Charlie2b
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000020 |
|---|---|
| TE superfamily | Charlie |
| TE order | 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 | EREB29 | 489 | 498 | - | 16.66 | TCCGCCGCCC |
| Charlie2b | DREB2D | 490 | 503 | - | 16.61 | TCACTTCCGCCGCC |
| Charlie2b | NR3C1 | 1322 | 1336 | - | 16.45 | GGAACATTTTGTCCT |
| Charlie2b | Stat5b | 1766 | 1774 | + | 16.36 | TTCCCAGAA |
| Charlie2b | ZHD9 | 336 | 350 | + | 16.27 | TTTAATGATTAATCA |
| Charlie2b | HNF1A | 336 | 348 | - | 16.21 | ATTAATCATTAAA |
| Charlie2b | Pgr | 1321 | 1337 | + | 16.18 | TAGGACAAAATGTTCCC |
| Charlie2b | skn-1 | 497 | 510 | + | 16.13 | GAAGTGATGACAAT |
| Charlie2b | Zfp961 | 286 | 293 | + | 15.99 | GGGCGCCA |
| Charlie2b | ETV6 | 494 | 502 | + | 15.77 | GCGGAAGTG |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
