Charlie30a
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0001193 |
|---|---|
| TE superfamily | Charlie |
| TE order | DNA |
| Species | Mammalia |
| Length | 791 |
| Kimura value | 32.97 |
| Tau index | 0.0000 |
| Description | hAT-Charlie DNA transposon, Charlie30a subfamily |
| Comment | 16 bp TIRs. Non-autonomous - shows no remnants of coding region. Termini shared with many Charlies, currently strongest with elements in the pika and little brown bat genomes. Pyrimidine-rich region at pos. 350-550 is very poorly defined and prone to give false positives. Present in placentals, marsupials and monotremes. |
| Sequence |
CAGGGGTGGGGAACCTCCGGCCCGCGGGCCGGACCCGGCCCTCGGCTTGATTTCATCCGGCCCCTGGGGTGATATTGCTCTGGTCACTGCCGCTGCAGCCCAGAGAATAATTTCTCCCCTGGTGGGCTGCTGTGGCTATCCCATTCAGAGCAGAGCCTCTGAAGGTTTAAGGATAAAGAGCAGTTGAAGAGCTGTGAACAGTGGTTAATCAGCTAATCAGCATTTCAAAGGGCAGTGATAANAGGTGATAATACTCTGAAGCCCACGGCCCAAGTGAACAGCAGGGTGTGACAAAATCAGTTTACTAACACTTCAGAACCTACCGAGCCTCTCTTTCCGCGCCTNGTNTTTCCTNCCCCTTTGCCTNTTCTCGTCTCCCTCCCGGTTTCTCTCTGTCTGTNNCTCTCTGCCTCCTTTCTCCGCCCCCGAGTCTTNTTCCCTCTCNCNGTCCCTCTTGGTCTCTGTCTCTCTGTCTCTGCCTCTNTNTCTCTCTTTCTCTTCTTCTCTCATTTCCCCACTCTCTTTCTATCTCTTTCCCCCTACTTTTTCTCCCTTAACTGGCCATAATATAGAACTGAAGTATATTTTTTATTATTTGTTGTATTTATTGAATAGAGTTTTATGTTCCCTGTTCTTAATTTTAAAAGCAGATGAGTTGAACATTTTATATTTCTCTTTCTAAAAAAAAAAAATAAACCAAATTAAGTTGCTTTTTACTTGTATGTGGCCCTCGATTGATTTTTTTTCTGTGGGTCAGTGGCCCTCGATAGAAAAAAGGTTCCCCACCCCTG
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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 |
|---|---|---|---|---|---|---|
| Charlie30a | SREBF2 | 64 | 73 | + | 15.54 | CTGGGGTGAT |
| Charlie30a | KLF4 | 4 | 11 | - | 15.48 | CCCCACCC |
| Charlie30a | KLF4 | 781 | 788 | + | 15.48 | CCCCACCC |
| Charlie30a | NR4A2::RXRA | 751 | 763 | - | 15.37 | GGGCCACTGACCC |
| Charlie30a | RAMOSA1 | 463 | 476 | - | 15.33 | GAGACAGAGAGACA |
| Charlie30a | ZNF93 | 87 | 100 | - | 15.21 | GGCTGCAGCGGCAG |
| Charlie30a | KLF10 | 3 | 11 | + | 15.20 | GGGGTGGGG |
| Charlie30a | KLF10 | 781 | 789 | - | 15.20 | GGGGTGGGG |
| Charlie30a | KLF5 | 3 | 12 | - | 14.84 | TCCCCACCCC |
| Charlie30a | KLF5 | 780 | 789 | + | 14.84 | TCCCCACCCC |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
