Charlie5
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000027 |
|---|---|
| TE superfamily | Charlie |
| TE class | DNA |
| Species | Eutheria |
| Length | 2624 |
| Kimura value | 17.76 |
| Tau index | 0.9941 |
| Description | hAT-Charlie DNA transposon, Charlie5 subfamily |
| Comment | Transposose (roughly <841 to 2439) is 50% similar to the human protein AC004883. MER3 appears to be a recombinant product of 5' end fragments of Charlie5. |
| Sequence |
CTGCGCTGTCCAATACGGTAGCCACTAGCCACATGTGGCTATTGAGCACTTGAAATGTGGCTAGTGCGACTGAGGAACTGAATTTTTAATTTTATTTAATTTTAATTAATTTAAATTTAAAAACTGAAGCAGTGTAAAATATTTTTCCGTTAAACACAACTTTATTGTTTTGGTAGGACTACATTTCACTTTAACCGTTGCATCGCGTAAGATATTATTGTTGTATTGTAGTGCGCGTGTCGGGCACGTGCGTCGTTTCTAGTATTACACATAAACACATCACCGATCTAGTCGGTGTCAACGGATTGATTCAGTTCGAATGATTTTTTTCTACGCACCGATGTAACATTGTAATGTGTTTATTTGAATATTTTATGCAGACAGCACGAGTTACAGTGATACCTATGTAAATCGTAATTGGTAATTAAATTGAAATACTTATTATTTTAATTATAATATAATTAAATTATTTTTCTAGTTTAAAAAATAAGTATGGACAAATTTTTAAATTTAAAACGAAGGCATACTACTGATGCAGAATCGAGTGGAGATGCAGAAGCTAGTACTACGACCGGAACAGTAAAGAAAAAAAGAGACTGGAAGAAGGTATGTCGCAAATTTCACGATGAATGGCAATTGCAATTTGCTGCGGCAGAGCAAAACGAAAAAGCTGTTTGTTTGTTGTGTAAAAAAATTTTTAAAGATAATAAAGTGGACAATATTAAGAGACATTTTCAGCAAATACATAGTGAATTTGATAAGAAGTTTCCTCTCAACAGTCAAAAAAGAATCGATGAAATTAGTCGCCTGAAATCAGAATTAAATGTCCAACAAAAATTTTTTAAATAATTTTTAACAGGATCTGAGCTTGTAACTTTGGCCAGCTATAAAACGGCTTGGATTCTTGCACAAAAAAGAAAACCATTTTTAGATGGAGAGATGGTAAAANAAATTATTATTTCAGTTATGGAAATTTTGTTAGAAAATTATGAGGAAAAGACTAAAAAAGATATTTTACAAAAAGTGAAAGATCTTCAATTAAGCCACCAAACAATTGCCCGTAGAATACAAGACCTTTCTAACAATATCAAAGATCAATTGATTCAAAATTTGAAAAATTGCAAGTACTTTTCTTTAGCTTTAGATGAGTCGTGCGATATAAGAGACACTGCCCAATTAATACTTTGGGTACGTTTTGTCTCAAAGGACTTCCAAATTTACAAAGAAATGTTGNCAATTCGCGGCCTAAAAAATCGAACTCGTGGCGTAGATATTTTTNAATCTTTTACATCTGTCAAAGAAGAATTTCAGCTAGATATGAAAAAATTAGTTTCTATCACGACGGACGGTGCTCCAGCTATGTTAGGTCAAAAATCCGGATTTATTGGAATTTTAAAACAAGAGACTGATGTTTCCCTTATTGCTTCGTTCCACTGTATGATACATATTGAAAATATTTGTGCTCAGTTTTCTGAAGCAGACTCTATGAAAAGTGTCATGGATACAGTTGTTAAAATCGTTCAGTATATACGTGCAAATGCTATGAATCATCGCCAGTTTATGGAACTGTTGAAAGAAATAGAAGACAATGAATTTAATGATCTTGTGTTCTTTGCCAATGCTCGTTGGTTGAGTCGTGGAAGAGTTTTACAAAGATTTACTGTACTGTTAACTCCAATTCAAGATTTTCTTGAAACAAAAGGAATGCTTGCCAAATATTCAATAATCAAAGACAAAAAATGGCAGTGTGATTTACGTTTTCTCACCGATATCACACTGCATATGAACGAGCTAAATTTGAAGCTCCAAGGAAAGGAAAAGCTTATTTGTGACCTAGCTAGACAGGTACGAGAATTTATGTTGAAATTGAAACTTTTCATAATACAAATCAATAATAATGATTTTACACATTTTTCTAACATGAATCAATATGCAGAAGATTTTAATTGTAATCGACAGCATTATGTAAATTGGCTGCAAAAACTACAAGAAAAATTTGAAGAACGCTTTGTTGATATTGATAAATTTAGAGTTGCTTTTCAATTTATGCAATACCCCTTTGAATTCGATGTTAATAATACTGAGTTGACACAAGAGTTAGTGAATTTACTTAACTTGGACAGACGTAGTTTTGAAACTGATATGCTTTTGCTTCAAAGTCAAATCAATTCTTCTAAAAAAGATGAACCAGTTTTGTCAATGTGGATGCGAATATTAAAGGAAAATGATTTTTTGATACTCGATTCAGTTATTGGAAAACTTTTAAGTATGTTTGGAACAACTTGGGTATGTGAATCTACTTTTTCAACTGTAAATTTTATGAAATCTAAATACAGATCAAGTATTTCCGATGAAAATTTAGCGTCCGAATTGAGATGTGCTGTAAGTGTAAAATACACACCGGATTTCGAAGACTTAGTACGAAAAAAAGAATGTAAAATATCTCATTAATAATTTTTATATTGATTACATGTTGAAATGATAATATTTTGGATATATTGGGTTAAATAAAATATATTATTAAAATTAATTTCACCTGTTTCTTTTTACTTTTTTNAATGTGGCTACTAGAAAATTTAAAATTACATATGTGGCTCGCATTATATTTCTATTGGACAGCGCTG
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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 |
|---|---|---|---|---|---|---|
| Charlie5 | RVE7 | 2437 | 2445 | + | 16.38 | AAAATATCT |
| Charlie5 | TCX6 | 109 | 123 | + | 16.37 | ATTTAAATTTAAAAA |
| Charlie5 | TCX2 | 1102 | 1116 | - | 16.31 | TTTCAAATTTTGAAT |
| Charlie5 | YPR015C | 1748 | 1758 | - | 16.31 | ACGTAAATCAC |
| Charlie5 | bHLH78 | 244 | 251 | + | 16.29 | GCACGTGC |
| Charlie5 | bHLH78 | 244 | 251 | - | 16.29 | GCACGTGC |
| Charlie5 | SOL1 | 1102 | 1116 | - | 16.27 | TTTCAAATTTTGAAT |
| Charlie5 | RVE6 | 1008 | 1016 | + | 16.23 | AGATATTTT |
| Charlie5 | RVE6 | 1269 | 1277 | + | 16.23 | AGATATTTT |
| Charlie5 | RVE6 | 2437 | 2445 | - | 16.23 | AGATATTTT |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
