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 | ONECUT3 | 1312 | 1323 | - | 15.30 | ATAAATCAATAT |
| Charlie2a | ETV2::FOXI1 | 374 | 384 | - | 15.28 | AGACAGGAAGC |
| Charlie2a | Kr | 1738 | 1746 | + | 15.21 | CAACCCTTT |
| Charlie2a | STAT3 | 1845 | 1853 | - | 15.20 | TTCTGGGAA |
| Charlie2a | STAT1 | 1845 | 1853 | - | 15.13 | TTCTGGGAA |
| Charlie2a | Stat5a::Stat5b | 1845 | 1853 | + | 15.12 | TTCCCAGAA |
| Charlie2a | ERF055 | 489 | 497 | + | 14.95 | GGGCGGTGG |
| Charlie2a | PKNOX1 | 2047 | 2056 | + | 14.87 | TGAGTGACAT |
| Charlie2a | DOF3.2 | 2269 | 2284 | + | 14.86 | TTACTTTTTATGTTTA |
| Charlie2a | AP4 | 1961 | 1970 | - | 14.85 | ATCAGCTGAC |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
