MSTC
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0001044 |
|---|---|
| TE superfamily | MaLR |
| TE class | 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 | ERF095 | 252 | 264 | - | 17.08 | GAGGCGGCGCAGG |
| MSTC | ERF091 | 252 | 264 | - | 17.03 | GAGGCGGCGCAGG |
| MSTC | ZIM3 | 407 | 417 | + | 16.97 | CAACAGAAAAC |
| MSTC | Spi1 | 199 | 211 | + | 16.76 | GAAGAGGAAGAGA |
| MSTC | NR6A1 | 320 | 333 | - | 16.34 | GAAGTCCAAGGTCG |
| MSTC | ERF2 | 252 | 264 | + | 16.32 | CCTGCGCCGCCTC |
| MSTC | SPIB | 199 | 211 | - | 15.79 | TCTCTTCCTCTTC |
| MSTC | ERF109 | 255 | 262 | + | 15.56 | GCGCCGCC |
| MSTC | ARALYDRAFT_495258 | 74 | 81 | - | 15.43 | GGCCCCAC |
| MSTC | ARALYDRAFT_484486 | 74 | 81 | - | 15.43 | GGCCCCAC |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
