Charlie1a
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000021 |
|---|---|
| TE superfamily | Charlie |
| TE order | 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 | PHOX2B | 302 | 313 | - | 14.18 | TAATAAAATTAA |
| Charlie1a | vnd | 487 | 495 | - | 14.11 | TTTCAAGTA |
| Charlie1a | ATHB-20 | 1400 | 1407 | + | 14.11 | CAATAATT |
| Charlie1a | pnr | 1354 | 1362 | - | 14.05 | TATCGATAT |
| Charlie1a | ceh-39 | 1353 | 1363 | + | 14.01 | AATATCGATAG |
| Charlie1a | BZIP30 | 1143 | 1151 | - | 14.00 | GACAGCTGG |
| Charlie1a | let-381 | 1375 | 1382 | + | 13.99 | ATAAACAA |
| Charlie1a | Sox100B | 1267 | 1274 | + | 13.99 | TGTTAACA |
| Charlie1a | Sox100B | 1267 | 1274 | - | 13.99 | TGTTAACA |
| Charlie1a | SPIC | 358 | 370 | + | 13.96 | GAAATGGGAAGTA |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
