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 | ZNF454 | 14 | 30 | - | 15.54 | GGTCCGTGGCCCGGGGG |
| Charlie3 | ATMYB31 | 2116 | 2130 | + | 15.51 | TACTTCCCAACCACA |
| Charlie3 | MYB31 | 2116 | 2130 | + | 15.51 | TACTTCCCAACCACA |
| Charlie3 | KLF4 | 2633 | 2640 | + | 15.48 | CCCCACCC |
| Charlie3 | NDT80 | 2323 | 2331 | + | 15.46 | GCCACAAAA |
| Charlie3 | ewg | 216 | 225 | + | 15.45 | GCGCATGCGA |
| Charlie3 | ewg | 216 | 225 | - | 15.45 | TCGCATGCGC |
| Charlie3 | HES2 | 1149 | 1157 | + | 15.44 | GGCACGTGT |
| Charlie3 | ZNF320 | 2453 | 2472 | - | 15.40 | GGGGGTGATGGGAGACAGTG |
| Charlie3 | MAF | 705 | 717 | + | 15.24 | TGATGAGACAGCA |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
