Charlie3
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000023 |
|---|---|
| TE superfamily | Charlie |
| TE class | DNA |
| Species | Simiiformes |
| Length | 2706 |
| Kimura value | 8.31 |
| Tau index | 0.9037 |
| Description | hAT-Charlie DNA transposon, Charlie3 subfamily |
| Comment | ORF (roughly 625-2526) encodes a transposase 59% identical to that of CHARLIE1. Common internal deletion products of CHARLIE3 are roughly: 1-272<>2456-2710 (MER1A), and 1-96<>135-272<>2621-2710 (MER1B). |
| Sequence |
CAGGGGTCCCCAACCCCCGGGCCACGGACCGGTACCGGTCCGTGGCCTGTTAGGAACCGGGCCGCACAGCAGGAGGTGAGCGGCGGGCGAGCGAGCGAAGCTTCATCTGTATTTACAGCCGCTCCCCATCGCTCGCATTACCGCCTGAGCTCCGCCTCCTGTCAGATCAGCGGCGGCATTAGATTCTCATAGGAGCGCGAACCCTATTGTGAACTGCGCATGCGAGGGATCTAGGTTGCGCGCTCCTTATGAGAATCTAATGCCTGATGATCTGAGGTGGAGCTGAGGCGGTGATGCTAGCGCTGGGGAGCGGCTGCAAATACAGATTAACATTAGCAGAGAGGTTTGACTGCACAGAGACCATAATAAATCAATTGCTTGCAGACTCATATCAAAACCCTATCAGTGAGTGGCAAGTGACAATTAAGCTGCATCTGGTGGCAGGCTTTATAGTGGCAAGTGAGTTGATGTACTTCAATTGTACAGCTGCATCTGGTGGCAGGCTTTAAGTCAGAATCCGACACTTATTTTAGTCCGCGCGTGGCCCGCCCATTATTTTATTTACCACTTCCGTCCGCGCCTCTTTCCCGCACTGCGCACTTGTCTCAGTCACAGTTTTGGTAAGCCCACAAGCTAACCCTAGCCAAAATGAGTAAAAAACAAACGTCACTGGAGAGCTTCTTTGAAAAGGGGGAAAGACCCAATGATGAGACAGCAGAAGACTCTAAGACTGCCAACAAAAAGAAAGCTGCATTTAAAAGAAAATACCAAGAGTCCTACTTAAATTACGGGTTCATTGCAACAGGTGATTCACATTCTCCAAGCCCGCTTTGTATAATATGTGGCGACCGGCTATCCAACGAAGCCATGAAACCTTCAAAACTGCTTCGCCACATGGAGACCAAGCACCCTGCATTAAAAGACAAGCCTTTGGAGTTTTTCAAAAGAAAAAAACGTGAACACGAAGAACAGAAGCAATTATTGAAGGCCACCACTTCATCAAATGTGTCTGCACTGAGAGCATCATTCTTAGTGGCTAACCGCATTGCTAAAGCTAAGAAGCCCTTTACTATTGGTGAAGAGTTGATCCTGCCTGCTGCTAAGGACATTTGTCGTGAACTTTTAGGAGAGGCTGCAGTTCAAAAGGTGGCACGTGTTCCTCTTTCGGCTAGCACCATAACTAGACGAATTGATGAAATAGCAGAGGATATTGAGGCACAATTGTTAGAGAGGATTAATGAGTCACCGTGGTACGCAATCCAGGTTGACGAGTCTACCGATGTTGACAACAAGGCAACAATGCTTGTTTTTGTGCGATATATTTTTCAGGAGGATGTGCATGAGGATATGTTATGTGCACTTTTGTTGCCAACCAACACCACAGCTGCAGAACTATTCAAGTCTTTGAATGATTACATATCAGGAAAACTGAATTGGTCATTTTGTGTCGGTATATGCACGGACGGAGCGGCTGCCATGACTGGACGGCTTTCTGGTTTCACTACTCGGGTCAAAGAGGTCGCTTCTGAATGTGAGTCTACGCACTGTGTCATCCATAGAGAAATGCTGGCTAGCCGAAAAATGTCACCTGAACTTAACAACGTTTTGCAGGATGTGATTAAAATTATCAACCACATTAAAGTACATGCCCTTAACTCACGTCTGTTCGCGCAGCTCTGTGAGGAGATGGACGCAGAGCACACACGTCTTCTCTTATACACAGAAGTGAGATGGCTTTCTAAAGGTAGATCACTGGCCAGAGTTTTTGAGTTACGAGAGCCGCTCCAGAGATTTCTTTTAGAAAAACAGTCACCACTGGCAGCACATTTCAGTGACACAGAATGGGTCGCAAAACTTGCTTACTTGTGTGACATATTCAACCTGCTCAACGAACTCAATCTGTCACTTCAGGGGAGAACGACAACTGTGTTCAAGTCGGCAGATAAAGTGGCTGCATTCAAAGCCAAACTGGAATTATGGGGGCGACGAGTGAACATTGGGATTTCTGACATGTTTCAAACATTAGCAGAGATTTTGAAAGAGACTGAGCCAGGGCCTTCTTTCTCCCAGCTGGTGCATGATCACCTATCTCAGCTTTCAAAAGAGTTTGAGCATTACTTCCCAACCACAAAAGACCCCCGAACTGGGAAGGAATGGATCCGCGACCCATTTGTGAATAAGCCAGGTGAATCGACTTTGTCCGTGCTAGAAGAGGATCAACTGCTTGAGATCGCAAATGACGGTGGCCTTAAAAGTATGTTTGAGACAACTTCAAATCTCCATACGTTCTGGATTAAAGTCAAGGCGGAATATCCTGAGATTGCCACAAAAGCACTGAAAAGCCTGCTTCCATTTCCAACATCCTATCTTTGTGAAGCAGGGTTTTCTGCAGTGACAGCAACCAAAACGAGATTACGGAGTAGACTGGACATAAGCAACACACTTCGGGTGTCACTGTCTCCCATCACCCCCAGATGGGACCGTCTAGTTGCAGGAAAACAAGCTCAGGGCTCCCACTGATTCTACATTATGGTGAGTTGTATAATTATTTCATTATATATTACAATGTAATAATAATAGAAATAAAGTGCACAATAAATGTAATGCGCTTGAATCATCCCGAAACCATCCCCCCCACCCCCGGTCCGTGGAAAAATTGTCTTCCACGAAACCGGTCCCTGGTGCCAAAAAGGTTGGGGACCGCTG
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TF motifs of the concenus sequence
Use FIMO to detect transcription factor motifs in the concenus sequence of the TE family.
| TE_family | TFBS | Start | End | Strand | Score | Matched sequence |
|---|---|---|---|---|---|---|
| Charlie3 | Clamp | 85 | 98 | + | 18.94 | GGGCGAGCGAGCGA |
| Charlie3 | HES6 | 1149 | 1158 | + | 18.14 | GGCACGTGTT |
| Charlie3 | HOXD12::ELK1 | 561 | 573 | - | 18.12 | CGGAAGTGGTAAA |
| Charlie3 | PATZ1 | 2632 | 2642 | - | 17.64 | GGGGGTGGGGG |
| Charlie3 | SCRT2 | 799 | 808 | + | 17.62 | GCAACAGGTG |
| Charlie3 | scrt | 799 | 809 | + | 17.31 | GCAACAGGTGA |
| Charlie3 | ZNF281 | 2633 | 2642 | - | 17.16 | GGGGGTGGGG |
| Charlie3 | ERF::HOXB13 | 561 | 573 | - | 17.03 | CGGAAGTGGTAAA |
| Charlie3 | Klf15 | 2620 | 2641 | + | 16.98 | CCGAAACCATCCCCCCCACCCC |
| Charlie3 | SCRT1 | 799 | 808 | + | 16.90 | GCAACAGGTG |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
