MER102b
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000697 |
|---|---|
| TE superfamily | Charlie |
| TE class | DNA |
| Species | Eutheria |
| Length | 341 |
| Kimura value | 28.60 |
| Tau index | 0.9597 |
| Description | hAT-Charlie DNA transposon, MER102b subfamily |
| Comment | Present in Sus scrofa. Originally classified as a putative DNA transposon based on a weak nucleotide identity to MER58B. Final classification as a hAT DNA transposon is based on identification of 15 bp TIRs and 8 bp TSDs with MER1-like NTCTAGAN bias. MER stands for MEdium Reiteration frequency interspersed repeat. As such, MERs as a group are a grab bag of DNA transposons and retrotransposons. |
| Sequence |
CAGAGGTCGCAAACTGGCGGCCCGCGGGCCGAATCCGGCCCGCAGACGTGTTTTGTTTGGCCCGCACAGTGTTTTNAAANATTTTTGAATTAGTTGCCAACATTTAAAAATCGGGAGATTTCACATAAAAATCCGGATTTCCGGCTTCTCTTGAAAAATCAGAAGATCTGGCAACACTGGGCCCGCATTCCCGCATGGCAACAATCGGCTGGAGCTGAGTAGCAGCTGCCCCCTTTAGACGGGGCATGCGCTCTCCAGTTCGCCACAGTCCCCACCCGGCCCGCTTCACTCATTTACGTTACCTGCCTGGCCCCTGTAGGCATTTGAGTTTGCGACCCCTG
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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 |
|---|---|---|---|---|---|---|
| MER102b | Ascl2 | 221 | 230 | + | 16.23 | AGCAGCTGCC |
| MER102b | KLF4 | 270 | 277 | + | 15.48 | CCCCACCC |
| MER102b | Ascl2 | 221 | 230 | - | 15.29 | GGCAGCTGCT |
| MER102b | sc | 221 | 230 | + | 15.25 | AGCAGCTGCC |
| MER102b | NHLH1 | 221 | 229 | + | 15.19 | AGCAGCTGC |
| MER102b | sc | 221 | 230 | - | 15.10 | GGCAGCTGCT |
| MER102b | NHLH2 | 218 | 233 | + | 15.02 | AGTAGCAGCTGCCCCC |
| MER102b | KLF1 | 270 | 277 | - | 14.64 | GGGTGGGG |
| MER102b | ZNF692 | 177 | 184 | - | 14.58 | GGGCCCAG |
| MER102b | ac | 222 | 229 | + | 14.47 | GCAGCTGC |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
