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 | SIZF2 | 594 | 602 | - | 14.50 | ACTGTCAGT |
| Charlie1a | BZIP69 | 1142 | 1152 | - | 14.48 | AGACAGCTGGA |
| Charlie1a | BEAF-32 | 1355 | 1362 | + | 14.46 | TATCGATA |
| Charlie1a | BEAF-32 | 1355 | 1362 | - | 14.46 | TATCGATA |
| Charlie1a | Dref | 1355 | 1362 | + | 14.38 | TATCGATA |
| Charlie1a | Dref | 1355 | 1362 | - | 14.38 | TATCGATA |
| Charlie1a | PK16335.1 | 1144 | 1151 | - | 14.35 | GACAGCTG |
| Charlie1a | nit-4 | 21 | 27 | + | 14.25 | TCCGCGG |
| Charlie1a | nit-4 | 22 | 28 | - | 14.25 | TCCGCGG |
| Charlie1a | PPARG | 33 | 51 | - | 14.21 | AGGGTCTCGGGGACCCCCA |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
