ZRdb KZFP & Repeats
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LTR_LTR1D1

  • Name
    LTR1D1
  • Repbase
    LTR1D1
  • Type
    LTR
  • Emergence
    43.0 Mya
  • Dfam Id
    DF0000444
Description :

Consensus oscillates between two apparent subs, but coseg can notseparate these.
Consensus sequence The consensus sequences obtained from Dfam are derived from the seed alignment using a specialized caller. :
tgatagggacaggaggcagggaaattctgggcagaagagggcgggtccccggcgagggccccaccctcaagccaaagcctggaaccgcggcccaaagtgagaacntacatccctgttttcccgctcgaatgttgccttttccaaaaccacccatggcccgccccgccccccatcctgtgcccataaaaaccccaggctcngccggcagagaggagaagcagctggacgtcggagactacggttggacgtcggagagaagcggcttgacttcagagggacggcttgacggcgtagcttcggagaggagtccggccggggacggccggactccgggggaagattaccttcccgctccgtccccttttcagctccccttcccgctgagagccactttcatcggcaataaaatcccccgcatttaccatccttcaattcgttcgtgcgacctcattcctcctggacgccggacaagaactcgggtgccacgagtgcgggtgcaaaaggctgtcacactgaccctccgnnnncgncgncgnnnnncgnncgnnncgcgcgnnnnnncgnnnnnnccactgagctgttnaacacttaagccgtccgcggacggcaaagctaaaagagcactgtaacactccctctggggcttcaggggtcgcgggcacccccccctagacgctgccgcggggccngcacggagttttgctcctgccggcgcccaaaagcgctcgccccggctcctgcacccgctcacctgcgcgccccctcccgcgaggggtggagcgcagcgggtccgagtgagtggagttcgcccctgccggcgccgaagcggccggctagttccagcgcccgtgcactccagttcccgcccgcgaaggggtcagggaaaatntcctgcttca
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 ZNF347 185 43.0 Highly correlated
2 ZNF736 62 43.0 Highly correlated
3 ZNF680 43 28.9 Moderately correlated
4 ZNF263 16 180.0 Weakly correlated
5 ZNF382 10 99.0 Weakly correlated
6 ZNF274 8 99.0 Weakly correlated
7 ZNF317 8 99.0 Weakly correlated
8 ZNF394 8 99.0 Weakly correlated
9 ZNF534 6 19.6 Weakly correlated
10 ZNF92 6 28.9 Moderately correlated
11 ZNF18 4 160.0 Weakly correlated
12 ZNF251 4 94.0 Weakly correlated
13 ZNF705B 4 28.9 Moderately correlated
14 ZNF823 3 43.0 Highly correlated
15 ZNF84 3 99.0 Weakly correlated
16 ZNF679 3 28.9 Moderately correlated
17 ZNF28 3 28.9 Moderately correlated
18 ZNF468 3 28.9 Moderately correlated
19 ZNF766 2 43.0 Highly correlated
20 ZFP69B 2 99.0 Weakly correlated
21 ZFP37 2 99.0 Weakly correlated
22 ZNF320 2 28.9 Moderately correlated
23 ZNF343 2 74.0 Weakly correlated
24 ZNF257 1 0.0 Weakly correlated
25 ZIM3 1 87.0 Weakly correlated
26 ZKSCAN1 1 160.0 Weakly correlated
27 ZNF789 1 99.0 Weakly correlated
28 ZNF778 1 74.0 Weakly correlated
29 ZNF101 1 43.0 Highly correlated
30 ZNF75D 1 94.0 Weakly correlated
31 ZNF140 1 99.0 Weakly correlated
32 ZNF735 1 28.9 Moderately correlated
33 ZNF723 1 15.2 Weakly correlated
34 ZNF705D 1 28.9 Moderately correlated
35 ZNF253 1 19.6 Weakly correlated
36 ZNF282 1 319.0 Weakly correlated
37 ZNF677 1 99.0 Weakly correlated
38 ZNF675 1 8.6 Weakly correlated
39 ZNF563 1 28.9 Moderately correlated
40 ZNF558 1 99.0 Weakly correlated
41 ZNF554 1 99.0 Weakly correlated
42 ZNF528 1 43.0 Highly correlated
43 ZNF519 1 19.6 Weakly correlated
44 ZNF490 1 43.0 Highly correlated
45 ZNF479 1 6.4 Weakly correlated
46 ZNF33A 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 ZNF347 179 43.0 Highly correlated
2 ZNF736 61 43.0 Highly correlated
3 ZNF680 20 28.9 Moderately correlated
4 ZNF534 5 19.6 Weakly correlated
5 ZNF263 5 180.0 Weakly correlated
6 ZNF28 3 28.9 Moderately correlated
7 ZNF468 3 28.9 Moderately correlated
8 ZNF18 2 160.0 Weakly correlated
9 ZNF679 2 28.9 Moderately correlated
10 ZNF274 1 99.0 Weakly correlated
11 ZNF320 1 28.9 Moderately correlated
12 ZNF789 1 99.0 Weakly correlated
13 ZNF528 1 43.0 Highly correlated
14 ZNF317 1 99.0 Weakly correlated
15 ZNF343 1 74.0 Weakly correlated
16 ZNF251 1 94.0 Weakly correlated
17 ZFP69B 1 99.0 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
1 ZNF347 43.0 Highly correlated