ZRdb KZFP & Repeats
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LTR_MER11D

  • Name
    MER11D
  • Repbase
    MER11D
  • Type
    LTR
  • Emergence
    19.6 Mya
  • Dfam Id
    DF0000718
Description :

MER11D is a retroviral LTR that has been proliferated by the HERVK-related retrovirus HERVK11. Generates 6 bp TSDs. MER11D is a very youngsubfamily of MER11 LTRs, 98% similarity to the consensus sequence.MER11D consensus sequence is only 64% similar to MER11A,B,C consensussequences, which are also young subfamilies (~90% similarity). Note thatMER stands for MEdium Reiteration frequency interspersed repeat. Assuch, MERs as a group are a grab bag of DNA transposons andretrotransposons.
Consensus sequence The consensus sequences obtained from Dfam are derived from the seed alignment using a specialized caller. :
tgtagggagaccccctgaaactattgctacggaataaaagatgaaatgctcctgattattgtaaatacaaaattgcatgcaggattgtgtaaagacaatgccaggttggactgccagaacgagccaacagcgcgtgatgtgcttccccctgcagagagcctatgaatggacgtgcagtcagggaggtttcacatcaccaagattcctatcccagaaaagcagatgttcatagctctgggaatggaatgcgacccttgtggagagcctataaacggacgcatggggggcgcctgtccatatggataagatagggctataaacgccctcatcttgccacggctcttctaggcctctttagggttaaggcatactcccttctgagaatttctggtctaaccggttgtctagcttcacgtcctgtttctatggattgtttgtaaccagcttttgctgcaactgttactgctgattaatatcttgctaatcataggttatggaaagactgtgtttctgttttaaggctctgttagaaattactgatgcacacactatattgtaaattcttatctctgtatactgtacttctgcatacagatgtactgtacttctacatacaaatgttatgttaaagaattacttcatccccatgtgaccatctcacctcataatcaaatgaccctaaatccctcactaacctacccccgccctcactaaacttaataataaatgctggtatatccagtgcattgttggcaccgcgggaccagaaggcggtgacccccctggacccagctttcactatcttgtgtgtgtctattatttctcgacctgccgatccgcctgggaacaaagagagagccccgttgcattgcgggctgctggccagatcccgcaata
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 ZNF611 144 19.6 Highly correlated
2 ZNF382 26 99.0 Weakly correlated
3 ZNF701 20 28.9 Weakly correlated
4 ZNF766 15 43.0 Weakly correlated
5 ZNF589 10 28.9 Weakly correlated
6 ZKSCAN8 7 160.0 Weakly correlated
7 ZFP37 6 99.0 Weakly correlated
8 ZNF175 6 94.0 Weakly correlated
9 ZNF197 5 99.0 Weakly correlated
10 ZNF28 4 28.9 Weakly correlated
11 ZNF141 3 43.0 Weakly correlated
12 ZNF584 3 99.0 Weakly correlated
13 ZNF394 3 99.0 Weakly correlated
14 ZNF597 3 94.0 Weakly correlated
15 ZNF18 3 160.0 Weakly correlated
16 ZNF274 2 99.0 Weakly correlated
17 ZNF257 2 0.0 Weakly correlated
18 ZNF317 2 99.0 Weakly correlated
19 ZNF417 2 28.9 Weakly correlated
20 ZNF587 2 28.9 Weakly correlated
21 ZNF534 2 19.6 Highly correlated
22 ZNF605 1 99.0 Weakly correlated
23 ZNF723 1 15.2 Moderately correlated
24 ZNF84 1 99.0 Weakly correlated
25 ZNF679 1 28.9 Weakly correlated
26 ZNF92 1 28.9 Weakly correlated
27 ZNF549 1 87.0 Weakly correlated
28 ZNF506 1 28.9 Weakly correlated
29 ZNF485 1 94.0 Weakly correlated
30 ZNF273 1 28.9 Weakly correlated
31 ZNF26 1 99.0 Weakly correlated
32 ZNF264 1 99.0 Weakly correlated
33 ZNF251 1 94.0 Weakly correlated
34 ZNF184 1 99.0 Weakly correlated
35 ZNF133 1 99.0 Weakly correlated
36 ZNF101 1 43.0 Weakly correlated
37 ZKSCAN1 1 160.0 Weakly correlated
38 ZFP57 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 ZNF611 52 19.6 Highly correlated
2 ZNF766 6 43.0 Weakly correlated
3 ZNF589 5 28.9 Weakly correlated
4 ZNF175 4 94.0 Weakly correlated
5 ZNF197 3 99.0 Weakly correlated
6 ZNF28 3 28.9 Weakly correlated
7 ZNF584 2 99.0 Weakly correlated
8 ZNF417 2 28.9 Weakly correlated
9 ZNF257 2 0.0 Weakly correlated
10 ZNF141 1 43.0 Weakly correlated
11 ZNF534 1 19.6 Highly correlated
12 ZNF605 1 99.0 Weakly correlated
13 ZNF549 1 87.0 Weakly correlated
14 ZNF264 1 99.0 Weakly correlated
15 ZNF701 1 28.9 Weakly correlated
16 ZNF506 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
1 ZNF766 43.0 Weakly correlated