Charlie2a
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000019 |
|---|---|
| TE superfamily | Charlie |
| TE class | DNA |
| Species | Eutheria |
| Length | 2861 |
| Kimura value | 27.60 |
| Tau index | 0.9897 |
| Description | hAT-Charlie DNA transposon, Charlie2a subfamily |
| Comment | 15-16bp TIR; 8bp TSD. Contains an internal deletion. ORF (roughly 1456-2247) is 56% similar to the C terminal region of the Charlie3 transposase. |
| Sequence |
CAGTGGTCTTCAAACTGGGGTATGCATACCCCTGGGGGTACGCGAAGACTTTCCAAGGGGTACGCGGGCACGGATAGTTTTAAGGGAATCAATTTCCAGATCCTCAACTTCCATATGTACTCTTTCCTAAAACTGATCTGCCTGAGAACGTACCTGTGGCGAAGTCTGCCCTTTCCCACCTCCCCTTTCACAATCGCCCTTCTCCCACTTTACAAAAGAAAGGCATACCTCTCACCCATCCCGAATCTTACTATGGTGCATTGCCCCGGGGTGTAAAAACCTCCGGGGCGCCAAACAAAGGGACAATTCGAAATATTGGTGTTGGGGAAGCCTCCTTTAATGATTAATCAAGGCACCATAAACCCATGGTAGGGCTTCCTGTCTTTCCCTGTCTTATACATATTTCTGTTAAGGGTGAAGCNTGGCGTTAGAAACGGGGTATTTTGGCCCNTGTTGGGATGTTCTGAATTCAGATATATNGTAGAGTGGGGCGGTGGGAGTGATGACAATTTTCGTTTAACGACCTTGCCTCTTCCATTCCCCGACTATTGTCAAAGAATGCATCGCTCTTGAGGGAGAGTCCCGTGAGAGCAAAGCAAAGAGAGCATCGGTAAGAAATACTGAACGCTAAAAACGGCTTTTTTCACGTATTTAAACGTAAGCAATTCTTTTCAGCTATTCTCAATACTCATCCCTAGGACGTGTCATTAGCTGGAAAGAAAAGCACCTTCGAACAGCCGAAGCAGTATAGGTTAGTGACGCTGATTCTTTTAAATGTAACTGGAATGTTTTCCGGGACTACCAAATTTTTCAAGATACATTGGATAAAACCCACGGATAAAANTTTTACGTGATTTCTTTCAGATTCGGTGTGCGTTATTCAATAAGGTAGTTAAAACCTATTTTATCAAATCATATCATGAAATATTTATTCCAATTACAGTCAATCCTCATCTTATTTCATCTTATAAAATGTTTAATATTTTCTACCTCCTATTAACAAAAAATAAAATTATATGCTAGCTGCCGGACCGATTAGTTTTTAGCAGTATATACCTTTCTCTTTCATTAAATACATAGGAAAAGTTTGATCATGATGTCTAACGAAATTAATGGAGTTATTTCTGATTTTTATACATGATTCTTATTTAATTATTCCCAAAAGCCGAACACCAGAGTTCGATATACACATGCACACACATTTACCAAAGGAATACCATGCCTTTTATCATACTCCTCGCTTCATAAATAACTTATAATTTTAGCTACACATTACATTGCATTATTACAAATTAAGTAATGAGAAACAGCATATTGATTTATTATCTTGTTTTTATAACTTATTATAAAAATAGATNAATTATATTAGATCTACATNATTTTAATCTTGACTGCTTTTAGTAATCTATCTTACAAGATGCATTCCATAATTTATTTCTCAGTGGTTTTTATAATATTCCTCGAAATGCATATTAACACGTTTATTTGAATTGAAAAATGAAGTCAGACTTTTTCTGACAGAAAGTAAGTCTGATTTGGCTGATTGGTTTGACAATGAGGACTGGCTTTGCCAATTAGGTTATATGGCGGACATTTTCCATAAATTGAATGAGCTAAATCTGCAGCTCCAAGGTTTTGACGAAAATATATTTAAAGCACGTAATAAGATAAAAGCATTTTATCAAAAAATATTGTATTGGCAAAGGTGTATTGAAATTAACAATATTTCGATTTTCCCAACCCTTTCTGAGTATATCGGGTTAAACAAGGTGCCTCTAAGTGAAAGAGTAACAGGTATAATTAATAGTCATTTGATAAGTCTTGGTAAAGCCTTTTTGGTATACTTCCCAGAAATTGAGAAAGTGAATGACTCTAATGACTGGGTAACAAATCCTTTTGCAAGTCAGGTGGTTTCCAATTCTTTGCTTTCAACAAAATTGAAGGAGGACCTAATCGAGTTGTCAGCTGATAGATCATTAAAAATAATTTTTGATGATAGATCACTATGTGATTTTTGGCATATAACTCGGAAGGAGTTCAAAGAATTGAGTGACATTGCTATAACAAAACTCCTTCCATTCCCATCTACTTATTTATGTGAACAAGGTTTCTCAGCGCTTACATCTATAAAAATGAAAAATAGGAATAGAATTGATGCTGAACCCTGTCTCATTCTAGCAATAAGTAATATTCATCCACGGATACATGAACTAATTGGGAAAANAAAGCCCCATCCATCTCATTAAGAGATGCATTTCCAATAAAATTTTACTTTTTATGTTTAATATTTATCAAAATTTGTAATATATTTATGTTGTTTTGATCAATTGTGTACTAATAATAATTGTAATGATAACTCAATCCAGAAGAAAATTTTTAACACTTAGAGCCTTATGGTCACAGGAAATNTAAAAAATTAAATTTCAATTTATATACATATTTTTGTTGCAGAGAAGTATGATAGGGTGATCAATAAAAGACTTTCAAGCATAAAAATATATTACATTAGGATAAAATTCTGTGGGGGAAGTGGAATGGAAATACGAGTTCAAGGAGAAAAAGAGAACGATGTAAAATTTCCGACTGTTAAAGAAGAGCTTGTTCATGTATTTTTTAAATGGATGATGGTGGGTATCAAATCGCTATGGTATTTAGATTCCATTGGATACATTTAAAAGAGTGATGTAACAGTTTTATTTTAAAATGTCAATATTTACAATACGCCAGAAATTACATCCTTTGCAACTATTTAAACTTATGATGAAAAATTTTAGATGTCAACTTAAAAATGTGCGAGGGGGTACATAGTTTTTCAAAATTCTTTTAGGGGGTACGCGAGCAAAAANGTTTGAAGACCACTG
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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 |
|---|---|---|---|---|---|---|
| Charlie2a | AT5G05790 | 947 | 960 | + | 14.85 | ATCCTCATCTTATT |
| Charlie2a | ERF::FOXO1 | 375 | 386 | - | 14.79 | AAAGACAGGAAG |
| Charlie2a | SFP1 | 2763 | 2772 | + | 14.76 | GAAAAATTTT |
| Charlie2a | ZNF257 | 523 | 532 | - | 14.75 | GAGGCAAGGT |
| Charlie2a | AP4 | 1961 | 1970 | + | 14.73 | GTCAGCTGAT |
| Charlie2a | MEF2C | 1346 | 1356 | + | 14.73 | ATAAAAATAGA |
| Charlie2a | AT3G10580 | 2505 | 2518 | + | 14.70 | ATTAGGATAAAATT |
| Charlie2a | Stat2 | 1058 | 1067 | - | 14.70 | GAAAGAGAAA |
| Charlie2a | GATA6 | 1368 | 1377 | + | 14.67 | AGATCTACAT |
| Charlie2a | ZNF417 | 287 | 293 | + | 14.55 | GGCGCCA |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
