Charlie31a
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0001244 |
|---|---|
| TE superfamily | Charlie |
| TE class | DNA |
| Species | Eutheria |
| Length | 554 |
| Kimura value | 31.04 |
| Tau index | 0.9730 |
| Description | hAT-Charlie DNA transposon, Charlie31a subfamily |
| Comment | 8 bp TSDs with NNCTAGNN preference. Terminal 80-90 bp similar to those of autonomous Charlies (like Chaplin6_FR and Charlie17), on which the orientation is based. Present in elephant, sloth, human, absent in marsupials. |
| Sequence |
CAGTGGTTCTCAACCGGTGTGCCGCGGCACACCGGTGTACCGCGAACCCTTCACAGGTGTGCCGCCAAATTTTGATCAATGTGTAAAATTTATTTTTGCTACAACTGAGTATACATACTGTTACGGCGATGTCTGTCAGACGGAACGTTGAGCTGAGCGGGTCGTGCGACGCGGTGTAGAGCGGGGTACAACTTGCTGCGAGTAAGAGGTAAGAGGCATAGCGTAACGTCAAGCCGGCGCCAAAGAAAGATCGCGTGTTTACTGGAACATGCGAGAACTTTGCCTCGTGAGTATATAAGAGAGCGCGGTCAGGGCAGTAAACAGTTCTACTCAAACAGCGACACAGTGCTGAAGGGCGACCAAGTGAATAGTGCGATAACTGTGGATGCTTTTATAGACACTGTGAGACATTGTTATACTGTAGTAGTGATTGCGTTGTAATTATTGCTGACTTGTTTAGTGTTGTTTTGAGTCTTTTAATCCCTTCAAGTGTGCCGCCAAAAATTCTAGTATTCGAAAGTGTGCCGCGAACACAAAAAGGTTGAGAACCACTG
|
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 |
|---|---|---|---|---|---|---|
| Charlie31a | E2F7 | 490 | 503 | + | 0.62 | GTGTGCCGCCAAAA |
| Charlie31a | E2F7 | 57 | 70 | + | -0.44 | GTGTGCCGCCAAAT |
| Charlie31a | E2FD | 57 | 71 | - | -1.84 | AATTTGGCGGCACAC |
| Charlie31a | E2FE | 57 | 71 | - | -1.84 | AATTTGGCGGCACAC |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
