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 | MGP | 345 | 357 | - | 14.97 | AAAAAGACAAATG |
| LTR6A | TCF7L2 | 153 | 161 | + | 14.93 | ACATCAAAG |
| LTR6A | DOF4.2 | 347 | 357 | - | 14.89 | AAAAAGACAAA |
| LTR6A | ZNF184 | 407 | 419 | - | 14.58 | TAGAAAGGGGAGG |
| LTR6A | CEBPD | 132 | 139 | - | 14.47 | TTGCACAA |
| LTR6A | SP2 | 405 | 413 | - | 14.29 | GGGGAGGGG |
| LTR6A | GATA1::TAL1 | 163 | 179 | - | 14.27 | TTATCAGTTAATTGCAC |
| LTR6A | Klf15 | 99 | 120 | + | 14.24 | CTCCTTACCCACCCCCTTCCTC |
| LTR6A | KLF5 | 404 | 413 | + | 14.20 | CCCCCTCCCC |
| LTR6A | OSR2 | 376 | 383 | - | 14.17 | ACAGAAGC |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
