ZRdb KZFP & Repeats
...

LTR_MER50C

  • Name
    MER50C
  • Repbase
    MER50C
  • Type
    LTR
  • Emergence
    43.0 Mya
  • Dfam Id
    DF0000808
Description :

MER50C is a minor variant of the MER50-type LTRs. Possibly primatespecific, or perhaps restricted to Euarchontoglires. Note that MERstands for MEdium Reiteration frequency interspersed repeat. As such,MERs as a group 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. :
tgttagagtaggtagttagacatgagcagggcaggagagagggcccccaggaatgtcgggcantcgtcaggcgatggtcaggcagttatnaanctgtccctctgaaataatgagcagggcaggggagggaccccagaantgtcnggcgnccatcgggtgatggncaggcggncgtnaaactgtccctctaaaataataantggtcacggccggcgccgggagggaaaggagtctcccaacagatagaaaacacctgaagctggcgagccgcaattcccgataaggtctcaagcatgcgcagtaanggggcaaaatggcggagtttgaccggtatatgaccttcctctgggggcgctcgaccggtaagggaaaatcgccccaagtgagcatgcgcacaacttcagtaaacacactgcgcatgcggcccctcccaagtgctggcaggccactgcgcatgcggcgattagncaacagcccgcccaagggaagaacgaagggaggagacagagagcccgggaaaagatacggngtataaaagccccgagccaagggtcgagcggggcactcgatctctcaagtcgcccgcttggccctcttccaagtgtactttnctttctttaataaactctcactttgcttaaaataaactttcnctcctgctttaaancttgcctntgtctctcggccgaattctttcttccgagaagacaaggnaccgaggttgctgcggacccgccactccggagtttctccggatagctgcagactcaccgccggtaaca
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 ZNF382 8 99.0 Weakly correlated
2 ZNF766 7 43.0 Highly correlated
3 ZNF263 5 180.0 Weakly correlated
4 ZNF793 4 99.0 Weakly correlated
5 ZKSCAN1 4 160.0 Weakly correlated
6 ZNF680 4 28.9 Moderately correlated
7 ZNF394 4 99.0 Weakly correlated
8 ZFP37 3 99.0 Weakly correlated
9 ZNF18 3 160.0 Weakly correlated
10 ZFP57 2 87.0 Weakly correlated
11 ZNF786 2 99.0 Weakly correlated
12 ZNF441 2 43.0 Highly correlated
13 ZNF197 2 99.0 Weakly correlated
14 ZNF324 2 99.0 Weakly correlated
15 ZNF182 1 99.0 Weakly correlated
16 ZNF85 1 28.9 Moderately correlated
17 ZNF7 1 99.0 Weakly correlated
18 ZFP69B 1 99.0 Weakly correlated
19 ZNF133 1 99.0 Weakly correlated
20 ZNF175 1 94.0 Weakly correlated
21 ZNF705D 1 28.9 Moderately correlated
22 ZNF705B 1 28.9 Moderately correlated
23 ZNF701 1 28.9 Moderately correlated
24 ZNF607 1 43.0 Highly correlated
25 ZNF554 1 99.0 Weakly correlated
26 ZNF549 1 87.0 Weakly correlated
27 ZNF534 1 19.6 Weakly correlated
28 ZNF519 1 19.6 Weakly correlated
29 ZNF274 1 99.0 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 ZNF263 2 180.0 Weakly correlated
2 ZNF680 2 28.9 Moderately correlated
3 ZFP57 1 87.0 Weakly correlated
4 ZNF382 1 99.0 Weakly correlated
5 ZNF607 1 43.0 Highly correlated
6 ZNF793 1 99.0 Weakly correlated
7 ZNF766 1 43.0 Highly correlated
8 ZNF549 1 87.0 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