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 | ZNF558 | 345 | 373 | - | 1.20 | AACAGGCAAAAAAGTTAAAAAGACAAATG |
| LTR6A | ZSCAN31 | 234 | 251 | + | 0.21 | CCCTAAAGCCCCCGCGTT |
| LTR6A | GLIS1 | 238 | 252 | + | -10.62 | AAAGCCCCCGCGTTT |
| LTR6A | BCL6B | 203 | 219 | + | -12.60 | CAGTTCCCAGGAATTCG |
| LTR6A | EWSR1-FLI1 | 101 | 118 | - | -16.03 | GGAAGGGGGTGGGTAAGG |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
