P. falciparum genes harboring G-quadruplexes
The striking genomic features of P. falciparum, wherein GC richness is uniquely localized in parasite's AT rich genome hint towards existence of regulatory elements in GC rich regions. G-stretches have the potential to form non Watson-Crick secondary structures called G-quadruplexes. Studies in different genomes suggest that DNA or RNA quadruplexes can regulate gene expression.
Bhartiya D, Chawla V, Ghosh S, Shankar R, Kumar N. Genome-wide regulatory dynamics of G-quadruplexes in human malaria parasite Plasmodium falciparum. Genomics. 2016 Oct 24. pii: S0888-7543(16)30094-5.PMID: 27789319.
Functional category PFID New Annotation E.C Transcript
21663 DNA metabolism PF3D7_0318600 cleavage and polyadenylation specificity factor, putative
21950 PF3D7_1425400 DEAD/DEAH box helicase, putative
21860 PF3D7_1117800
DNA mismatch repair protein MLH
21778 PF3D7_0726300 DNA mismatch repair protein PMS1, putative
21681 PF3D7_0411900 DNA polymerase alpha
21784 PF3D7_0803400 DNA repair and recombination protein RAD54, putative
29829 PF3D7_1368800 DNA repair endonuclease XPF, putative
21762 PF3D7_0710400 DNA repair protein RAD14, putative
21876 PF3D7_1211700 DNA replication licensing factor MCM5, putative
21794 PF3D7_0814200
DNA/RNA-binding protein Alba 1
21737 PF3D7_0614800 endonuclease III homologue, putative
25792 PF3D7_1360900 RNA-binding protein, putative
21854 PF3D7_1107300 polyadenylate-binding protein-interacting protein 1, putative
21680 PF3D7_0409600 replication protein A1, large subunit
21744 PF3D7_0623900 ribonuclease H2 subunit A, putative
21900 RNA metabolism PF3D7_1243100 zinc finger protein, putative
21838 PF3D7_1031500
ATP-dependent DNA helicase ddx3x
21662 PF3D7_0318200 DNA-directed RNA polymerase II subunit RPB1
21974 PF3D7_1472700 DNA-directed RNA polymerase, alpha subunit, putative
21901 PF3D7_1244000 glucose inhibited division protein a homologue, putative
21735 PF3D7_0611900 lsm12, putative
21796 PF3D7_0822100 mediator of RNA polymerase II transcription subunit 7, putative
21891 PF3D7_1235500 mRNA methyltransferase, putative, METTL14
21817 PF3D7_0917600
pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43, putative
21714 PF3D7_0515000 pre-mRNA-splicing factor CWC2, putative
21698 PF3D7_0422500 pre-mRNA-splicing helicase BRR2, putative
21827 PF3D7_1005500 regulator of nonsense transcripts 1, putative
21710 PF3D7_0509400
RNA polymerase I
21664 PF3D7_0319500 RNA-binding protein, putative
21689 PF3D7_0416000 RNA-binding protein, putative
21911 PF3D7_1310700
PhIL1-interacting protein PhIP
21920 PF3D7_1326300 RNA-binding protein, putative
21943 PF3D7_1407100
rRNA 2'-O-methyltransferase fibrillarin, putative
25894 PF3D7_0422900 methyltransferase, putative
21718 PF3D7_0517300
serine/arginine-rich splicing factor 1
21878 PF3D7_1217200 multiple rna-binding domain-containing protein 1
21890 PF3D7_1234800 splicing factor 3B subunit 3, putative
21949 PF3D7_1420000 splicing factor 3B subunit 4, putative
23746 PF3D7_0420300 AP2 domain transcription factor
21893 PF3D7_1239200 transcription factor with AP2 domain(s)
21915 PF3D7_1317200 AP2 domain transcription factor AP2-FG
23958 PF3D7_1342900 ap2 domain transcription factor ap2-hs
30430 PF3D7_1466400 AP2 domain transcription factor AP2-SP/EXP
21743 PF3D7_0623600 splicing factor-like protein, putative
21832 PF3D7_1014600 transcriptional coactivator ADA2
22041 PF3D7_0408900
tRNA N6-adenosine threonylcarbamoyltransferase
21853 PF3D7_1105700 tRNA-splicing ligase RTCB
21907 PF3D7_1306900 U1 small nuclear ribonucleoprotein A, putative
21825 PF3D7_0935000 U2 small nuclear ribonucleoprotein B'', putative
21960 PF3D7_1448000 U3 small nucleolar RNA-associated protein 12, putative
21909 PF3D7_1309300 U4/U6 small nuclear ribonucleoprotein PRP3, putative
21829 PF3D7_1009400 zinc finger protein, putative
21978 Translation PF3D7_0801100 28S ribosomal RNA
21716 PF3D7_0516200 40S ribosomal protein S11
21661 PF3D7_0317600 40S ribosomal protein S11, putative
21916 PF3D7_1317800 40S ribosomal protein S19
21760 PF3D7_0705700 40S ribosomal protein S29, putative
21818 PF3D7_0918200 50S ribosomal protein L3, apicoplast, putative
21923 PF3D7_1331800 60S ribosomal protein L23, putative
21711 PF3D7_0509600
asparagine--tRNA ligase
21713 PF3D7_0514300 aspartate--tRNA ligase, putative
21922 PF3D7_1331700
glutamine--tRNA ligase, putative
21954 PF3D7_1431300 large subunit GTPase 1, putative
21932 PF3D7_1350100
lysine--tRNA ligase
21948 PF3D7_1416800
lysine--tRNA ligase, putative
21643 PF3D7_0212300 eukaryotic peptide chain release factor subunit 1, putative; ERF1
21758 PF3D7_0704900 peptide chain release factor 2
21729 PF3D7_0603700
phenylalanine--tRNA ligase
21877 PF3D7_1213800
prolyl-tRNA synthetase proline--tRNA ligase
21640 PF3D7_0203700 protein MAK16, putative
21930 PF3D7_1346100
protein transport protein SEC61 subunit alpha
21830 PF3D7_1010000 ribosomal protein L43, mitochondrial, putative
21862 PF3D7_1123400 eukaryotic peptide chain release factor GTP-binding subunit, putative, erf3
21799 PF3D7_0828500 translation initiation factor eIF-2B subunit alpha, putative
21763 Post-translational modifications PF3D7_0711000
AAA family ATPase, CDC48 subfamily
21886 PF3D7_1230400
ATP-dependent protease subunit ClpQ
21946 PF3D7_1414500
atypical protein kinase, ABC-1 family, putative 1.14.13.-
21963 PF3D7_1453700 co-chaperone p23
21906 PF3D7_1302600
deoxyhypusine hydroxylase
21813 PF3D7_0911900
inhibitor of cysteine proteases falstatin
25710 PF3D7_0409400
chaperone protein dnaj; heat shock protein 40
25887 PF3D7_1108700
heat shock protein 40, type ii
21749 PF3D7_0628100
hect domain-containing protein 1, putative
21837 PF3D7_1028000 methyltransferase, putative
21634 PF3D7_0109500 N-acetyltransferase, putative
21884 PF3D7_1228300
NIMA related kinase 1
21707 PF3D7_0507700 nuclear protein localization protein 4, putative
21641 PF3D7_0205400 PCI domain-containing protein, putative
21931 PF3D7_1349700 peptidase, putative
21666 PF3D7_0322000
peptidyl-prolyl cis-trans isomerase
21722 PF3D7_0528700
peptidyl-prolyl cis-trans isomerase
21873 PF3D7_1202400
peptidyl-prolyl cis-trans isomerase
21912 PF3D7_1313300 peptidyl-prolyl cis-trans isomerase, putative
21657 PF3D7_0311700
plasmepsin VI 3.4.23.-
21952 PF3D7_1428300 proliferation-associated protein 2g4, putative
21831 PF3D7_1011400
proteasome subunit beta type-5
21951 PF3D7_1426200
protein arginine N-methyltransferase 1
21750 PF3D7_0628200
eukaryotic translation initiation factor 2-alpha kinase
33636 PF3D7_0311400 kinase-related protein pkrp
21776 PF3D7_0724600 protein kinase, putative
21821 PF3D7_0926100 protein kinase, putative
21822 PF3D7_0926300 protein kinase, putative
25810 PF3D7_1315100
serine/threonine protein kinase PK9
21869 PF3D7_1148000
serine/threonine protein kinase, putative
21858 PF3D7_1114700
cyclin-dependent-like kinase clk3
21783 PF3D7_0802800
serine/threonine protein phosphatase 2B catalytic subunit A
21833 PF3D7_1018200 serine/threonine protein phosphatase 8, putative
21863 PF3D7_1136900
subtilisin-like protease 2
21815 PF3D7_0915100
SUMO-conjugating enzyme UBC9
21717 PF3D7_0516700 ubiquitin carboxyl-terminal hydrolase 2, putative
21936 PF3D7_1365400 adenylyltransferase and sulfurtransferase uba4, putative 2.7.7.-
23907 PF3D7_1033900 ubiquitin-conjugating enzyme e2, putative
21913 PF3D7_1314800
ubiquitin-like protein, putative
21730 Chromosome structure PF3D7_0603800 NdP2 protein, putative
21709 PF3D7_0509100
structural maintenance of chromosomes protein 4
21793 PF3D7_0813200 CS domain protein, putative
21924 PF3D7_1336800 nuclear movement protein, putative
21765 PF3D7_0711500 regulator of chromosome condensation, putative
21745 PF3D7_0624600
iswi chromatin-remodeling complex atpase
21734 PF3D7_0608700 T-complex protein 1 subunit zeta
21889 Histone modifications PF3D7_1234100
bromodomain protein 5
21836 PF3D7_1023900
SNF2 helicase, putative chromodomain-helicase-DNA-binding protein 1 homolog, putative
21834 PF3D7_1020700 histone acetyltransferase, putative
21690 PF3D7_0416400
histone acetyltransferase, putative
21820 PF3D7_0925700
histone deacetylase 1
21764 PF3D7_0711400 histone deacetylase complex subunit SAP18, putative
21973 PF3D7_1472200
histone deacetylase, putative
21665 PF3D7_0320900
21852 PF3D7_1105000
histone H4
21676 PF3D7_0403900 SET domain protein, putative
21677 Amino acid metabolism PF3D7_0405700
lysine decarboxylase, putative
21687 PF3D7_0413700 lysine decarboxylase-like protein, putative
21953 PF3D7_1430700
NADP-specific glutamate dehydrogenase
21874 PF3D7_1205100 O-phosphoseryl-tRNA(Sec) selenium transferase, putative