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 | hr3 | 83 | 90 | - | 13.92 | GGTCACAC |
| HERV1_LTRc | l(3)neo38 | 89 | 95 | + | 13.75 | CCCCCCC |
| HERV1_LTRc | l(3)neo38 | 90 | 96 | + | 13.75 | CCCCCCC |
| HERV1_LTRc | PHOX2B | 430 | 441 | - | 13.75 | TTATTAAATTAA |
| HERV1_LTRc | Sox6 | 297 | 306 | + | 13.71 | CCTTTGTTTC |
| HERV1_LTRc | nhr-142 | 227 | 234 | + | 13.62 | GGTCACAA |
| HERV1_LTRc | AT5G56840 | 152 | 165 | + | 13.56 | GACCTTATCTATAC |
| HERV1_LTRc | AT2G38300 | 113 | 122 | - | 13.52 | AATATTCTCT |
| HERV1_LTRc | THI2 | 63 | 77 | - | 13.51 | AGCAACTTTAAGAGG |
| HERV1_LTRc | UGA3 | 325 | 331 | - | 13.34 | GGCGGGA |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
