MSTC
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0001044 |
|---|---|
| TE superfamily | MaLR |
| TE order | LTR |
| Species | Primates |
| Length | 428 |
| Kimura value | 14.57 |
| Tau index | 0.9296 |
| Description | MSTC Long Terminal Repeat for ERVL-MaLR retrotransposon |
| Comment | MSTC has 5 bp TSDs. It represents an intermediate subfamily between MSTB1 and MSTD. 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 |
TGCTATGGTTTGAATGTTTGTCCCCTCCAAAACTCATGTTGAAACTTAATCCCCAATGTGGCAGTATTGAGAGGTGGGGCCTTTAAGAGGTGATTGGGTCATGAGGGCTCTGCCCTCATGAATGGATTAATCCATTCATGGATTAATGGATTAATGGATTAATGGGTTATCATGGGAGTGGGACTGGTGGCTTTATAAGAAGAGGAAGAGAGACCTGAGCTAGCACGCTCAGCCCCCTCGCCATGTGATGCCCTGCGCCGCCTCGGGACTCTGCAGAGAGTCCCCACCAGCAAGAAGGCCCTCACCAGATGCGGCCCCTCGACCTTGGACTTCTCAGCCTCCANAACTGTAAGAAATAAATTCCTTTTCTTTATAAATTACCCAGTTTCAGGTATTCTGTTATAAGCAACAGAAAACGGACTAAGACA
|
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 |
|---|---|---|---|---|---|---|
| MSTC | BPC6 | 194 | 214 | - | -2.64 | GTCTCTCTTCCTCTTCTTATA |
| MSTC | Rarb | 94 | 109 | + | -2.97 | TTGGGTCATGAGGGCT |
| MSTC | Rarb | 312 | 327 | - | -3.22 | CAAGGTCGAGGGGCCG |
| MSTC | Rarg | 312 | 326 | - | -3.79 | AAGGTCGAGGGGCCG |
| MSTC | TRP1 | 36 | 56 | + | -4.04 | ATGTTGAAACTTAATCCCCAA |
| MSTC | E2F7 | 19 | 32 | + | -4.33 | TGTCCCCTCCAAAA |
| MSTC | THI2 | 368 | 382 | - | -6.44 | GGTAATTTATAAAGA |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
