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 | TRP2 | 1016 | 1036 | - | 4.27 | AACTATAAAACCAAAACAAAT |
| Charlie29b | RREB1 | 982 | 1000 | - | 3.78 | AAACAAAACTACAAAACCA |
| Charlie29b | RLM1 | 858 | 871 | - | 3.76 | TTCTATATTTAATC |
| Charlie29b | RREB1 | 927 | 945 | + | 3.05 | CAGCAAAACAACATCATCC |
| Charlie29b | CG4360 | 934 | 946 | + | 3.03 | ACAACATCATCCG |
| Charlie29b | BACH2 | 303 | 321 | + | 2.51 | GCCAAATGACGTCACGGCG |
| Charlie29b | IRF4 | 1018 | 1031 | - | 0.85 | TAAAACCAAAACAA |
| Charlie29b | Rarg | 300 | 316 | + | -3.71 | AAGGCCAAATGACGTCA |
| Charlie29b | E2F7 | 285 | 298 | + | -4.74 | CGTTCGCGCCAAGT |
| Charlie29b | E2F7 | 363 | 376 | - | -6.07 | TTCTCCCACCACTT |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
