ZRdb KZFP & Repeats
...

LTR_HERVH48

  • Name
    HERVH48
  • Repbase
    HERVH48I
  • Type
    LTR
  • Emergence
    28.9 Mya
  • Dfam Id
    DF0000184
Description :

HERVH48 is flanked by MER48 LTRs. ORFs found in the reconstruction: Gag(~657-2237) and Pol + partial Env (~3927-6455).
Consensus sequence The consensus sequences obtained from Dfam are derived from the seed alignment using a specialized caller. :
tctggtgccgaaacccgggaggggctcaggtccgcgtcccccgtggacctacccctccaccccggagagcaggccacagcagccggacaaaggaagctcctcagcctccagtcgcctctctgtgcatgcacatcggtcactgatctcgcctactggtaagtttccccgggagcccggttaacagggaaaaatccgcacggcctctcttggtttctccggtccgaaaatccaacgttggtccaagaaggctccggcgtgtgccaggcactcgctgatcatctggtcttagggggacgcctctaagccatttgatcccgttccgggaacgaaaaaggcagcggtgacgatcgctccttttatcgtctccctccggccgtccaggacggtctccttttccctgttctcccgagcctaccctccgttatgggaaactcccggtcctccattccaaaaaacagccctctaggctgcctcataaaaaancctgcaaaccttaggcctcaggcaagatatccgccctaagcgccttgtctttttttnnnnnnncgcaattcagtctggccacagtacgaattagataacgggtccaaatggcccgcaaatggaacattcgactttacaattttaactgacttaagcaattattgccgacgactggagaaatggggagaaattccttatgtccaggcctttttgcactcagatcacaacccgacctctgcaattcttgctcacctgttcaaatccttctcctccattctcgccgccctgatcgcctttctcctcccgaccctacctctttttccntcgttngatccagcagactgctgtccacccctcccangcccctacctctccctctcaaccgtcttctttaaccccccaagcctcctctttgtcttctcagccgccatcttcccagncgccancntntcagccgccatcttcccagccgccatcttctcagccgccatcttcccagccgccatcttcccagtcagcagtatccacttcttttcctacaccgtcccctcctcaggacaattctagtattgcctgtacccattctcctcccccaccgccctctcctgaggcctgtaaacccatcccgccaccttacgcccctatctatcctccactgcctgttaactcaacncccccttcccccttcaaaccctcagcaggaaccacttccggcttcttccttctctcccgcccatactcgctcaggcgccatctttggcccatgccccacccttacttcagcgcctgcgctagagtgcccccttcgggaagtagcaggagctgaaggtattgttagagttcatgttcccttctccctcactgatctctctcaaattaacaaaagactcggttcatttccagaagaccctacctcttatattagagtttcagtacctnacccagtcttatgaacttggcgtgacctctacgttatcctctcttccaccctcaccccagaagaccgggaccgtatctggaccctagctcaggcgcatgctgatacaattcatcaccaggctcctgcccagcctactggcgcagaggcagtccccaancaggacccccactgggattatcaagacggggcccccggacgccgccatcgagaccacatgattgcgtgcctccttgcaggactcaaaaaggntgcccataaagcngtnaactatgaaaaacttncagaaatcacccaaggtccngacgaaaacccagcccnnttcctctctcgtttagcngaagccatgagaaantataccgncctagacccagccggcccagaaggaaccttcggttcatcncccaatccgcccccgacattcggcgcaagcttcagaagcttgacgacggccctcaaaccccacaacgagacctncttaacctngccttcaaagtctttaacaatcgtgatgaggaaagtaaaaggcaaaaacaggcagagtttcaaatgcttgcctccgccgtcaggggccctgcaggcccacggggccgcagctccacacggaagcctcctagcaatccacctccacctggcgcctgtttcaagtgcggcaatgaaggccactggtccagacaatgcccaaacccaggtaagcccaccaggccgtgccccnctctgcggaggaccccactggaagtcggactgtgagcggcccccgcaaggaccgcccccatcccttcctgagccggccaaaacctcctactcggatctcatcggccttgccgctgaagactgacggtgccctggaacggacgccccggcaactaccatcgcttcatccgagccaagggtaaccctgacggtggcgggtaggccagtacgcttttttnaaattaataccggggcaacctactccgctttacctaatttttcaggacccacccagtcctcccaagtctctgttgtgggaattgacggacaagtctccaaaccccgagccacccctccactcttctgctccctncacaccttttccttcactcactctttcttagtcctgccctcatgcccaactccgctcctaggcagagacatcctttcaaaactccacactactctccacttccacgttccccatagtacccaacgcatcaacccagacccctcnncggngcttctaactttcttctactcctccaacctcccaccttaaaacatgcaacctttccttatcccccatccgtagttaaccccgctgtttgggatacttccacaccnnnnnnctcagtcgcaaaacaccacacccccgtccgcattacccttaaagagcccacccagttcctatcacagaagcagtatcccatcccccaagcagctctcataggcctaaagcctatcatttctcgcctcctcgccagtcacctactccgcccaacaaactccccttttaacacaccaattctacctgttaaaaagccagacggaacttatcgcttagtccaggacctcaggctcattaaccaagctgtactcccagtacgtccagtagttcctaacccatacactttactttccgcaattccctccaataccacccatttttctgtctagacctaaaggatgcttttttcacaattcctttacaccctgattcccaaaacctctttgcctttacgtgggaaaaccccgacacccacctttcacgtcagctcacctggtgcgtactacctcaaggtttcagagacagcccccacctttttgcgnccgacaggcccttgctcgcgacctctgtaccttatccctaaaaccgtccactctccttcaatatgttgatgatctgctcctgtgtagcccctctcaaagagactgcaacgcccatactatctctcttttaaacttcttggcagaacgggggtatcgggtctcccctaagaaagcacaaatatgcacccccntcagtcacctatctaggcctagctcttaccccgcgaacccgagggctcacaaccgaccgcatatccctcctccagtccctcccgcctccgcaaactaagcaagaaattctctcttttctaggactagcgggatattttaggctctgggttccctccttcgctctacttgccaaaccgttataccaagctgctaaaggccctctccatgagcctttaaaccctgctaaaggccctctccatgagcctttaaaccctgcacagcctattacccaacctttccgtctactccagaaggctctcacctcagccccgtcctcactctcccagacctcaccaaacctttctccctctataccgacgaacggcgtggagttgcactaggtgttctaacccagtctaagggacccaccctccaggttgttgcctacctctctaaacagcttgaagccacagttctcggatggcctgcctgcctccgagcattggcggcagctgctgtcctcacccttgaaagcctaaaactatctctccatgccaacctaacagtttattcaacccataacatcaaagacatgctagctcaccgcagtgtactaagtctcatctctgccccacggctcctccaactgtatgctctattcgtagaaaccccccncccgcnaatcaccatgctaaccagctcccgtctaaacccggccacgctcttacctgaagctacaaccgcccaagaccctacacacttctgtgtgaacactgttcaaacctttcttataccttttccaaacctaacagaccaaccccttccagatgcctcctttacttggtttattgatggcagttccaccctacatcanngccactagcaggcaggctatgctatagtatcttcccgcgnacatctatcattgaggccactctgccccccctcnccactacctctcagcaagccgaactcattgccttaactcgagccctcactcttgcaaagggactacgcgtcaatatttatactgactctaaatatgccttccatatcctgcacccacgctcgttcatatgggcngaaagaggtttcctcactacacaaggntcccccatcattaatgcctctttaataannaaactctttcaagccgctttacttccaaaggaagctggagtcattcactgcaagggccatcaaaagncggangatcccatctcagctggcaacggcttagctgataaggtagctaaanaagtagcnttccaacttctgcacggccagtttttctccttctcatcggtcactcccacctactcccccgctgaaannnnnnncttccanncccaancccttcccacgcaaggcaaatggtacgccaaggaaaantatctcnttcttccncagcctcacagncccnctctnctccgncgtcttcataacctcttccatgtaggttacaagcctctcttacaacctctccgccctattctcacttntcctcacctttccagccatgctcgagaaatcactcagtnncgttccatctgctattcantaccaccccagggattgttcaggccccctcccttccctacacatcaagctcggggccntgtgcccgggcaggactggcaaattgactttactcacatgccggtcaggaaacgnntaaaatacctcttggtctgggtagacactttcactggatgggtagaggcctttcccacagggtcagaaggcgccaccgtcgtcacttnnnctcccctcntgtacataattcctcggtttggccttcccacctctatacagtccgataacggaccggcctttattagtcaaatcacccaagcagtttctacgctcttnggtattcagtggaaccttcataccccttaccgtcctcaatcttcaggaaaggtagaacggactaacgctgtctttaaagcacacctcaccaagctggctctagaaacccgccagtcgtggacaaaaaatctccctttcgccctcatgagactccgcgcaacaccaaaagcaccctctttttatagtccctttgaaatcatgtatggccgaacttttgtcttggggcctccacccttaccagactctgagccactcgggaattacctcccctccttaatccagacacggtctttcattcgtgaagcagcaaatgaggccatgcctctccctgtcgacacctccttgtcctctcaacataactgtcttgcaggcacagacgtgtttatctgccaacccgaccctcacnaaaagctacaaccgaagtggacaggccctacactgtgatactcagcacgccaactgcagtgagagtccaaggactcccccactgggtccatcgcaccagggtcaagctcaccccgcaaggctactccttcctccaaaacattaacggcgggcaacaccctcggagtccctgtatatgataacctaaacagagaaaaacgatccttaaaggtaggaggaagccaaanncgncgnnnnnncgnnnnncgnngatggcgagaggacgaatggcctccgcaacggatcatcgaatattacggtcctgccacttgggctgaggatggttcatggggttatcgcactcccatatatatgctaaatagaataattagactacaggctgttctagagataatcactaaccaaaccgcctcagccctggaaatgctcgcgcaacaacaaaaccaaatgcgcgcggcaatttatcaaaacaggctagcactagactacttattagcagaagagggtggggtctgtggtaagtttaatatctccaattgctgtcttaacatagacgataacggaaaagcggttctagaaatcgcttcaaacatcagaaaagtagcccatgtaccagtccaaacctggaagggatgggacccaacaaaccttctaggagggtggttctctaatttaggaggatttaaaacgctggtagggacagtaatcttcatcattgggctcctcctgtttctcccctgtgttatcccactgataataaaagccattaaaactcttgttgaaactacagttaaccgccagacaatccagacgatgctcctgctacaacgacacgatggataccaacccgtctctcaagaataccccaaaaattaagtttttctttttccaaggtgcccacgccaccccctatgtcacgcctgaagtagttattgagaaagtcgtcccttttcccttttctataaccaaatagacaggaa
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 ZNF680 32 28.9 Highly correlated
2 ZNF175 26 94.0 Weakly correlated
3 ZNF793 21 99.0 Weakly correlated
4 ZFP57 20 87.0 Weakly correlated
5 ZNF766 15 43.0 Weakly correlated
6 ZNF589 14 28.9 Highly correlated
7 ZNF18 11 160.0 Weakly correlated
8 ZNF2 11 99.0 Weakly correlated
9 ZKSCAN1 10 160.0 Weakly correlated
10 ZNF382 10 99.0 Weakly correlated
11 ZNF320 10 28.9 Highly correlated
12 ZNF251 10 94.0 Weakly correlated
13 ZNF610 9 28.9 Highly correlated
14 ZNF324 9 99.0 Weakly correlated
15 ZFP37 8 99.0 Weakly correlated
16 ZNF584 8 99.0 Weakly correlated
17 ZNF792 8 94.0 Weakly correlated
18 ZNF394 8 99.0 Weakly correlated
19 ZNF197 8 99.0 Weakly correlated
20 ZNF528 7 43.0 Weakly correlated
21 ZNF723 7 15.2 Moderately correlated
22 ZNF479 7 6.4 Weakly correlated
23 ZNF101 7 43.0 Weakly correlated
24 ZNF140 5 99.0 Weakly correlated
25 ZNF317 5 99.0 Weakly correlated
26 ZKSCAN8 5 160.0 Weakly correlated
27 ZFP69B 5 99.0 Weakly correlated
28 ZNF641 5 99.0 Weakly correlated
29 ZNF679 5 28.9 Highly correlated
30 ZNF534 5 19.6 Moderately correlated
31 ZNF707 4 74.0 Weakly correlated
32 ZNF202 4 160.0 Weakly correlated
33 ZNF585B 4 99.0 Weakly correlated
34 ZNF263 4 180.0 Weakly correlated
35 ZNF695 3 28.9 Highly correlated
36 ZNF558 3 99.0 Weakly correlated
37 ZNF490 3 43.0 Weakly correlated
38 ZNF468 3 28.9 Highly correlated
39 ZNF445 3 99.0 Weakly correlated
40 ZKSCAN5 3 160.0 Weakly correlated
41 ZNF8 3 99.0 Weakly correlated
42 ZNF519 2 19.6 Moderately correlated
43 ZNF547 2 74.0 Weakly correlated
44 ZNF75D 2 94.0 Weakly correlated
45 ZNF557 2 15.2 Moderately correlated
46 ZNF418 2 43.0 Weakly correlated
47 ZNF354C 2 99.0 Weakly correlated
48 ZNF264 2 99.0 Weakly correlated
49 ZNF705B 2 28.9 Highly correlated
50 ZNF92 1 28.9 Highly correlated
51 ZNF701 1 28.9 Highly correlated
52 ZNF816 1 28.9 Highly correlated
53 ZNF778 1 74.0 Weakly correlated
54 ZNF735 1 28.9 Highly correlated
55 ZNF671 1 94.0 Weakly correlated
56 ZNF658 1 99.0 Weakly correlated
57 ZNF597 1 94.0 Weakly correlated
58 ZNF554 1 99.0 Weakly correlated
59 ZNF510 1 99.0 Weakly correlated
60 ZNF486 1 8.6 Weakly correlated
61 ZNF44 1 43.0 Weakly correlated
62 ZNF441 1 43.0 Weakly correlated
63 ZNF417 1 28.9 Highly correlated
64 ZNF347 1 43.0 Weakly correlated
65 ZNF30 1 94.0 Weakly correlated
66 ZNF284 1 43.0 Weakly correlated
67 ZNF257 1 0.0 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 ZNF793 12 99.0 Weakly correlated
2 ZFP57 11 87.0 Weakly correlated
3 ZNF680 7 28.9 Highly correlated
4 ZNF723 7 15.2 Moderately correlated
5 ZNF2 5 99.0 Weakly correlated
6 ZNF479 5 6.4 Weakly correlated
7 ZKSCAN5 3 160.0 Weakly correlated
8 ZNF320 3 28.9 Highly correlated
9 ZNF534 3 19.6 Moderately correlated
10 ZNF468 3 28.9 Highly correlated
11 ZNF585B 2 99.0 Weakly correlated
12 ZNF485 1 94.0 Weakly correlated
13 ZNF75D 1 94.0 Weakly correlated
14 ZNF197 1 99.0 Weakly correlated
15 ZNF417 1 28.9 Highly correlated
16 ZNF735 1 28.9 Highly correlated
17 ZNF317 1 99.0 Weakly correlated
18 ZNF679 1 28.9 Highly correlated
19 ZNF641 1 99.0 Weakly correlated
20 ZNF175 1 94.0 Weakly correlated
21 ZNF347 1 43.0 Weakly correlated
22 ZNF324 1 99.0 Weakly correlated
23 ZNF251 1 94.0 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 ZFP57 87.0 Weakly correlated
2 ZNF680 28.9 Highly correlated
3 ZNF723 15.2 Moderately correlated
4 ZNF793 99.0 Weakly correlated