HERV1_LTRb
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000165 |
|---|---|
| TE superfamily | ERV1 |
| TE class | LTR |
| Species | Catarrhini |
| Length | 511 |
| Kimura value | 5.98 |
| Tau index | 0.0000 |
| Description | LTRb (Long Terminal Repeat) of endogenous retrovirus HERV1 |
| Comment | - |
| Sequence |
TGAAGGGGGAATTAATGAATTTTATAAGTATAATAGTCGAGAAATTTATTCTTTTCCTTGAAGGTAGAATGTAATATAGCCCCCCAACCCGGAGGCCTGGGTTAAGAGAGAATATTAACTGCTTATTTCTCCTCTATGCNCAGAGAGGCTTATCTGTGTTCCATCGTTTCACATTCCTTGAGGCACGGCGAGTTCTTGCTTCCCTCCCTAGCGCGGCTGTAAAGTCACAAGGTTGATAAGCAANTGCTACAAAAGCATGTATTCCCAAGGATGTAAGACATGTGGTGTAACAAATGTAAAAGAGTAATTAACTGCCTTTGTTCTCGCTTCCGCAAGTACGCTTCCTGCAGCACGTAACTCCCGCCACAAACTGCTTAAAAGGTGATTGATCCCTTTGTTCGGGGCTCAGACTTTCTGGACCCTAGTCCGACTGAGCCGGTGATCACCTTAATAATAAAGGGCTCTCCTGAACTCTGCTCGGTCTCTCCCGTCTCTGATTTGTCCCGCAACA
|
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_LTRb | E2F6 | 358 | 365 | - | 13.22 | GGCGGGAG |
| HERV1_LTRb | Sox7 | 315 | 324 | - | 13.18 | AGAACAAAGG |
| HERV1_LTRb | SOX4 | 315 | 322 | - | 13.17 | AACAAAGG |
| HERV1_LTRb | SOX4 | 392 | 399 | - | 13.17 | AACAAAGG |
| HERV1_LTRb | Sox17 | 315 | 324 | - | 13.15 | AGAACAAAGG |
| HERV1_LTRb | RELB | 6 | 12 | - | 13.14 | ATTCCCC |
| HERV1_LTRb | JUB1 | 185 | 191 | + | 13.11 | ACGGCGA |
| HERV1_LTRb | Erg | 339 | 348 | - | 13.11 | GCAGGAAGCG |
| HERV1_LTRb | pal-1 | 304 | 311 | + | 13.09 | GTAATTAA |
| HERV1_LTRb | RDR1 | 328 | 334 | - | 13.06 | TGCGGAA |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
