HERV1_LTRc
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000166 |
|---|---|
| TE superfamily | ERV1 |
| TE order | LTR |
| Species | Catarrhini |
| Length | 491 |
| Kimura value | 4.44 |
| Tau index | 0.9897 |
| Description | LTRc (Long Terminal Repeat) of endogenous retrovirus HERV1 |
| Comment | - |
| Sequence |
TGAAGAAGGAATTAATGAAATCAACTATAACCTAATAGTAGTAGTAATAGAAATTTTAAAATCCTCTTAAAGTTGCTGCAAAGTGTGACCCCCCCCTTACACTCAAGTTAAAAGAGAATATTAACAGCCTGTCTTCTCTCTGTGGACAGTGGACCTTATCTATACTCCCCAACTCCACATTCCTCAAAGTTTATTACAGGCCCAGCGAGTTCCTGCACGGCTGCAGGGTCACAAGACCGATAAGTTTAGGTTGCAAGACATGTTTCTCTCAAGATGTAAGAAATGTTGTAATGCTGCCTTTGTTTCTTGCTTCTGTAACTCGCTTCCCGCCTCACGTAGTTCCCGCCTTAAGATGTTTAAAAGTAGGAAAAGCCCTTTGTTCGGGGCTCAGACTTTCTGGACATATGTCCGGCTGAGCCGGTGATCACCTTAATTTAATAAACTCTCCTGAACCTTTTTCGGTCTCTCCAGTCTTTGATTGTCCCGCAACA
|
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_LTRc | NEUROG2 | 400 | 409 | + | 16.45 | GACATATGTC |
| HERV1_LTRc | NEUROG2 | 400 | 409 | - | 16.45 | GACATATGTC |
| HERV1_LTRc | Sox14 | 372 | 382 | + | 15.89 | GCCCTTTGTTC |
| HERV1_LTRc | NEUROG1 | 400 | 409 | + | 15.87 | GACATATGTC |
| HERV1_LTRc | NEUROG1 | 400 | 409 | - | 15.87 | GACATATGTC |
| HERV1_LTRc | E2F6 | 324 | 331 | - | 15.29 | GGCGGGAA |
| HERV1_LTRc | E2F6 | 340 | 347 | - | 15.29 | GGCGGGAA |
| HERV1_LTRc | SOL1 | 47 | 61 | + | 15.04 | ATAGAAATTTTAAAA |
| HERV1_LTRc | SRM1 | 153 | 161 | - | 15.02 | AGATAAGGT |
| HERV1_LTRc | KAN2 | 113 | 122 | - | 14.94 | AATATTCTCT |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
