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 | DOF1.5 | 355 | 370 | - | 14.15 | AGGCAAAAAAGTTAAA |
| LTR6A | ZNF85 | 384 | 395 | + | 14.12 | AAGATTGCTTCA |
| LTR6A | GTL1 | 18 | 25 | - | 14.09 | GGTTAAAA |
| LTR6A | DOF1.7 | 355 | 365 | - | 14.08 | AAAAAGTTAAA |
| LTR6A | pqm-1 | 172 | 179 | + | 13.89 | ACTGATAA |
| LTR6A | DOF4.7 | 357 | 365 | + | 13.89 | TAACTTTTT |
| LTR6A | KLF14 | 405 | 413 | - | 13.88 | GGGGAGGGG |
| LTR6A | Zm00001d027846 | 432 | 439 | + | 13.75 | AAAGAAAA |
| LTR6A | Stat4 | 334 | 343 | - | 13.74 | TTACAGGAAA |
| LTR6A | RAP2-11 | 489 | 499 | + | 13.67 | CGGTCGCCGGC |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
