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 | ZNF331 | 105 | 114 | - | 15.09 | GGCAGAGCCC |
| MSTC | THAP1 | 249 | 256 | - | 14.80 | GCAGGGCA |
| MSTC | CRF2 | 255 | 262 | + | 14.74 | GCGCCGCC |
| MSTC | ERF073 | 253 | 263 | + | 14.69 | CTGCGCCGCCT |
| MSTC | ARALYDRAFT_493022 | 74 | 81 | - | 14.64 | GGCCCCAC |
| MSTC | ABR1 | 253 | 264 | - | 14.64 | GAGGCGGCGCAG |
| MSTC | MZF1 | 48 | 55 | + | 14.60 | AATCCCCA |
| MSTC | LEP | 253 | 262 | + | 14.58 | CTGCGCCGCC |
| MSTC | ERF086 | 252 | 261 | + | 14.50 | CCTGCGCCGC |
| MSTC | RAP2-3 | 255 | 262 | + | 14.44 | GCGCCGCC |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
