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 | KLF7 | 270 | 277 | - | 13.19 | GGGTGGGG |
| MER102b | GCM1 | 179 | 188 | - | 13.17 | ATGCGGGCCC |
| MER102b | FERD3L | 219 | 232 | - | 13.06 | GGGGCAGCTGCTAC |
| MER102b | ASCL1 | 222 | 230 | + | 12.99 | GCAGCTGCC |
| MER102b | Hmga1 | 104 | 111 | - | 12.99 | ATTTTTAA |
| MER102b | ETS1 | 137 | 145 | - | 12.89 | GCCGGAAAT |
| MER102b | Plagl1 | 308 | 315 | - | 12.85 | AGGGGCCA |
| MER102b | GRF4 | 222 | 229 | + | 12.83 | GCAGCTGC |
| MER102b | GRF4 | 222 | 229 | - | 12.83 | GCAGCTGC |
| MER102b | NAC043 | 294 | 301 | - | 12.80 | TAACGTAA |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
