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 | ARALYDRAFT_484486 | 177 | 184 | - | 7.07 | GGGCCCAG |
| MER102b | MTF1 | 269 | 282 | + | 5.98 | TCCCCACCCGGCCC |
| MER102b | ZNF157 | 42 | 62 | - | 5.74 | GGCCAAACAAAACACGTCTGC |
| MER102b | phol | 10 | 19 | - | 2.41 | CGCCAGTTTG |
| MER102b | PAX9 | 277 | 292 | + | 1.65 | CGGCCCGCTTCACTCA |
| MER102b | ZSCAN16 | 162 | 179 | - | -14.13 | CAGTGTTGCCAGATCTTC |
| MER102b | DAL81 | 32 | 50 | - | -39.14 | CACGTCTGCGGGCCGGATT |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
