ZRdb KZFP & Repeats
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LTR_LTR28

  • Name
    LTR28
  • Repbase
    LTR28
  • Type
    LTR
  • Emergence
    43.0 Mya
  • Dfam Id
    DF0000480
Description :

LTR of endogenous retroviruses related to MER4-int, MER41-int,MER57-int, and MER65-int. LTR28 elements share common fragments withMER52, MER61, MER61B, MER61C, LTR1 and LTR27.
Consensus sequence The consensus sequences obtained from Dfam are derived from the seed alignment using a specialized caller. :
tgatagcgacaggaggcagccaaatgcctaggcagataggggcgggtacccggtgaaaccccacctccaagccgaagacagtttaaagcctgaaagccaagctacaagtcccgnntaaatcctcggaccggattgagaacttgtcttcctgtttggcgcgctttcctctgattgatccccacccttcacctattttacatatacctaccctttcctaattggttttctacactgtcgtgcccacctttgagtggtgtcttcgctttaaccttttttgcatactcacaaaccaatcagcacgcactnnnccccatcctgtgcctataaagaccccagactcagtcggtagaggaggagacggcctgacttcacgnncgnnnnncgnnntgggaaagagacaacctgacttcggggaagacgacctgcccttcccgtcccctctccagctcccctctccgctgagagccgttttcatcgctcaataaaattctccgccttcaccatccttcaatcgtccgcgtgacctcattcttcttggacgccggacaagagctcgggacccaccgagtgcgggtacccagaaaggctgtcacaccggccctttgccctcgccggcggagggcagccgccccacgcgacgnncgcgncgncgnnnncgnnncgnnnccgnnnncgcgnnncgnnntgaggcaaggggccaactgagctgctaacacgccgccgtccgcggacggcggaactaaaggagcnnnnnnncgnactgtaacaccccctctggggcttcggggtcgcgggcaccctcacctgggcgccgccgcgttcccctcgaggcgacacgcctggtctggccgcgggccccgcacggagcttgctcctgtgtcggcgcccggagcggccggccggatcccgcactcgctcgctcacgtgctccctcccgcaaggggctgagcgcggcgggccgagtagacggggcgcccctgccgcgagtccggcgaaggggccgagaaaaatcctgcatca
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 ZNF680 294 28.9 Moderately correlated
2 ZNF347 50 43.0 Highly correlated
3 ZNF736 41 43.0 Highly correlated
4 ZNF28 17 28.9 Moderately correlated
5 ZNF382 7 99.0 Weakly correlated
6 ZNF320 6 28.9 Moderately correlated
7 ZNF486 5 8.6 Weakly correlated
8 ZNF263 4 180.0 Weakly correlated
9 ZNF519 4 19.6 Weakly correlated
10 ZNF766 4 43.0 Highly correlated
11 ZNF554 3 99.0 Weakly correlated
12 ZNF257 3 0.0 Weakly correlated
13 ZNF558 3 99.0 Weakly correlated
14 ZNF534 3 19.6 Weakly correlated
15 ZFP69B 2 99.0 Weakly correlated
16 ZNF679 2 28.9 Moderately correlated
17 ZNF705B 2 28.9 Moderately correlated
18 ZNF793 2 99.0 Weakly correlated
19 ZNF506 2 28.9 Moderately correlated
20 ZFP57 2 87.0 Weakly correlated
21 ZNF141 2 43.0 Highly correlated
22 ZNF816 1 28.9 Moderately correlated
23 ZNF799 1 43.0 Highly correlated
24 ZIM3 1 87.0 Weakly correlated
25 ZKSCAN1 1 160.0 Weakly correlated
26 ZNF124 1 43.0 Highly correlated
27 ZNF701 1 28.9 Moderately correlated
28 ZNF140 1 99.0 Weakly correlated
29 ZNF610 1 28.9 Moderately correlated
30 ZNF605 1 99.0 Weakly correlated
31 ZNF157 1 99.0 Weakly correlated
32 ZNF274 1 99.0 Weakly correlated
33 ZNF479 1 6.4 Weakly correlated
34 ZNF530 1 28.9 Moderately correlated
35 ZNF490 1 43.0 Highly correlated
36 ZNF514 1 94.0 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 ZNF680 64 28.9 Moderately correlated
2 ZNF347 49 43.0 Highly correlated
3 ZNF736 41 43.0 Highly correlated
4 ZNF28 15 28.9 Moderately correlated
5 ZNF534 3 19.6 Weakly correlated
6 ZNF257 3 0.0 Weakly correlated
7 ZNF141 2 43.0 Highly correlated
8 ZNF320 2 28.9 Moderately correlated
9 ZFP69B 1 99.0 Weakly correlated
10 ZIM3 1 87.0 Weakly correlated
11 ZNF157 1 99.0 Weakly correlated
12 ZNF793 1 99.0 Weakly correlated
13 ZNF554 1 99.0 Weakly correlated
14 ZNF263 1 180.0 Weakly correlated
15 ZNF816 1 28.9 Moderately 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 ZNF28 28.9 Moderately correlated
2 ZNF347 43.0 Highly correlated