HERV1_LTRe
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000168 |
|---|---|
| TE superfamily | ERV1 |
| TE class | 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
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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 | SREBF2 | 327 | 336 | - | 5.92 | ATCATGTGAC |
| HERV1_LTRe | RAMOSA1 | 201 | 214 | - | 5.63 | GGGGGAGAGATATG |
| HERV1_LTRe | RAMOSA1 | 203 | 216 | - | 5.23 | GCGGGGGAGAGATA |
| HERV1_LTRe | RAX3 | 140 | 151 | - | 3.89 | CGGGGGGGGTGG |
| HERV1_LTRe | IXR1 | 211 | 225 | - | 1.51 | ACAAAATATGCGGGG |
| HERV1_LTRe | BPC1 | 203 | 226 | - | -2.03 | TACAAAATATGCGGGGGAGAGATA |
| HERV1_LTRe | IRF9 | 43 | 57 | + | -2.40 | AATAATAGCGAAAGT |
| HERV1_LTRe | IRF8 | 45 | 57 | + | -2.87 | TAATAGCGAAAGT |
| HERV1_LTRe | BPC5 | 182 | 211 | - | -48.78 | GGAGAGATATGGTTAATGTTTCACAGAGAG |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
