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 | REST | 316 | 335 | + | 20.33 | TTAGCACCCGGGCCAGCGGC |
| LTR12E | HAP5 | 912 | 925 | - | 18.78 | GGGCGCTGATTGGT |
| LTR12E | HAP5 | 743 | 756 | - | 17.96 | GGGTGCTGATTGGT |
| LTR12E | TFAP2A | 414 | 426 | - | 17.33 | TGCCCCGCGGGGA |
| LTR12E | ZNF460 | 452 | 467 | + | 17.25 | GCCTGAGCCTCCCACC |
| LTR12E | TFAP2C | 414 | 426 | + | 17.10 | TCCCCGCGGGGCA |
| LTR12E | dar1 | 976 | 986 | - | 17.08 | GCCCCACCCAC |
| LTR12E | KLF9 | 976 | 986 | - | 17.03 | GCCCCACCCAC |
| LTR12E | Clamp | 33 | 46 | - | 17.02 | GAGCGAGCGAGGGC |
| LTR12E | Mad | 370 | 384 | - | 16.95 | GCGGCGCCGGCGGGC |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
