ZRdb KZFP & Repeats
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LTR_HERVFH21

  • Name
    HERVFH21
  • Repbase
    HERVFH21I
  • Type
    LTR
  • Emergence
    28.9 Mya
  • Dfam Id
    DF0000182
Description :

HERVFH21 is the internal region of HERVH-related endogenous retrovirus,and is flanked by LTR21 long terminal repeats, and has 5 bp TSDs. Ithas a PBS site similar to Phe tRNA binding site in intracisternalA-particles from mouse and hamster genomes.
Consensus sequence The consensus sequences obtained from Dfam are derived from the seed alignment using a specialized caller. :
ttctggtgccgaaacccgggaaggggataggctctggccgggantcactctctctctctctctctctctctctctctctccctctccctcccctatcacccctctcccggccganctcccccttcccgaacctgccgaagacccggaggatctcctagaccctcccattgctggcgaccncatccancaccagggcctccgcaggggtgagtnaaaagagactcttgccattccccggaacccttgaccgtccgtctctccnttcccgaaagacccagcgctgggccaagggcttcctcccgcctccgggcctccaggcgnccctcggttcctccgtttcagggacgcctgacncggcggttacctcccctattccggacaagncccgcgggacaggggacgccctctcccgccgtccttgtcaccggcagtctcttcttcctctacccccccctcctccattcaccatgggagcctctcagtctactccctcnaagacnncccccctgggtgtctcctccgcaacctcaacgccctcggcctccgttcagaaatccgnccnaaaaggcttatctttttcaacatnctcagacctagataatttttgccatcgaaatgggaaatggtctgaggtgccttacgtccaggcatttttcacacttcgtncccnccctnccctctgtcagtcccgttccacttcccaaatcctcctcncccnctccnancctgnctcgcctcctancccccnccccacagccccagctgacgattcctcttcctttgacccnnccgactttccccttccccgncggcatcacgntcctccgccagagcgtcccgatcctccaccgtatgcccccgctccggctctacctttctcccctcctctccccaaccacccngcttctgactctgggtcctctccntctccacccctcacccgctctcnggcccaacntgcccagcaaccagctcccctgcttcctcttagagaggtggctggagctgaaggcatagtcagggtacatgtncctttttctctatcagacctttcccaaatcagccagcgtttaggctctttctcatcagaccccgncacttatatacaggaattccaatatctaactcngtcctacaatttaacctggagtgacttaaatgtcatcctgacttctaccctctccccagatgaacgggaaagatttntctcntagcccaatctcacgctgataaccttcatgagccagaccccannaaggcnntagaggccgccgcagttccccgagagganccccnncgggantaccagcccgcagaccccggccgggcatctcgagattacatggtttcctgcctagttgaagggcttaaaaaggcagcntacaaagctgttaattatgacaagcttaaagaaactacccaaggtaaagacgaaaacccagcccagttcatggcccgcttngcagcgaccctnagacgctntaccgccctagacccnganggnccggaaggccgccttattcttaatatgcattttatcacccagtccgctcccgacattaggaaaaagcttcaaaaattagantccggccctcaaaccccacaacaggacttaatcaacctcgccttcaaggtgtncaataatagngangaggnaagnnaggcagcaacangcagagttncaantacttgcctccgctgtnagangccctncagnccacgggacgcagctccacacggaagcctcctagcagttcacctccnccnggancttgcttcaagtgcggcaangaaggccactgggccaaggaatgccccagcccaggnattcctcctaagccgtgcccctctgtgcgggaccccactggaagtcggactgtnantngcccccgcaaggaccgcccccancccttcccgagccggccgaaacctccttcccagatctcctcggcttagcggctgaagactgacgctgcccnggaacggacgccccggnagctaccatcacngcatccgagcttcgggtaactcttacagtggagggtaagtcngtccccttnntttnatcgatacgggggctacccactccgcattaccttcttttcaagggcccgctccgtcctcccnngtctctgttgtgggtattgacggccaggcttcnaaaccccttaaaactccccnactctggtgccacttggacaacattncttttacgcactcttttttagttatccccacctgcccagctcccttattaggccgagacattttancnaaattntccgcttcccntgtnttcctggcnactacagccacantccctcccgcccctctccgccagtccagcccctnacccctctccccggcatccnctccccacctcccncgttaacccacaagtatgggacacctctactccctccctggcgaccgatcacgaccccattaccatcccattaaaaaatccccctaacccgcccaacgntcnccaatatcccatcccacnagcacgcttaaaaggattaaagcctgttatcancnngctctgctcacgncgtcttctaaaacctacaaactctccttacaattcccccattctacctgtccaaaaaccggacaagtcttacaggttagttcaggatctncgccttatcaaccaaattgtcttgcctatccaccccgtggtgccnaacccgtatactctcctntcnctcatnccttcctccacaacccactattccgttcttgacctnaaagatgctttcttcactattcccctgcacccctcntcccagcctctctttgctttcacctggactgaccctgacacccatcagtcccagcagcttacctgggctgtactgccgcaaggcttcagggacagccctcattacttcggccaagctctttctcatgatcttacttccttnnatccgtcccccngccaccttattcaatatattgatgaccttctnctttgtagcccctccttngaannctcccaaacncacactnccgcccttctaaacttctttnctaanaaaggatatcgggtatcccctccaaagcncaaatttctncctccatcgttacctacctcggcatnnaactcttcntnaaaacacgngctntgacccctgcccgagcggccttaatngataantaatctaccccanccccttctaaaaacgaaatcctttccttcctaggcatggttggatactttcgnctttggatacccggttttgccatcctaacnaaaccattatataaactcgcaaaaggccccctcgatgancccctaaacccctcncntaacctactccccancttccgtnnactccaaacagctctngnnaccgcncccgctctanccctncccgacntctcccaacccttctcnctncacacagccgaagnccgaggnntngcnctcggngtcttaggacaacagaagggaantcctccntcctttgcccctgtagcctttctgtccaaacaacttgaccttactgttttaggctggccntcatgtctccgngcgncggcngcngccgccacttttagccctcgaaatcacgaaactaacgctcaactnnnncgncactctctacagttctcataacttccaaaatctattttcctcccgagcattangctccctttctgctccccggctccnnttnctctatncnctctttgttgagtctcccaaattcagtcttgccaanagtgctcccttcaatccggcctccttattcccgatatccncctccccncctacccattcntgcactgatatcctgatccacctgcattcacnctttccccatatttccttctttcctgttcctcaccccgntgatcaactgtttattgatggcagttccaccaggcctaatcgctcacccaaagnngcaggctatgctattgtcttccacatctanntcattgaggctacnnccctgcctccannnactacctctcagcaagccgaactcattgcctntaactcgagccctcactcttgcaaaaggactacgcgtcaatatttatactgactctaaatatgccttccatatcctgcaccaccatgctgttatatgggcngaaagaggtttcctcactacgcaagggtcctccatcattaatgcctccnnttaattaaaaactccttnaggccgctttacttccaaaggaagctggagtcattcactgcaagggccatcaaanaggctcagannnnccnntganncgncgnatcaatctcaagaggnaacannaangccgataaggcagcaaaaaacagnacctcaaaagggatcaganntgaaatctcaagaggnaacgnnnangccgatgaggcagcaaaagaagcctccctttcttctgtccctgcctctctcctcctcattaccccngcantccnacccaagtactcccccactnagaaanngcttcgctactacagcaaggagcctccctccaaggggactggatagtcaaagatcaaaagctcntcctcccccaagagcaagccaannnnattctgacatcncttcaccaacccttccatgtnggtgcgcgcccccngtacctgccccttcgccctcatttctcctccccccatctattcacctcactaaaggacataacctcnaactgtcncatntgctntgctacttcctcccaaggggccctccgctctccccccatccctacacatcagctcagaggancgctcccagggnaggactggcaaatngacttcacccacatgcctcccgtcaagaaaacaaaatatcttcttantctngtagacactttcnctggntgggtagaggcntttcccacnncntcngagaaggccgcngnagtctcccaaattctcgtaacaganatnatccctnggtttggcctccccanctccatacagtcngacaacggnccntagcttcatcnnccaaatcacccaaccggtttctcagncccttggtattcagtggcgcctccatatcccntaccgnccccagtcntcaggaaaagtcgaaagggcaaatggnattctnaaaacncagttnaccaaactcaccctcgaagtcnaaaaaccntggacctcccttttacccatagcnctggcccgcatcagagccagtccaaaagcaccctccttcctcagtccatttgagttaatgtatggacgccctttcctcttacaaaacaggccccctcctaactctcagttaggagaatacctcccaacactctccctcatccgccatctcctccgcgaacaagcngaccaggnccctcccaaaaccccacgaaggcccttgacacctcccacctccttaacaaaaattcagggtactgcaacggccgacacctcccctgtttatccctcttcccttggctcccctctccgtgcaccatccctgcccnnnacccaccacccgcgactgtctccttatcccancgttcaacaacactcccacangnntcttagtggacacaaaacgcttcctcctacactgggaaaaaaaaaaannaacncaaagagccncccagcctaanccaaacacccccttacaaccactcnccgcagcggccctagccggcaccctaggagcatggatgcacgaggacaacaaaattntacacctttttagcatacacaaccagttctgcctaccnagccaaggcatattcttcctatgcggcacctcnacctatntctgcctccccnccaactggacaggcacctncgcaccctggttttcctcagcccnaaaatcgacgttgccccaggagaccaacccctaccaatcccngttaanacccanatccgacaccgccgngccatacagctcatacccctnctagtaggcctaggaatnacngcagnagtnggaaccggagtngcgggattngcnacctccctntcctattaccaatccctctccaaagaccttacgganagcttggaagacatngccaantccattncnaccctccaancncaaatagactcttagcagcagtcgccctncaaaaccgcagaggcctngacctnctcaccgccgaaaaaggaggnctctgcntctttctagatgaanagtgctgcttttatctcaaccagtcaggcttagtncaagatgcngtcaaaaaactnaaagaccgagcncaaaaaatcaaagaaaacgtcctctgctggcccncntggccctcntggtccctcagcncctgggctccctggctactgcccctcctnggcccngccataaccnttcttctccttctagcnttcggnccctgcctcntacgcctcctcacccagtttttacaggaccgtatcagagccttcacccacggaacaatacaagatatgatgctgctccaggaataccgacggctccaagaacggcagtccctaccntccagcctttccccncaaccgccgccccttcccagcnngaagcagccagacgacaacggcgcccctcttctattacctattaaaaggctggaa
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 ZNF766 15 43.0 Weakly correlated
2 ZNF263 14 180.0 Weakly correlated
3 ZNF723 12 15.2 Moderately correlated
4 ZNF705B 10 28.9 Highly correlated
5 ZNF486 10 8.6 Weakly correlated
6 ZNF382 10 99.0 Weakly correlated
7 ZNF2 10 99.0 Weakly correlated
8 ZNF101 9 43.0 Weakly correlated
9 ZNF705D 8 28.9 Highly correlated
10 ZNF394 8 99.0 Weakly correlated
11 ZFP37 7 99.0 Weakly correlated
12 ZNF680 6 28.9 Highly correlated
13 ZNF479 6 6.4 Weakly correlated
14 ZNF679 5 28.9 Highly correlated
15 ZNF589 5 28.9 Highly correlated
16 ZNF793 4 99.0 Weakly correlated
17 ZNF554 4 99.0 Weakly correlated
18 ZNF534 4 19.6 Moderately correlated
19 ZNF18 4 160.0 Weakly correlated
20 ZNF197 4 99.0 Weakly correlated
21 ZNF257 4 0.0 Weakly correlated
22 ZNF324 4 99.0 Weakly correlated
23 ZFP69B 4 99.0 Weakly correlated
24 ZKSCAN8 3 160.0 Weakly correlated
25 ZNF792 3 94.0 Weakly correlated
26 ZNF610 3 28.9 Highly correlated
27 ZNF320 3 28.9 Highly correlated
28 ZNF175 3 94.0 Weakly correlated
29 ZNF735 2 28.9 Highly correlated
30 ZIM3 2 87.0 Weakly correlated
31 ZNF584 2 99.0 Weakly correlated
32 ZNF141 2 43.0 Weakly correlated
33 ZNF558 2 99.0 Weakly correlated
34 ZNF8 2 99.0 Weakly correlated
35 ZNF468 2 28.9 Highly correlated
36 ZNF282 2 319.0 Weakly correlated
37 ZNF701 2 28.9 Highly correlated
38 ZNF92 1 28.9 Highly correlated
39 ZNF75D 1 94.0 Weakly correlated
40 ZNF780A 1 43.0 Weakly correlated
41 ZNF823 1 43.0 Weakly correlated
42 ZNF790 1 99.0 Weakly correlated
43 ZNF671 1 94.0 Weakly correlated
44 ZNF641 1 99.0 Weakly correlated
45 ZNF596 1 94.0 Weakly correlated
46 ZNF563 1 28.9 Highly correlated
47 ZNF547 1 74.0 Weakly correlated
48 ZNF528 1 43.0 Weakly correlated
49 ZNF519 1 19.6 Moderately correlated
50 ZNF425 1 94.0 Weakly correlated
51 ZNF383 1 99.0 Weakly correlated
52 ZNF354C 1 99.0 Weakly correlated
53 ZNF343 1 74.0 Weakly correlated
54 ZNF317 1 99.0 Weakly correlated
55 ZNF264 1 99.0 Weakly correlated
56 ZNF17 1 69.0 Weakly correlated
57 ZKSCAN1 1 160.0 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 ZNF723 10 15.2 Moderately correlated
2 ZNF263 8 180.0 Weakly correlated
3 ZNF705D 4 28.9 Highly correlated
4 ZNF479 4 6.4 Weakly correlated
5 ZNF534 3 19.6 Moderately correlated
6 ZNF793 3 99.0 Weakly correlated
7 ZNF680 3 28.9 Highly correlated
8 ZNF705B 3 28.9 Highly correlated
9 ZNF257 3 0.0 Weakly correlated
10 ZNF141 2 43.0 Weakly correlated
11 ZNF735 2 28.9 Highly correlated
12 ZNF468 2 28.9 Highly correlated
13 ZIM3 2 87.0 Weakly correlated
14 ZNF766 1 43.0 Weakly correlated
15 ZNF197 1 99.0 Weakly correlated
16 ZNF679 1 28.9 Highly correlated
17 ZNF282 1 319.0 Weakly correlated
18 ZNF823 1 43.0 Weakly correlated
19 ZNF264 1 99.0 Weakly correlated
20 ZNF425 1 94.0 Weakly correlated
21 ZNF382 1 99.0 Weakly correlated
22 ZNF75D 1 94.0 Weakly correlated
23 ZNF780A 1 43.0 Weakly correlated
24 ZNF175 1 94.0 Weakly correlated
25 ZNF383 1 99.0 Weakly correlated
26 ZNF596 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 ZNF263 180.0 Weakly correlated
2 ZNF723 15.2 Moderately correlated