MSTA
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0001041 |
|---|---|
| TE superfamily | MaLR |
| TE class | LTR |
| Species | Haplorrhini |
| Length | 428 |
| Kimura value | 12.64 |
| Tau index | 0.8869 |
| Description | MSTA Long Terminal Repeat for ERVL-MaLR retrotransposon |
| Comment | MSTA has 5 bp TSDs. This represents an intermediate subfamily between THE1C and MSTB. 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 |
TGATATGGTTTGGATCTGTGTCCCCGCCCAAATCTCATGTCGAATTGTAATCCCCAGTGTTGGAGGNGGGGCCTGGTGGGAGGTGATTGGATCATGGGGGCGGATTTCTCATGANCGGTTTAGCACCATCCCCTTGGTGCTGTTCTCGTGATAGTGAGTGAGTTCTCACGAGATCTGGTTGTTTAAAAGTGTGTGGCACCTCCCCCCTCGCTCTCTCTTNCTCCTGCTCCGGCCATGTGACGTGCCTGCTTCCCCTTCGCCTTCCGCCATGATTGTAAGTTTCCTGAGGCCTCCCCAGAAGCCGANNAGATGCCANCGCCATGCTTCCTGTACAGCCTGCGGAACCGTGAGCCAATTAAACCTCTTTTCTTTATAAATTACCCAGTCTCAGGTATTTCTTTATAGCAGTGCGAGAACGGACTAATACA
|
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 |
|---|---|---|---|---|---|---|
| MSTA | IRF2 | 250 | 265 | - | 4.46 | GGAAGGCGAAGGGGAA |
| MSTA | BPC1 | 194 | 217 | - | 0.26 | GAGAGAGCGAGGGGGGAGGTGCCA |
| MSTA | BPC6 | 199 | 219 | + | -0.82 | CCTCCCCCCTCGCTCTCTCTT |
| MSTA | RARA | 80 | 97 | + | -2.03 | GAGGTGATTGGATCATGG |
| MSTA | BPC6 | 197 | 217 | + | -2.05 | CACCTCCCCCCTCGCTCTCTC |
| MSTA | E2F7 | 19 | 32 | + | -4.03 | TGTCCCCGCCCAAA |
| MSTA | THI2 | 368 | 382 | - | -6.44 | GGTAATTTATAAAGA |
| MSTA | EWSR1-FLI1 | 241 | 258 | - | -15.37 | GAAGGGGAAGCAGGCACG |
| MSTA | BPC5 | 189 | 218 | - | -36.94 | AGAGAGAGCGAGGGGGGAGGTGCCACACAC |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
