ZRdb KZFP & Repeats
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LINE_MAM_R4

  • Name
    MAM_R4
  • Repbase
    Plat_R4
  • Type
    LINE
  • Emergence
    99.0 Mya
  • Dfam Id
    DF0000984
Description :

This is the first Dong retrotransposon found in tetrapods, originallyidentified in platypus as Plat_R4. Because closely related sequences arefound in Theria (non-monotreme mammals), this has been renamed toMam_R4. This reconstruction contains all of "ORF2" (roughly pos.244-3732), although the start condon is unclear. ORF1 is usually absentin Dong elements, and is not evident here.
Consensus sequence The consensus sequences obtained from Dfam are derived from the seed alignment using a specialized caller. :
aaatccaactctatatccttagggactttangtccttaaacgtgcgaggcgggcggcatagccggctaacagggctctggtaacccacgaatgtgttggcagctcatcacggagtttggaattgctacgccaaggaaaagaagaattaaaggtgaagcaacagtggagactgatgttgctttcaccgagggacagtctcacgttgtggaaagtggagcaagtggcgctacccaatggtctggaaccgcgagaaacagaagcagcacccaagaccaacgagttgtaactgctccaagngttttgcctgatggaagtcaggcaaccaccagagcaggactgccgagacagcgcattaaatggacagcagaaatgaataagantataatgcgccgttattttgaaaccacacaattagaaaccgagacgacagcgtatagaccagcaacgtatcagcattttatagccaaatatcctgaattgacagcgagactaactgaacaaaatgtagcagatcggaggcgggccattatgacgagaaacctgcttaccgaaactgaaattaataccatcagacgtgaggtctcagaacagttaggaatcaacagaaaagcagatgaagaggcccctgttgataatgaatcagaagatggagatacgcccctgagnaagaagagcgaaatgaaggaagaaccagcagtaattgtgaatgaaagtcatgaggatcaacagttgtttcaganagtagaacatcattttaatgctgccatgactgcgtttggaggtactgacccaacacaacgacgtagtatcccgaagatacgcgcctctaaaaagatgggtatcataatgggctacctgaataaccaggttttacctcaatatcttaatgaaacatcagacccggaatatgtacgttatataatttactgcgcagcagtcgcagcaataagatcaatgggtctaaaaacaattccncagcataacaataaacgagtcaacagggtgaaatgtgagccagaatggagaagacgactagaacaaaaaatcagtaagctcagaaaacagctgggaaggcttacccaatacaaaaataacaaccgatcaagaaaattaattaataaagttgcccggataattactccccttgcactgaatgacttaagcaaagataaattgatagaaataacggatacacgcacgcaaaaattaactgcttactcaaaaagattacgaagatataaagaaagccgagagaggaaaaatcaaaatcagggcttccagagtaatcaaaanaaattttatcgggacttgcaacgggaaaaaatcaattatagtgagggtgtaccaccgattgaagatgtgacggaattctggtcaagtatttgggaggtccctaaaagccataacactgaagcaacgtggttgcgagaagagaaaacccggacagatggaatcatggaaatgtcacctattggaatatctgaacaggaggttactgaagcaatcaaagcggctagtaattggaaagcaccaggtcctgacttgttgcagaacttctggctcaagaagctcacgacagcacatggagctattgcaagatgtttcatgaaaatactgcgcgagccagaagaaatgcctgattttatgacntctggaaacagctttcttttgccaaaagataacaatacttcaaatccagcgaagtatagaccgataacatgnttgcctaccatctacaagctaatgacatccattttggcgaagaagatttactcgcattgtgagagaaataatatcangactgaagaacagaaaggatgtcgcaaattatcacagggatgtaaagaacaggtcattatagactctgtgatagttaatcaggctattaaaaaacaacgaaatctgagcatgagctatattgattacaaaaaagcctatgactcagttccccattcgtatctaatagagattttgaaggtttataagatcgatccttcgattgttaattttttgcagcatgcaatgagcaaatggaataccacgttacatctttcaaatggtgaaaggactgtcaaatcgagggccatacttataaagcggggaatatttcaaggagactcgcttagtccattatggttctgtttgggactgaatcccctaagcagaaaactaaataataccggtcatggctttaagataaaacacgaggatgaacatcatatcgtcagccatttgctctacgtggacgatctgaagctctatgccaactctaaaacgcagcttcataagctactaaaaattacaaagaactttagtgatgatatacaaatggagtttggtatggataaatgcaagtcgatacaaatggtgaaaggacaacttactgtgacggacgggttcactgtcagtaaagaccaaattattgaagacttagtgcaaggggaagcctacaaatacctgggcttcctgcagttgagagggattaaccacatcgcaattaaagaaaagctgaagaaaacattcagtttacgtgcggagaaaatattaaaaacttacctcaacgcaggcaataagaccaaggcaataaatgcatttgcggtaccggttctaacatattcatttggtattataaaatggtccgatacagacctagaggccatcacacgtaacatcagagtgttaatgacaaagcatcgtacgcatcacccgaaagctgcaatcgagaggatcactctaccatatgaagaaggtggaagaggagtaattaacatttacaatctgtattactcccagattgcaaaaccgagggactatttttacagcaagtcagattgtaacctgtataaatcggtcattaaaaccgatcgcagtttcacaccactaaagcttgggaatatagagtatgatccagcagcaaatctacaaacgattcaacagcaaattcagacttggaaacaaaaagagttgcacggtacctacccgcatcagcttagccaaaattatgtagataaaactgtgtctaatttacggctgaagcgaggtttactgtttgctgagaccgaagggtttgctgtggcgattcaggatagggtgattggcactaaaaattatcgcaagtatatactgaaggaaaacttacttgacgataagtgcagacgatgtgtggcggctaacgagacaattgaacacgtaattggaggatgtactaccttggctgctgtggattataccaacaggcacaataacgttgctaagattgtacatcaacagttagccttcaattgcaagttagtgaatggattaacaccatattataagtatgaacccaagaatgtgatggaaaacagctgttataaattgtactgggacagagccgtgataacagaccaacaaatcctggccaacagaccagacattctgctgcttgataaacttaataaaacagtggagcttattgatattgctgttcccctaagcagaaatattccaagaacatatgcagagaagataaataagtacgtgggtctggtagaggagctgaaacaaatgtggagattgaagtncagcaaagtaaagccaattatcatctcggcgactggggtggttccgcatacactagttaaacatcttaaggaactggggattcattatacgctggcctcaattcagaaggcggtacttctggatacctgtcacataaccaggagatttttatctcaacaatagataattataatgtacttggctaatgcccgtattgttataatgtgtaaagaccagattaatctgagaaataaaaataataataa
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 ZNF382 40 99.0 Highly correlated
2 ZNF18 11 160.0 Weakly correlated
3 ZNF394 10 99.0 Highly correlated
4 ZIM3 7 87.0 Moderately correlated
5 ZNF2 6 99.0 Highly correlated
6 ZFP37 5 99.0 Highly correlated
7 ZNF101 5 43.0 Weakly correlated
8 ZNF766 5 43.0 Weakly correlated
9 ZNF723 5 15.2 Weakly correlated
10 ZKSCAN1 4 160.0 Weakly correlated
11 ZNF175 4 94.0 Moderately correlated
12 ZNF610 3 28.9 Weakly correlated
13 ZNF317 3 99.0 Highly correlated
14 ZNF263 3 180.0 Weakly correlated
15 ZNF133 3 99.0 Highly correlated
16 ZNF75D 2 94.0 Moderately correlated
17 ZKSCAN8 2 160.0 Weakly correlated
18 ZNF792 2 94.0 Moderately correlated
19 ZNF324 2 99.0 Highly correlated
20 ZFP69B 2 99.0 Highly correlated
21 ZNF589 2 28.9 Weakly correlated
22 ZNF584 2 99.0 Highly correlated
23 ZNF558 2 99.0 Highly correlated
24 ZNF479 2 6.4 Weakly correlated
25 ZNF554 2 99.0 Highly correlated
26 ZNF679 2 28.9 Weakly correlated
27 ZNF547 2 74.0 Weakly correlated
28 ZNF793 1 99.0 Highly correlated
29 ZNF695 1 28.9 Weakly correlated
30 ZNF701 1 28.9 Weakly correlated
31 ZNF705B 1 28.9 Weakly correlated
32 PRDM9 1 0.0 Weakly correlated
33 ZNF705D 1 28.9 Weakly correlated
34 ZNF627 1 74.0 Weakly correlated
35 ZNF528 1 43.0 Weakly correlated
36 ZNF486 1 8.6 Weakly correlated
37 ZNF429 1 28.9 Weakly correlated
38 ZNF418 1 43.0 Weakly correlated
39 ZNF273 1 28.9 Weakly correlated
40 ZNF251 1 94.0 Moderately correlated
41 ZNF197 1 99.0 Highly correlated
42 ZNF169 1 94.0 Moderately correlated
43 ZFP69 1 99.0 Highly correlated
44 ZFP57 1 87.0 Moderately 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 ZNF133 3 99.0 Highly correlated
2 ZNF723 3 15.2 Weakly correlated
3 ZNF382 3 99.0 Highly correlated
4 ZFP57 1 87.0 Moderately correlated
5 ZIM3 1 87.0 Moderately correlated
6 ZNF554 1 99.0 Highly correlated
7 ZNF584 1 99.0 Highly correlated
8 ZNF101 1 43.0 Weakly correlated
9 ZNF558 1 99.0 Highly correlated
10 ZNF766 1 43.0 Weakly correlated
11 ZNF589 1 28.9 Weakly correlated
12 ZNF679 1 28.9 Weakly correlated
13 ZNF175 1 94.0 Moderately correlated
14 ZNF18 1 160.0 Weakly correlated
15 ZNF429 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