LTR12E
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000404 |
|---|---|
| TE superfamily | ERV1 |
| TE class | LTR |
| Species | Hominoidea |
| Length | 1322 |
| Kimura value | 6.49 |
| Tau index | 0.9390 |
| Description | LTR12E (Long Terminal Repeat) for HERV9-like endogenous retrovirus |
| Comment | Another subfamily obtained primarily by variation of the R66-like minisatellite. |
| Sequence |
TGAGAGGTGACAGCGTGCTGGCAGCCCTCGCAGCCCTCGCTCGCTCTCGGCGCCTCCTCGGCCTCGGCGCCCACTCTGGCCGCGCTTGAGGAGCCCTTCAGCCCGCCGCTGCACTGTGGGAGCCCCTCTCTGGGCTGGCCGAGGCCGGAGCCGGCTCCCTCNGCTTGCGGGGAGGTGTGGAGGGAGAGGCGCGGGCGGGAACCGGGGCTGCGCGCGGCGCTCGCGGGCCAGCGCGAGTTCCGGGTGGGCGCGGGCTCGGCGGGCCCCGCACTCGGAGCGGCCGGCCGGCCCCGCCGGCCCCGGGCAGTGAGGGGCTTAGCACCCGGGCCAGCGGCTGCGGAGGGTGCGCCGGGTCCCCCAGCAGTGCCGGCCCGCCGGCGCCGCGCTCGANTTCTCGCCGGGCCTCAGCCGCCTCCCCGCGGGGCAGGGCTCGGGACCTGCAGCCCGCCATGCCTGAGCCTCCCACCCNCTCCGTGGGCTCCTGCGCGGCCCGAGCCTCCCCGACGAGCGCCGCCCCCTGCTCCGCGGCGCCCGGTCCCATCGACCGCCCAAGGGCTGAGGAGTGCGGGCGCACGGCGCGGGACTGGCGGGCAGCTCCACCCGCGGCCCCGGTGCGGGATCCACTGGGTGAAGCCAGCTGGGCTCCTGAGTCTGGTGGGGACTTGGAGAACCTTTATGTCTAGCTAAGGGATTGTAAATACACCAATCGGCACTCTGTGTCTAGCTCAAGGTTTGTAAACGCACCAATCAGCACCCTGTGTCTAGCTCAGGGTTTGTGAATGCACCAATCGGCGCTCTGTATCTAGCTAATCTGGTGGGGACTTGGAGAACCTTTGTGTCNANGNNCTGTANCGNACCAATCNGNCGGGGNCGCGNAGNACCTCTGTGTCTAGCTCAGGGATTGTAAACGCACCAATCAGCGCCCTGTCAAAACGGACCAATCGGCTCTCTGTAAAATGGACCAATCAGCAGGATGTGGGTGGGGCCAGATAAGAGAATAAAAGCAGGCTGCCCGAGCCAGCAGCGGCAACCCGCTCGGGTCCCCTTCCACGCTGTGGAAGCTTTGTTCTTTCGCTCTTTGCAATAAATCTTGCTGCTGCTCACTCTTTGGGTCCGCGCTGCCTTTATGAGCTGTAACACTCACCGCGAAGGTCTGCAGCTTCACTCCTGAAGCCAGCGAGACCACGAACCCACCGGGAGGAACGAACAACTCCGGACGCGCCGCCTTTAAGAGCTGTAACACTCACCGCGAGGGTCCGCGGCTTCATTCTTGAAGTCCAGCGAGACCAAGAACCCACCAGAAGGAAGAAACTCCGGACACA
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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 |
|---|---|---|---|---|---|---|
| LTR12E | ZNF93 | 327 | 340 | + | 15.83 | GCCAGCGGCTGCGG |
| LTR12E | opa | 411 | 422 | + | 15.81 | GCCTCCCCGCGG |
| LTR12E | CTCFL | 513 | 520 | - | 15.72 | CAGGGGGC |
| LTR12E | ERF5 | 329 | 343 | - | 15.70 | CCTCCGCAGCCGCTG |
| LTR12E | ERF109 | 1219 | 1226 | + | 15.56 | GCGCCGCC |
| LTR12E | ERF109 | 508 | 515 | + | 15.56 | GCGCCGCC |
| LTR12E | KLF4 | 978 | 985 | - | 15.48 | CCCCACCC |
| LTR12E | BAD1 | 293 | 304 | - | 15.45 | CCCGGGGCCGGC |
| LTR12E | ARALYDRAFT_495258 | 980 | 987 | - | 15.43 | GGCCCCAC |
| LTR12E | ARALYDRAFT_484486 | 980 | 987 | - | 15.43 | GGCCCCAC |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
