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 | Trl | 204 | 212 | - | 14.81 | GAGAGAGAG |
| MSTD | Trl | 206 | 214 | - | 14.81 | GAGAGAGAG |
| MSTD | Trl | 208 | 216 | - | 14.81 | GAGAGAGAG |
| MSTD | ARALYDRAFT_493022 | 73 | 80 | - | 14.64 | GGCCCCAC |
| MSTD | Mafg | 247 | 258 | + | 14.60 | GATGACGCAGCA |
| MSTD | MZF1 | 47 | 54 | + | 14.60 | AATCCCCA |
| MSTD | Nfe2l2 | 248 | 258 | + | 14.59 | ATGACGCAGCA |
| MSTD | CTCF | 223 | 253 | + | 14.47 | TTGCCCTTCCGCCTTCCGCCATGGGATGACG |
| MSTD | MAFG::NFE2L1 | 248 | 258 | + | 14.34 | ATGACGCAGCA |
| MSTD | ZBTB26 | 306 | 313 | + | 14.32 | CTCCAGAA |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
