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
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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 |
|---|---|---|---|---|---|---|
| Charlie3 | Zic2 | 65 | 73 | + | 16.82 | CACAGCAGG |
| Charlie3 | CG12605 | 800 | 808 | - | 16.69 | CACCTGTTG |
| Charlie3 | E(spl)m3-HLH | 1148 | 1156 | - | 16.56 | CACGTGCCA |
| Charlie3 | ZNF610 | 116 | 125 | + | 16.46 | CAGCCGCTCC |
| Charlie3 | ZNF610 | 1465 | 1474 | - | 16.46 | CAGCCGCTCC |
| Charlie3 | ZNF610 | 307 | 316 | - | 16.46 | CAGCCGCTCC |
| Charlie3 | ZKSCAN5 | 72 | 80 | + | 16.46 | GGAGGTGAG |
| Charlie3 | ZIC1 | 65 | 78 | - | 16.40 | CACCTCCTGCTGTG |
| Charlie3 | Jra | 1238 | 1247 | + | 16.30 | ATGAGTCACC |
| Charlie3 | HAT5 | 976 | 984 | - | 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.
