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 | BPC1 | 1847 | 1870 | + | -1.41 | CCCAGAAATTGAGAAAGTGAATGA |
| Charlie2a | BPC1 | 1046 | 1069 | - | -1.74 | ATGAAAGAGAAAGGTATATACTGC |
| Charlie2a | IRF9 | 1056 | 1070 | - | -1.76 | AATGAAAGAGAAAGG |
| Charlie2a | ZAP1 | 25 | 39 | - | -2.21 | ACCCCCAGGGGTATG |
| Charlie2a | BPC6 | 2550 | 2570 | - | -3.53 | ATCGTTCTCTTTTTCTCCTTG |
| Charlie2a | IRF8 | 1056 | 1068 | - | -3.62 | TGAAAGAGAAAGG |
| Charlie2a | BCL6B | 1842 | 1858 | + | -9.76 | TACTTCCCAGAAATTGA |
| Charlie2a | EWSR1-FLI1 | 524 | 541 | - | -11.61 | GGAATGGAAGAGGCAAGG |
| Charlie2a | BPC5 | 171 | 200 | - | -43.21 | AGGGCGATTGTGAAAGGGGAGGTGGGAAAG |
| Charlie2a | BPC5 | 167 | 196 | - | -46.48 | CGATTGTGAAAGGGGAGGTGGGAAAGGGCA |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
