ZRdb KZFP & Repeats
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LTR_LTR88A

  • Name
    LTR88A
  • Repbase
    LTR88a
  • Type
    LTR
  • Emergence
    99.0 Mya
  • Dfam Id
    DF0000612
Description :

4 bp TSDs. 3' end matches LTR85, which is tentatively a Gypsy LTR. ~80%similar to LTR88b. Many CpGs. Middle region least well defined.Outrageous substitution level (>35% in borEut13) partly due to CpGs.
Consensus sequence The consensus sequences obtained from Dfam are derived from the seed alignment using a specialized caller. :
tgtagcgggagtcccagcttgagcctaaactgggattcagacgtgtctgggcgtgtctgatgaaccggtggggcgggcccgccaggcgtctatttgcatgagttgatttgcatgggggggaagggagagctgggggnggngntttgtatgtggggccntggggnagaggggaagggggaaacggggatggagaggacagcacggtgtctgtctctgacggcccggcctccacggactcgcgtctgagccccgtggagagaggggctgcaggcagaagctgaaggagctgttttcacgagggactttgtgagacncgggggcacaagcagcgctgcttcggggcccaggtgacaaagtgcgacacagagtnggggagaggggcattctccccacttctgcgcggaacgcagcgcggctccggcgcggcgaggactncggggaacgcagcgccgttcggcacctcgagggtctgcagcttcgggagcgccgggagacagcgccctcggcacggacatcagcgttctcacggagggcgccggcagcagtggcagcggcgaggcgccgccctcaagtggcttcgcgggcagcggacatcaacgaggaggnccggagcggaagaggaagagcgggccggctgtgagcacacgtgagacaccccctggggactcccagaaataactgggggagactttgcagggggctgaggtcctgcgtcgngcaggtgggggcaagagccagcgaaatttgggttattaccgttaatgtgacctcatttgtacccacaggctggtgaggcctggggaaactcgggttaca
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 ZNF382 52 99.0 Highly correlated
2 ZNF263 26 180.0 Weakly correlated
3 ZFP37 21 99.0 Highly correlated
4 ZNF2 17 99.0 Highly correlated
5 ZNF394 17 99.0 Highly correlated
6 ZNF766 17 43.0 Weakly correlated
7 ZKSCAN1 13 160.0 Weakly correlated
8 ZNF18 13 160.0 Weakly correlated
9 ZNF534 11 19.6 Weakly correlated
10 ZNF680 11 28.9 Weakly correlated
11 ZFP69B 8 99.0 Highly correlated
12 ZNF324 7 99.0 Highly correlated
13 ZNF585B 7 99.0 Highly correlated
14 ZNF479 7 6.4 Weakly correlated
15 ZNF701 6 28.9 Weakly correlated
16 ZNF793 6 99.0 Highly correlated
17 ZNF610 5 28.9 Weakly correlated
18 ZNF425 5 94.0 Moderately correlated
19 ZNF175 5 94.0 Moderately correlated
20 ZNF101 5 43.0 Weakly correlated
21 ZKSCAN8 5 160.0 Weakly correlated
22 ZNF485 4 94.0 Moderately correlated
23 ZNF584 4 99.0 Highly correlated
24 ZNF554 4 99.0 Highly correlated
25 ZNF705B 4 28.9 Weakly correlated
26 ZNF589 3 28.9 Weakly correlated
27 ZIM3 3 87.0 Moderately correlated
28 ZNF528 3 43.0 Weakly correlated
29 ZNF133 3 99.0 Highly correlated
30 ZNF317 3 99.0 Highly correlated
31 ZNF705D 3 28.9 Weakly correlated
32 ZNF75D 2 94.0 Moderately correlated
33 ZNF597 2 94.0 Moderately correlated
34 ZNF675 2 8.6 Weakly correlated
35 ZNF786 2 99.0 Highly correlated
36 ZNF792 2 94.0 Moderately correlated
37 ZNF736 2 43.0 Weakly correlated
38 ZNF8 2 99.0 Highly correlated
39 ZNF558 2 99.0 Highly correlated
40 ZNF707 2 74.0 Weakly correlated
41 ZNF92 2 28.9 Weakly correlated
42 ZNF320 2 28.9 Weakly correlated
43 ZNF486 2 8.6 Weakly correlated
44 ZNF441 2 43.0 Weakly correlated
45 ZNF257 2 0.0 Weakly correlated
46 ZNF251 2 94.0 Moderately correlated
47 ZNF429 2 28.9 Weakly correlated
48 ZNF202 1 160.0 Weakly correlated
49 ZNF274 1 99.0 Highly correlated
50 ZNF273 1 28.9 Weakly correlated
51 ZNF264 1 99.0 Highly correlated
52 ZNF778 1 74.0 Weakly correlated
53 RBAK 1 99.0 Highly correlated
54 ZNF140 1 99.0 Highly correlated
55 ZNF808 1 19.6 Weakly correlated
56 ZNF816 1 28.9 Weakly correlated
57 ZKSCAN5 1 160.0 Weakly correlated
58 ZNF547 1 74.0 Weakly correlated
59 ZNF284 1 43.0 Weakly correlated
60 ZNF28 1 28.9 Weakly correlated
61 ZNF695 1 28.9 Weakly correlated
62 ZNF682 1 28.9 Weakly correlated
63 ZNF34 1 99.0 Highly correlated
64 ZNF611 1 19.6 Weakly correlated
65 ZNF433 1 43.0 Weakly correlated
66 ZNF440 1 28.9 Weakly correlated
67 ZNF586 1 43.0 Weakly correlated
68 ZNF585A 1 99.0 Highly correlated
69 ZNF490 1 43.0 Weakly correlated
70 ZNF506 1 28.9 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 ZNF534 6 19.6 Weakly correlated
2 ZNF263 5 180.0 Weakly correlated
3 ZNF479 3 6.4 Weakly correlated
4 ZNF133 2 99.0 Highly correlated
5 ZNF680 2 28.9 Weakly correlated
6 ZNF485 2 94.0 Moderately correlated
7 ZNF793 2 99.0 Highly correlated
8 ZNF2 2 99.0 Highly correlated
9 ZNF440 1 28.9 Weakly correlated
10 ZKSCAN8 1 160.0 Weakly correlated
11 ZNF528 1 43.0 Weakly correlated
12 ZNF92 1 28.9 Weakly correlated
13 ZNF705D 1 28.9 Weakly correlated
14 ZNF597 1 94.0 Moderately correlated
15 ZNF589 1 28.9 Weakly correlated
16 ZNF701 1 28.9 Weakly correlated
17 ZNF429 1 28.9 Weakly correlated
18 ZNF320 1 28.9 Weakly correlated
19 ZNF34 1 99.0 Highly correlated
20 ZNF264 1 99.0 Highly correlated
21 ZNF257 1 0.0 Weakly correlated
22 ZNF585A 1 99.0 Highly correlated
23 ZNF736 1 43.0 Weakly correlated
24 ZNF273 1 28.9 Weakly correlated
25 ZNF75D 1 94.0 Moderately correlated
26 ZNF584 1 99.0 Highly 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