MER67C
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000909 |
|---|---|
| TE superfamily | ERV1 |
| TE class | LTR |
| Species | Boreoeutheria |
| Length | 711 |
| Kimura value | 20.40 |
| Tau index | 1.0000 |
| Description | MER67C Long Terminal Repeat for ERV1 endogenous retrovirus |
| Comment | MER67C is an LTR for a MER4-int type ERV with distant similarity to LTR70. It has 4 bp TSDs and is found in humans and rodents. 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 |
TGTAAGGGCAAATACAAATTAAAAATAAGAGGCTTAATTCTCCCTGTTGAAAATAAGGGAAAGAGACTTCCCTCCCTCCCTTTTCTTAGAGCATTTACTTTAGAAAACTTGTAATTGTAAATTCTTTCTCTGTCTCTTTGAAATGTATGTAAATCTTTTTAAAAGCTAAATAAGCCTCTTGCCAGCTTTACGACCCAGGAATGTCTTTCTCAAGGACCTGGGAGCCATCTCTTTGAAATGTAANCATCAAGGAAGATAGCGCCCCTATCTCCCAGTTTCTGTGGGAGGGTAGGAGCCTAACTTCGGTGGGCGCCTTGCTCCAAGTTGCAAAACTACCTCCTGTCATAAAGATATGAGAAGTTTATTTTTCCTTTGGATAAAGCCAATTAGCNAACACAGATGGTCACCCCAATTACCAGGTGAATTTAGGATGAACTATGTGTGACAAATGGTGCTGTCAAGTCCTCTTACTTGAGGACTAGTTATTGTTTATCTTGAGAACATGTATGTAATGGGTTGTATCTGCTTGGCTATATAAAAGGGTGAGATTTCTTTCTGTCTTTGCAATCTCTTAGCGGATTGCCTGTGATGCGCATCACATTCTGGTTTAATGCTTATTCAATAATAAAACTGTTTTCTTTCTCTTCTACCTTTGTGGAGAGGTTTTCTGGGTTGGGAGGAGATTTTGTTTTTAATTATATTTCCCCAACA
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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 |
|---|---|---|---|---|---|---|
| MER67C | BPC1 | 119 | 142 | - | 0.92 | TTCAAAGAGACAGAGAAAGAATTT |
| MER67C | BPC6 | 120 | 140 | + | 0.24 | AATTCTTTCTCTGTCTCTTTG |
| MER67C | BPC6 | 124 | 144 | + | -2.22 | CTTTCTCTGTCTCTTTGAAAT |
| MER67C | EWSR1-FLI1 | 67 | 84 | - | -9.54 | AAAAGGGAGGGAGGGAAG |
| MER67C | EWSR1-FLI1 | 66 | 83 | - | -11.38 | AAAGGGAGGGAGGGAAGT |
| MER67C | ZSCAN16 | 161 | 178 | + | -23.85 | AAAAGCTAAATAAGCCTC |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
