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 | BPC1 | 201 | 224 | - | 25.76 | AAGAGAGCGAGAGAGAGAGAGCAA |
| MSTD | BPC6 | 196 | 216 | + | 23.14 | CCCTTTTGCTCTCTCTCTCTC |
| MSTD | BPC6 | 204 | 224 | + | 22.50 | CTCTCTCTCTCTCGCTCTCTT |
| MSTD | RAMOSA1 | 205 | 218 | - | 21.91 | GCGAGAGAGAGAGA |
| MSTD | RAMOSA1 | 203 | 216 | - | 21.47 | GAGAGAGAGAGAGC |
| MSTD | RAMOSA1 | 207 | 220 | - | 21.40 | GAGCGAGAGAGAGA |
| MSTD | BPC1 | 203 | 226 | - | 20.50 | GCAAGAGAGCGAGAGAGAGAGAGC |
| MSTD | Clamp | 207 | 220 | - | 19.59 | GAGCGAGAGAGAGA |
| MSTD | BPC6 | 198 | 218 | + | 19.32 | CTTTTGCTCTCTCTCTCTCGC |
| MSTD | Clamp | 211 | 224 | - | 18.53 | AAGAGAGCGAGAGA |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
