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. 2001 Jan;75(2):891–902. doi: 10.1128/JVI.75.2.891-902.2001

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Copyright © 2001, American Society for Microbiology

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FIG. 5 — (A) Alignment of DNA binding domains of the human IRFs IRF-4 (GI:2497445) and ICSB-1 (GI:4504567) with those of vIRF-1 (GI:1718311), vIRF-2 (GI:3152729), K10.1, and a novel putative ORF, K10.7. The amino acid sequences for K10.1 and K10.7 were translated from the genomic sequence of KSHV (U75698). The sequence shown for each protein is bounded by the amino acid positions shown on either side. The alignment was performed with ClustalW (46). (B) RT-PCR products showing transcripts encoding vIRF-1 and the putative ORFs K10/10.1, K10.5/10.7, and K11/vIRF-2. The primers used are complementary to either end of the putative long ORFs (see Materials and Methods). RNA was extracted from BC-3 cells 24 h after the addition of TPA. RT-negative controls and positive controls from KSHV genomic DNA are included for each RT-PCR. The RT-PCR product sizes are predicted to be 1,350 (K9), 2,736 (K10/10.1), 1,701 (K10.5/10.7), and 2,043 (K11/vIRF-2) bp. (C) Positions (relative to genomic sequence U75698) and organization of the IRF-related genes of KSHV. The location of the novel putative ORF K10.7 is shown. Secondary lytic genes are shaded in black. The region of each ORF whose translated sequence is shown in panel A is indicated by the grey bars above. Sequenced transcripts shown in panel B are drawn below the corresponding ORFs. Each transcript encodes a predicted protein with full-length homology to known IRFs. The predicted size of the encoded protein is indicated below each transcript. Introns are located between 88343 and 88443 (K10/10.1), 90846 and 90939 (K10.5/10.7), and 93519 and 93639 (K11/vIRF-2). (D) Sequenced transcripts encoding K10/10.1 and K10. The positions of start and stop codons and introns are shown relative to U75698. RT-PCR products corresponding to the two transcripts are shown on the right. The primers used (see Materials and Methods) are labeled (small arrows). RNA templates was taken from BC-3 cells 0 (latent) and 24 (lytic) h after the addition of TPA. The PCR product from KSHV genomic DNA is shown for size comparison.

FIG. 5 — (A) Alignment of DNA binding domains of the human IRFs IRF-4 (GI:2497445) and ICSB-1 (GI:4504567) with those of vIRF-1 (GI:1718311), vIRF-2 (GI:3152729), K10.1, and a novel putative ORF, K10.7. The amino acid sequences for K10.1 and K10.7 were translated from the genomic sequence of KSHV (U75698). The sequence shown for each protein is bounded by the amino acid positions shown on either side. The alignment was performed with ClustalW (46). (B) RT-PCR products showing transcripts encoding vIRF-1 and the putative ORFs K10/10.1, K10.5/10.7, and K11/vIRF-2. The primers used are complementary to either end of the putative long ORFs (see Materials and Methods). RNA was extracted from BC-3 cells 24 h after the addition of TPA. RT-negative controls and positive controls from KSHV genomic DNA are included for each RT-PCR. The RT-PCR product sizes are predicted to be 1,350 (K9), 2,736 (K10/10.1), 1,701 (K10.5/10.7), and 2,043 (K11/vIRF-2) bp. (C) Positions (relative to genomic sequence U75698) and organization of the IRF-related genes of KSHV. The location of the novel putative ORF K10.7 is shown. Secondary lytic genes are shaded in black. The region of each ORF whose translated sequence is shown in panel A is indicated by the grey bars above. Sequenced transcripts shown in panel B are drawn below the corresponding ORFs. Each transcript encodes a predicted protein with full-length homology to known IRFs. The predicted size of the encoded protein is indicated below each transcript. Introns are located between 88343 and 88443 (K10/10.1), 90846 and 90939 (K10.5/10.7), and 93519 and 93639 (K11/vIRF-2). (D) Sequenced transcripts encoding K10/10.1 and K10. The positions of start and stop codons and introns are shown relative to U75698. RT-PCR products corresponding to the two transcripts are shown on the right. The primers used (see Materials and Methods) are labeled (small arrows). RNA templates was taken from BC-3 cells 0 (latent) and 24 (lytic) h after the addition of TPA. The PCR product from KSHV genomic DNA is shown for size comparison.