ZRdb KZFP & Repeats
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LTR_MSTC

  • Name
    MSTC
  • Repbase
    MSTC
  • Type
    LTR
  • Emergence
    74.0 Mya
  • Dfam Id
    DF0001044
Description :

MSTC has 5 bp TSDs. It represents an intermediate subfamily betweenMSTB1 and MSTD. Note that a full-length ERV-MaLR (Mammalianapparent LTR retrotransposon) element is derived from an ERV (EndogenousRetrovirus), but only contains the Gag gene (that is, no Pol or Env).
Consensus sequence The consensus sequences obtained from Dfam are derived from the seed alignment using a specialized caller. :
tgctatggtttgaatgtttgtcccctccaaaactcatgttgaaacttaatccccaatgtggcagtattgagaggtggggcctttaagaggtgattgggtcatgagggctctgccctcatgaatggattaatccattcatggattaatggattaatggattaatgggttatcatgggagtgggactggtggctttataagaagaggaagagagacctgagctagcacgctcagccccctcgccatgtgatgccctgcgccgcctcgggactctgcagagagtccccaccagcaagaaggccctcaccagatgcggcccctcgaccttggacttctcagcctccanaactgtaagaaataaattccttttctttataaattacccagtttcaggtattctgttataagcaacagaaaacggactaagaca
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 ZNF585B 47 99.0 Weakly correlated
2 ZNF547 31 74.0 Highly correlated
3 ZNF707 27 74.0 Highly correlated
4 ZNF675 20 8.6 Weakly correlated
5 ZNF586 19 43.0 Weakly correlated
6 ZNF486 11 8.6 Weakly correlated
7 ZNF680 6 28.9 Weakly correlated
8 ZIM3 5 87.0 Weakly correlated
9 ZNF382 4 99.0 Weakly correlated
10 ZNF479 3 6.4 Weakly correlated
11 ZNF263 2 180.0 Weakly correlated
12 ZNF766 2 43.0 Weakly correlated
13 ZNF793 2 99.0 Weakly correlated
14 ZNF554 1 99.0 Weakly correlated
15 ZNF701 1 28.9 Weakly correlated
16 ZNF705B 1 28.9 Weakly correlated
17 ZNF705D 1 28.9 Weakly correlated
18 ZNF679 1 28.9 Weakly correlated
19 ZNF778 1 74.0 Highly correlated
20 ZNF610 1 28.9 Weakly correlated
21 ZNF585A 1 99.0 Weakly correlated
22 ZNF528 1 43.0 Weakly correlated
23 ZNF506 1 28.9 Weakly correlated
24 ZNF471 1 94.0 Weakly correlated
25 ZNF394 1 99.0 Weakly correlated
26 ZNF347 1 43.0 Weakly correlated
27 ZNF169 1 94.0 Weakly correlated
28 ZNF140 1 99.0 Weakly correlated
29 ZNF101 1 43.0 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 ZNF585B 23 99.0 Weakly correlated
2 ZNF675 20 8.6 Weakly correlated
3 ZNF586 19 43.0 Weakly correlated
4 ZNF707 13 74.0 Highly correlated
5 ZNF680 3 28.9 Weakly correlated
6 ZNF479 3 6.4 Weakly correlated
7 ZNF793 2 99.0 Weakly correlated
8 ZIM3 1 87.0 Weakly correlated
9 ZNF486 1 8.6 Weakly correlated
10 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