Charlie3
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000023 |
|---|---|
| TE superfamily | Charlie |
| TE class | DNA |
| Species | Simiiformes |
| Length | 2706 |
| Kimura value | 8.31 |
| Tau index | 0.9037 |
| Description | hAT-Charlie DNA transposon, Charlie3 subfamily |
| Comment | ORF (roughly 625-2526) encodes a transposase 59% identical to that of CHARLIE1. Common internal deletion products of CHARLIE3 are roughly: 1-272<>2456-2710 (MER1A), and 1-96<>135-272<>2621-2710 (MER1B). |
| Sequence |
CAGGGGTCCCCAACCCCCGGGCCACGGACCGGTACCGGTCCGTGGCCTGTTAGGAACCGGGCCGCACAGCAGGAGGTGAGCGGCGGGCGAGCGAGCGAAGCTTCATCTGTATTTACAGCCGCTCCCCATCGCTCGCATTACCGCCTGAGCTCCGCCTCCTGTCAGATCAGCGGCGGCATTAGATTCTCATAGGAGCGCGAACCCTATTGTGAACTGCGCATGCGAGGGATCTAGGTTGCGCGCTCCTTATGAGAATCTAATGCCTGATGATCTGAGGTGGAGCTGAGGCGGTGATGCTAGCGCTGGGGAGCGGCTGCAAATACAGATTAACATTAGCAGAGAGGTTTGACTGCACAGAGACCATAATAAATCAATTGCTTGCAGACTCATATCAAAACCCTATCAGTGAGTGGCAAGTGACAATTAAGCTGCATCTGGTGGCAGGCTTTATAGTGGCAAGTGAGTTGATGTACTTCAATTGTACAGCTGCATCTGGTGGCAGGCTTTAAGTCAGAATCCGACACTTATTTTAGTCCGCGCGTGGCCCGCCCATTATTTTATTTACCACTTCCGTCCGCGCCTCTTTCCCGCACTGCGCACTTGTCTCAGTCACAGTTTTGGTAAGCCCACAAGCTAACCCTAGCCAAAATGAGTAAAAAACAAACGTCACTGGAGAGCTTCTTTGAAAAGGGGGAAAGACCCAATGATGAGACAGCAGAAGACTCTAAGACTGCCAACAAAAAGAAAGCTGCATTTAAAAGAAAATACCAAGAGTCCTACTTAAATTACGGGTTCATTGCAACAGGTGATTCACATTCTCCAAGCCCGCTTTGTATAATATGTGGCGACCGGCTATCCAACGAAGCCATGAAACCTTCAAAACTGCTTCGCCACATGGAGACCAAGCACCCTGCATTAAAAGACAAGCCTTTGGAGTTTTTCAAAAGAAAAAAACGTGAACACGAAGAACAGAAGCAATTATTGAAGGCCACCACTTCATCAAATGTGTCTGCACTGAGAGCATCATTCTTAGTGGCTAACCGCATTGCTAAAGCTAAGAAGCCCTTTACTATTGGTGAAGAGTTGATCCTGCCTGCTGCTAAGGACATTTGTCGTGAACTTTTAGGAGAGGCTGCAGTTCAAAAGGTGGCACGTGTTCCTCTTTCGGCTAGCACCATAACTAGACGAATTGATGAAATAGCAGAGGATATTGAGGCACAATTGTTAGAGAGGATTAATGAGTCACCGTGGTACGCAATCCAGGTTGACGAGTCTACCGATGTTGACAACAAGGCAACAATGCTTGTTTTTGTGCGATATATTTTTCAGGAGGATGTGCATGAGGATATGTTATGTGCACTTTTGTTGCCAACCAACACCACAGCTGCAGAACTATTCAAGTCTTTGAATGATTACATATCAGGAAAACTGAATTGGTCATTTTGTGTCGGTATATGCACGGACGGAGCGGCTGCCATGACTGGACGGCTTTCTGGTTTCACTACTCGGGTCAAAGAGGTCGCTTCTGAATGTGAGTCTACGCACTGTGTCATCCATAGAGAAATGCTGGCTAGCCGAAAAATGTCACCTGAACTTAACAACGTTTTGCAGGATGTGATTAAAATTATCAACCACATTAAAGTACATGCCCTTAACTCACGTCTGTTCGCGCAGCTCTGTGAGGAGATGGACGCAGAGCACACACGTCTTCTCTTATACACAGAAGTGAGATGGCTTTCTAAAGGTAGATCACTGGCCAGAGTTTTTGAGTTACGAGAGCCGCTCCAGAGATTTCTTTTAGAAAAACAGTCACCACTGGCAGCACATTTCAGTGACACAGAATGGGTCGCAAAACTTGCTTACTTGTGTGACATATTCAACCTGCTCAACGAACTCAATCTGTCACTTCAGGGGAGAACGACAACTGTGTTCAAGTCGGCAGATAAAGTGGCTGCATTCAAAGCCAAACTGGAATTATGGGGGCGACGAGTGAACATTGGGATTTCTGACATGTTTCAAACATTAGCAGAGATTTTGAAAGAGACTGAGCCAGGGCCTTCTTTCTCCCAGCTGGTGCATGATCACCTATCTCAGCTTTCAAAAGAGTTTGAGCATTACTTCCCAACCACAAAAGACCCCCGAACTGGGAAGGAATGGATCCGCGACCCATTTGTGAATAAGCCAGGTGAATCGACTTTGTCCGTGCTAGAAGAGGATCAACTGCTTGAGATCGCAAATGACGGTGGCCTTAAAAGTATGTTTGAGACAACTTCAAATCTCCATACGTTCTGGATTAAAGTCAAGGCGGAATATCCTGAGATTGCCACAAAAGCACTGAAAAGCCTGCTTCCATTTCCAACATCCTATCTTTGTGAAGCAGGGTTTTCTGCAGTGACAGCAACCAAAACGAGATTACGGAGTAGACTGGACATAAGCAACACACTTCGGGTGTCACTGTCTCCCATCACCCCCAGATGGGACCGTCTAGTTGCAGGAAAACAAGCTCAGGGCTCCCACTGATTCTACATTATGGTGAGTTGTATAATTATTTCATTATATATTACAATGTAATAATAATAGAAATAAAGTGCACAATAAATGTAATGCGCTTGAATCATCCCGAAACCATCCCCCCCACCCCCGGTCCGTGGAAAAATTGTCTTCCACGAAACCGGTCCCTGGTGCCAAAAAGGTTGGGGACCGCTG
|
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 |
|---|---|---|---|---|---|---|
| Charlie3 | E(spl)mdelta-HLH | 1148 | 1156 | - | 16.15 | CACGTGCCA |
| Charlie3 | Nrf1 | 214 | 225 | + | 16.08 | CTGCGCATGCGA |
| Charlie3 | ZHD3 | 976 | 984 | + | 15.98 | CAATTATTG |
| Charlie3 | ELK1::HOXB13 | 561 | 575 | - | 15.96 | GACGGAAGTGGTAAA |
| Charlie3 | HAT22 | 976 | 984 | - | 15.87 | CAATAATTG |
| Charlie3 | ATHB-53 | 976 | 984 | - | 15.87 | CAATAATTG |
| Charlie3 | ZNF707 | 2633 | 2647 | + | 15.84 | CCCCACCCCCGGTCC |
| Charlie3 | MYB30 | 1369 | 1380 | + | 15.75 | CCAACCAACACC |
| Charlie3 | ZNF610 | 1777 | 1786 | + | 15.73 | GAGCCGCTCC |
| Charlie3 | FOSL2 | 1238 | 1247 | - | 15.69 | GGTGACTCAT |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
