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. 2014 Jan 14;6(1):223–242. doi: 10.3390/v6010223

Figure 2.

Figure 2

(A) Genome organization of the DNA-A component of CLCuBuV. Five ORFs are shown with the arrows. V1 and V2 (coat protein) are located on the plus strand, C1 (replication associated protein), C3 (replication enhancer protein) and C4 (unnamed) are located on the complementary sense strand. The 455 bp large intergenic region (LIR) contains the potential stem-loop with nonanucleotides conserved among all geminiviruses. Sequence numbering begins at base 8 of the conserved nonamer; (B) A schematic drawing of the CLCuBuV LIR. Shown, is the invariant loop sequence with the nonanucleotide sequence (grey box) flanked by inverted repeats (short arrows); the viral protein start sites and replication associated proteins; (C) A schematic representation of both expression vectors shows the cloning of the C1 and V1 promoters; (D) Schematic representation of important features of large intergenic region (LIR) of CLCuBuV including REP-binding sites (iterons), TATA box and structure of hair pin showing nonanucleotide (underlined). The TATA box for Rep promoter was to be present at position 2660–2664 in the genome. Two directly repeats iteron motifs AAATTC were predicted at position 2709–2715; 2715–2721 present downstream to TATA box and immediate upstream to stem-loop motif .The stem-loop motif composed of 35 bp was predicted at position 2738–15 in the CLCuBuV genome.