Figure 2

Redefining the structure of the 205 SICAvar gene. A. Schematic representing the genomic organization of the exons and introns of the original (10 exon) and redefined (12 exon) 205 SICAvar gene. Blue boxes denote exons, black lines denote introns, and dotted lines represent the estimated sizes of uncharacterized 12 kb and 3 kb introns, drawn roughly to scale. B. Schematic representing the discovery of the PkH_051981 two-exon gene fragment and its relationship with the 205 SICAvar gene. The color-coded bars are drawn to depict the relationship of the newly defined start of the 205 SICAvar gene with its originally defined 5'UTR and exons 1 through 3. The originally defined 5'UTR and exon 1 sequence are identical to sequence in the PkH_051981 fragment. Part of the originally defined exon 1 was also found to be identical to sequence from the unmapped contig PkH_000630, revealing that the original exon 1 actually contains an internal intron. Previously, this sequence was only available from cDNA generated via 5'RACE experiments and this intron went undetected. See Additional file 1: Alignment of PkH_051981, genomic sequence surrounding PkH_051981, PkH_000630, and sequenced clones. C. Synteny map of the region surrounding PkH_051981 showing many orthologous genes in P. knowlesi, P. vivax and P. falciparum. PkH_051981 is near the end of a contiguous syntenic block that extends upstream for 70,449 bp. D. Northern blot data supports the premise that the PkH_051981 sequences are part of the 205 SICAvar transcript. Individual lanes of P. knowlesi [Pk1(B+)1+] ring-stage total RNA were hybridized with a PkH_051981 antisense riboprobe and an oligonucleotide probe representing exon 11. The 205 SICAvar transcript signal (9.5 kb) is attained with each probe. The standard sizes noted are based on the Millennium RNA markers from Invitrogen.