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 | DOF3.6 | 2268 | 2288 | + | 17.67 | TTTACTTTTTATGTTTAATAT |
| Charlie2a | HOXC11 | 516 | 526 | - | 17.41 | AGGTCGTTAAA |
| Charlie2a | nfya-1 | 1540 | 1549 | - | 17.16 | AACCAATCAG |
| Charlie2a | NTL9 | 1293 | 1301 | + | 16.85 | TTAAGTAAT |
| Charlie2a | DOF1.5 | 2267 | 2282 | - | 16.74 | AACATAAAAAGTAAAA |
| Charlie2a | Stat5b | 1845 | 1853 | + | 16.36 | TTCCCAGAA |
| Charlie2a | ZHD9 | 336 | 350 | + | 16.27 | TTTAATGATTAATCA |
| Charlie2a | TEAD1 | 781 | 789 | - | 16.23 | ACATTCCAG |
| Charlie2a | HNF1A | 336 | 348 | - | 16.21 | ATTAATCATTAAA |
| Charlie2a | Zfp961 | 286 | 293 | + | 15.99 | GGGCGCCA |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
