Charlie30a
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0001193 |
|---|---|
| TE superfamily | Charlie |
| TE order | 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
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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 | BPC1 | 459 | 482 | - | 17.56 | GAGGCAGAGACAGAGAGACAGAGA |
| Charlie30a | ZNF454 | 14 | 30 | - | 17.20 | GGCCCGCGGGCCGGAGG |
| Charlie30a | BPC1 | 511 | 534 | - | 16.70 | AAGAGATAGAAAGAGAGTGGGGAA |
| Charlie30a | BPC1 | 487 | 510 | - | 16.55 | ATGAGAGAAGAAGAGAAAGAGAGA |
| Charlie30a | BPC1 | 453 | 476 | - | 16.48 | GAGACAGAGAGACAGAGACCAAGA |
| Charlie30a | Pou5f1::Sox2 | 216 | 230 | - | 16.23 | CTTTGAAATGCTGAT |
| Charlie30a | SP1 | 418 | 426 | - | 16.13 | GGGGCGGAG |
| Charlie30a | SP4 | 418 | 426 | - | 16.07 | GGGGCGGAG |
| Charlie30a | btd | 419 | 427 | - | 15.92 | GGGGGCGGA |
| Charlie30a | BPC6 | 518 | 538 | + | 15.76 | CTCTCTTTCTATCTCTTTCCC |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
