Charlie6
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000105 |
|---|---|
| TE superfamily | Charlie |
| TE class | DNA |
| Species | Eutheria |
| Length | 3519 |
| Kimura value | 23.01 |
| Tau index | 0.0000 |
| Description | hAT-Charlie DNA transposon, Charlie6 subfamily (autonomous) |
| Comment | Imperfect 16bp TIR. TSD: NTCTAGAN. Charlie6 is unusual in that no common deletion products have been amplified. A member of the MER1-group. ORF roughly at pos. 607-2496. |
| Sequence |
CAGAGTTTCTCAAATGGGGTTTCTGCGGAACCTAGGGTTCCGCGAGATGTCGCTAGGGGCTCCGCGAGANATTGTGATTGAAAAAAATATAGATTTTTGAACTTCGCGCGCCGCGCGATGCTAGCACTCGCAGTGATGGACAGTGACCGAGCAGCCCCGTTAGCAATTTCGTTAGAGGTCTTTCAGCCTCGTATGGCAGTGCGCAGTAGGACCATGTTCATTTGGNTGAGTCCATTCTCAGTTTTTGACGCAAGATAGGGGAGGCCGTTGATAANTGGTGAGTGCTGTATTGCACGGAGGGGAGGACGGTAGGCTGATGACGTCAGCCTCTCCCTCCCGAATTACCTCCCCCAACCTCCCCTTNCGCGCCGCCGACTGACTTACGGGAGCGAACAAGCTCTACCGGTGTAATAGAAAATCGGAGGGAAATTTTCATTCTAAAGAAGGAATTTTTACGCGCCGCGACTCAGCTGCCCCCCTGCCGCTTTGCTGTTGTTGTAAACGTTGCAAAACGTGGATTGTGTAGGTTAGAAGTGAATTGTATTGTGAAGTTTTCGTATTTTTTGCGATTTTCTCGTTTAGTTATTTATTATGCCCTTCTGTTTTATATTTTATTAGCGTTTGTGTTTTACAAACATGTCTGACGGTCCAATGTGGCGATTTTTGAAGACGAGGTGTGAGACGGAAGAGGAGGATTCTAGGCCTAGGCCTACGGACAATTCTGATAAGGTTAGTGATGAAGAATTACAATCTTCTGAGTCATTTCACTGCACTAGTGCAACAAGGGACACAAAAAAAGTCCGTCTTTACAATGAAAGCTACTTATCAATGGGTTTTACGTGGNCTGGTAATCCAAGTTGTCCTATTCCATTGTGCGTCGTCTGTGGCAAACAACTTACAAATGCAGCAATGGCTCCAGCAAAATTGAAAAGACACTTAACTACAAATCACAGCCATTTGACAAGTAAAGGTGCTGATTATTTTAAACGGCTATTGGAATCTCAAAACAAACAGAGTAAAGCTTTTGTTNAAAAAGTCACATTCAGTGAAAAGGCTCAGGAAGCAAGTTATTTAGTAGCAGAACTTATTGCCCAGAAAAGGAAAAGTCACACAGTTGGTGAGAACCTAATAATGCCAGCATGTAAAATTATAGTGAGTAAAATGCTAGGACAAGATGCAGTACGAGAAATTGAAAAGGTTCCACTCTCAAACAGTACGATAAGTCGACGTATTGATGACATGTCACATGATGCTGAAGAGGTTTTGTGTAATAAACTGAAAAACAACAGCTTCTCTATCCAGGTTGATGAGTCAACAGATTTCACCAATAAATGTCATGCTGTAGCATTTGTAAGATTTGTAAATGATGGTGAAATTCAAGAAAACTTTTTCTGCTGCAAAGAGCTGCCCGAAACAAGCAAAGGCCAAGATATATTTAATGTTTTGTCTTCATATCTGGAAACAAAAGGTCTGTCTTGGAGGAACTGTGTTGGCATCTGTACTGATGGTGCCCCATCAATGGTTGGCTCCATGAGAGGTTTCGCCTCTCTTGTAAAAAAAGAAAATCCTGACGTTGTCACAACACACTGCTTTCTTCACAGAGAGGTGCTGGTGTCAAAAACTCTTGGAGATGAAATGAAAAAAGTTCTGGATGATGCTACAAAAATGGTTAACTTTATTAAACAAAGACCAGTTCACTCGAGAATGTTTNAAAAACTGTGTGAAAACCTGGACAAAGAGCACATAAATCTCCTGCTACATACAGAAATCCGGTGGCTTAGCAGAGGAAGAGTTCTCAACAGGGTGTTTGAGCTGAAAGGTGAATTGCAGGAGTACTTTCAAGAAAATAGTAGGCCAGATTTTGCTGAGTGCTTTGAAGATGAAGAATGGCTGCAGAAACTAGCCTACTTAGCAGACATTTTTCATCACATGAACCAGTTGAACAAGTCTCTGCAAGGCCCTGGAGAAAATGTTTTGACTTCAAGTGACAAGATTCTTGGATTTAAAAGGAAACTGAATCTTTGGAAAAATCATGTTGCAAAAGGAAATCTTGAAATGTTTCCACTGCTGCTTGGGCTTGAGAGTGAGGAAGGATATCAGCAAGTCTCAAGTCTTATTGAAAACCACCTGGAAGAACTGCAGAACAAAATTGAACAGTATTTTCCCTCCCTTTCAACACAAGTGTATGACTGGGTGAGGGACCCTTTCTCTGAATCTTCTGCTCAGCCTGAGAACTTGACTTTGAGAGAAGAGGAAGAACTTTGTGAGCTGCAGTCTGATCGTACACTCAAGATGAGATTTACTGATCTGCCCCTAGACGAGTTCTGGATTTCTGTGAAAGAAGAGTATCCTGCCATTCACAGGAAAGCAATGAACATTTTGCTGCAGTTTTCAACTTCTTACATGTGTGAGCAAGCTTTTTCTTGTTTAACAAGCATCAAGAGCAAGGACAGAAATCGTCTCATTTCAGTTGAAAATGAAATCCGTGTGTGCTTATCTCAAGTTCGACCCAGAATTGAGTATTTGTGCAGCAAAAAACAAGCACAGGTTTCACATTAAAGAGGTAAATTTCATTCTTTATTTTTAGTTTCAAAAATAACACTTTTTATGCATATATAGGCCTATAAAAGAGATCAAGAAACCAACACATGTGTATAATAATTTTGTAACTGCTAGGCCTATATTTGAGCCTGATCATGTCACTCAGTAAGAAAATATTTTTTCAAAGTCTTATATAAAATTGTGTCTTAGGCTATATTTTTATTCATATTGCTTTGGCTTATGGTTTTAGTAGCTTTACTATTCAACATTGTCAATAAATTTTCATGTTGTAAATAACATTAATTAAAATCAATTTACAACCTTTATTTAAATTAAATCTACCGAGCCTACCTTTAGAAAAATTAAATCCCATTTTGGCTTAAGCCAGTTATTTAACAGAAATTTATTATGTTTGCCTTATGAGTTTTTAAAATTTATGAAAAGGAAAGAAATTAATTTCAAGAAAGGTAAGCTAAGCTTAATACCTTNTTTTTTTCAAGAAAGNTTGGCTAAAAAGTCATTTTTAGTTTTAAATAGGGAGAAAAACTACTCTTGCACATACCATATACCACATACCATACCTCATTAGCATCTTGTATAGTAGAAATTTGTGATAAGACTTTTAGGCCTACTTGGATAAGGTNAAAAAATCAAGTAGGAAATTTTTTAAAAAAGAAAAACTGAAGTTTCCTCTACCTACACTACTGACTTGCATTAGAGTTGATATCCTTTGTGGGGAGGGGGAACCACACAAAAAGAGTAGGCTAATAAGTTGGCCAAAATAAACAGATCCACAGAAAAATATCATTCTCTACTCAAAAGAGCATTGACAATTATTATTGGATTATTATATCTACAACTTACTGATCACGCTAATGTACCATGAGCTGTAGATATAATAATTTTTATGCAGGGGTTCCCTGAGACCTGAAAATTATTTCAAGGGCTCCTCCAGGGTAAAAAGATTGAGAAAGGCTG
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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 |
|---|---|---|---|---|---|---|
| Charlie6 | NAC038 | 2420 | 2438 | + | 16.58 | TTTCTTGTTTAACAAGCAT |
| Charlie6 | TGA7 | 317 | 326 | + | 16.56 | ATGACGTCAG |
| Charlie6 | lmd | 473 | 484 | + | 16.52 | GCCCCCCTGCCG |
| Charlie6 | Gfi1B | 945 | 954 | + | 16.50 | AAATCACAGC |
| Charlie6 | zip-8 | 317 | 325 | + | 16.50 | ATGACGTCA |
| Charlie6 | NAC010 | 2420 | 2440 | + | 16.42 | TTTCTTGTTTAACAAGCATCA |
| Charlie6 | TGA2 | 317 | 326 | - | 16.40 | CTGACGTCAT |
| Charlie6 | TGA5 | 317 | 325 | + | 16.33 | ATGACGTCA |
| Charlie6 | Zm00001d020595 | 367 | 376 | - | 16.31 | GTCGGCGGCG |
| Charlie6 | FLC | 1092 | 1105 | + | 16.27 | CCAGAAAAGGAAAA |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
