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 | Znf423 | 26 | 40 | + | 19.38 | GGACCCCTGGGGGTC |
| Charlie1a | GT-4 | 511 | 522 | + | 18.06 | AAACTATGGTTA |
| Charlie1a | ZNF680 | 993 | 1003 | + | 17.27 | CAAAGAAGAAT |
| Charlie1a | DOF4.2 | 104 | 114 | - | 17.21 | AAAAAGGCAAA |
| Charlie1a | PDR3 | 21 | 28 | + | 16.61 | TCCGCGGA |
| Charlie1a | PDR3 | 21 | 28 | - | 16.61 | TCCGCGGA |
| Charlie1a | CUP2 | 380 | 390 | - | 16.27 | CAGCAGAAGTG |
| Charlie1a | F10B5.3 | 549 | 559 | - | 15.99 | TTTTCGAGAAA |
| Charlie1a | USV1 | 52 | 61 | - | 15.98 | ACCCCCTGAA |
| Charlie1a | SIZF2 | 594 | 602 | + | 15.69 | ACTGACAGT |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
