Charlie29b
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0001176 |
|---|---|
| TE superfamily | Charlie |
| TE class | DNA |
| Species | Eutheria |
| Length | 1194 |
| Kimura value | 27.74 |
| Tau index | 0.0000 |
| Description | hAT-Charlie DNA transposon, Charlie29b subfamily |
| Comment | ORF remnant from 467-955 encodes the C-term of a transposase with consensus 49% identical (66% similar) to Charlie25_tp in mammals, hAT-1_MEu in marsupials, and Chaplin5_FR_tp in Fugu. Positions 1-467 and 913-1194 comprise the previously described subfamily Charlie29a. Present at orthologous sites throughout Eutheria, but not in marsupials. |
| Sequence |
CAGTGTTTCTCAAACTGGGGTCCGCGGACGTATTCTCGGGGGTCCGCGAGTTCTCTACGAGAATTTTTNAATTTTGTGTTTTCATTTCGATGATAATCTAAAAAAATTAATATAAGCATATTCTGGATCATCTGGATGACCACCTTATAACCGAGTACTGCCACGCGATTTCAGTGCCCGCGTTTGCGTTTGTGTTTACGATCGCGTTGGCGCCAAGTAGTACTACTTTAATTGTCGCGGGCTAATGAGAAAAGAACAGAGGCGGACTTAATACGTAAATGATGCGTTCGCGCCAAGTGAAGGCCAAATGACGTCACGGCGCGCTGTACGAACGAAGGTTTCGCAGTAGTTCGAATAGAGAAAAGTGGTGGGAGAATTGAGTCATCACACGGCACACGGTAGTATAGGCATGCCGAACTCAAAAGAACCTGCGCCGTAGCAGTCAGTACCATATTCACGTTGCGAGCAGATGTATTGCGCGGATCCCGTCTTTGTACGTACCAACTTGCAACAGTTCATTAGCAGTAAGTGTAGTAGTAAATACGCAATGAAGAATTTTTCTGTTCCCGATTCCAGCAATAATTGGATTAGATACCCATTTAATGCAGATTTCAATAACGCCGCAATGCTAACCTTATCTTCAAGTGAACAAGACAGCTTTACAGAGTTATCAAGTGACACCTCATTAAAATTGGCATTCGAGGATTGCTCGCTGGCAGAGTTTTGGTTAAGTATGAGGTCTGATTATCCTGAACTAGCAAACAAAGCCTTGAAGTTATTAATACCATTTTGTACAACATACTTATGCGAACAGGCATTCTCTGCATTAGTATTATTGAAGTCAAAATACAGAAACAGATTAAATATAGAACCGGACCTGAGGCTACATCTTTCTACTATTAAACCCAACATCGGCGATTTAGTTTCAGCAAAACAACATCATCCGTCACATTAAATTAATGTTGTTAATTTGAATTTTATTGGTTTTGTAGTTTTGTTTGTATTTAATTTGTAAATTTGTTTTGGTTTTATAGTTGTATAAGAGCTATAAGCATAAGGAGTTTATACCTAGTTTTATGTTTGTACATATTTAAGTAACATTATAATAAAAATAATTTAAGTCAACACTGGGGGTCCGCGAGAATTTTTTTCCTTAAAAGGGGTCCGTACATTACTCAAGTTTGAGAAACACTG
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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 |
|---|---|---|---|---|---|---|
| Charlie29b | CrebB | 308 | 317 | - | 16.92 | GTGACGTCAT |
| Charlie29b | CrebB | 308 | 317 | + | 16.91 | ATGACGTCAC |
| Charlie29b | TGA7 | 308 | 317 | + | 16.89 | ATGACGTCAC |
| Charlie29b | At3g11280 | 631 | 644 | + | 16.86 | AACCTTATCTTCAA |
| Charlie29b | PDR3 | 21 | 28 | + | 16.61 | TCCGCGGA |
| Charlie29b | PDR3 | 21 | 28 | - | 16.61 | TCCGCGGA |
| Charlie29b | TGA2 | 308 | 317 | - | 16.60 | GTGACGTCAT |
| Charlie29b | ATF7 | 308 | 317 | - | 16.57 | GTGACGTCAT |
| Charlie29b | AT5G05790 | 631 | 644 | + | 16.55 | AACCTTATCTTCAA |
| Charlie29b | zip-8 | 308 | 316 | + | 16.50 | ATGACGTCA |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
