Charlie23a
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000100 |
|---|---|
| TE superfamily | Charlie |
| TE class | DNA |
| Species | Theria_mammals |
| Length | 339 |
| Kimura value | 29.77 |
| Tau index | 0.8944 |
| Description | hAT-Charlie DNA transposon, Charlie23a subfamily (non-autonomous) |
| Comment | Charlie23a has 16bp TIRs. The TIR sequence is shared with Charlie18a, and similar to that of Charlie15a and Charlie21a. Present in marsupials; absent from platypus. |
| Sequence |
CAGTGGTTCCCAACCTGTGGGCCGCGGACCCTGGGGGGCTNCGGAGTTATTGCAAGGGGTCCGCGAATCCATATGCGCACCAAGCATTGTCTGTAGACTGAATAAATAATATGTCTCGCACATATATGTACTACTATTTTTCAAATGTATGTAGATGCTGTTGTGATTAATAAAATACAAATTCATTTAAAAGCGTTACTGAATTCATAGTAGCTTTTTGTCATTATGTATTTTCTCAATCAACGGATACTAAAAGTACAACTACTATCATGTGGGGATCCGCGAAATTTTTTGACGTTAAAAAGGGGTCCTCATACTCGAAAAGGTTGGGAACCACTG
|
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 |
|---|---|---|---|---|---|---|
| Charlie23a | TCP3 | 57 | 64 | + | 8.50 | GGGTCCGC |
| Charlie23a | ARF14 | 9 | 24 | - | 7.99 | CGGCCCACAGGTTGGG |
| Charlie23a | GAF1 | 216 | 230 | - | 7.61 | TACATAATGACAAAA |
| Charlie23a | TCP13 | 54 | 64 | + | 7.41 | AAGGGGTCCGC |
| Charlie23a | NR2F1 | 18 | 32 | + | 7.20 | TGGGCCGCGGACCCT |
| Charlie23a | Rel | 274 | 284 | - | 6.74 | CGCGGATCCCC |
| Charlie23a | ZNF558 | 213 | 241 | - | 5.26 | GATTGAGAAAATACATAATGACAAAAAGC |
| Charlie23a | PDR3 | 21 | 28 | + | 3.75 | GCCGCGGA |
| Charlie23a | PDR3 | 21 | 28 | - | 3.75 | TCCGCGGC |
| Charlie23a | TCP14 | 320 | 337 | + | -1.55 | GAAAAGGTTGGGAACCAC |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
