Charlie2b
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000020 |
|---|---|
| TE superfamily | Charlie |
| TE class | DNA |
| Species | Eutheria |
| Length | 2782 |
| Kimura value | 26.18 |
| Tau index | 0.9970 |
| Description | hAT-Charlie DNA transposon, Charlie2b |
| Comment | 15-16bp TIR; 8bp TSD. Charlie2b is an alternative internal deletion product of this superfamily. |
| Sequence |
CAGTGGTCTTCAAACTGGGGTATACATACCCCTGGGGGTACGTGAAGACTTTCCAAGGGGTACGCGGGCACGGATAGTTTTAAGGGAATCAATTTCCAGATCCTCAACTTCCATATGTACTCTTTCCTAAAACTGATCTGCCTGAGAACGTGCCTGTGGCGAAGTCTGCCCTTTCCCACTTCCCCTTTCACAATTGCCCTTCTCCCACTTTACAAAAGAAAGGCATATCTCTCACCCATCCCGAATCTTACTATGGTGCATTGCCCCGGGGTGTAAAAACCTCCAGGGCGCCAAACAAAGGGACAATTCGAAATATTGGTGTTGGGGAAGCCTCCTTTAATGATTAATCAAGGCACCATAAACCCATGGTAGGGCTTCCTGTCTTTCCCTGTCTTATACATATTTCTGTTAAGGGCGAAGCGTGGCGTTAGAAACGGGGTATTTTGGCCCGTGTTGGGATGTTCTGAATTCAGATATATTGTAGAGTGGGGCGGCGGAAGTGATGACAATTTTCGTTTAATGACCTCGCCTCTTCCATTCCCCGACTATTGTCAAAGAATGCATCGCTCCTGAGGGAGAGTCCCGTGAGAGCAAAGCAAAGAGAGCGTCGGTAAGAAATACTGAAGGTGGCAGTGCCTTATTTCATCCAGGCGACAAACTCATGGCAAGGTCTNTTTGCCTCAGAATTAGAATATTCGAGATTTGCGANAAGCATNCTGGGAAATACCAATNNGCTACGAAGCNCANCTTCTCTGCATTTTCNCCATTCTCAGTAATGAGAAAGAGCTTGGNGAGTACTCTCATTCACCTGCGTCTTGATCTGTGTCTCAGNTGCATATTTTGCATGATTTCAAGGAGGNGGAGGTGAAAAGTTCCACATTTACTTCCGACAGATCAACGTTACATCTTCAAGTAAAAGGAACACATATTGGAGGTAAGTTAGCGTTTTATATTTTCTTAAACATTTATTCAGACTCGTAGGAGAAACATTTTCATTAACTTTTGCCAAAGATTATTGGATACTGTAAATCCATATTCATTTTTTACTTGGGCACAAGTCTCCTGCTCGCTGTCACTCGTCAACCACTTCTCTGCTCATTTATTCATTCCTACCATGTACTTATTAGATTTAGATTAACTTAACGGGAATATGTTGTGGATTCTACTGTAAATAATGCACTTAAAACAATCATTAATNCACCTTTTGTAAGCCCTACACTTACTAGTGGCCCAATACCTTCTCTCTCCTTTTGCTGTTAATTTCCACAAAGTAGATTAAANTGNACTCTTAAAAGCAGAACATCTACTTATGTACGGGTGTAGGACAAAATGTTCCCAAAATGCAATCTAGGACGTAATGCCCTGAACTTTAGAAAACCAGCTTCATTTAATTAGGATTAATTTCTCCCTCTCAGATGTTGATATGCTGTTCTAATTCTGTCAAATGCATAATTATAAACAATCGTTTTCAACNATGAAATGAAATTACTAATCTATNTATACATAAAAATTCTCAAGNATGTNTCTCTGTCCATCCGTCACGTCTTTTNAAGGCGCTTTGAGACGACCTAGAAAANTGAAATTTGGCATGAATATNTAGGTCTTTGTTCACAGTCAATGGGAAAAGTCCTAAAATGCACAATTTNATTTTTTTANGCTGNTNTNATCTAATTNNAGNTTCANAAACAAGGTGCCTCTAAGCGAAAGAGTAANAGGTATAATTAATAGTCATTTGATAAGTCTTGGTAAAGCCTTTTTGGTATACTTCCCAGAAATTGAGAAAGTGAATGACTCTAATGACTGGGTAACAAATCCTTTTGCAAGTCAGGTGGTTTCCAATTCTTTGCTTTCAACAAAATTGAAGGAGGACCTAATCGAGTTGTCAGCTGATAGATCATTAAAAATAATTTTTGATGATAGATCACTATGTGATTTTTGGCATATAACTCGGAAGGAGTTCAAAGAATTGAGTGACATTGCTATAACAAAACTCCTTCCATTCCCATCTACTTATTTATGTGAACAAGGTTTCTCAGCGCTTACATCTATAAAAATGAAAAATAGGAATAGAATTGATGCTGAACCCTGTCTCATTCTAGCAATAAGTAATATTCATCCACGGATACATGAACTAATTGGGAAAANAAAGCCCCATCCATCTCATTAAGAGATGCATTTCCAATAAAATTTTACTTTTTATGTTTAATATTTATCAAAATTTGTAATATATTTATGTTGTTTTGATCAATTGTGTACTAATAATAATTGTAATGATAACTCAATCCAGAAGAAAATTTTTAACACTTAGAGCCTTATGGTCACAGGAAATNTAAAAAATTAAATTTCAATTTATATACATATTTTTGTTGCAGAGAAGTATGATAGGGTGATCAATAAAAGACTTTCAAGCATAAAAATATATTACATTAGGATAAAATTCTGTGGGGGAAGTGGAATGGAAATACGAGTTCAAGGAGAAAAAGAGAACGATGTAAAATTTCCGACTGTTAAAGAAGAGCTTGTTCATGTATTTTTTAAATGGATGATGGTGGGTATCAAATCGCTATGGTATTTAGATTCCATTGGATACATTTAAAAGAGTGATGTAACAGTTTTATTTTAAAATGTCAATATTTACAATATGCCGGAAATTACATCCTTTGCAACTATTTAAACTTATGATGAAAAATTTTAGATGTCAACTTAAAAATGTGCGAGGGGGTACATAGTTTTTCAAAATTCTTTTAGGGGGTACGCGAGCAAAAANGTTTGAAGACCACTG
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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 |
|---|---|---|---|---|---|---|
| Charlie2b | STAT3 | 1766 | 1774 | - | 15.20 | TTCTGGGAA |
| Charlie2b | CRF2 | 490 | 497 | - | 15.20 | CCGCCGCC |
| Charlie2b | FKH1 | 1451 | 1463 | + | 15.18 | AATTATAAACAAT |
| Charlie2b | DREB2F | 490 | 500 | - | 15.17 | CTTCCGCCGCC |
| Charlie2b | STAT1 | 1766 | 1774 | - | 15.13 | TTCTGGGAA |
| Charlie2b | Stat5a::Stat5b | 1766 | 1774 | + | 15.12 | TTCCCAGAA |
| Charlie2b | ETV7 | 494 | 502 | + | 15.00 | GCGGAAGTG |
| Charlie2b | PKNOX1 | 1968 | 1977 | + | 14.87 | TGAGTGACAT |
| Charlie2b | DOF3.2 | 2190 | 2205 | + | 14.86 | TTACTTTTTATGTTTA |
| Charlie2b | AP4 | 1882 | 1891 | - | 14.85 | ATCAGCTGAC |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
