Table S33: Characteristics
of the 53 P. falciparum-specific intersyntenic genes. A list of 53 P. falciparum-specific genes located in indels
between SBs (intersyntenic genes) including all intersyntenic pseudogenes.
Groups of genes forming a cluster (8 indels) are separated by a black line
Proteins with a TM domain in the first 100 amino acids (TM-N) as well as var
and rif genes are considered proteins potentially targeted to the
surface membrane of the parasite or erythrocyte (37 of 42 genes and 11 of 11 pseudogenes
marked with an asterisk, genes with a PEXEL/VTS (Marti et al. 2004;
Hiller et al. 2004) are marked with two asterisks). |
|||||||||
Pf gene |
Product |
pf-fama |
Size indel (bp) |
trans. |
exp. |
SP |
AP |
TM-N |
TM |
PFD0615c ** |
erythrocyte membrane
protein 1 (PfEMP1) |
var |
70,195 |
|
|
|
|
|
|
chr4.phat_143/ chr4.glm_148 * |
var internal cluster
associated repeat gene 4a |
vicar |
70,195 |
- |
- |
X |
- |
X |
X |
PFD0620c ** |
rifin--related
protein |
rif |
70,195 |
|
|
|
|
|
|
PFD0625c ** |
erythrocyte membrane
protein 1 (PfEMP1) |
var |
70,195 |
|
|
|
|
|
|
- * |
vicar pseudogene |
vicar |
70,195 |
|
|
|
|
|
|
PFD0630c ** |
erythrocyte membrane
protein 1 (PfEMP1) |
var |
70,195 |
|
|
|
|
|
|
- * |
vicar pseudogene |
vicar |
70,195 |
|
|
|
|
|
|
PFD0635c ** |
erythrocyte membrane
protein 1 (PfEMP1) |
var |
70,195 |
|
|
|
|
|
|
PFD0640c ** |
rifin |
rif |
70,195 |
|
|
|
|
|
|
PFD0645w ** |
rifin |
rif |
70,195 |
|
|
|
|
|
|
PFD0650w |
hypothetical protein |
- |
70,195 |
- |
- |
- |
- |
- |
- |
PFD0655w ** |
var-related
pseudogene |
var |
70,195 |
|
|
|
|
|
|
MAL7P1.39 * |
var internal cluster
associated repeat gene 7a |
vicar |
105,155 |
S,M |
- |
X |
- |
X |
X |
PF07_0048 ** |
erythrocyte membrane
protein 1 (PfEMP1) |
var |
105,155 |
|
|
|
|
|
|
chr7.phat_103/ chr7.glm_101 * |
var internal cluster
associated repeat gene 7b |
vicar |
105,155 |
- |
- |
X |
- |
X |
X |
MAL7P1.43 ** |
rif pseudogene |
rif |
105,155 |
|
|
|
|
|
|
PF07_0049 ** |
erythrocyte membrane
protein 1 (PfEMP1) |
var |
105,155 |
|
|
|
|
|
|
chr7.phat_108/ chr7.glm_105 * |
var internal cluster
associated repeat gene 7c |
vicar |
105,155 |
- |
- |
X |
- |
X |
X |
MAL7P1.47 ** |
rif pseudogene |
rif |
105,155 |
|
|
|
|
|
|
MAL7P1.50 ** |
erythrocyte membrane
protein 1 (PfEMP1) |
var |
105,155 |
|
|
|
|
|
|
PF07_0050 ** |
erythrocyte membrane
protein 1 (PfEMP1) |
var |
105,155 |
|
|
|
|
|
|
MAL7P1.52 ** |
rif pseudogene |
rif |
105,155 |
|
|
|
|
|
|
PF07_0051 ** |
erythrocyte membrane
protein 1 (PfEMP1) |
var |
105,155 |
|
|
|
|
|
|
chr7.phat_114 * |
vicar pseudogene |
vicar |
105,155 |
|
|
|
|
|
|
MAL7P1.55 ** |
erythrocyte membrane
protein 1 (PfEMP1) |
var |
105,155 |
|
|
|
|
|
|
MAL7P1.56 ** |
erythrocyte membrane
protein 1 (PfEMP1) |
var |
105,155 |
|
|
|
|
|
|
MAL7P1.57 ** |
rifin |
rif |
105,155 |
|
|
|
|
|
|
MAL7P1.58 * |
hypothetical protein,
conserved in Pf |
pfmc-2tm |
105,155 |
ET |
- |
- |
- |
X |
X |
MAL7P1.59 |
hypothetical protein,
conserved in Pf |
- |
105,155 |
- |
- |
- |
- |
- |
- |
MAL7P1.60 ** |
var fragment,
pseudogene |
var |
105,155 |
|
|
|
|
|
|
MAL7P1.62 ** |
var fragment,
pseudogene |
var |
105,155 |
|
|
|
|
|
|
MAL7P1.63 ** |
var fragment,
pseudogene |
var |
105,155 |
|
|
|
|
|
|
PF07_0107 * |
hypothetical protein |
- |
13,799 |
M-LR |
- |
- |
- |
X |
X |
MAL7P1.144 ** |
pftstk7a |
tstk |
13,799 |
ER-LT,G |
S |
- |
- |
- |
X |
PF08_0103 ** |
erythrocyte membrane
protein 1 (PfEMP1) |
var |
43,407 |
|
|
|
|
|
|
- * |
vicar pseudogene |
vicar |
43,407 |
|
|
|
|
|
|
PF08_0104 ** |
rifin |
rif |
43,407 |
|
|
|
|
|
|
PF08_0105 ** |
rifin |
rif |
43,407 |
|
|
|
|
|
|
PF08_0106 ** |
erythrocyte membrane
protein 1 (PfEMP1) |
var |
43,407 |
|
|
|
|
|
|
PF08_0107 ** |
erythrocyte membrane
protein 1 (PfEMP1) |
var |
43,407 |
|
|
|
|
|
|
chr8.phat_232/ chr8.glm_253 * |
var internal cluster
associated repeat gene 8 |
vicar |
43,407 |
- |
- |
X |
- |
X |
X |
PFI0330c |
hypothetical protein |
- |
11,729 |
LR-LT |
- |
- |
- |
- |
X |
PF10_0159 ** |
glycophorin-binding
protein 130 precursor |
gbp |
37,843 |
ER-LS |
T |
- |
- |
X |
X |
PF10_0160 ** |
3.8 protein -
pftstk10a |
tstk |
37,843 |
ER-ES |
T |
- |
- |
X |
X |
PF10_0161 |
hypothetical protein |
- |
37,843 |
ER-LR |
S |
- |
- |
- |
- |
PF10_0162 |
hypothetical protein |
- |
37,843 |
ET,M |
- |
- |
- |
- |
- |
PF10_0163 ** |
hypothetical protein |
- |
37,843 |
LS-ER |
- |
X |
X |
X |
X |
PF10_0164 * |
hypothetical protein |
etramp |
37,843 |
S,G |
G |
X |
- |
X |
X |
MAL13P1.268 * |
hypothetical protein |
- |
18,712 |
M-ER |
- |
X |
- |
X |
X |
MAL13P1.269 * |
hypothetical protein |
- |
18,712 |
B,G |
T |
- |
- |
X |
X |
PF13_0275 ** |
hypothetical protein |
- |
18,712 |
M-ET |
T,G,M |
- |
- |
X |
X |
PF13_0276 * |
hypothetical protein |
- |
18,712 |
M-LR |
- |
- |
- |
X |
X |
PF14_0708 * |
hypothetical protein |
- |
13,194 |
G |
- |
- |
- |
X |
X |
a References to the papers describing the gene families are as follows:
var (Baruch et al. 1995; Smith et
al. 1995; Su et al. 1995); vicar, var internal
cluster associated repeat gene (this paper); rif (Kyes et al.
1999); pfmc-2tm, P. falciparum Maurer’s cleft localized 2
transmembrane domain proteins (Sam-Yellowe et al. 2004); tstk,
transforming growth factor β (TGF-β) receptor-like serine/threonine
protein kinases (this paper); gbp, glycophorin-binding protein (Nolte et
al. 1991; Perkins et al. 1984; Rudolph et al. 1994); etramp,
early transcribed membrane proteins (Spielmann et al. 2003). Abbreviations:SB,
synteny block; PEXEL, Plasmodium export element; VTS, vacuolar
transport signal; Pf, P. falciparum; pf-fam, described P. falciparum gene
family; SP, predicted signal peptide; AP, predicted apicoplast transit
peptide; TM, transmembrane domain; TM-N, N-terminal TM-domain; trans.,
approximate stage of (highest) transcription for all genes except the var,
rif and vicar genes
based on transcriptome data (Le Roch et al. 2003; Bozdech et al. 2003); M, merozoite; ER, early
ring; LR, late ring; ET, early trophozoite; LT, late trophozoite; ES, early
schizont; LS, late schizont; G, gametocyte; S, sporozoite; B, asexual blood
stages; exp., expression of those genes based on proteome data (Florens et
al. 2002; Lasonder et al. 2002); M, merozoite; T, trophozoite; G,
gametocyte; S, sporozoite. |