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 | Clamp | 204 | 217 | - | 17.40 | GAGAGAGCGAGGGG |
| MSTA | KLF15 | 22 | 29 | + | 16.27 | CCCCGCCC |
| MSTA | KLF14 | 22 | 30 | - | 16.15 | TGGGCGGGG |
| MSTA | btd | 96 | 104 | + | 15.92 | GGGGGCGGA |
| MSTA | USF1 | 232 | 241 | + | 15.90 | GCCATGTGAC |
| MSTA | KLF12 | 22 | 30 | - | 15.81 | TGGGCGGGG |
| MSTA | KLF7 | 22 | 29 | - | 15.72 | GGGCGGGG |
| MSTA | Trl | 211 | 219 | - | 15.63 | AAGAGAGAG |
| MSTA | KLF1 | 22 | 29 | - | 15.53 | GGGCGGGG |
| MSTA | SP4 | 22 | 30 | - | 15.52 | TGGGCGGGG |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
