Charlie4
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000024 |
|---|---|
| TE superfamily | Charlie |
| TE class | DNA |
| Species | Metatheria,Eutheria |
| Length | 3378 |
| Kimura value | 23.67 |
| Tau index | 0.0000 |
| Description | hAT-Charlie DNA transposon, Charlie4 subfamily (autonomous) |
| Comment | Active in common ancestor of all eutherians. |
| Sequence |
CAGGGGTTCTTAACCTGGGGTCCACGGACCCCCAAGGGGTCCGTGGATAGAATTCAGGGGGTCCGTGAACTTGGATGGGAAAAAATTACATCTTTATTTTCACTAACCTCTAACTGAAATTTAGCATTTCCTTCAATTATGAATGTAGGCAACAAACCACAGTAGTATTAGCAGTACCTGTGACTTTGTCACCAATAGAAATCACAGATATTTTCATATCACATTACAGTTGTTGCAGATATCTCGAAATATCGTTTACGCTCATCACTACTTCGAAATTACGGTAGTTATTAGACCCGCCGCTAGATCGCACGTGATCGCAGTCTTCCTGTCTACAGATGCTCGTGCGACGTAGCTGGCCAACTATCGGGCAACTCTGCGCCTAGTAGTCGTTCAGCCACCAAACGGTGAAGTCGCGTGTTCTCACATTGGTGACCCAGACATCTACGTTGCTTTCCAGTATTCCCTATCTACAATTGTTTGTTGATCAATACGTGGAAGGAGGTGAGTCGTTTTCATTGTTTGNTAAAGTTTTGCAAAACTGGACGGTTCAAATGAGAATTCTTAACTCTCCGTAAGGCAGCGCGGCCTTTTGTAACACGGATAGGCGCGCGGGCTACGAGTGTAGACCAGGCAAGTTCAAATACATCTGACGGTTGAGATAACTGCTGAAGTGTGTTATTTAAAGTAACTTNTTATTGCTAACAGATTGCGCAGTGACGTAGGTCATGCACAGTGTTGTAAGCTCTGTGAAGCAGAGNTTCTTTTCTATTTGTTTTTCTCTTTGTACTCCTTTTTTGTACACTGTCTGTGTTACGAAGTAAAGGCATGCACATACANTGTGTTGTACAAGTGGTATTCGTGTATTATTNTTCCGTGAAAATACCGCATATTTNAAAAATAACTTCGCGAGAAACANTGACAATATCAGAAATGAGAACCATTATTTCTAAGAAGGCACAGAAAGCCACGCGACTCCACGCTCGACACTAGCTAAATTTCAGGAAGGACATGNCTTCTGAACTNCTGCTGTAATCCNCGCGTCTACGTAAGGNTTAAAANNATTAAAAGTGCTNAAANNTTGGATAAATTATAAAACCTGTCTTATTTTACTCGCTNGTCATACAAATTTCCGAATATCNTACANTCTACTTAATTAACATACAAATTACTTCNTTCTATGCAGATTTATCAAANAAATTANTTAAAAGCCNTACGAAAATATNGAGTTTCAAAGNATGTCAGTTGAATCAAACGTTTTATTTTAGCATTATTTATTTTATTTTTTACAGACCCAATTTAAGTTGNAGTGTCGAAGAAAAGGACGNATGATGAAGACCGTGTATTATACGGTTTCGCTTNCATTANTGAACGTGATGGGACACAAAAGCCACAGTGTTTTTTGTGTGNAAAAATTCTTGTGAATNGAAGTATGAAACCAGNGAAACTGAAAGAGNACNTCACATCTGCCCATCCTGAAAACGCATCTAAANACGCGAGTTTTTTTNGTGTGAGGAAAGTTCAACTCGAAAAAGCTGGGACACTTCCNAAACGTNGATTTGCCGTTTCACAAAAACCTTTTCTCGAAGCATCCTATAAAGTTGCNNNNCCGNTCGCCAAACGNAAGAAGCCTCACACTACTGGAGAGGCTTTAGTAAAGCCATGTGCGCTGGAAATGGTCGAGCTGGTTTGTGGACTGGAACAGAGGAAAAAGCTGGAAGTGGTTCTTTTGTCAAATGATGTGATACGTTNTGGAATAGTTGACATNTCTTTTAACATTTTGAAGCGAGTCATCGAGGAATTGGCGNCCTCGCCATTCCCCTTCANTATGCGACTGGATGAAACTACAGACATCTCTCAATGTAGCCANCTCCCTNTTTTTGTTCACTATGTGCATGCTGACGCCATCAAAGAAGAATTCTTATTTTGTGAGTCCCTTTTGGAAACTACAAAGGCTGCCGATGTTTTGGAAATGGTAAAAGGTTTTTTTGCCAAACAAAACTTTGACTGGAAANAAAAGCTTCATACTCTTTGCACAGATGGAGCTCCTACAATGCNTGGCGATGCATCTGGTTTTGCTACTTTAGTGAAAAAGGAAGCNCCTCACGTCGTCGTCACTCATTGCNTTTTACACAGNCGTGCACTGGCAACAAAGACTCTTCCAACAATCCCGAAAGAAGTTTTGTCAACAGCCATAAANGTCATCAACTTTATCAGAAGTAGGTCTCTGAATCACGNCATTTTNAAAAAATTTTGTTAAGAAATGGGAGCAGAATATGAAGTGCTTCTCTACCACACAGAAGTTCGCTGGCTTTCAAGAGGACAAGTCTTGAAGCGCTTGTTCAAACTAAGGGCAGAAGTTTTACNTTTTCTGAAAGAAAAAGAAAACCCACTCTCGGAACACTTTGAAAGAAAGNATTTTATCCATGGGTTGGCTTACCTGGCAGATATTTTTAACCATATGAATGAGATAAATCTTTCAATTCAAGGTCCTGAAGTCACCATTATGGATGCTACTGAAAAATTACAAGCTTTCTTGGCTAAGCTGCCGATATGGAAGAAGAGAGTAGAGGCCGACGTCCTTGCAAACTTTCGAATGCTGGAGGAAGTGCTTTNCCANGACGAAGTTGAGATACAAAATTCTCTGTCAATTTCTTTGAAAAGAGAAATCTGCAAACACCTGGAAACACTTCAGAACTCTTTCAAAAGTTATTTCTATCTTGATGGCATCAAAGTTGAACCATGGATCCGCAATCCTTTTCTTTCTGATATAAACTGTATCGAAGATGTTGACCTAGCCAAAGATGAACTCATTGATCTTAGGACAAAAAACTTACTACAACTGGAGTTTAACTCAAAAAGCCTTGGAGAATTCTGGTGTTCCTTGAGAGAAGCCTATCCTCGCCTTGTAAAGCGAGCTACGGAAGCTTTAATTCCATTTGCAACAATATATCTTTGTAAATCGGGATTTTCAACACTTGTAACCATCAAAACAAAAAATCAAAATCGACTGGATGTCCAACATGACATGCGTGTTGCCTTGTCAAAGACCACCCCACAGTTTAATGTTCTTATTCAAGCTAAGCAACAACAGCCTTCACACTGATATGTCTTTAAAAAATAAAATTTAACTTTAACTTGCCTATATTTTAAATGTATTGTCTTATTATTTAATGCGTTAATAAAGAAGCACATATATTACTATATCACAAATTTGTTTTTAAATATTTTGATAACTATATTTCAATATAATTGGTTTCCTTTGTAATCCTATGTATTTTATTTTATGCATTTAAAAACATTATTCTGAGAAGGGGTCCATAGGCTTCACCAGACTGCCAAAGGGGTCCATGGCACAAAAAAGGTTAAGAACCCCTG
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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 |
|---|---|---|---|---|---|---|
| Charlie4 | Sox21b | 801 | 815 | - | -6.18 | AACACAGACAGTGTA |
| Charlie4 | RARA | 2468 | 2485 | + | -10.47 | GAGATAAATCTTTCAATT |
| Charlie4 | AT4G12670 | 2981 | 3009 | + | -11.89 | GTAACCATCAAAACAAAAAATCAAAATCG |
| Charlie4 | ZSCAN16 | 2177 | 2194 | - | -15.45 | GGCTGTTGACAAAACTTC |
| Charlie4 | BPC5 | 767 | 796 | - | -41.10 | AAAGGAGTACAAAGAGAAAAACAAATAGAA |
| Charlie4 | BPC5 | 765 | 794 | - | -44.94 | AGGAGTACAAAGAGAAAAACAAATAGAAAA |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
