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 | Spi1 | 176 | 188 | - | 18.90 | AAAGGGGAAGTGG |
| Charlie2b | NR3C2 | 1322 | 1336 | + | 18.85 | AGGACAAAATGTTCC |
| Charlie2b | RAP1 | 1310 | 1321 | + | 18.29 | ATGTACGGGTGT |
| Charlie2b | SPIB | 176 | 188 | + | 18.15 | CCACTTCCCCTTT |
| Charlie2b | DOF3.6 | 2189 | 2209 | + | 17.67 | TTTACTTTTTATGTTTAATAT |
| Charlie2b | ZNF24 | 1097 | 1109 | + | 17.64 | CATTTATTCATTC |
| Charlie2b | NR3C1 | 1322 | 1336 | + | 17.47 | AGGACAAAATGTTCC |
| Charlie2b | NR3C2 | 1322 | 1336 | - | 17.06 | GGAACATTTTGTCCT |
| Charlie2b | ERF057 | 490 | 503 | - | 16.93 | TCACTTCCGCCGCC |
| Charlie2b | DOF1.5 | 2188 | 2203 | - | 16.74 | AACATAAAAAGTAAAA |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
