Charlie12
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000085 |
|---|---|
| TE superfamily | Charlie |
| TE class | DNA |
| Species | Rodentia,Strepsirrhini,Haplorrhini |
| Length | 2870 |
| Kimura value | 6.16 |
| Tau index | 0.0000 |
| Description | hAT-Charlie DNA transposon, Charlie12 subfamily (autonomous) |
| Comment | A largely internally deleted Charlie12 is the source of MER30 elements. |
| Sequence |
CAAGCTTGTCCAACCCGCGGCCCGCGGGCCTCATGCAGTCCAGGACGGCTTTGAATGTGNCCCAACACAAATTTGTAAACTTTCTTAAAACATTNTGAGATTTTTTTGCAATTTTTTTTGTAATTTTGTNATTTGNCTATGTGATTCTCAAGTGTGAACTTCGTAGACAACAATGGAATGGAAAGGGGTAATCAGAGTATGTCACATCCACAAATAATGGACTAGTATCCATAATTTGCATTATAATTGCAAACAGTTCAGCAAGAAGAAATTAAAAGCCATTAAAATTAACTAACAAAGAGCGAGAGGACGCTATTGCAGTGCCACGTGAAGTGAATTGTGACAAAGAATTCAAGTGTGTATTCTGGACAAGGCAGAGCGCTGCTGTACACCAGACACTGTCGCCATTTGTACGCATGTGTGGCTTCAGTTTTATGGTGGTGTGCGACTTCCAGTGTGTTATCTTCTAATCACGGACAGTTGAATTGACACCGTCAGGCGTTANGTGTGCTTNTGGCGACTTGAGCAATNATATTCGATAATATTTCAACCTACCTTTGTAGATGATAGGTGTTTAATATTANTTAGAAGACNTGTAAGTATTAGTCTTCTTATTTGGTTATTAAACCTTGCTTTCTATTTTCCTGTCTGTTAATTTCCATAATAAANGTAAATNNAGTTGCTTATCTATTATNATCTTTTAAAATTCCAGNATATGGCTTCCACAATGTCTCAAAAGAAAACAAACCCCCCNNAAAACAAAAANTACGGATGAGGGAAGATTGCTCAACGAAAAGTGGACAGATGACTACTTTCTTGTCGAGGCAAATAGCGAGGCACTCTGCTTGATTTNCANGGAATTTGTGCCAGTTTCAAAGACTACAATTTGAAGAGGCATTATATGCAAAGACGTGCTGNCAAATTTGGTGCGTATCAAGGAATGTGTCGTAAGGACAAAAATAGCAGAACTGAAAAAANGTCTGTCTTCACAAAAAAGATTTTTTNNAAAGTTGCAACTCGGACAGTCTANNGTAAAANCTAGTTATGTGGTAGCAAATTTAATAGCAAAAAGCAAAACCATTTACNGATGGTGAGTTTATTAAGCAACGTNTGGGAGGCGTGGCANATATCATTTGCCCTGANAAANNAGAAGATATCTCTAAAATCAGTTTGTCTCGCCGGANTATAGCCAGGNGAATTGGAGAAATTGGGAAGTCTATGAAAGGAGNGTAAAACTGCTAATTTNAAATTTTGTGCTTTGGCGATGGATGAAGGCACTGACGCTACANATACGGCACAACTTGCCATTTTTATTAGAGGCATTGATGACGAATANAATGTCACCATTATATAAAGCCATATAATGAAGAAATNATAAACCCATATAATGAAGAAATGGCTTTTTCAGTGCCATTAAAAGACANAGTAAATCAAGAGATTTATACGAAGCAGTGAAAGATGCGTTAAAGCAATTTTCTTTGTNCNTTGTGAACATACGTGGTATAGCTACNGATGNTGCCCCGGCGATGGTANGTAAAAGAGAGGGANTTGTANAATTAATAGAAAATGATGCAGTTGCCGCNCGAAACTCACNTTTGATGANGTGTCATTGCATAGTACATCAAGAAAATTTATGTACAAAAGCTTTAAAAATGGATAACGTCATGCAAATTGTCATCAAGGCTGTGAATTTCACAGGGGCCNAGGGATTGAATCATCGCCAGTTCCAGGAATTCCTTAAAAGTATGGATGCTGACTNTAGCAACGTCATTCACTTTTCGGAAGTAAAGTCGAGGCAGATGTTGAAAAGATTTTATGNTTTGCGACGTGAAATCGAGCTGTTTATGGTATCAAAAACAAAATTNGTGCCAGAACTTGACGACGAAAACTGGCTTACAGATTTAGCATTTTTAGTGGGTTTGACCGCCCATTTAAGTGAGTTAAACNTGNGTCTTCAAGNTGAAAACCAACTTNNCAATACAATGTTTCAAACCATAACAGCGTTCCANATGNAACTGAAATTATGGCAAGCTNAAATTAAGGCAAACAGTTTTACGNATTTCGACACGTTNGCTAAACACGGNCCTGTNAACAGCNAAAAGTACGCNGCCTTGCTTTTCGATTTGATANAGGAATTTGAAAACAGGTTTCAAGATTTCTGGAAAAATNATCAATATTTTGGTATANTTGCAACTCCATTTTCAGCCGACATANATATGTTACCTGCGAATGCNTANAGCTGCAATNTGACGTTCAACTTANAGAAAAATCTNATCNNGCCTCTTTNCTGGACTTTGTAAGACCTGTCTTCCCAGNGACAAATATCCCTCGCTTCACAGTCACGCCTTGCTCATGTCGTCGNTTTTTGGCAGCACCTGCGTTTGTGAGCNACTGTTTTCAAGGATGAAGNACACGAAGAGTAAAATTAGAACCAAAATATCTGANGAGCACCTTGAGAACTCGCTGAGAATTGCAACTACTTCCATCGAGCCAGATACTGATGNATTAGTTTCTCAAAAACAATGTCAAGTACCCCACTAGTTTTATGTTGTCCTCTTTTACTTTTATAATAAAAANTATCAAAAAANTAGTGANGTTTTATTANCTAGATACGTACATTTTCTGTGTCAGTGATTGCAAANTTGGGACCTGCTCGACGATTTTGAAAGACCCTCTGAANGGGGCAGCGCATGGTTAGATTATNATGCGAGGACTTTTTTGCTTATCTGTGGTGGCGGATATCACGAAAATTATNCACGGACCTTTTTTCTTTAGCTCATCAGCTGTCGTTAGTGTTTGTGTATTTTNTGTGTNGCNCAAGACAATTCTTCTTCCNGTGTGGCCCAGGGAAGCCGAAAGATTGGACACCC
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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 |
|---|---|---|---|---|---|---|
| Charlie12 | BACH2 | 1652 | 1670 | + | 19.83 | AATGGATAACGTCATGCAA |
| Charlie12 | Fer1 | 2778 | 2790 | - | 17.70 | ACGACAGCTGATG |
| Charlie12 | BZIP16 | 322 | 331 | - | 17.65 | TCACGTGGCA |
| Charlie12 | F10B5.3 | 2156 | 2166 | - | 17.46 | TTTTCCAGAAA |
| Charlie12 | BZIP68 | 322 | 331 | + | 16.88 | TGCCACGTGA |
| Charlie12 | ROX1 | 166 | 177 | - | 16.80 | TCCATTGTTGTC |
| Charlie12 | ZNF530 | 176 | 189 | + | 16.77 | GAATGGAAAGGGGT |
| Charlie12 | RVE4 | 2434 | 2442 | - | 16.53 | AGATATTTT |
| Charlie12 | ZNF454 | 19 | 35 | + | 16.43 | GGCCCGCGGGCCTCATG |
| Charlie12 | AT1G19000 | 1651 | 1663 | + | 16.39 | AAATGGATAACGT |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
