LTR18B
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000429 |
|---|---|
| TE superfamily | ERV3 |
| TE class | LTR |
| Species | Primates |
| Length | 614 |
| Kimura value | 10.99 |
| Tau index | 0.9287 |
| Description | LTR18B (Long Terminal Repeat) for HERV18 endogenous retrovirus |
| Comment | LTR of HERVL endogenous retrovirus HERV18. 5 bp target site duplications. Not observed in other mammals. |
| Sequence |
TGTAAGGTACATGGATGTGCTTTGGTCAAGGAATAGGCCGAGGCGGACATCCAGGCCTGCGTGACTCAGCGAGTTTGGNGCGCAGGCGCATANCTCCACTTGTTATATAACCTGTTTGTGTAAGNTCATACTTGGCTCTGAGCCACTATTGTCTGTAAAAGGTATAACTGCCCTGCTGACGCTGTACAGGGGCTCTTGGGGCTCGGCTCGGCTCAACATGGCTTGACATGGCGGGCGCGCTGGCGCCCAGAGAAAGAGAGAGAGAGCCAGAGCTGTCCGTCTTGCAGACGGACAGGGGGGAGCCAGGACACAGCTCGGCTCGCTCGTGCCCAGAGAGAGAAAGAGTTAAGCTGCTGACCCTGAAGGCAAGGGAGAGCCGGCCGCGCAGCTGTGCGTGGGGGCGGCAGGAGCCGCAGAGCCGGANCAAGCAGCCGAGACAGAGGCGGACAGTGTGAGAGAGCTGCTGAAGTGTGAGAAGCTGCTGATGAGAGAGCTGCTGAATAAAACCATATTTCACCTGCCTACGGCCCCCCGAGTGTTCTTTCAGCTATCTGCCCATCCACCCACTCCCCTCGGACCTCAGCATGGGCTGGAACCTGACCCCGGGCCTGACA
|
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 |
|---|---|---|---|---|---|---|
| LTR18B | ss | 58 | 65 | + | 15.56 | TGCGTGAC |
| LTR18B | ZNF652 | 341 | 349 | + | 15.51 | AAGAGTTAA |
| LTR18B | Wt1 | 395 | 404 | - | 15.11 | CCGCCCCCAC |
| LTR18B | blmp-1 | 252 | 262 | + | 15.04 | GAAAGAGAGAG |
| LTR18B | eor-1 | 253 | 265 | + | 15.00 | AAAGAGAGAGAGA |
| LTR18B | MAFG::NFE2L1 | 61 | 71 | + | 14.89 | GTGACTCAGCG |
| LTR18B | NFIB | 131 | 147 | - | 14.82 | AGTGGCTCAGAGCCAAG |
| LTR18B | Trl | 256 | 264 | + | 14.81 | GAGAGAGAG |
| LTR18B | Trl | 258 | 266 | + | 14.81 | GAGAGAGAG |
| LTR18B | THAP1 | 169 | 176 | - | 14.80 | GCAGGGCA |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
