HERV1_LTRe
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000168 |
|---|---|
| TE superfamily | ERV1 |
| TE order | LTR |
| Species | Catarrhini |
| Length | 537 |
| Kimura value | 12.32 |
| Tau index | 0.0000 |
| Description | LTRe (Long Terminal Repeat) of endogenous retrovirus HERV1 |
| Comment | HERV1_LTRe represents a mixture of low copy number subfamilies, probably all <10% diverged. |
| Sequence |
TGAAGTAGGAAATTAGGAAAATAACAGAATAATGGCANAAGTAATAATAGCGAAAGTNATAGTAATAGAAANATAATAATAGTTCATAGAATGAATTGCTGTNTTAACCTAGGCTGAAAAGGCTTTAGGTAGCGCACCCCCACCCCCCCCGAAGTNAGAGTTAAGAAAGAATATTAACTGCCTCTCTGTGAAACATTAACCATATCTCTCCCCCGCATATTTTGTAAGTTCTGTAAGTTCCTGTTTTTCTTGCTGTGCAGCTGCAAGGTCACAAGATAGATAAGCGTAAGCTGCAAGACATGTTTTCCCTAAGATGTAAGACTCATGTCACATGATGATTAACTGCTTTTGTTCTCGCTTCTGTAAGCCTGCTTCCTGCNTCACGTANTTCCCGCCTCAAGATGCNTAAAAGGCGCTTGCCTTCTTTGTTCGGTGCTCAGACTTTCAGGACGCATGTCCGCTGAGCCGGTGTACACCTTAAAATAAANCCCTCCTGNACCCCNATCGGTCTCTCCGGTTCCCTGATTTCCCGCTACA
|
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 |
|---|---|---|---|---|---|---|
| HERV1_LTRe | ERR | 264 | 271 | + | 14.77 | CAAGGTCA |
| HERV1_LTRe | TFDP1 | 389 | 396 | - | 14.70 | GGCGGGAA |
| HERV1_LTRe | SOX12 | 425 | 434 | - | 14.69 | ACCGAACAAA |
| HERV1_LTRe | KLF16 | 137 | 147 | + | 14.67 | CCCCCACCCCC |
| HERV1_LTRe | KLF1 | 138 | 145 | - | 14.64 | GGGTGGGG |
| HERV1_LTRe | Sox14 | 421 | 431 | + | 14.61 | CTTCTTTGTTC |
| HERV1_LTRe | AT2G40260 | 166 | 175 | - | 14.55 | AATATTCTTT |
| HERV1_LTRe | Sox11 | 424 | 431 | - | 14.51 | GAACAAAG |
| HERV1_LTRe | ac | 257 | 264 | + | 14.47 | GCAGCTGC |
| HERV1_LTRe | ac | 257 | 264 | - | 14.47 | GCAGCTGC |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
