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 | NR4A2::RXRA | 1084 | 1096 | - | 15.37 | GGGCCACTGACCC |
| Charlie30b | Clamp | 793 | 806 | - | 15.35 | GAGAGAGAGAGAAG |
| Charlie30b | Fer2 | 675 | 684 | + | 15.28 | ACAGGTGACG |
| Charlie30b | BPC6 | 788 | 808 | + | 15.26 | TCTTCCTTCTCTCTCTCTCTT |
| Charlie30b | MYB96 | 743 | 753 | + | 15.20 | CCCAACTTCCA |
| Charlie30b | blmp-1 | 840 | 850 | - | 15.15 | AAAAGAGAGAG |
| Charlie30b | Fer1 | 672 | 684 | + | 15.13 | ATAACAGGTGACG |
| Charlie30b | ceh-38 | 1022 | 1035 | + | 15.00 | AAAAATAAATAATT |
| Charlie30b | Trl | 764 | 772 | - | 14.81 | GAGAGAGAG |
| Charlie30b | Trl | 796 | 804 | - | 14.81 | GAGAGAGAG |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
