Charlie9
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000108 |
|---|---|
| TE superfamily | Charlie |
| TE class | DNA |
| Species | Eutheria |
| Length | 2787 |
| Kimura value | 23.76 |
| Tau index | 1.0000 |
| Description | hAT-Charlie DNA transposon, Charlie9 subfamily (autonomous) |
| Comment | Present in all eutherians, but absent in opossum & monotremes |
| Sequence |
CAGTGTTTTTCAAACTGCGGGTCGCGACCCATTAGTGGGTCGTGAAATCAATTTAGTGGGTCGCAACCAGCATTTTTAAAAGTAAAATGAAATAGAATAGAATAGAAAATATCAGAGTGCATCGCACGGATCCTTAGCAAGAACTGCGCACATTGCAACAAATACCGCGGCCAATTGCAATGNGCGAGAAGACAGTTAGTGGAGGGGATGTGATGAANACACGCATATTGGCTAGGAATGGGTCATTCGATCTTTTGCTCACTGGCATCTCNTTNGATTTTCNGGTATACGATGGTCAATTTGATCATCACCGTAACGGGAGGGTTAACGTTGTACAGTTTAATTTTATATTAACATAATTTGCAGTTAGTTGTGAAGCGAAGTGCGGGAGAATTTTATCCGCTGTCGGCAAAANTGTCGAGACTTTCAACCGAGTTTCGGTTACGAACTTTCAGTGTGTTTTTCAGAAAGGACGTTATCGAGTGTGACATTTTTCAAGTTCGTGACAATTGTAACATTTTAATCGAACTAGTACAAATTGCCCTTAAAATGGATCGCTTTATTATTAGAAGAAAAAAGAATGATGAAGTGAAAAATACAGAGGCATGTTCAAGTTCAACTGCTGGATCTGGAAGTGTAAATAGTGACAATATTGAGAAAAATGTTGACTCTAATCAGCAAACTTCGACTTCATTTGAGCCGCATTCTAAAAAGAAAAAAGTAAGTGCAAGACTTTATAATGAAGATTATTTAAAATATGGTTTTATCAAATGTGCAAAACCCANTGAAAATGACAGACCCCAATGTATTATTTGTAATGATATTCTTGCAAATGAAAGCTTAAAACCTTCAAAATTAAAAAGACACTTGGAAACACAGCATGCTGAACTTGTCGATAAGCCCCTCGAATATTTTCAAAGAAAGAAAAAAGACGTAAAGTTATCGGCACAATTTCTTAGTCGTTCTACGACTGTTAATGAGAAAGCCTTATTATCATCATATTTAGTTGCATATCGTGTGGCAAAAGAGAAAATGGCTCACACAGCTGCTGAAAAAATTATTCTTCCAGCATGTATGGATATGGTGCGTACGATTTTTGATGATAAATCAGCTGATAAATTAAAAACTATACCTCTTAGTGATAACACAGTATCTCGTCGAATCTNTACTATTGCAGAACATTTAGAAGCAATGCTTATTACGCGGTTACAGTCTGGTATAGATTTTGCGATCCAACTCGATGAGAGCACTGATATTGCAAGTTGCGCAACACTTTTAGTTTATGTCAGATATGCGTGGCAAGACGATTTTATGGAGGATTTGTTGTGTTGTTTAAATTTAACCTCACACACAACTGAATTAGACATATTTACAGAATTGGAAAAGCGCATTGTTGGTCAANATAAATTAAACTGGAAAAACTGTAAAGGAATNACGAGTGATGGAATAGCAAATATGACTGGAAAACACGGNAGAGNTATTAAAAAATTGTTAGAAGCTACTAATAACGGTGCTATTTGGAATCACTGTTTTATACATCGCGAAGCTTTGGCGTCCAAAGAAATTCTACCGAATCTCATGGATATATTGAAAAACGCAGCGAAAGTTGTTAATTTTATTAAAGGAAGCTCACTGAATAGCCGACTTTTTGAAATATTTTGTTCAGAGATTGGAGCTAACCATNCCCGCTTACTGTATCANACCGAAGTTCGTTGGTTGTCGCGAGGGAAAGTGCTAAGCAGGGTGTATGAACTCAGGAATGAGATTCACATTTTTCTAATTGAAAAGCAATCTCATTTGGCAAATATTTTCGAAGATGATATTTGAGTAANAAAATTGGCATATTTAACTGATATTTTCGGCATTCTTAACGAACTAAATTTGAAACTNCAGGGGAAAAACAACGATATATTTCAACATGTCGAACATATCCAAGGATTCCAAAAGACATTATTGTTATGGCAAGCAAGACTTAAAAGTAATCGCCCTAGCTACTATATGTTCCCAACATTGTTGCAACATATCGAAGAGAACATTATTAATGAAGACAGTTTGAANGAAATAAAATTAGAGATATTGTTGCATCTCACTTCTCTGTCTCAAACTTTTAATCATTACTTTCCAGAAGAGAAATTTGAAACATTAAAGAAAAATANTCGGATAAAAGATCCATTTGCTTTTCAAAACCCTGAATCAATAATTGAGTTAAACTTGGTGCCCGAAGAAGAGAATGAATTATTGCAGCTTAGTTCTTCATTTACACTGAAGAATGATTATAAGACATTAAGTNTATCATTATTTTGGATTAAGATTAAAGAAGAATTTCCATTGCTAAGTAGAAAGAGTGTATTGCTATTATTACCATTCACAACGACCNATTTGTNTGAACTAGGATTTTCAACCTTGACCCAATTAAAAACAAAGGAAAGAAACAGGCTCAACAGTGCACCAGATATGCGNGTAGCATTGTCCTCGTGTGTTCCGGACTGGAATGAACTTATGAACAGGCAAGCACACCCGTCGCATTAAATAAAATCTTTCCTAATTTTTGTTTTTGTATTGTTTATTTTGGANTATTTTTCTATGTTGTATTTAAATATTAATAAAATCATATTTGATATTAACTTTATGTTTTTACTTTTATCATACGTAGTAAGAGTAAGTATTGTTTCATGAAACTTTGTTTCAGTTGATATNTGTGCGTTATACGCGTATGTGTGTACTGGGTCGCGATGTAAAATGTATTTCTTACTGTGGGTCGCGGTCAAAAAAGTTTGAAAAACACTG
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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 |
|---|---|---|---|---|---|---|
| Charlie9 | RARA | 2490 | 2507 | - | -5.00 | CTGTTCATAAGTTCATTC |
| Charlie9 | Nr2F6 | 2493 | 2507 | - | -6.61 | CTGTTCATAAGTTCA |
| Charlie9 | Sox21b | 1246 | 1260 | - | -9.05 | TGCAATATCAGTGCT |
| Charlie9 | BCL6B | 127 | 143 | - | -10.84 | TTCTTGCTAAGGATCCG |
| Charlie9 | AT4G12670 | 322 | 350 | - | -13.31 | TATAAAATTAAACTGTACAACGTTAACCC |
| Charlie9 | ZSCAN16 | 1137 | 1154 | + | -16.96 | TAGTGATAACACAGTATC |
| Charlie9 | BPC5 | 578 | 607 | + | -31.38 | AGAATGATGAAGTGAAAAATACAGAGGCAT |
| Charlie9 | BPC5 | 572 | 601 | + | -35.89 | GAAAAAAGAATGATGAAGTGAAAAATACAG |
| Charlie9 | BPC5 | 574 | 603 | + | -44.13 | AAAAAGAATGATGAAGTGAAAAATACAGAG |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
