ZRdb KZFP & Repeats
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LTR_PRIMA4-INT

  • Name
    PRIMA4-INT
  • Repbase
    PRIMA4_I
  • Type
    LTR
  • Emergence
    74.0 Mya
  • Dfam Id
    DF0001053
Description :

PRIMA4 is an autonomous, endogenous retrovirus with 4bp TSDs. The fullelement is comprised of this internal region, and the long terminalrepeats, PRIMA4_LTR. The PRIMA4 is an ancient ERV, related to the ClassI retroviruses, including leukemia viruses. PRIMA4 is also one of thekey factors in the MER4-group evolution. MER4-int is a non-autonomousderivative of PRIMA4 (analogous to a relation between MER41-int andPRIMA41).
Consensus sequence The consensus sequences obtained from Dfam are derived from the seed alignment using a specialized caller. :
tctggtaaccacggagggattctgagtggaggtgncccggcctncggcaantctcctatcggtgcttggtaccggcttgggcaccttatggctcaaaccgataggacgatttgctgaggtctggganctcccccctccagagatccctgatctcccaaaatttttcggttgggggtctgaggtttatttgctgttaaaaaaaaaacaaacaacgaggacggcaagaactccttttttcgtgggagtttttcagctcgcttccaacagggaaggcgagtttgtctgcttctgnancggtagagagcagtcttcagcctgagncccatccctaggtaagtagctgaattggggttttgtcttgnaaattctcttnaatgactaaagttaagattaacaaccagctggtcttaatttcntccttaccattagagcgctcagtaatcatataanttgtgcgatcgttgttngttttgcttaactgttttgttgtttgtttctgtgtttgtgtgtgtgtatattttgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtatgtgtgtgtttcggtcctttcccctatcggatttgaccaactccgaaccctctagctcatgagtgtggaatcttccactccgaagaaataagagcaccttgctcccctcagcctttcggggcattctcaggcgactgagaatcacgtgagggtgtctgggaggaacgctccctaagacgtgcagcggctctaaataggtttccccctcagaagaacatacttagggtctaatctcagccggcaggtgcatataaggagctgacccctcccgcaccttgagcccctgacacactgtgccaggtagccgcgacacgggtggaccgaaccggttcagggggtaacggccctgaaaagctaggtctgcaagcagcacattttgggtccgacacacntcccgacttggtcaaatccgaangagaattccaaattatggggaacaaggcctctgaattggctaaaaccccngcagctgcaaaacanaaagttccacctttagaaactccggccgggtatatgcaaaatacttatggcgaatcgtcatgcaaatatttaaccaagtggaccactataaccaaagcagattctaagttacaatggcctaaatggggatcttttgagatgcccaaattagtgtacctgtgaaccaggatggaaaacgcaggcacaaaaactaagcaaccagaatgggagagctactttcagtggtacctggagagtagcaaaaggggggaagaccgcctcatctccctacaggaggccaacaaacaacttagaaatgctaatcgagaactctctaatcttttatctctcttaaagaaatcctcggaatcccttacttcccccttggcacctcccccacctccacctacacccccactctaccctgacctctctgaacttcccggaccagatctgttccctccttctcctgcatgttcnannctancgtnttccnctcnntgtctgccactcgctcaacagaaggcagtngggagtctgacttcaaagaccccacctcctgacgattccctgacagccccagtggcagcctctcatctggaagatgtggaaaagggggaccctgcagggacatctctcatgatcgccccatttcgggaacaaccggtaacaggtaggggaaccccggcgattgtctaccaaccctggtcaaaggctgagttgcgaggcatagttaaagaatttcctgacccccataaagatccaattgggtttgcccgagaatttgagctcattatcagaacctatgacccaggtcattcagacctttatcagctggtccacatgttggtctcagaagctaaagctaaggaatggctggaaaaagcacagtggtcagaccctatagcagatttgacccctgaaggcccaatagagccacaacaaccagcccccanaaatccagaagacaggcgcaaagatgcgcgggaacgagcgaccgctctgttaaatatcattccttcagtgttccaaagggttgtggattggaataaaatccagcaatgccgccagaacccaaatgaatcagttttagattatttcacacgttttgataaaactttaagacaatattgcgggatgtcagctgattgctttgaaaacaataaaaatgatacattattaaatgcaaatttcttaaacggactagatgatgatttagccacccttgtaaaacgccacatgacaaattgggccacggccagaactaatgaactagttaacttagctgaccaattatcccgcactatgataaaaaaggaaaaacagaagattgcccgagttatgcatttacagctaaagcaattaacttctcaaacctctcagccccagaaagattttaagctccctcggtctgaggactcttccctcccagtctgttactactgtaaaagaccgggacaccttaagagggattgccttaggctgaaacgaaagaaaaggcaggagaatgcaactcaggaagactagggatgctccgaggaagtacaggggtttcacctctccaaatattctaccctgacaaacaaattgggagagattaatataataataaaccatgagcttacaactgccttaattgacacaggcgcgactatatctctgataaatcccaccttatttagaaaccccattcctcggagtaatgaaagaattaacatggtgggtgtgtctaataaaacgatctcatgttttaagtccaaacctataccttaccgtttcatcgggttcagctcccccgccgcaggctctaagtgtgacacgctcagtaggtcccatatgtttctnatatgccctggggcccctgtcaatcttttgggccgtgatctcctcaacatccataatgcccatatctctttttcatcaaaaggtgaactttttttagaattggagccaggggaccaaaaataccaaattaaaaaatgtcctgacaatgtaccacaatttagtactagtaatgttaaaacgtcatcttgtgaccgggaaaatgaaatggagacagagaaggaaatattaggggagaagagagaacattggaataaagagcaggaaacggtaaaactccttttagcttccccaatcttcctgttaacnccagaagcggagcacttgctcaaggatgtcccctcccacttatggtctcagtcaaatacagatatagggaaaatattctcagccactccaataaaggtagagataaacccaaagaaacccctacccaaccttaaacaatatcctctacgacaggaagccatagatggaattgcccctatcatacaagattatctgaaaaaggggctcattattccctgcacaagcccctgcaacagccctatattccctgtaaagaaaccaagcgggagaggatggagatttgtgcaggacttgagggcaataaacaatatcgtaatacccaggcacccagtagtccccaacccacatacccttctatcagctatacccactaccagccagtatttctcagttgtggatctctgcagtgccttctttagtattcctgtagatccagacagccagtatttgtttgcctttacttggaaagaatggcaatatacgtggactgtaatgccccaagggtatacagaaagtcccacttacttttcccaaatattaaaagctgatttagaggatttaatttttccccagggctcaacactcatccagtatgtggatgaccttctcctttgttcagacacactntcttcctctcaggaagatagtctatatttactcaaacagtnagccaccaagggacacaaagtgtccaaagacaaacttcagctatgcttaccgcaagttaagtatttggggcatattatctcggtcaaaggactgagtattaaccctgacagagtgagaggaattttagctttcccaatgcccgtcactaagaaacaacttagaggattttngggcctggcnggctattgtagaaactggataccaaatttctcccttatggctcaacctctgtatgcatacctaaaaaatgaacaacctgatcccatcatgtggactccagagggacaatcagctgtacaacaaataaaggaaattctaactaatgccccagccttagggcacccaaactacaaattgcctttctcccttttcgtacacgaaactggaggtactgcatccggggtactgacccagaaacatggtgatcatcagagacctataggctattatagccaacagctggaccctgtggctcgagggctgcctccttgtgtgagagcaatagcagccacggcccttctgtacaagtctgttgaagaaataattatgggttccccccttaccatttttgtgccgcattctcttgagacccttctaaactctcatcatactcaacatctgtctgtcaaccggttagcctcttatgaaattttgcttttatcatctcccaatattaccatttcccgctgtaataatcttaatccggccactctcttgccgggcccttccgacgaaacccctcatgactgtgttctgatgactgaccgacttctcacccccaggacagacctacaagagatgccactggataatgctgagatagaatggtatacagatgggtcttatttaagaggagaggatggaaattttagagcaggatatgctgtggtttccttactagaggtaattgaagccggtcctcttccccaagccagatcagctcaagtggccgaattgattgccctgacccgagcttgtcaattggcaaaagacaaggctgcgaacatttacactgacagccgctatgcntttggggttgctcatgactttgggatgctatggaaagagagaggatatttaacctcctcagggcaacccataaaaaatggacaacaagtatcagagctgttagaagctattctaaaaccaaaacgtttggcaattataaaaatcccaggtcactcnaaattagacaccacagaaagtcggggtaaccaattggctgatgctacagctaaaagagcagcattcgagccaccagccccaatccgggaaatggccataaaacccgaaacacttaaaaacatgttgaaagaaacccagagcatagctccnacaaaagagaaatctacttggaaacaggcagggggatacttgtctcccgaaactgaaatatggtgtggacctaataataaacccattattccaatgggatgtcaggtgccccttatggaatatgttcataatctgacccattggaatccagataaaatgatatcctggtgtaaacaatattactggaaaccgtccttcacggtggcacaaaaggtttactctcgatgtgttatttgtcccaaatataacccaggaaagcccctccatggggcccagggtcattttccccttccggctggaccttttgaggtatggcagcttgattttatccagctgccatcatctcaaggttacaagtatgttttagtaatggtctgcatgttttcccattgggttgaagcttttccctgcaggcaagcaacagccatggcagttggaaaaatcctactagaaaaaattatcccactgtggggagtcccctgtgaacttcacagtgacaggggaactcactttactggccaggttattcaaaatatttgtaaaatttggcccatatttcaacatttccattgtgcctaccatccccagtcctcaggcctggtggagaggaccaatggaataattaaaacacaattggctaagttcacagaggcatttcacctcccctggcccaaagcactccccctagtgctgcttacactccgatccaccccttttggaaaacatcaactgtccccttatgaaattataacgggaaggcccatgtgtatgggaacgaaaataaccaacccaacttttctcaagggagatatattgcaatattgtgagggactcatttatcatcttaaaaaaagccaagatttggtaaagaattcctttcacagtgcgctccctgaagataaggtncctggtcacgatctgcagcccggagattttgtctattggaaaagacatctaataaaggactccctccaaccccgatggaagggcccataccaggtactattgactaatccatgtgccgcnaaattagagggtatngactcatggatncacatctctcatcttaaaaaggcacaacctcctgagtggactgtaactcccaccaaagatcttcgcctccagttcactaaacatcgaccttcgacccaggactagaagcagacgacagctgttgtggactgcttaaacccaagacacaggaccaggcctgtatacaaaagaacgcctatgtttattgtataatagccattacaattattgtcctagagatactggcaactgctgtcttatgcagaacagggcacttgccttgtctgatttaacgtcctttagtagctaaaatgaatttcacaaccttgctnctatttatcctatgtccctacgccttcttgccactgccacccactgttgcccatgaaacaaacctgtttctacaatgggctcaggattatgcagacagattacaaaaggacgcctgctggatatgcggactcatgcctctttccagtggctccggcctgccatggtgggtatcccccttccaaggtcaggactggatagaataccaaaaatttattacatcacagaaacggtctggtatccttagtgctggcataacaaaagacaatatatataattggcccattaaaaacactcttaagagcaagggacatgggaaaagnttttcaatggaaaggaccagctcactagctctcactttagcatccccccaactaaaagagaaggtggtaaccacgccccaaacaacggcccattttcaaaatgggataatgcaaatttgggatggatttatctggctcaccccttcatttggccaactcagccaaaatgctcctttgtgctgggaacaaagaaaccacaccaaggaccnatggccaaacagtacgagagatatggggtggatacctggagaacgttgtgaccacattatcatattacaagacactgactggcatgccaccgattgggtgcagcgaccaggtatttattggctagctccaaatgggacatattggctatgtggcactaacttatggccgtggttacctccagggtggttaggacgatgttccctaggttatgcttgggcacaaggacgagtaattcagaccctgccaaaaccagcaaacctttttcatttacaatctcgctggacacgttcggtattccaatggtatgatcacttagcttcaatctttgtaccacagataggtattgaagatgttatatggcatatagaggccttaacgaattacacccaaaaggccctaaatgatagccgcatgagtatctctttgctaaacaatgaggtcacgcttatgaggaaagctgtgctgcaaaaccgtatggctttagatatactcacggcagcacaaggggggacctgcgccatcataaaaactgaatgttgtgtgtatattccagatgaatcgaagaacataacccgacttatgactgatatgaaaacccagataaccaacctgtcagatccaaaaccctcactaatcgattggttgagtggttggtttggatcctggggaacttggtggcagaagctattgcttataataggaataataataataatttgtgttctgtcctgtttttgcttacaatgttgttatggtatgtgcttgcaaataagtcaacgtgcaactgaaagggctagggtaatgattgcccagagaattgctctaattgaggaggcggtaatatagcctgaaccagcttccaggnttgctttccttttgttgctataaatctggcctnggtccctatatanntntttttctctctttcttttttcctttcctttttccttctttcctccccctnttttttttntntcttcatgggacangacttcctaggaatgagccttcctagcgacgngggacatgacctcctaggaatgagccttcctagcgacgtgggacctgaacttctaggaataaaccatcctagcgacgagaaaccagctcaaaaaaaggagagaaaaaacaacctgagaccagagactcatntttcttctaaaatgctttnctccaaaagattttaaaaaagaaaaggggggaaa
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 ZNF2 22 99.0 Weakly correlated
2 ZNF680 21 28.9 Weakly correlated
3 ZNF18 21 160.0 Weakly correlated
4 ZFP37 20 99.0 Weakly correlated
5 ZKSCAN1 20 160.0 Weakly correlated
6 ZNF8 19 99.0 Weakly correlated
7 ZNF792 19 94.0 Weakly correlated
8 ZFP69B 18 99.0 Weakly correlated
9 ZNF723 18 15.2 Weakly correlated
10 ZNF707 18 74.0 Highly correlated
11 ZNF175 18 94.0 Weakly correlated
12 ZNF547 17 74.0 Highly correlated
13 ZNF202 15 160.0 Weakly correlated
14 ZNF324 15 99.0 Weakly correlated
15 ZNF641 14 99.0 Weakly correlated
16 ZNF382 14 99.0 Weakly correlated
17 ZNF585B 13 99.0 Weakly correlated
18 ZNF394 13 99.0 Weakly correlated
19 ZNF354C 13 99.0 Weakly correlated
20 ZNF140 12 99.0 Weakly correlated
21 ZNF610 11 28.9 Weakly correlated
22 ZNF766 10 43.0 Weakly correlated
23 ZNF558 6 99.0 Weakly correlated
24 ZNF320 6 28.9 Weakly correlated
25 ZNF264 6 99.0 Weakly correlated
26 ZNF263 5 180.0 Weakly correlated
27 ZNF534 5 19.6 Weakly correlated
28 ZNF101 4 43.0 Weakly correlated
29 ZNF679 4 28.9 Weakly correlated
30 ZNF658 4 99.0 Weakly correlated
31 ZNF479 3 6.4 Weakly correlated
32 ZNF490 3 43.0 Weakly correlated
33 ZNF157 3 99.0 Weakly correlated
34 ZIM3 2 87.0 Weakly correlated
35 ZNF793 2 99.0 Weakly correlated
36 ZNF317 2 99.0 Weakly correlated
37 ZNF485 2 94.0 Weakly correlated
38 ZNF705D 1 28.9 Weakly correlated
39 ZNF418 1 43.0 Weakly correlated
40 ZNF823 1 43.0 Weakly correlated
41 ZNF808 1 19.6 Weakly correlated
42 ZNF7 1 99.0 Weakly correlated
43 ZNF440 1 28.9 Weakly correlated
44 ZNF442 1 43.0 Weakly correlated
45 ZNF786 1 99.0 Weakly correlated
46 ZNF257 1 0.0 Weakly correlated
47 ZNF133 1 99.0 Weakly correlated
48 ZNF716 1 19.6 Weakly correlated
49 ZNF563 1 28.9 Weakly correlated
50 ZNF705B 1 28.9 Weakly correlated
51 ZNF701 1 28.9 Weakly correlated
52 ZNF700 1 28.9 Weakly correlated
53 ZNF528 1 43.0 Weakly correlated
54 ZNF554 1 99.0 Weakly correlated
55 ZNF182 1 99.0 Weakly correlated
56 ZNF28 1 28.9 Weakly correlated
57 ZNF596 1 94.0 Weakly correlated
58 ZNF30 1 94.0 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 17 15.2 Weakly correlated
2 ZNF792 11 94.0 Weakly correlated
3 ZNF202 9 160.0 Weakly correlated
4 ZNF547 9 74.0 Highly correlated
5 ZNF354C 8 99.0 Weakly correlated
6 ZNF641 8 99.0 Weakly correlated
7 ZNF157 3 99.0 Weakly correlated
8 ZNF766 3 43.0 Weakly correlated
9 ZNF534 3 19.6 Weakly correlated
10 ZNF558 3 99.0 Weakly correlated
11 ZIM3 2 87.0 Weakly correlated
12 ZNF680 2 28.9 Weakly correlated
13 ZNF479 1 6.4 Weakly correlated
14 ZNF382 1 99.0 Weakly correlated
15 ZNF264 1 99.0 Weakly correlated
16 ZNF596 1 94.0 Weakly correlated
17 ZNF485 1 94.0 Weakly correlated
18 ZNF786 1 99.0 Weakly correlated
19 ZNF793 1 99.0 Weakly correlated
20 ZNF705D 1 28.9 Weakly correlated
21 ZNF140 1 99.0 Weakly correlated
22 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
1 ZNF202 160.0 Weakly correlated
2 ZNF641 99.0 Weakly correlated
3 ZNF723 15.2 Weakly correlated