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 | BPC1 | 791 | 814 | - | 30.29 | GAGAGGAAGAGAGAGAGAGAAGGA |
| Charlie30b | BPC1 | 793 | 816 | - | 26.14 | GGGAGAGGAAGAGAGAGAGAGAAG |
| Charlie30b | BPC6 | 794 | 814 | + | 25.61 | TTCTCTCTCTCTCTTCCTCTC |
| Charlie30b | BPC1 | 789 | 812 | - | 22.98 | GAGGAAGAGAGAGAGAGAAGGAAG |
| Charlie30b | RAMOSA1 | 795 | 808 | - | 22.89 | AAGAGAGAGAGAGA |
| Charlie30b | RAMOSA1 | 793 | 806 | - | 20.46 | GAGAGAGAGAGAAG |
| Charlie30b | RAMOSA1 | 797 | 810 | - | 20.40 | GGAAGAGAGAGAGA |
| Charlie30b | BPC6 | 792 | 812 | + | 19.70 | CCTTCTCTCTCTCTCTTCCTC |
| Charlie30b | ZNF530 | 823 | 836 | - | 19.05 | GAAGGGAAAGGGGA |
| Charlie30b | BPC6 | 790 | 810 | + | 18.88 | TTCCTTCTCTCTCTCTCTTCC |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
