ZRdb KZFP & Repeats
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LTR_PRIMA41-INT

  • Name
    PRIMA41-INT
  • Repbase
    PRIMA41
  • Type
    LTR
  • Emergence
    74.0 Mya
  • Dfam Id
    DF0001052
Description :

This is the internal region of the PRIMA41, an endogenous retrovirus,complete with Gag, Pol and Env genes and flanked by MER41C/B LTRs. Itlost the main part of its internal coding sequence during formation ofMER41A LTRs. The lost part has been replaced by non-coding sequencescommon for the MER4-group. PRIMA41 is related to leukemia viruses.
Consensus sequence The consensus sequences obtained from Dfam are derived from the seed alignment using a specialized caller. :
tctttctggcgaaccacggaagggacgatactgaagaaaccccccnaacccaaaggaaatagactgcagcaccgattggncgactttgggtaagtggtggggntncgnnnnntacccgggtaaagaatgggattgggttagaggcccaacttaggggagttagagtctctcctaagacagagtgggttagaggcccctcttaataaaaggcaaggacgcttgaccgaccttgggttagaggcccgacttaggagggttagagtcccttctaagatttagggggttagaggcccctctcagtaaagtccctctcggctaagaacgggtttggcaccgcgggatgttaaccgctatgctctttgtattaatctgccttgtcctctttgctgcatgaatcaatttcttggttgctgtctctgtttcactgtcattttcaggagacttcatttaactggtcttagggattttaacttactcttttcctatgcgcctcccgatttccgtccgtttgcttgtgaaacattgggaacaaaaagcattgaaggctccgtctctaaaattgctgattgagatttggtatttaacagctatgagcaataagattagatagatgtggttatgttttgttgccgctatgccgactaggtgtgatcgagaagcactaggatggaaatcaggggacttttctccttgctgttttgtttcattttgcacactaaaaaaacttctttcctttcttggattcgggcaaaccggctttgcttgtccaatccacgctgccgctattgcccagaacctgcttgctctggtcattcccatctaaatcctcttcatttcctttgccttattcgacatttttgtcgaagtccatgttgtggtttatctaagattcatggctcggctcacttatattatttggataatgtgaataagagaattcaattttcggcagggatcccctcataatgcagctggccttaaaaactctctcctttttagtggaactcggccagtggcaatacaatctcgcaggtttggaacttttctttcaacgtcacctgcctccttcatgggaaccacggcatcgattccaaagaactcaccgctaggatgtattcttgaacattgggaccagtttaaactgaatgggcttaagaagagaaaactggtgtttctatgtaatactgtttggcctcggnntattatnnttggaaaaacaagagaaatggcctcctactggaactacggcctttaatactatacttcaactcgatttgttttgtaagcgggagggaaaatgggatgaaatccatatgttcaagcatttttgctgctcggtcaggataaaaccctgcagcgggcgtgtgcatgtttgatgagaggaaaagaagnaaaannngaaaaagagctagacatactagatgatcctttaatgcaagcccccctncccgcccccgccgnncncggttcagcgggcanttttgggtggagcagaacctccttctgtcagctctgaaggttcagatgtgtcggtcccttcttctagtccacctgaaagttctattgagaacccttcgtcccctcctccttacccgtctagtcccactctatacccaccactccccgaggaactnagcccagcgagtactactcgnagtggagcctcctatcagcctccaaagggaaatctttgtccacttagagaggtggcaaatggggangaaggcactgtnagagtacatgtncccttttctatgtctgatttggctctatgcaaggagaagtttggtcgnttctcngaggatccaggaaaattcatagacgagtttgagaagttaactctgacctntgatttaacttggcaggatctgcatattttgttgtctccgtgttgtacggtggaagagaaacaacgcattttggggacggctaggacccatgcagatggggtancggctcgcaacccgagccatgacatntatcaggcaggaggtatagcagttccagatcaagacccanagtggaactatcaaaggggcagtgaggacttggggaggagagatcatatggtcacttgtttnntggaagggatgaagaaatgtatganaaagcctgttaactatganaaggttagggaagttnctcagggnaaagatgaaaatccagctttgtttcaagggcgtttagttgaggcantcaggaaatatactaacactgaccctgnctcaagggaaggacaaacccttctgggagtacattttataacccagtctgcccctgatatccgnaggaagctacaaaaagcagctatgggnccccaaactcctatggancagcttttggacgtggcntttnnagttttcaataacagggacagggcagaggaagcagaaagagcaagaaggacctcccanaaggcgcagctnttggctgcagccttaagctcacctcccacatggggttgccctcctggctcttggcctgaacaagggaagctgaaaggtgggaagcccaaanctgggcgtccgagtcaccgtgccttgggcataaatcagtgtgcncnctgtaagaaagnnggccactggaagagggactgcccagcgctccgaagggagccatcggcacccgaaccnatgatggccgaaatagccaggcaagcccaagagtgacggggcccgagaccttccgccacggctcccatcggacaactagccatatctccggaggagcctcgggtaacccttgacgtggcaggtaagaatattaacttcctnttggatacgggagccgcttactctgttctgacccattataatgggccnctgtcnccccaaaactgtacggtcacggggatngatggacaagcccanagacgccattttacctatcctctaagctgctcttcagggactttggttttctcacatgccttttcttatcatgcctgaatgccccaccccttgctgggaagggatttattnactcagctgcaagcngtggtnnctttcggagatcacaaggcagacgaggaattgctccttctcctttcctgtgataagggaggaaagtcaanagggacctatcnnacttaccnactgaagtaacctctcaagtaaatcctnnngtttgggacacggaggttccgggnaaagcnntaaacgttcccccagttcgnatccaacttaagcccggtgttcnntacccntggaagagacaataccctttaaggccngaggcacgaggggggatccagcccctaatagcnaagtttctgcaatatggnttattaaggccctgtnagtccccttgtaataccccnatcttnccngttaaaaagccaaatggggantacagatttgttcaagacctnngggcngttaatgaggcngtcgttcccatncacccnatagtncccaatccttacacgntgttagcccaggtcccnggggatgcnaattggttcacagtnttagacctnaaggatgctttttttttntgcatttcagtacacccngattcncaatntatntttgcttttgaatggactgatccnngatantcattcggcntctcaattaacctggacagtccttccccagggntttagggacagcccccatctntttggaaatgcnttggcnaaagaattaaggaagctacagttgaataggggcnctattattcaatatgtggatgacttgttnattnctagcccnactaaagaagactcggataaaaataccattaagttnctaaatttcctgggaactaacgggtatagggtntcnccgcacaaggcccagatttcnactcaaaaggttaaatatttgggatacgtnctaacccctggnacccgggcantagccccnagaangaaaagaggccatcttggnnntcccgganccccagaccaagaaacagctgngggcttttttgggaatggcnggattctgctnttnatgggtncccggatttgggcntatagcnaagcctttatatgaggctctaaaaggagcggacgtgancccttngaatgggatagnaactgcaaaacanacttttaataccctnaaagagaaactgggancagctccngccttgggantccccaanttnganaagccntttcctttatgtggctgaaaaacaagggacgccctgggtgtcctngcccaaaggctgggaaatatccccgaccagtggcntatttttctaagcagctagaccaggtggcntcggggtggccnggatgcctnagggcngtngcngcnaccgctctnttggtagangaagccagtaaactnacnttgggacaacanctagaggttttgaccccncaccaagtacagggggtcctagaagcnaaaggacaccagtggntgacagggggacanttactnaaatatcaggctttnttgctagacaccccgatgtaactcttaaagtatgccaaactttgaacccagctacctntttgccngaacccacaggcaccctagatcattcttgtatacaagttatggagcaaatttactccagcnggccggacttaaaggatgagcccctagataatcccgaggtagaatggtttacagatggaagtagctttgtgcacnagggaaacagaaaggcngggtatgctgtngttagccaacangaggtnatcgaggcnnaggccttaccggcttcnacctcagctcaaaaggcggaattaatngctctnattagggccctncaattgggaaaggacttaagagtcaacatntncactgattccaagtatgnntttctggtgctccatgctcatgcngccatntggaaggaanggggactnctaacngctaagggntcccccataaaacatcactcagaaattctgaatctnttagatgctgtttngctgcccaaggaagtagcngtnattcattgcagaggacatcaaaaaggggactccantgtnactaagggaaactccctngcagacgnagcagctaaggccgcagcattaaagganccagttggacttgtcggcgcgctagtgccctcagccacggtaatgacagaaccgngatatactaaagaggaacgagaatgggctaaaggtcagggtttaattcaagatccctctggntggcttatcgangacaacaaactnttgataccaggtgctaatcagtggaaaatagttaagcatttncatgactctnctcatttgggaagggattccctgtttcaattaatgtctcagctttttataggaaaaggcttactcaaaacngtaaagcaggtaactcgggcctgtgaactntgtgcccggaataacccaaanagccaacctttacctcctcctctagtnaggcctgttcagcacaggggaacgtaccctggngaagactggcaaatagactttactcagatgcccccatgtagagggtttaaatatttgctagtattcgtngacaccttcaccggntggatngaggcttttcccaccnggncngaaaaggcaattgaggtntctaaactcctactaaaggaaataattcctaggtttgggctgcctaagagcttgcagagtgataatggcccatctttcacagcnanagtnacccaaaacgtntcttcagccctaggaattcagtaccgccttcactccgcntggaggccacagtcctcaggnaaagtagaaagagctaatcaaactctaaaaaggactctngcnaaactatgccaggagacntcagagacctggntgtctctattacccgtagccttnttacgggtncgaatggccccnaagggaaatctgnagctcagcccttttgaaatgacgtatggaaggcctttcttaactncagacctcctaatagacgnagatactttcaagctacagaattatgtnatcaacttaggncaggtncaaaaggcnctccntgaatatggaaatnaaagactnccttcccccacnaaggaagagaatctcgttacaacccagccaggagactnagtcctactaaaaacttggaaagaaggatccccngcggatcaactncnnccaaaatggaagggnccctatcaggtnctnctnagtaccccaactgcngttaaacttcagggaataancagctgggtncacctgtcccgaattaaacctgtttcttatgaagtcccacaggccgacggaacacaagagactgatcccgtttattcctgtgagccaatcagtgacctccgactcctgttcagaagaaacgaaagggatgggtaacataaagatatggattggcattctacttttgggtataagttggaatcatgcagagagtaacttatttactgagtgggcacagactttagcctctctacataatcagacaaactgttgggtatgtggagaattgccnctttcctccacttccggnttgccctggcatattcaaccggccaacctaagtttatggggnattttattatgattgggaaactgaacattataaacatannccctcttttcccatgtaccatagccnangnggccttagcccntttcccctcctacggagagacaagaaggcaccttttttttnnatctaattaggaaacagctaaactccaccccaacttaggttatgctgtacacgatggacttgggcggatgacaggtatcaggcaaagcgcctctatgtntcgaaaggcacaataacagtcaccaccagactggaacccatgatatgggatggctgccacctcaacaatgtaaccagacccttcttctaacngaccanatgtggntgggatggcaaaataattcgccaaaaatgggtgcctacccttccccttggggatggctatgggcntgcggnactcatggctggccntacttaccttataactggactggaaggtgcacgtggggtcgcccttatctnccgggacgtatcctcaccaanttggactctctcccatctaactgggaaantgtaaaggctcgccataggcgacaaaaacgggcatcctggtggttctacccgntggctatnttttccccgcaggcagcnaccaaattagatatngagttacaagtngaagcgnccttggccaagcacacggctgcagccttcaataatacncgccatgccgccttacccttncctnactgaggaaacttctcagattaggcaggtggccttacaaaaccgtatggctttggacattttaacngcggcccaagggggaacttgtgctttgatcaaaaccgaatgttgtgtgtatgttccagactattcncataatatnacccaggctatgaaagctttagacactcatatctctgccattgatgcgctgtcagtcgaccctatatcggcttggttccaacaactgcccagttcttggaaagccttcctgtttagtttacttggaatgattttacttattttgctttgctgttgtggaatatattgcggttgtactctttgtgtaggaatgcaagacaagctcactcaacgctttcttaaattggacacttattaatcttccagatatcaccttttgtcggaactcggagttatgaacgaccctcaccataccaacgctctctgactgagctcctctctaccctgaatgcaagagaccctaatagttaggcaggaatatcatcgcccctattcagcctgaagaagttacagaagacggatcttcgtccctctgcaacccttaggattaagggtcctcttgtaaagggaggggggagata
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 ZNF723 18 15.2 Weakly correlated
2 ZNF382 16 99.0 Weakly correlated
3 ZNF175 14 94.0 Weakly correlated
4 ZNF766 14 43.0 Weakly correlated
5 ZNF589 11 28.9 Weakly correlated
6 ZNF584 10 99.0 Weakly correlated
7 ZKSCAN8 8 160.0 Weakly correlated
8 ZNF197 8 99.0 Weakly correlated
9 ZNF101 7 43.0 Weakly correlated
10 ZNF486 5 8.6 Weakly correlated
11 ZNF479 5 6.4 Weakly correlated
12 ZFP57 4 87.0 Weakly correlated
13 ZNF528 4 43.0 Weakly correlated
14 ZNF394 4 99.0 Weakly correlated
15 ZNF251 4 94.0 Weakly correlated
16 ZNF263 3 180.0 Weakly correlated
17 ZNF793 3 99.0 Weakly correlated
18 ZNF679 3 28.9 Weakly correlated
19 ZNF786 3 99.0 Weakly correlated
20 ZNF680 3 28.9 Weakly correlated
21 ZNF549 2 87.0 Weakly correlated
22 ZNF547 2 74.0 Highly correlated
23 ZIM3 2 87.0 Weakly correlated
24 ZNF445 2 99.0 Weakly correlated
25 ZNF320 2 28.9 Weakly correlated
26 ZNF317 2 99.0 Weakly correlated
27 ZNF182 2 99.0 Weakly correlated
28 ZNF274 2 99.0 Weakly correlated
29 ZNF26 2 99.0 Weakly correlated
30 ZNF75D 2 94.0 Weakly correlated
31 ZNF701 1 28.9 Weakly correlated
32 ZNF77 1 87.0 Weakly correlated
33 ZNF705B 1 28.9 Weakly correlated
34 ZNF649 1 28.9 Weakly correlated
35 ZNF597 1 94.0 Weakly correlated
36 ZNF735 1 28.9 Weakly correlated
37 ZNF85 1 28.9 Weakly correlated
38 ZFP37 1 99.0 Weakly correlated
39 ZNF878 1 43.0 Weakly correlated
40 ZNF554 1 99.0 Weakly correlated
41 ZNF287 1 99.0 Weakly correlated
42 ZFP69B 1 99.0 Weakly correlated
43 ZFP90 1 99.0 Weakly correlated
44 ZNF124 1 43.0 Weakly correlated
45 ZNF133 1 99.0 Weakly correlated
46 ZNF140 1 99.0 Weakly correlated
47 ZNF18 1 160.0 Weakly correlated
48 ZNF257 1 0.0 Weakly correlated
49 ZNF273 1 28.9 Weakly correlated
50 ZNF534 1 19.6 Weakly correlated
51 ZNF2 1 99.0 Weakly correlated
52 ZNF334 1 99.0 Weakly correlated
53 ZNF347 1 43.0 Weakly correlated
54 ZNF429 1 28.9 Weakly correlated
55 ZNF43 1 43.0 Weakly correlated
56 ZNF441 1 43.0 Weakly correlated
57 ZNF471 1 94.0 Weakly correlated
58 ZNF506 1 28.9 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 ZNF793 4 99.0 Weakly correlated
3 ZNF479 2 6.4 Weakly correlated
4 ZNF701 1 28.9 Weakly correlated
5 ZIM3 1 87.0 Weakly correlated
6 ZNF382 1 99.0 Weakly correlated
7 ZNF471 1 94.0 Weakly correlated
8 ZNF263 1 180.0 Weakly correlated
9 ZNF705B 1 28.9 Weakly correlated
10 ZNF549 1 87.0 Weakly correlated
11 ZNF287 1 99.0 Weakly correlated
12 ZNF597 1 94.0 Weakly correlated
13 ZNF534 1 19.6 Weakly correlated
14 ZNF101 1 43.0 Weakly correlated
15 ZNF680 1 28.9 Weakly correlated
16 ZNF766 1 43.0 Weakly correlated
17 ZNF429 1 28.9 Weakly correlated
18 ZNF133 1 99.0 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 ZNF723 15.2 Weakly correlated