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
|
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 | FOSL2::JUND | 308 | 317 | - | 16.36 | GTGACGTCAT |
| Charlie29b | lin-54 | 968 | 980 | - | 16.34 | TAAAATTCAAATT |
| Charlie29b | FOSL2::JUND | 308 | 317 | + | 16.34 | ATGACGTCAC |
| Charlie29b | TGA5 | 308 | 316 | + | 16.33 | ATGACGTCA |
| Charlie29b | FOSL2::JUNB | 308 | 317 | - | 16.31 | GTGACGTCAT |
| Charlie29b | FOSL2::JUNB | 308 | 317 | + | 16.30 | ATGACGTCAC |
| Charlie29b | AT3G10580 | 631 | 644 | - | 16.25 | TTGAAGATAAGGTT |
| Charlie29b | SPL5 | 1163 | 1171 | - | 16.23 | TGTACGGAC |
| Charlie29b | FOSL2::JUN | 308 | 317 | - | 16.17 | GTGACGTCAT |
| Charlie29b | HAT5 | 577 | 585 | + | 16.17 | CAATAATTG |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
