Charlie30b
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0001199 |
|---|---|
| TE superfamily | Charlie |
| TE class | 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 | BPC5 | 867 | 896 | - | -46.40 | GTTAAGGGAGAGAGACAGGAAGGGAAGGAA |
| Charlie30b | BPC5 | 869 | 898 | - | -47.38 | CAGTTAAGGGAGAGAGACAGGAAGGGAAGG |
| Charlie30b | BPC5 | 844 | 873 | - | -47.76 | GAAGGAAGACGGAAAGTGAGGAGAAAAGAG |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
