MSTB
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0001042 |
|---|---|
| TE superfamily | MaLR |
| TE order | 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 | FEZF2 | 379 | 386 | + | 15.03 | CCCAGCCT |
| MSTB | Clamp | 218 | 231 | - | 15.02 | GCGAGAGCGGGAGC |
| MSTB | Trl | 207 | 215 | - | 14.81 | GAGAGAGAG |
| MSTB | Bteb2 | 93 | 105 | - | 14.79 | GATCCGCCCCCAT |
| MSTB | BPC1 | 206 | 229 | - | 14.71 | GAGAGCGGGAGCAAGAGAGAGAGG |
| MSTB | ZNF454 | 335 | 351 | - | 14.68 | GGCTCACGGTTCTGCAG |
| MSTB | ARALYDRAFT_493022 | 65 | 72 | - | 14.64 | GGCCCCAC |
| MSTB | ZNF417 | 120 | 126 | - | 14.55 | GGCGCCA |
| MSTB | ZNF417 | 313 | 319 | + | 14.55 | GGCGCCA |
| MSTB | ZBTB33 | 164 | 173 | - | 14.30 | TCTCGCGTGA |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
