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 | ETV1 | 323 | 331 | - | 13.30 | ACAGGAAGC |
| MSTA | NFYA | 83 | 90 | - | 13.28 | CCAATCAC |
| MSTA | TFAP2C | 282 | 290 | + | 13.25 | TCCTGAGGC |
| MSTA | SP1 | 22 | 30 | - | 13.19 | TGGGCGGGG |
| MSTA | TFAP2A | 282 | 290 | - | 13.19 | GCCTCAGGA |
| MSTA | bowl | 295 | 302 | - | 13.18 | GCTTCTGG |
| MSTA | pho | 230 | 236 | - | 13.17 | ATGGCCG |
| MSTA | Vsx2 | 352 | 360 | - | 13.17 | TTTAATTGG |
| MSTA | sptf-3 | 97 | 103 | - | 13.11 | CCGCCCC |
| MSTA | PIF5 | 233 | 240 | - | 13.10 | TCACATGG |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
