MSTD
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0001045 |
|---|---|
| TE superfamily | MaLR |
| TE class | LTR |
| Species | Euarchontoglires |
| Length | 396 |
| Kimura value | 18.61 |
| Tau index | 0.9910 |
| Description | MSTD Long Terminal Repeat for ERVL-MaLR retrotransposon |
| Comment | MSTD has 5 bp TSDs, and it represents an intermediate subfamily between MSTC and MLT1A LTRs. 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 |
TGCTATGGTTTGAATGTGTCCCCCAAAGTTCATGTGTTGGAAACTTAATCCCCAATGCAACAGTGTTGGGAGGTGGGGCCTNNTAAGAGGTGATTAGGTCATGAGGGCTCCGCCCTCATGAATGGATTAATGCCGTTATCGCGGGAGTGGGTTAGTTATCGCGGGAGTGGGTTCGTTATAAAAGNAAGTTCGGCCCCCTTTTGCTCTCTCTCTCTCGCTCTCTTGCCCTTCCGCCTTCCGCCATGGGATGACGCAGCAAGAAGGCCCTCGCCAGATGCCGGCNCCTCGATCTTGGACTTCCCAGCCTCCAGAACCGTGAGCCAAATAAATTTCTGTTCTTTATAAATTACCCAGTCTGTGGTATTCTGTTATAGCAGCACAAAACGGACTAAGACA
|
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 |
|---|---|---|---|---|---|---|
| MSTD | RAMOSA1 | 209 | 222 | - | 18.19 | GAGAGCGAGAGAGA |
| MSTD | BPC1 | 199 | 222 | - | 17.98 | GAGAGCGAGAGAGAGAGAGCAAAA |
| MSTD | RAMOSA1 | 201 | 214 | - | 17.73 | GAGAGAGAGAGCAA |
| MSTD | Clamp | 205 | 218 | - | 17.46 | GCGAGAGAGAGAGA |
| MSTD | BPC1 | 205 | 228 | - | 17.30 | GGGCAAGAGAGCGAGAGAGAGAGA |
| MSTD | Bach1::Mafk | 247 | 258 | + | 16.84 | GATGACGCAGCA |
| MSTD | Clamp | 203 | 216 | - | 16.76 | GAGAGAGAGAGAGC |
| MSTD | Zfp809 | 298 | 306 | + | 15.73 | TTCCCAGCC |
| MSTD | BPC6 | 206 | 226 | + | 15.61 | CTCTCTCTCTCGCTCTCTTGC |
| MSTD | ARALYDRAFT_495258 | 73 | 80 | - | 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.
