Charlie30b
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0001199 |
|---|---|
| TE superfamily | Charlie |
| TE order | DNA |
| Species | Eutheria |
| Length | 1124 |
| Kimura value | 31.73 |
| Tau index | 0.0000 |
| Description | hAT-Charlie DNA transposon, Charlie30b subfamily |
| Comment | 16 bp TIRs. No coding remnants, but termini similar to a number of other Charlies. Still apparently not at orthologous sites in marsupials. |
| Sequence |
CAGGGNTGGNGAACCTCCGGCCCATAGNCCAGATCTGGCCCTCGGCTTGATTTCATCCGGTNCGTGGGATGATATTGTTCTGGCCACTGNTNCTGCAGCCCAGAGAATAATTTCTCCCCTGGTGGGCTGCTGTGGCTATCCCATTCAGAGCGGAGCCTCTGAAGGTTTGATAAGAGCAGTTGAAGAGCTGTGAACAGCGGTTAACCCATTTATTCCTGAAGGTTTTTTCCGAATTNTTTTTGGTTTCTACTNTATATTATCCCCACTAGGACCCAACTAGACCAAAAAACTGGATTTGATTTGGAGAAAAAAGGCTCAGAACAATGAAATAAATGCTGGTTCCAAATGTAACCTTCAGGCATTGTGGAATGAGGCAGCCCTAATCTCTCAAAGAACAAAGATAAGGCAATCTGACAGCTTTTGAATGTCAAAGGGACTTTCAGGCGATAGCTAGTAAATTGACAGACACCTCTAAGGTTCCAAAGTAAATTTCTAAAACCTAAGTCATTCCTTCACACATGTGCAAAACCTTCAGAATTCCATGGGAAAATAAACCTTTATTTCAAAAATAAACTTTGAAGTTTGAAAATAAAAGCAGACAAGCTGTTTCCCAGTGCAGAAAGGACTGTTCTAAACTGCTGGAGAGCTAATCAGAATTTCAAAGGGCAGTGATAACAGGTGACGACTTACTCTGATGCCCACAGCCCAAGCGAACAGCGGAATCTCAACAGCCGNGCTTACCCCCAACTTCCACGCAGACCTCCTCTCTCTCCTCGCTTTNCCCCGTTCTTCCTTCTCTCTCTCTCTTCCTCTCCCNCTTTGTCCCCTTTCCCTTCCATCTCTCTCTTTTCTCCTCACTTTCCGTCTTCCTTCCCTTCCTGTCTCTCTCCCTTAACTGGCCATAATATGGAACTGAAGTATATTTTTNANTATTTGTTGTATTTATTGAATAAAGTTTTATGTTTCCCGTTCTTAATTTTAAAAGCGAGTGAGTNGAACGTTTTATATTTCTCTTCCTAAAAAAAATAAATAATTAAGTTGCTTTTTACTTACGTGTGGCCCTCGATTGATTTTTTCTCCTGTGGGTCAGTGGCCCTCGATAGAAAAAAGATTTCCCACCCCTG
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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 |
|---|---|---|---|---|---|---|
| Charlie30b | Trl | 798 | 806 | - | 14.81 | GAGAGAGAG |
| Charlie30b | ZNF257 | 766 | 775 | - | 14.67 | GAGGAGAGAG |
| Charlie30b | BPC1 | 787 | 810 | - | 14.64 | GGAAGAGAGAGAGAGAAGGAAGAA |
| Charlie30b | Erg | 873 | 882 | - | 14.61 | ACAGGAAGGG |
| Charlie30b | Pou5f1::Sox2 | 419 | 433 | - | 14.56 | CTTTGACATTCAAAA |
| Charlie30b | elt-3 | 168 | 175 | - | 14.52 | TCTTATCA |
| Charlie30b | Sox11 | 393 | 400 | + | 14.51 | GAACAAAG |
| Charlie30b | Sox7 | 318 | 327 | + | 14.49 | AGAACAATGA |
| Charlie30b | SPIB | 803 | 815 | + | 14.46 | TCTCTTCCTCTCC |
| Charlie30b | BPC1 | 783 | 806 | - | 14.45 | GAGAGAGAGAGAAGGAAGAACGGG |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
