Charlie30a
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0001193 |
|---|---|
| TE superfamily | Charlie |
| TE class | 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 | DOF5.1 | 530 | 548 | - | 14.82 | AAAAAGTAGGGGGAAAGAG |
| Charlie30a | MYB55 | 318 | 325 | + | 14.77 | ACCTACCG |
| Charlie30a | Stat2 | 670 | 679 | - | 14.70 | GAAAGAGAAA |
| Charlie30a | SREBF1 | 64 | 73 | - | 14.68 | ATCACCCCAG |
| Charlie30a | KLF1 | 4 | 11 | + | 14.64 | GGGTGGGG |
| Charlie30a | KLF1 | 781 | 788 | - | 14.64 | GGGTGGGG |
| Charlie30a | ZNF784 | 318 | 325 | + | 14.64 | ACCTACCG |
| Charlie30a | ZHD9 | 205 | 219 | + | 14.60 | TTAATCAGCTAATCA |
| Charlie30a | eor-1 | 471 | 483 | - | 14.48 | AGAGGCAGAGACA |
| Charlie30a | LOB | 87 | 99 | + | 14.46 | CTGCCGCTGCAGC |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
