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 | RXRB | 123 | 136 | - | 0.89 | CAGTGCAAATGTCA |
| Charlie1a | ZNF143 | 396 | 411 | - | 0.07 | CAACCATCGTACTTCG |
| Charlie1a | NR1H2::RXRA | 121 | 137 | - | -0.04 | TCAGTGCAAATGTCAAC |
| Charlie1a | IRF4 | 926 | 939 | - | -0.11 | GGAATCTGAAACCA |
| Charlie1a | Poxm | 841 | 855 | - | -0.51 | TACCCATGCATGATT |
| Charlie1a | IRF9 | 927 | 941 | - | -1.22 | GTGGAATCTGAAACC |
| Charlie1a | TGIF1 | 762 | 773 | - | -1.39 | TGACACATTTCA |
| Charlie1a | IRF8 | 554 | 566 | + | -1.50 | CGAAAATGAACGA |
| Charlie1a | NR1H2::RXRA | 849 | 865 | + | -6.03 | ATGGGTAAAAGATCCAT |
| Charlie1a | Sox21b | 1193 | 1207 | - | -10.51 | AAGAGTGGCATTGTT |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
