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 | DOF1.7 | 2188 | 2198 | - | 15.76 | AAAAAGTAAAA |
| Charlie2b | HOXB13 | 2179 | 2187 | + | 15.62 | CCAATAAAA |
| Charlie2b | AT5G61620 | 2426 | 2439 | + | 15.59 | ATTAGGATAAAATT |
| Charlie2b | ERF118 | 490 | 497 | - | 15.56 | CCGCCGCC |
| Charlie2b | HNF1B | 336 | 348 | + | 15.50 | TTTAATGATTAAT |
| Charlie2b | CDF5 | 2189 | 2209 | + | 15.50 | TTTACTTTTTATGTTTAATAT |
| Charlie2b | FoxB | 2628 | 2638 | - | 15.48 | GTAAATATTGA |
| Charlie2b | Foxq1 | 1454 | 1463 | - | 15.29 | ATTGTTTATA |
| Charlie2b | ETV2::FOXI1 | 374 | 384 | - | 15.28 | AGACAGGAAGC |
| Charlie2b | EFM | 689 | 697 | + | 15.24 | AGAATATTC |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
