MSTD
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0001045 |
|---|---|
| TE superfamily | MaLR |
| TE order | 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 | ARALYDRAFT_484486 | 73 | 80 | - | 15.43 | GGCCCCAC |
| MSTD | Spps | 107 | 117 | + | 15.38 | GCTCCGCCCTC |
| MSTD | eor-1 | 211 | 223 | - | 15.35 | AGAGAGCGAGAGA |
| MSTD | ARF36 | 13 | 24 | - | 15.35 | GGGGGACACATT |
| MSTD | eor-1 | 205 | 217 | - | 15.24 | CGAGAGAGAGAGA |
| MSTD | ZNF454 | 306 | 322 | - | 15.22 | GGCTCACGGTTCTGGAG |
| MSTD | RAMOSA1 | 211 | 224 | - | 15.11 | AAGAGAGCGAGAGA |
| MSTD | PATZ1 | 69 | 79 | + | 15.04 | GGAGGTGGGGC |
| MSTD | FEZF2 | 300 | 307 | + | 15.03 | CCCAGCCT |
| MSTD | ARF39 | 14 | 24 | - | 14.85 | GGGGGACACAT |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
