MSTB
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0001042 |
|---|---|
| TE superfamily | MaLR |
| TE class | LTR |
| Species | Haplorrhini |
| Length | 426 |
| Kimura value | 14.57 |
| Tau index | 0.9951 |
| Description | MSTB Long Terminal Repeat for ERVL-MaLR retrotransposon |
| Comment | MSTB has 5 bp TSDs. This is an intermediate subfamily between MSTA and MSTB1. Note that a full-length ERV-MaLR (Mammalian apparent LTR retrotransposon) element is derived from an ERV (Endogenous Retrovirus), but only contains the Gag gene (that is, no Pol or Env). |
| Sequence |
TGATATGGTTTGGATGTTTGTCCCCTCCAAATCTCATGTTGAAATGTGATCCCCAGTGTTGGAGGTGGGGCCTGGTGGGAGGTGTTTGGGTCATGGGGGCGGATCCCTCATGAATGGCTTGGCGCCGTCCCCNTGGTGATGAGTGAGTTCTCGCTCTGTTAGTTCACGCGAGATCTGGTTGTTTAAAAGAGTNTGGCACCTCCCCCCTCTCTCTCTTGCTCCCGCTCTCGCCATGTGACGCGCCTGCTCCCCCTTCGCCTTCCGCCATGATTGNAAGCTTCCTGAGGCCTCACCAGAAGCCGAGCAGATGCCGGCGCCATGCTTCCTGTACAGCCTGCAGAACCGTGAGCCAANTAAACCTCTTTTCTTTATAAATTACCCAGCCTCAGGTATTCCTTTATAGCAACGCAAGAACGGACTAACACA
|
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 |
|---|---|---|---|---|---|---|
| MSTB | RAMOSA1 | 204 | 217 | - | 18.46 | AAGAGAGAGAGGGG |
| MSTB | RAMOSA1 | 206 | 219 | - | 16.69 | GCAAGAGAGAGAGG |
| MSTB | btd | 95 | 103 | + | 15.92 | GGGGGCGGA |
| MSTB | USF1 | 230 | 239 | + | 15.90 | GCCATGTGAC |
| MSTB | Trl | 209 | 217 | - | 15.63 | AAGAGAGAG |
| MSTB | ZNF274 | 142 | 153 | + | 15.49 | AGTGAGTTCTCG |
| MSTB | ARALYDRAFT_495258 | 65 | 72 | - | 15.43 | GGCCCCAC |
| MSTB | ARALYDRAFT_484486 | 65 | 72 | - | 15.43 | GGCCCCAC |
| MSTB | RAMOSA1 | 208 | 221 | - | 15.11 | GAGCAAGAGAGAGA |
| MSTB | PATZ1 | 61 | 71 | + | 15.04 | GGAGGTGGGGC |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
