LTR6A
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000569 |
|---|---|
| TE superfamily | ERV1 |
| TE class | LTR |
| Species | Catarrhini |
| Length | 564 |
| Kimura value | 14.78 |
| Tau index | 0.9907 |
| Description | LTR6A (Long Terminal Repeat) for HERVS71 endogenous retrovirus |
| Comment | Some copies present at orthologous site in old world monkeys, others specific to apes. |
| Sequence |
TGTGATACCCTACCTTGTTTTAACCTGAATNGACTCTCCCTTAGCTGAGAGAGCCGGACGGACTCCATTTGGCTCCTTCACTTGCAAGACATCAAGGGCTCCTTACCCACCCCCTTCCTCAAGGACTTAACTTGTGCAAGCTGACTCCCAGCACATCAAAGAGTGCAATTAACTGATAAGGTACTGNGGCAAGCTATGTCCGCAGTTCCCAGGAATTCGCCCGGNTGATAGTACCCTAAAGCCCCCGCGTTTGTGTCCGGTNGATAGCACCCAAAGCCCCCGCACCTATCACCTTGTGATGGATTTAAAGCCCCTGCACCTGGAACTGTTTGTTTTCCTGTAACCATTTGTCTTTTTAACTTTTTTGCCTGTTTTGCTTCTGTAAGATTGCTTCAGCTAGGCTCCCCCTCCCCTTTCTAAACCAAAGTATAAAAGAAAATCTAGCCCCTTCTTCGGGGCCGAGAGAATTTTGAGCGCTAGCCGTCTCTCGGTCGCCGGCTAATAAAGGACTCCTGAATTCGTCTCAAAGTGTGGCGTTTCTCTATAACTCGCTCGGTTACAACA
|
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 |
|---|---|---|---|---|---|---|
| LTR6A | MAZ | 405 | 412 | + | 16.08 | CCCCTCCC |
| LTR6A | SP1 | 405 | 413 | - | 16.06 | GGGGAGGGG |
| LTR6A | IDD1 | 346 | 357 | + | 16.03 | ATTTGTCTTTTT |
| LTR6A | SP4 | 405 | 413 | - | 15.85 | GGGGAGGGG |
| LTR6A | NUC | 346 | 357 | + | 15.82 | ATTTGTCTTTTT |
| LTR6A | SGR5 | 346 | 358 | - | 15.59 | TAAAAAGACAAAT |
| LTR6A | Six3 | 3 | 13 | - | 15.38 | GTAGGGTATCA |
| LTR6A | EcR::usp | 161 | 175 | - | 15.32 | CAGTTAATTGCACTC |
| LTR6A | egl-27 | 171 | 181 | - | 15.11 | CCTTATCAGTT |
| LTR6A | Stat6 | 206 | 215 | - | 15.09 | TTCCTGGGAA |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
