Charlie1a
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000021 |
|---|---|
| TE superfamily | Charlie |
| TE class | DNA |
| Species | Eutheria |
| Length | 1455 |
| Kimura value | 21.18 |
| Tau index | 0.9047 |
| Description | hAT-Charlie DNA transposon, Charlie1a subfamily |
| Comment | This is an internal deletion product of Charlie1 which is much more common than the full-length element. |
| Sequence |
CAGCGGTTCTCAAAGTGTGGTCCGCGGACCCCTGGGGGTCCCCGAGACCCTTTCAGGGGGTCCGCGAGGTCAAAACTATTTTCATAATAATACTAAGACGTTATTTGCCTTTTTCACTGTGTTGACATTTGCACTGATGGTGCAAAAGCAATGGTGGGTAAAACTGCTGGCGCCTTAGCACGAATCAAGGCAGTGGCACCAAACTGTACTAGTAGTCATTGTATTCTTCACCGCCACGCACTCGCAGTNAAAAAAAAGCCAGTTTCACTTAAGAATGTCCTTGATGAAGCAGTAAAAATTATTAATTTTATTAAATCTCGACCCTTGAGTACACGTCTTTTTAATATTCTGTGTGACGAAATGGGAAGTACGCATAAAGCACTTCTGCTGCATACCGAAGTACGATGGTTGTCTCGAGGAAAAGCACTTGTGCGATTGTTTGAGTTGCGAGCTGAACTAGCCGCTTTTTTCATGGAACACCATTTTTACTTGAAAGAACGACTGACAGACAAACTATGGTTATTCAGACTTGGGTATTTGGCAGACATTTTCTCGAAAATGAACGAAGTGAGCCTGTCACTTCAAGGAAAACAACTGACAGTATTTGTTGCCAATGATAAAATTCGAGCTTTCAAGCGAAAATTAGAATTTTGGAAAACTTGTATCCGCCACCGTGAGCTTGACAGCTTCCCAATACTTAAAGACTTTTCTGATGAGATCGGTGGTGATATTAACGAATGTGATTTTTTGATATTGTATAATGAAATGTGTCAACATTTGGAAGATCTGCATAACTCAGTGAACCAATATTTTCCAAATGACCAATGCATGATGTTACAAAATCATGCATGGGTAAAAGATCCATTCAAAGTGCAAGATAGACCAATGGATTTTAATGTAACAGAGTACGAAAAGTTCATTGATATGGTTTCAGATTCCACATTGCAACTAACCTTTAAGAAACTACCACTTGTCGAGTTTTGGTGTAGTATCAAAGAAGAATATCCACAATTATCTGAAAAGGCTATTAAAATACTCCTCCCTTTTCCAACTACATATCTGTGTGAGGCCGGATTTTCTTCATATACTTCAACCAAAACAACATATCGCAACAGATTGAATGCAGAAGCAGATATGAGAATCCAGCTGTCTTCTATTAAGCCAGACATTAAAGAGATTTGCAAAAATGTAAAACAATGCCACTCTTCTCACTAAATTTTTTTGTTTTGGAAAATATAGTTATTTTTCATAAAAATATGTTATTTATGTTAACATGTAATGGGTTTATTATTATTTTTAAATGAATTAATAAATATTTTAAAAATTTCTCAGTTTTAATTTCTAATATGGTAAATATCGATAGATATAACCCACATAAACAAAAGCTCTTTGGGGTCCTCAATAATTTTTAAGAGTGTAAAGGGGTCCTGAGACCAAAAAGTTTGAGAACCGCTG
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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 |
|---|---|---|---|---|---|---|
| Charlie1a | pnr | 1355 | 1363 | + | 15.64 | TATCGATAG |
| Charlie1a | ZFP42 | 540 | 552 | - | 15.47 | GAAAATGTCTGCC |
| Charlie1a | NAC071 | 226 | 240 | + | 15.44 | CTTCACCGCCACGCA |
| Charlie1a | sug | 29 | 40 | - | 15.13 | GACCCCCAGGGG |
| Charlie1a | ZNF770 | 1065 | 1072 | - | 14.94 | CGGCCTCA |
| Charlie1a | MYB107 | 197 | 204 | + | 14.64 | CACCAAAC |
| Charlie1a | GT-4 | 511 | 522 | - | 14.62 | TAACCATAGTTT |
| Charlie1a | PK27109.1 | 1144 | 1151 | - | 14.60 | GACAGCTG |
| Charlie1a | ZNF417 | 168 | 174 | - | 14.55 | GGCGCCA |
| Charlie1a | ARF27 | 541 | 548 | + | 14.52 | GCAGACAT |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
