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 | BPC5 | 241 | 270 | + | -40.35 | TGGCGCCCAGAGAAAGAGAGAGAGAGCCAG |
| LTR18B | BPC5 | 427 | 456 | + | -43.70 | AGCAGCCGAGACAGAGGCGGACAGTGTGAG |
| LTR18B | BPC5 | 429 | 458 | + | -44.06 | CAGCCGAGACAGAGGCGGACAGTGTGAGAG |
| LTR18B | BPC5 | 239 | 268 | + | -45.40 | GCTGGCGCCCAGAGAAAGAGAGAGAGAGCC |
| LTR18B | BPC5 | 439 | 468 | + | -46.20 | AGAGGCGGACAGTGTGAGAGAGCTGCTGAA |
| LTR18B | BPC5 | 435 | 464 | + | -46.46 | AGACAGAGGCGGACAGTGTGAGAGAGCTGC |
| LTR18B | BPC5 | 237 | 266 | + | -47.41 | GCGCTGGCGCCCAGAGAAAGAGAGAGAGAG |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
