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 | BPC6 | 514 | 534 | + | 21.58 | CCCACTCTCTTTCTATCTCTT |
| Charlie30a | BPC6 | 516 | 536 | + | 19.93 | CACTCTCTTTCTATCTCTTTC |
| Charlie30a | BPC1 | 517 | 540 | - | 19.29 | GGGGGAAAGAGATAGAAAGAGAGT |
| Charlie30a | BPC1 | 519 | 542 | - | 19.29 | TAGGGGGAAAGAGATAGAAAGAGA |
| Charlie30a | eor-1 | 465 | 477 | - | 19.26 | AGAGACAGAGAGA |
| Charlie30a | eor-1 | 459 | 471 | - | 18.79 | AGAGAGACAGAGA |
| Charlie30a | BPC1 | 515 | 538 | - | 18.35 | GGGAAAGAGATAGAAAGAGAGTGG |
| Charlie30a | eor-1 | 487 | 499 | - | 17.79 | AGAGAAAGAGAGA |
| Charlie30a | BPC1 | 513 | 536 | - | 17.76 | GAAAGAGATAGAAAGAGAGTGGGG |
| Charlie30a | eor-1 | 495 | 507 | - | 17.71 | AGAGAAGAAGAGA |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
