ZRdb KZFP & Repeats
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LTR_LTR88C

  • Name
    LTR88C
  • Repbase
    LTR88c
  • Type
    LTR
  • Emergence
    99.0 Mya
  • Dfam Id
    DF0000614
Description :

4 bp TSD. 3' end matches LTR85, which is tentatively a Gypsy LTR. ~80%similar to LTR88b. Many CpGs. Middle region poorly defined. Outrageoussubstitution 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. :
tgtagcaggggtcccagcttgagcctaagctgtgttcaccctaggattcagacatgtctgggcatgtctggaggactggtggggcgggcccgccaggggtctatttgcatgagggaccgaggagcctcctgggaaagaactcatcctaagggaagagagagtcgaggcacacaagtttggtccaaggacagtgggccagngtcggaggggaggggcgattctgagtacagcacggtgtctgtcactcagattgtcctccggcccagcccccatggactcatgcctgagtcctagggagaggggactgcaataaaagagcaagtaaaaactaaaagagctgtttcactaaaatctccgtgggacattgagagcgcaaggcgtcagcagcattggcgccggcagcgncagcggcgatggtggcgtagcacagagtgnagaaagggggnancctctcccacctnnncngggancgcagtgcagctttggggacttgaggcagcagggctctnnnnnnnnnnnttgaggagctcctgcangccagcagcaggtggcagcgtcttcnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnggctgcccagcaggagcnggnatctggcgcgagacagtgcccggcggagcggcagnggcgccnagtggaancagacttgttcgtgagcacacgtgagacaccccctggggactcccagaaatanttggggaggantttgaagggggctggagttccgcgngagcgggtgggggcaagagccagagaaatatngnttattgctgttatgtgaccctatttttacccccaggctggtgtggcctggggaaacacgggttaca
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 70 99.0 Highly correlated
2 ZNF263 20 180.0 Weakly correlated
3 ZFP37 16 99.0 Highly correlated
4 ZNF394 15 99.0 Highly correlated
5 ZNF766 12 43.0 Weakly correlated
6 ZNF680 9 28.9 Weakly correlated
7 ZNF2 8 99.0 Highly correlated
8 ZNF324 7 99.0 Highly correlated
9 ZNF534 7 19.6 Weakly correlated
10 ZNF320 7 28.9 Weakly correlated
11 ZNF18 7 160.0 Weakly correlated
12 ZNF589 7 28.9 Weakly correlated
13 ZNF479 6 6.4 Weakly correlated
14 ZNF101 5 43.0 Weakly correlated
15 ZNF175 5 94.0 Moderately correlated
16 ZNF554 5 99.0 Highly correlated
17 ZIM3 4 87.0 Moderately correlated
18 ZNF705B 4 28.9 Weakly correlated
19 ZNF317 4 99.0 Highly correlated
20 ZNF701 4 28.9 Weakly correlated
21 ZNF558 4 99.0 Highly correlated
22 ZNF610 4 28.9 Weakly correlated
23 ZNF257 4 0.0 Weakly correlated
24 ZNF679 4 28.9 Weakly correlated
25 ZKSCAN1 4 160.0 Weakly correlated
26 ZFP69B 4 99.0 Highly correlated
27 ZNF584 3 99.0 Highly correlated
28 ZNF793 3 99.0 Highly correlated
29 ZKSCAN8 3 160.0 Weakly correlated
30 ZNF573 2 94.0 Moderately correlated
31 ZNF641 2 99.0 Highly correlated
32 ZNF597 2 94.0 Moderately correlated
33 ZNF705D 2 28.9 Weakly correlated
34 ZNF506 2 28.9 Weakly correlated
35 ZNF486 2 8.6 Weakly correlated
36 ZNF485 2 94.0 Moderately correlated
37 ZNF723 2 15.2 Weakly correlated
38 ZNF429 2 28.9 Weakly correlated
39 ZNF331 2 94.0 Moderately correlated
40 ZNF28 2 28.9 Weakly correlated
41 ZNF274 2 99.0 Highly correlated
42 ZNF778 2 74.0 Weakly correlated
43 ZNF251 2 94.0 Moderately correlated
44 ZNF248 2 99.0 Highly correlated
45 ZNF140 2 99.0 Highly correlated
46 ZNF816 2 28.9 Weakly correlated
47 ZFP28 2 99.0 Highly correlated
48 ZNF75D 1 94.0 Moderately correlated
49 ZNF765 1 8.6 Weakly correlated
50 ZNF93 1 8.6 Weakly correlated
51 ZNF596 1 94.0 Moderately correlated
52 ZNF585B 1 99.0 Highly correlated
53 ZNF567 1 99.0 Highly correlated
54 ZNF563 1 28.9 Weakly correlated
55 ZNF519 1 19.6 Weakly correlated
56 ZNF468 1 28.9 Weakly correlated
57 ZNF441 1 43.0 Weakly correlated
58 ZNF440 1 28.9 Weakly correlated
59 ZNF30 1 94.0 Moderately correlated
60 ZNF273 1 28.9 Weakly correlated
61 ZNF26 1 99.0 Highly correlated
62 ZNF133 1 99.0 Highly correlated
63 ZFP57 1 87.0 Moderately 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 5 19.6 Weakly correlated
2 ZNF479 4 6.4 Weakly correlated
3 ZNF257 3 0.0 Weakly correlated
4 ZNF18 2 160.0 Weakly correlated
5 ZNF324 2 99.0 Highly correlated
6 ZNF680 2 28.9 Weakly correlated
7 ZNF320 2 28.9 Weakly correlated
8 ZNF485 2 94.0 Moderately correlated
9 ZNF641 1 99.0 Highly correlated
10 ZIM3 1 87.0 Moderately correlated
11 ZNF596 1 94.0 Moderately correlated
12 ZNF573 1 94.0 Moderately correlated
13 ZNF28 1 28.9 Weakly correlated
14 ZNF705D 1 28.9 Weakly correlated
15 ZNF440 1 28.9 Weakly correlated
16 ZNF317 1 99.0 Highly correlated
17 ZNF816 1 28.9 Weakly correlated
18 ZNF793 1 99.0 Highly correlated
19 ZNF429 1 28.9 Weakly correlated
20 ZNF382 1 99.0 Highly correlated
21 ZNF705B 1 28.9 Weakly correlated
22 ZNF597 1 94.0 Moderately correlated
23 ZNF248 1 99.0 Highly correlated
24 ZNF101 1 43.0 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