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 | ZNF281 | 197 | 206 | - | 14.08 | GGGGGAGGTG |
| MSTA | PRDM9 | 246 | 265 | - | 14.06 | GGAAGGCGAAGGGGAAGCAG |
| MSTA | SP2 | 22 | 30 | - | 14.02 | TGGGCGGGG |
| MSTA | ZNF274 | 157 | 168 | + | 13.96 | AGTGAGTTCTCA |
| MSTA | Zm00001d027846 | 365 | 372 | - | 13.75 | AAAGAAAA |
| MSTA | KLF2 | 22 | 29 | + | 13.55 | CCCCGCCC |
| MSTA | YY2 | 264 | 270 | - | 13.54 | ATGGCGG |
| MSTA | RAMOSA1 | 204 | 217 | - | 13.44 | GAGAGAGCGAGGGG |
| MSTA | Sp1 | 96 | 104 | - | 13.41 | TCCGCCCCC |
| MSTA | LEU3 | 223 | 232 | + | 13.35 | CCTGCTCCGG |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
