ORF4Open Reading Frames 4
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Using specific primers pairs (Table 1), we performed an extensive expression analysis of PPARG1, PPARG2, PPARG3, PPARG4, and ORF4 in tissues and cells related to complications of metabolic syndrome--such as altered glucose and lipids' metabolism (liver), increased inflammatory response (macrophages), atherosclerosis (EPCs, heart, and macrophages), cancer (colon carcinoma and MCF7), and thyroid dysfunction (thyroid)--and in a widely used cell model, HEK293 [3, 6, 17, 39, 40].
Of note, the results shown in Figure 2 refer to ORF4 transcripts' total expression.
Given the existence of two different isoforms of [gamma]ORF4, previously described as dominant negative of PPAR[gamma] [28], we asked whether other ORF4 variants may be transcribed from the promoter upstream the AL1 exon of PPARG gene.
Given the discovery of such new transcript in hMSCs, we decided to investigate the expression of the entire pool of ORF4 variants (ORF4t in Figure 4(b)) during in vitro adipogenesis.
To quantitatively study ORF4 transcripts, the only way to discriminate among the different variants is through the analysis of large PCR amplicons (about 900-1000 bp, Figure 4(b)), unfeasible with qRT-PCR.
The primers were designed using a primer-designing tool (NCBI 2013) to amplify smaller products of the ORF4 gene in the OsHV-1 virus and variants to increase detection performance in tissues that had been stored in a variety of ways and over varying periods of time.
Zhou, "Identification and functional analysis of the novel ORF4 protein encoded by porcine circovirus type 2," Journal of Virology, vol.
The genome of PRRSV is 15 kb in length and contains nine open reading frames (ORFs) designated ORF1a, ORF1b, ORF2a, ORF2b,ORF3, ORF4, ORF5, ORF6, and ORF7 [21-23].
These latter ORFs are not conserved among cycloviruses and show low partial homology to bacterial enzymes, NAD-dependent DNA ligase of Psychrobacter (ORF3), transketolase of Sinorhizobium (ORF4), and dTDP-D-glucose 4,6-dehydratase of Actinomyces (ORF5).
Unlike R63 and R68, only 1 additional putative ORF, corresponding to ORF4 (nt residues 27-578), was found in V-105, suggesting that other putative ORFs, ORF5 and ORF6 found in R63 and R68, are not common in rat HEV.
The FRHEV genome organization was found to be slightly different from other HEVs and included a putative ORF (ORF4) of 552 nt that overlapped with ORF1 (online Technical Appendix Figure).