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. 2016 Mar 28;90(8):4093–4104. doi: 10.1128/JVI.02947-15

TABLE 1.

RT-PCR assays to detect unspliced and spliced SIV RNA

Target RNA Sequence (5′–3′)
 Amplicon size (bp) Splice junctiona
Forward primer Reverse primer Probe
SIV gag RNA GGGAGATGGGCGTGAGAAA CGTTGGGTCGTAGCCTAATTTT TCATCTGCTTTCTTCCCTGACAAGACGGA 78 None
SIV tat mRNA GGTCGGTACCAGACGGCGT GTTGGCAGTGCCGGGTCCTGTTG CTGCAACCGGAGGCCTCTTCCTCTCCC 386 SD1/SA4^SD3/SA8
SIV rev mRNA GGTCGGTACCAGACGGCGT GTTGGCAGTGCCGGGTCCTGTTG CTGCAACCGGAGGCCTCTTCCTCTCCC 171 SD1/SA6^SD3/SA7
SIV rev mRNA GGTCGGTACCAGACGGCGT GTTGGCAGTGCCGGGTCCTGTTG CTGCAACCGGAGGCCTCTTCCTCTCCC 174 SD1/SA6^SD3/SA8
SIV rev mRNA GGTCGGTACCAGACGGCGT GTTGGCAGTGCCGGGTCCTGTTG CTGCAACCGGAGGCCTCTTCCTCTCCC 293 SD1/SA5^SD3/SA7
SIV rev mRNA GGTCGGTACCAGACGGCGT GTTGGCAGTGCCGGGTCCTGTTG CTGCAACCGGAGGCCTCTTCCTCTCCC 296 SD1/SA5^SD3/SA8
SIV nef mRNA GGTCGGTACCAGACGGCGT GTTGGCAGTGCCGGGTCCTGTTG CTGCAACCGGAGGCCTCTTCCTCTCCC 85 SD1/SA7
SIV nef mRNA GGTCGGTACCAGACGGCGT GTTGGCAGTGCCGGGTCCTGTTG CTGCAACCGGAGGCCTCTTCCTCTCCC 88 SD1/SA8
SIV vif mRNA GGTCGGTACCAGACGGCGT CTTTAAGATGACTGCTCCTTCCC CTGCAACCGGAGGCCTCTTCCTCTCCC 126 SD1/SA1
a

mRNA splice junctions (21, 22) spanned by an amplicon.