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 | BPC1 | 1768 | 1791 | + | -1.41 | CCCAGAAATTGAGAAAGTGAATGA |
| Charlie2b | ZAP1 | 25 | 39 | - | -2.21 | ACCCCCAGGGGTATG |
| Charlie2b | BPC6 | 2471 | 2491 | - | -3.53 | ATCGTTCTCTTTTTCTCCTTG |
| Charlie2b | BCL6B | 1763 | 1779 | + | -9.76 | TACTTCCCAGAAATTGA |
| Charlie2b | EWSR1-FLI1 | 1097 | 1114 | - | -12.76 | GGTAGGAATGAATAAATG |
| Charlie2b | BCL6B | 1257 | 1273 | - | -15.83 | TACTTTGTGGAAATTAA |
| Charlie2b | BPC5 | 171 | 200 | - | -43.74 | AGGGCAATTGTGAAAGGGGAAGTGGGAAAG |
| Charlie2b | BPC5 | 167 | 196 | - | -45.45 | CAATTGTGAAAGGGGAAGTGGGAAAGGGCA |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
