MER52A
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000856 |
|---|---|
| TE superfamily | ERV1 |
| TE class | LTR |
| Species | Haplorrhini |
| Length | 1755 |
| Kimura value | 12.01 |
| Tau index | 0.9189 |
| Description | MER52A Long Terminal Repeat for ERV1 endogenous retrovirus |
| Comment | MER52A is associated with MER52-int, and has 4 bp TSDs. The originally reported orientation has been reversed. Note that MER stands for MEdium Reiteration frequency interspersed repeat. As such, MERs as a group are a grab bag of DNA transposons and retrotransposons. |
| Sequence |
TGATGGCAGCGGCGGCCCGTCTGGAGCGGCCGCTGCNANGACGCCGGCTGCAGCGGGGGAGGCGCGGCCGGGGCTGCGCGCTCCACGGAGCCGGCGGGAGCCGGGAACAGGCGGGAGCCCCGCCCCCTTCCGAGTTGGGGCGGGAGCNNCCCGGGTGCGGCTGCAGCCGCCCANNCGCGGACCCGGGCNTCCCCGTGCTCNTGGGGNCCGGGAGCAGGCAGGAGCCCCGCCCTCCCGGGCGCAGCTGCAGCCGCCCAGCCGCGGCTGCGGACCCGGGCATCCCTGCGCTCTCGGGGGCCCGGGAAGNCCCCCCTGCCCCCGCAGGCTTGGAAGTGCCTGCTCCCGCCGCGNNCGNCCCCGCCCCGNNNNCGNCGNNCGNNCCGCAGGCTCGGAAGTGCCTGCTCCCGCTGCCTGGCCTCTCCCCGCTCCCGGCGCCCGCTCCGATTTCGGAGCAAAGTTGNGGCCGAGCCCGGGCGCTGTCGCGACCCGGCCGGGTGTGCGCGCGCTCGGGGCGGCGCTGACACGCCAGCCCCCTGCCGCCTCGGCCCCCTCCGGACTTTGGGCGCCGACGAGCACGGGAGGGAGGCCGAGGGGGGGCTGAGGGCGGCTCGGCGCGGGCCTGCAGGCGCCCCTCGGCACGAACAGCCTGGGCGCCATGGACGGCAGCAGGAGGCAGACAGGCTCCTGGGCGGAAAGGGGCGGGTCCCCGGTGAAGCCCCACCTTCAAGCCAGGGACGGCCTGAAGCCTGGGGGCCGGGCTGCCAGTTCCGGGTGGAGTCCGCGGACCGGAGTGAGAACTTATGGTGCTTTTTCCGGGCCCGCCCATGGCCGCCCATGGACCAATCAGCACGCACTTCCTCCCCTCTGAAGCCCATAAAAACCCCGGACTCAGCCAGACTCGGGCAGACGTCGGGACGACCAGCTGCGGAGAGGAGCTACCCACTCCGGGNTCTCCTCTCTGCTGAGAGCTGNANAGNCGTCGGGACGACCTGCCTGCGGAGAGGAGCTACCCACTCCAGGGTCTCCTCTCTGCTGAGAGCTGAACACTCGTCGGGACGACCTGCCTGCGGAAAGGAGCTACCCACTNCGGGTCTCCTGNGAGCTGTTCTGTCGCTCAATAAAGCTCCTCTTCGCCTTGCTCACCCTCCANTTGTCCGCGTACCTCATTCTTCCTGGACGCGGGACAAGAACTCGGGACCCGCCGAATGGCGGGGCTGAAAGAGCTGTAACACAAACAGGGCTGAAACACGCCCCCTGCTCGCCACGTTGCGGGCGACGAGAAGGAGAGAAGAGCTGCGGCCCTTCGGGGAGCCCAGACCTAGGAGCTCCCCGAGCCAGGGCTGTGACACCCTCTTTGGGGCTCTGCGGTTCCTGGCGTCTCCAAGCTTCCGGGCGCCACCGCGTTCCCCGGTGCCCGCNGTGGAAGCCGCTTGCGGTACGCCTGGTCCAGCCGCAGCCTCGCAGGGAGCCGGCGCCCGTGCCGGCGCCTGGAGCTGCCCGCCCCGCCGCAGCCGGCGTGCCTGGCTGTGCGCAGTGGCCGGACCCCGCGCTCGCTCGCTCACACACCCCTCGCCGCTCCGCGCCTGGCTCGCCCTTGGCAGGCGTGGGATCCGGGCCGGTAGCGCGAGCCGAGCGCAGCCTGCCAGGCCGAGTGGGCGGAACGAGCCCAGCGGGCCCGAGCAAAACTCGGGCAAAGGCGCCACCGGCCACAGAGGTTTCCGGCCGGNAAAGCGACACCCCAAGGATCCCGTGACA
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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 |
|---|---|---|---|---|---|---|
| MER52A | SP4 | 118 | 126 | - | 17.54 | GGGGCGGGG |
| MER52A | SP4 | 356 | 364 | - | 17.54 | GGGGCGGGG |
| MER52A | Mad | 1476 | 1490 | - | 17.49 | CAGGCGCCGGCACGG |
| MER52A | Spps | 224 | 234 | + | 17.39 | GCCCCGCCCTC |
| MER52A | BAD1 | 428 | 439 | + | 17.32 | CCCGGCGCCCGC |
| MER52A | ZNF460 | 224 | 239 | + | 17.30 | GCCCCGCCCTCCCGGG |
| MER52A | CG3065 | 117 | 127 | + | 17.29 | GCCCCGCCCCC |
| MER52A | KLF14 | 118 | 126 | - | 17.26 | GGGGCGGGG |
| MER52A | KLF14 | 356 | 364 | - | 17.26 | GGGGCGGGG |
| MER52A | Mad | 59 | 73 | + | 17.26 | GAGGCGCGGCCGGGG |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
