaggaggcacctgcacgctgttaaatgaaacttgttgcttttacatcaatacctcaggtcaggtagaagaaagtttagaaaagataaaagaaaacatcaaaatattagagggccttcaaaaaggagttcctcaagattcctttttngcacaactatttcaaagcttctccagttgggttnggccacgggttgccccacttctcccgcctataataatgctcatattagttcgtttatttgcaccatgtattgttaatgcnanatatctcgttttgtgtcttctagaatacaacaatttcaaaccaaaatgttactgcagcgagggtatcagccactaagagaactccataactctcctttggacgcagcaggacaaaattttaggctgcaaatgctgttcccccatggtcccacagcgaccctgcccaatttaantcccaactcagggatttaggcccatgtaacctcctgacngactaacaatcctaggtagggccaactctacgcccctggtcagcaggaagcagttggaagatgagaccttcacccacatgccaaagatttgtcattgttgctctgtcaggggggaa
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 10 28.9 Weakly correlated
2 ZNF766 9 43.0 Weakly correlated
3 ZNF382 3 99.0 Highly correlated
4 ZFP69B 2 99.0 Highly correlated
5 ZNF878 2 43.0 Weakly correlated
6 ZNF534 2 19.6 Weakly correlated
7 ZNF263 2 180.0 Weakly correlated
8 ZNF197 2 99.0 Highly correlated
9 ZNF547 1 74.0 Weakly correlated
10 ZFP14 1 99.0 Highly correlated
11 ZNF793 1 99.0 Highly correlated
12 ZIM3 1 87.0 Moderately correlated
13 ZNF723 1 15.2 Weakly correlated
14 ZNF701 1 28.9 Weakly correlated
15 ZKSCAN8 1 160.0 Weakly correlated
16 ZNF584 1 99.0 Highly correlated
17 ZNF561 1 43.0 Weakly correlated
18 ZNF257 1 0.0 Weakly correlated
19 ZNF175 1 94.0 Moderately correlated
20 ZNF490 1 43.0 Weakly correlated
21 ZNF394 1 99.0 Highly correlated
22 ZNF347 1 43.0 Weakly correlated
23 ZNF324 1 99.0 Highly correlated
24 ZNF2 1 99.0 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 ZNF197 2 99.0 Highly correlated
2 ZFP14 1 99.0 Highly correlated
3 ZIM3 1 87.0 Moderately correlated
4 ZNF561 1 43.0 Weakly correlated
5 ZNF534 1 19.6 Weakly correlated
6 ZNF680 1 28.9 Weakly correlated
7 ZNF347 1 43.0 Weakly correlated
8 ZNF584 1 99.0 Highly correlated
9 ZNF257 1 0.0 Weakly correlated
10 ZNF723 1 15.2 Weakly correlated
11 ZNF701 1 28.9 Weakly correlated
12 ZNF793 1 99.0 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