Charlie15a
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000089 |
|---|---|
| TE superfamily | Charlie |
| TE class | DNA |
| Species | Eutheria |
| Length | 224 |
| Kimura value | 29.28 |
| Tau index | 0.7845 |
| Description | hAT-Charlie DNA transposon, Charlie15a subfamily (non-autonomous) |
| Comment | 8bp Charlie-type TSDs; 16 bp TIRs. |
| Sequence |
CAGTGGTTTTCAAACTGTGTTCCGCGGAGCCCTAGGGGTTCCGCGGAGGTGCCTCGGGGGCTGCTGGGNGGGNNGTGAGGCTGGGCGGGCGGGGCTCTGGGCCTCCCACCCCCGCTTCAACCAGAGCAGCTCCGCTTTTATCTGTTTTATATATTGGGCTTCCGCGTAAGATTTCATTTGAAGAAAGGGTTCTGCTGCTTAAAAAAAAAGTTTGAAAACCACTG
|
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 |
|---|---|---|---|---|---|---|
| Charlie15a | KLF7 | 87 | 94 | + | 15.72 | GGGCGGGG |
| Charlie15a | PDR1 | 20 | 29 | + | 15.57 | TTCCGCGGAG |
| Charlie15a | PDR1 | 39 | 48 | + | 15.57 | TTCCGCGGAG |
| Charlie15a | KLF1 | 87 | 94 | + | 15.53 | GGGCGGGG |
| Charlie15a | PDR1 | 20 | 29 | - | 15.33 | CTCCGCGGAA |
| Charlie15a | PDR1 | 39 | 48 | - | 15.33 | CTCCGCGGAA |
| Charlie15a | TFAP2A | 50 | 62 | + | 15.33 | TGCCTCGGGGGCT |
| Charlie15a | TFAP2B | 50 | 62 | + | 15.23 | TGCCTCGGGGGCT |
| Charlie15a | TFAP2A | 50 | 62 | - | 15.21 | AGCCCCCGAGGCA |
| Charlie15a | Klf15 | 79 | 100 | - | 15.09 | CCAGAGCCCCGCCCGCCCAGCC |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
