ZRdb KZFP & Repeats
...

LTR_MER57E2

  • Name
    MER57E2
  • Repbase
    MER57E2
  • Type
    LTR
  • Emergence
    87.0 Mya
  • Dfam Id
    DF0000870
Description :

MER57Es was originally known as MER93a_LTR. Note that MER stands forMEdium Reiteration frequency interspersed repeat. As such, MERs as agroup are a 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. :
tgttaaaataattaaatgggaggccattagactgaggtggctctaacgccctgggttcctacataagcaaaccgaaacctaactcaganncgnnncccgcgancgnnnaatttaaaagaaaacgaaacttaagctcagccaatcacaggcggccaactgggcattagttgtattgtcntgaacttcccaccgggatagtccaaataaggcaactgcccaaactttaaccaatcaaataatttctttgctctgcttctacattcaccctataaaagccttcccttcanacncctccggcggagccccnaaccacttccggtttggagctgcctgattcatgaatcgctgtttgctcaaataaactctttaaaattttaatgtgccnaagtttatcttttaaca
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 ZNF549 30 87.0 Highly correlated
2 ZNF382 4 99.0 Weakly correlated
3 ZIM3 3 87.0 Highly correlated
4 ZNF766 3 43.0 Weakly correlated
5 ZFP28 2 99.0 Weakly correlated
6 ZNF77 2 87.0 Highly correlated
7 ZNF793 2 99.0 Weakly correlated
8 ZFP37 1 99.0 Weakly correlated
9 ZNF133 1 99.0 Weakly correlated
10 ZNF394 1 99.0 Weakly correlated
11 ZNF589 1 28.9 Weakly correlated
12 ZNF823 1 43.0 Weakly correlated
13 ZNF92 1 28.9 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 ZNF549 17 87.0 Highly correlated
2 ZNF793 2 99.0 Weakly correlated
3 ZFP28 1 99.0 Weakly correlated
4 ZIM3 1 87.0 Highly correlated
5 ZNF133 1 99.0 Weakly correlated
6 ZNF766 1 43.0 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