Nucleic Acids Research, 2006, Vol. 34, No. 22 6703 Figure 5. Alignments of the divergent loop and flanking sequences for Stevor family members from isolates 3D7 Dd2, HB3 and Ghana. 3D7 isolate genes are denoted by their protein names; genes from other isolates are numbered in the order of their discovery. The TM domains are indicated by blue boxes and a green box indicates the hypervariable loop. Translated sequences corresponding to the sense and antisense PCR primers are indicated in lowercase font. The bottom line reflects 85% consensus. Cysteine residues are highlighted in yellow. of 3D7 isolate Pfmc-2TM loci, indicating the conservation of extended loci across isolates (data not shown). All ampliﬁed loci are found on multiple chromosomes in sub-telomeric regions, in association with riﬁn genes, and have conserved orientations with respect to the telomeres (chromosomal locations and orientations are indicated in the left-hand column, Figure 6A). An exception to this rule is the truncated locus containing the Pfmc-2TM gene, MAL7P1.58, which is located within the internal cluster of var and riﬁn genes on Chr7. Chr2 and Chr11 each harbor tandem copies of the locus (denoted by gray and black stars, respectively, in Figure 6A) and, in fact, the PFB0960c locus on Chr2 is truncated immediately downstream of the Pfmc-2TM gene due to fusion with the locus containing PFB0985c. The pairs of loci indicated by brackets in Figure 6A show similarities that may indicate relationships in the ancestral progression of the locus duplications. The ORFs within the extended loci predominantly encode Pexel/ VTS-containing proteins, PfEMP1 proteins or apparent pseudogenes (Figure 6B). The full-length versions of the ampliﬁed locus each contain one Pfmc-2TM gene; one gene from the 2TM paralogous family Hyp5 (e.g. PFF1535w); a gene encoding a Pexel/VTS-containing protein that may not possess a TM domain (e.g. PFF1530c); and one or more riﬁn gene. Additionally, a DnaJ domain-containing gene (e.g. PFF1520w) lies immediately downstream, and on the opposite strand, of each Pfmc-2TM gene. In contrast to the DnaJ domain-containing Pexel/VTS genes, these versions appear to be pseudogenes and lack an N-terminal exon and start methionine, with the notable exception of a predicted two exon, signal peptide/Pexel/VTS-containing version that has an insertion encoding a pronounced repeat region (PFA0675w). Although the loop region within the Pfmc-2TM proteins is variable across paralogs and across P.falciparum isolates, the ORFs adjacent these genes within the extended locus are relatively invariant across paralogs and in predicted orthologs within the HB3 isolate genome sequence (e.g. predicted orthologs for PFF1535w, PFF1530c and PFF1520w). The riﬁn gene (e.g. PFF1540w) is highly conserved in the dupli- cated versions, including a nearly identical copy on Chr11 that is also a predicted pseudogene. A predicted ortholog of