ZRdb KZFP & Repeats
...

Retroposon_SVA_B

  • Name
    SVA_B
  • Repbase
    SVA_B
  • Type
    Retroposon
  • Emergence
    15.2 Mya
  • Dfam Id
    DF0001068
Description :

SVA retroelements are hominid-specific chimeras, some of which are stillactive in the human population. These SINEs are a unique combination offeatures. The 5' end begins with hexamer repeats, followed by two Alusin reverse orientation. The center is comprised of a number of VNTRregions (Variable Number of Tandem Repeats) that may span a few hundredbasepairs, up to 2000bp. The 3' end is formed by a portion of a HERVKLTR (the SINE-R feature) .
Consensus sequence The consensus sequences obtained from Dfam are derived from the seed alignment using a specialized caller. :
ctctccctctccctctccctctccctctccctctccctctccctntcccctctttccacggtctccctctgatgccgagccgaggctggactgtactgccgccatctcggctcactgcaacctccctgcctgattctcctgcctcagcctgccgagtgcctgggattgcaggcgcgcgccgccacgcctgactggttttcgtattttttggtggagacggggtttcgccgtgttggccgggctggtctccagctcctgaccgcgagtgatctgccngcctcggcctcccgaggtgccgggattgcagacggagtctcgctcactcagtgctcaatgttgcccaggctggagtgcagtggcgtgatctcggctcgctacaacctccacctcccagccgcctgccttggcctcccaaagtgccgagattgcagcctctgcccggccgccaccccgtctgggaagtgaggagcgtctctgcctggccgcccatcgtctgggatgtgaggagcccctctgcccggccgcccagtctgggaagtgaggagcgcctcttcccggccgccatcccgtctgggaagtgaggagcgtctctgcccggccgcccatcgtctgggatgtggggagcgcctctgccccgccgccccgtctgggangtgaggagcgcctctgcccggccagccgccccgtctgggaggtgaggaggtcagccccccgcccggccagccgccccgtccgggaggaggtggggggnncagccccccgcccggccagccgccccgtccgggaggtggggggcgcctctgcccggccgccccgtctgggaagtgaggagcccctctgcccggccgccaccccgtctgggaggtgtacccaacagctcattgagaacgggccatgatgacgatggcggttttgtcgaatagaaaagggggaaatgtggggaaaagaaagagagatcagattgttactgtgtctgtgtagaaagaagtagacataggagactccattttgttctgtactaagaaaaattcttctgccttgggatgctgttaatctataaccttacccccaaccccgtgctctctgaaacatgtgctgtgtccactcagggttaaatggattaagggcggtgcaagatgtgctttgttaaacagatgcttgaaggcagcatgctcgttaagagtcatcaccactccctaatctcaagtacccagggacacaaacactgcggaaggccgcagggtcctctgcctaggaaaaccagagacccttgttcacatgtttatctgctgaccttccctccactattgtcctatgaccctgccaaatccccctctccgagaaacacccaagaatgatcaataaatactaaaaaaaaaaaaa
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 ZNF91 428 6.0 Moderately correlated
2 ZNF705B 286 28.9 Weakly correlated
3 ZNF611 249 19.6 Weakly correlated
4 ZNF705D 176 28.9 Weakly correlated
5 ZNF141 96 43.0 Weakly correlated
6 ZFP57 89 87.0 Weakly correlated
7 ZNF202 59 160.0 Weakly correlated
8 ZNF560 57 43.0 Weakly correlated
9 ZNF28 37 28.9 Weakly correlated
10 ZNF257 26 0.0 Weakly correlated
11 ZNF282 24 319.0 Weakly correlated
12 ZNF519 19 19.6 Weakly correlated
13 ZNF263 17 180.0 Weakly correlated
14 ZNF382 16 99.0 Weakly correlated
15 ZNF534 15 19.6 Weakly correlated
16 ZNF649 15 28.9 Weakly correlated
17 ZNF394 15 99.0 Weakly correlated
18 ZNF766 14 43.0 Weakly correlated
19 ZNF468 13 28.9 Weakly correlated
20 ZNF558 12 99.0 Weakly correlated
21 ZNF641 12 99.0 Weakly correlated
22 ZNF461 10 99.0 Weakly correlated
23 ZNF169 10 94.0 Weakly correlated
24 ZNF705E 9 0.0 Weakly correlated
25 ZNF317 8 99.0 Weakly correlated
26 ZNF589 8 28.9 Weakly correlated
27 ZNF2 8 99.0 Weakly correlated
28 ZKSCAN5 8 160.0 Weakly correlated
29 ZNF101 7 43.0 Weakly correlated
30 ZNF175 7 94.0 Weakly correlated
31 ZNF479 7 6.4 Moderately correlated
32 ZNF605 7 99.0 Weakly correlated
33 ZFP69B 6 99.0 Weakly correlated
34 ZFP37 6 99.0 Weakly correlated
35 ZNF18 6 160.0 Weakly correlated
36 ZNF486 6 8.6 Moderately correlated
37 ZNF347 5 43.0 Weakly correlated
38 ZKSCAN8 5 160.0 Weakly correlated
39 ZNF680 5 28.9 Weakly correlated
40 ZNF610 5 28.9 Weakly correlated
41 ZNF483 5 99.0 Weakly correlated
42 ZNF140 5 99.0 Weakly correlated
43 ZNF324 4 99.0 Weakly correlated
44 ZNF490 3 43.0 Weakly correlated
45 ZIM3 3 87.0 Weakly correlated
46 ZNF114 3 28.9 Weakly correlated
47 ZNF506 3 28.9 Weakly correlated
48 ZNF197 3 99.0 Weakly correlated
49 ZNF182 2 99.0 Weakly correlated
50 ZNF92 2 28.9 Weakly correlated
51 ZNF793 2 99.0 Weakly correlated
52 ZNF763 2 15.2 Highly correlated
53 ZNF735 2 28.9 Weakly correlated
54 ZNF707 2 74.0 Weakly correlated
55 ZNF675 2 8.6 Moderately correlated
56 ZNF251 2 94.0 Weakly correlated
57 ZNF334 2 99.0 Weakly correlated
58 ZNF425 2 94.0 Weakly correlated
59 ZNF584 2 99.0 Weakly correlated
60 ZNF57 2 28.9 Weakly correlated
61 ZNF302 2 43.0 Weakly correlated
62 ZNF75D 1 94.0 Weakly correlated
63 ZNF500 1 160.0 Weakly correlated
64 ZNF554 1 99.0 Weakly correlated
65 ZNF84 1 99.0 Weakly correlated
66 ZNF823 1 43.0 Weakly correlated
67 ZNF805 1 99.0 Weakly correlated
68 ZFP30 1 99.0 Weakly correlated
69 ZNF786 1 99.0 Weakly correlated
70 ZNF780A 1 43.0 Weakly correlated
71 ZNF77 1 87.0 Weakly correlated
72 ZNF778 1 74.0 Weakly correlated
73 ZNF429 1 28.9 Weakly correlated
74 ZNF562 1 28.9 Weakly correlated
75 ZNF578 1 15.2 Highly correlated
76 ZNF730 1 19.6 Weakly correlated
77 ZNF136 1 74.0 Weakly correlated
78 ZNF17 1 69.0 Weakly correlated
79 ZNF695 1 28.9 Weakly correlated
80 ZNF679 1 28.9 Weakly correlated
81 ZNF33A 1 99.0 Weakly correlated
82 ZNF284 1 43.0 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 ZNF91 358 6.0 Moderately correlated
2 ZNF611 248 19.6 Weakly correlated
3 ZNF705B 133 28.9 Weakly correlated
4 ZNF705D 107 28.9 Weakly correlated
5 ZNF141 93 43.0 Weakly correlated
6 ZNF28 33 28.9 Weakly correlated
7 ZNF202 20 160.0 Weakly correlated
8 ZFP57 14 87.0 Weakly correlated
9 ZNF282 13 319.0 Weakly correlated
10 ZNF461 10 99.0 Weakly correlated
11 ZKSCAN5 8 160.0 Weakly correlated
12 ZNF519 7 19.6 Weakly correlated
13 ZNF468 7 28.9 Weakly correlated
14 ZNF560 6 43.0 Weakly correlated
15 ZNF169 6 94.0 Weakly correlated
16 ZNF534 4 19.6 Weakly correlated
17 ZNF347 4 43.0 Weakly correlated
18 ZNF18 3 160.0 Weakly correlated
19 ZNF263 3 180.0 Weakly correlated
20 ZNF101 2 43.0 Weakly correlated
21 ZNF140 2 99.0 Weakly correlated
22 ZNF334 2 99.0 Weakly correlated
23 ZNF257 2 0.0 Weakly correlated
24 ZNF610 2 28.9 Weakly correlated
25 ZNF490 2 43.0 Weakly correlated
26 ZNF479 2 6.4 Moderately correlated
27 ZNF197 1 99.0 Weakly correlated
28 ZNF75D 1 94.0 Weakly correlated
29 ZNF680 1 28.9 Weakly correlated
30 ZFP30 1 99.0 Weakly correlated
31 ZNF823 1 43.0 Weakly correlated
32 ZNF780A 1 43.0 Weakly correlated
33 ZNF641 1 99.0 Weakly correlated
34 ZNF793 1 99.0 Weakly correlated
35 ZNF182 1 99.0 Weakly correlated
36 ZNF284 1 43.0 Weakly correlated
37 ZNF175 1 94.0 Weakly correlated
38 ZNF705E 1 0.0 Weakly correlated
39 ZNF57 1 28.9 Weakly correlated
40 ZNF506 1 28.9 Weakly correlated
41 ZFP37 1 99.0 Weakly correlated
42 ZNF707 1 74.0 Weakly correlated
43 ZNF589 1 28.9 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 ZFP57 87.0 Weakly correlated
2 ZKSCAN5 160.0 Weakly correlated
3 ZNF202 160.0 Weakly correlated
4 ZNF282 319.0 Weakly correlated
5 ZNF468 28.9 Weakly correlated
6 ZNF519 19.6 Weakly correlated
7 ZNF560 43.0 Weakly correlated
8 ZNF611 19.6 Weakly correlated
9 ZNF705D 28.9 Weakly correlated