Charlie23a
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000100 |
|---|---|
| TE superfamily | Charlie |
| TE order | 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 | NUC | 216 | 227 | + | 12.91 | TTTTGTCATTAT |
| Charlie23a | DOF3.2 | 211 | 226 | + | 12.89 | TAGCTTTTTGTCATTA |
| Charlie23a | HINFP | 24 | 31 | - | 12.82 | GGGTCCGC |
| Charlie23a | HINFP | 57 | 64 | + | 12.82 | GGGTCCGC |
| Charlie23a | Cf2 | 122 | 130 | + | 12.81 | ATATATGTA |
| Charlie23a | SGR5 | 216 | 228 | - | 12.79 | CATAATGACAAAA |
| Charlie23a | CG12605 | 12 | 20 | + | 12.79 | AACCTGTGG |
| Charlie23a | YLR278C | 42 | 48 | + | 12.66 | CGGAGTT |
| Charlie23a | ZNF692 | 17 | 24 | - | 12.62 | CGGCCCAC |
| Charlie23a | Aef1 | 259 | 266 | + | 12.61 | CAACTACT |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
