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 | TGA7 | 308 | 317 | - | 16.04 | GTGACGTCAT |
| Charlie29b | FOSB::JUNB | 308 | 317 | - | 16.04 | GTGACGTCAT |
| Charlie29b | ATHB-40 | 575 | 585 | + | 15.98 | AGCAATAATTG |
| Charlie29b | ZHD3 | 577 | 585 | - | 15.98 | CAATTATTG |
| Charlie29b | TGA3 | 307 | 317 | - | 15.89 | GTGACGTCATT |
| Charlie29b | HAT22 | 577 | 585 | + | 15.87 | CAATAATTG |
| Charlie29b | ATHB-53 | 577 | 585 | + | 15.87 | CAATAATTG |
| Charlie29b | bHLH80 | 502 | 510 | - | 15.85 | TGCAAGTTG |
| Charlie29b | Atf3 | 308 | 317 | + | 15.79 | ATGACGTCAC |
| Charlie29b | JUN::JUNB | 308 | 318 | - | 15.77 | CGTGACGTCAT |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
