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 | ERF087 | 253 | 262 | - | 14.44 | GGCGGCGCAG |
| MSTC | Glyma19g26560.1 | 74 | 81 | - | 14.23 | GGCCCCAC |
| MSTC | GLYMA19G26560 | 74 | 81 | - | 14.23 | GGCCCCAC |
| MSTC | LjSGA_053525.1 | 74 | 81 | - | 14.06 | GGCCCCAC |
| MSTC | eor-1 | 201 | 213 | + | 14.03 | AGAGGAAGAGAGA |
| MSTC | ERF5 | 252 | 266 | + | 14.03 | CCTGCGCCGCCTCGG |
| MSTC | ERF105 | 255 | 264 | - | 13.97 | GAGGCGGCGC |
| MSTC | Zm00001d027846 | 365 | 372 | - | 13.75 | AAAGAAAA |
| MSTC | ERF15 | 256 | 263 | + | 13.65 | CGCCGCCT |
| MSTC | ERF094 | 256 | 262 | + | 13.64 | CGCCGCC |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
