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 | KLF17 | 1182 | 1195 | + | 16.92 | ACCACGAACCCACC |
| LTR12E | ZNF610 | 274 | 283 | - | 16.89 | CGGCCGCTCC |
| LTR12E | TFAP2A | 414 | 426 | + | 16.82 | TCCCCGCGGGGCA |
| LTR12E | TFAP2C | 414 | 426 | - | 16.79 | TGCCCCGCGGGGA |
| LTR12E | nfya-1 | 960 | 969 | + | 16.78 | GACCAATCAG |
| LTR12E | LOB | 372 | 384 | + | 16.68 | CCGCCGGCGCCGC |
| LTR12E | LOB | 331 | 343 | - | 16.62 | CCTCCGCAGCCGC |
| LTR12E | GSM1 | 1309 | 1318 | + | 16.41 | AAACTCCGGA |
| LTR12E | ERF095 | 403 | 415 | - | 16.41 | GAGGCGGCTGAGG |
| LTR12E | AS2 | 335 | 352 | + | 16.34 | CTGCGGAGGGTGCGCCGG |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
