Charlie30b
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0001199 |
|---|---|
| TE superfamily | Charlie |
| TE class | DNA |
| Species | Eutheria |
| Length | 1124 |
| Kimura value | 31.73 |
| Tau index | 0.0000 |
| Description | hAT-Charlie DNA transposon, Charlie30b subfamily |
| Comment | 16 bp TIRs. No coding remnants, but termini similar to a number of other Charlies. Still apparently not at orthologous sites in marsupials. |
| Sequence |
CAGGGNTGGNGAACCTCCGGCCCATAGNCCAGATCTGGCCCTCGGCTTGATTTCATCCGGTNCGTGGGATGATATTGTTCTGGCCACTGNTNCTGCAGCCCAGAGAATAATTTCTCCCCTGGTGGGCTGCTGTGGCTATCCCATTCAGAGCGGAGCCTCTGAAGGTTTGATAAGAGCAGTTGAAGAGCTGTGAACAGCGGTTAACCCATTTATTCCTGAAGGTTTTTTCCGAATTNTTTTTGGTTTCTACTNTATATTATCCCCACTAGGACCCAACTAGACCAAAAAACTGGATTTGATTTGGAGAAAAAAGGCTCAGAACAATGAAATAAATGCTGGTTCCAAATGTAACCTTCAGGCATTGTGGAATGAGGCAGCCCTAATCTCTCAAAGAACAAAGATAAGGCAATCTGACAGCTTTTGAATGTCAAAGGGACTTTCAGGCGATAGCTAGTAAATTGACAGACACCTCTAAGGTTCCAAAGTAAATTTCTAAAACCTAAGTCATTCCTTCACACATGTGCAAAACCTTCAGAATTCCATGGGAAAATAAACCTTTATTTCAAAAATAAACTTTGAAGTTTGAAAATAAAAGCAGACAAGCTGTTTCCCAGTGCAGAAAGGACTGTTCTAAACTGCTGGAGAGCTAATCAGAATTTCAAAGGGCAGTGATAACAGGTGACGACTTACTCTGATGCCCACAGCCCAAGCGAACAGCGGAATCTCAACAGCCGNGCTTACCCCCAACTTCCACGCAGACCTCCTCTCTCTCCTCGCTTTNCCCCGTTCTTCCTTCTCTCTCTCTCTTCCTCTCCCNCTTTGTCCCCTTTCCCTTCCATCTCTCTCTTTTCTCCTCACTTTCCGTCTTCCTTCCCTTCCTGTCTCTCTCCCTTAACTGGCCATAATATGGAACTGAAGTATATTTTTNANTATTTGTTGTATTTATTGAATAAAGTTTTATGTTTCCCGTTCTTAATTTTAAAAGCGAGTGAGTNGAACGTTTTATATTTCTCTTCCTAAAAAAAATAAATAATTAAGTTGCTTTTTACTTACGTGTGGCCCTCGATTGATTTTTTCTCCTGTGGGTCAGTGGCCCTCGATAGAAAAAAGATTTCCCACCCCTG
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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 |
|---|---|---|---|---|---|---|
| Charlie30b | eor-1 | 795 | 807 | - | 18.35 | AGAGAGAGAGAGA |
| Charlie30b | BPC1 | 785 | 808 | - | 17.79 | AAGAGAGAGAGAGAAGGAAGAACG |
| Charlie30b | RAMOSA1 | 799 | 812 | - | 16.83 | GAGGAAGAGAGAGA |
| Charlie30b | ZNF75D | 1108 | 1119 | - | 16.82 | GTGGGAAATCTT |
| Charlie30b | eor-1 | 803 | 815 | - | 16.06 | GGAGAGGAAGAGA |
| Charlie30b | ROX1 | 317 | 328 | - | 15.92 | TTCATTGTTCTG |
| Charlie30b | Trl | 800 | 808 | - | 15.63 | AAGAGAGAG |
| Charlie30b | Trl | 840 | 848 | - | 15.63 | AAGAGAGAG |
| Charlie30b | Clamp | 795 | 808 | - | 15.62 | AAGAGAGAGAGAGA |
| Charlie30b | RAMOSA1 | 880 | 893 | - | 15.56 | AAGGGAGAGAGACA |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
