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
|
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 | BPC5 | 371 | 400 | - | -33.09 | ACAGACAGAGAGAAACCGGGAGGGAGACGA |
| Charlie30a | BPC5 | 490 | 519 | - | -34.33 | AGTGGGGAAATGAGAGAAGAAGAGAAAGAG |
| Charlie30a | BPC5 | 500 | 529 | - | -38.54 | ATAGAAAGAGAGTGGGGAAATGAGAGAAGA |
| Charlie30a | DAL81 | 32 | 50 | - | -38.87 | TCAAGCCGAGGGCCGGGTC |
| Charlie30a | BPC5 | 522 | 551 | - | -48.04 | GAGAAAAAGTAGGGGGAAAGAGATAGAAAG |
| Charlie30a | BPC5 | 369 | 398 | - | -48.62 | AGACAGAGAGAAACCGGGAGGGAGACGAGA |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
