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 | DOF1.7 | 2267 | 2277 | - | 15.76 | AAAAAGTAAAA |
| Charlie2a | blmp-1 | 1057 | 1067 | - | 15.73 | GAAAGAGAAAG |
| Charlie2a | At3g11280 | 947 | 960 | + | 15.65 | ATCCTCATCTTATT |
| Charlie2a | HOXB13 | 2258 | 2266 | + | 15.62 | CCAATAAAA |
| Charlie2a | AT5G61620 | 2505 | 2518 | + | 15.59 | ATTAGGATAAAATT |
| Charlie2a | HNF1B | 336 | 348 | + | 15.50 | TTTAATGATTAAT |
| Charlie2a | CDF5 | 2268 | 2288 | + | 15.50 | TTTACTTTTTATGTTTAATAT |
| Charlie2a | ONECUT1 | 1313 | 1321 | - | 15.50 | AAATCAATA |
| Charlie2a | FoxB | 2707 | 2717 | - | 15.48 | GTAAATATTGA |
| Charlie2a | PK08602.1 | 490 | 497 | - | 15.41 | CCACCGCC |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
