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 | GATA1 | 171 | 180 | + | 14.30 | AGATCTGGTT |
| MSTB | Os05g0497200 | 120 | 127 | - | 14.24 | CGGCGCCA |
| MSTB | Os05g0497200 | 312 | 319 | + | 14.24 | CGGCGCCA |
| MSTB | Glyma19g26560.1 | 65 | 72 | - | 14.23 | GGCCCCAC |
| MSTB | GLYMA19G26560 | 65 | 72 | - | 14.23 | GGCCCCAC |
| MSTB | Fer2 | 231 | 240 | + | 14.21 | CCATGTGACG |
| MSTB | Clamp | 208 | 221 | - | 14.21 | GAGCAAGAGAGAGA |
| MSTB | ZNF281 | 197 | 206 | - | 14.08 | GGGGGAGGTG |
| MSTB | LjSGA_053525.1 | 65 | 72 | - | 14.06 | GGCCCCAC |
| MSTB | Zm00001d027846 | 363 | 370 | - | 13.75 | AAAGAAAA |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
