Genome location: Pf3D7_10_v3:1,223,136..1,224,517(+)
Genome classification: Core
Product Description: transcription elongation factor SPT4, putative
SignalP Peptide: N/A
# Transmembrane Domains: 0
EC Numbers: None
Curated GO (PlasmoDB):
| Type | GO Term | Name |
|---|---|---|
| Component | GO:0032044 | DSIF complex |
| Component | GO:0005634 | nucleus |
| Function | GO:0003700 | DNA-binding transcription factor activity |
| Function | GO:0000993 | RNA polymerase II complex binding |
| Function | GO:0003682 | chromatin binding |
| Function | GO:0005515 | protein binding |
| Function | GO:0000182 | rDNA binding |
| Process | GO:0006325 | chromatin organization |
| Process | GO:0006397 | mRNA processing |
| Process | GO:0000398 | mRNA splicing, via spliceosome |
| Process | GO:0034243 | regulation of transcription elongation from RNA polymerase II promoter |
| Process | GO:0006355 | regulation of transcription, DNA-templated |
| Process | GO:0006351 | transcription, DNA-templated |
Expression by stage (LR - Le Roch et al., and MCA - Malaria Cell Atlas):
| Stage | LR class | MCA mean | MCA prop. zeros |
|---|---|---|---|
| Sporozoite | expressed | N/A | N/A |
| Ring | expressed | 0.02 | 0.99 |
| Trophozoite | expressed | 0.03 | 0.98 |
| Schizont | expressed | 0.02 | 0.99 |
| Gametocyte | expressed | 0.03 | 0.98 |
More info:
Old (Pf3D7v3) Gene ID: PF3D7_1030000
Resistome Missense Mutations: None
Resistome Compounds with Missense Mutations: None
Resistome # Samples with Disruptive Mutations: 0 (0 missense, 0 "interesting" missense)
Zhang Phenotype: Non - Mutable in CDS *tentative
MIS: 0.121 | MFS: -2.724 | #Insertions: 0
PlasmoGEM Phenotype: Essential (Pb ortholog: PBANKA_0514000)
RMgmDB ABS Phenotype: N/A
More info: PhenoPlasm Link
AlphaFill Uniprot ID: Q8IJA5
"Best" AlphaFill ligand hit: No AlphaFill hits
No associated EC numbersNo evidence of orthology to BindingDB entries
Ortholog Group (OrthoMCL): OG6_102281
Most Similar Human Ortholog: P63272
TM-align score: 0.77 | RMSD: 1.35
Seq Identity: 0.38 | Length: 95 / 133
All Human Orthologs (OrthoMCL):
| Gene ID | Description |
|---|---|
| ENSG00000213246 | SPT4 homolog, DSIF elongation factor subunit |
MalariaGEN Pf7 (worldwide samples) # unique SNV/indels:
Homozygous genotype calls only
| variant type | common | rare | doubleton | singleton |
|---|---|---|---|---|
| synonymous | 2 | 10 | 2 | 10 |
| disruptive | 1 | 11 | 4 | 15 |
| missense | 1 | 11 | 2 | 14 |
Any inclusion in genotype call
| variant type | common | rare | doubleton | singleton |
|---|---|---|---|---|
| synonymous | 2 | 19 | 6 | 9 |
| disruptive | 3 | 16 | 10 | 22 |
| missense | 3 | 13 | 9 | 21 |
PlasmoDB Total SNPs: 138
Non-coding: 137 | Synonymous: 1 | Nonsynonymous: 0 | Stop Codon: 0
Protein Length: 133 | Molecular Weight (kDa): 15.178
UniProt ID(s): Q8IJA5
PDB ID(s): None
Isoelectric Point: 9.18
Protein Domain Annotations:
| Source | Family ID | Description |
|---|---|---|
| InterPro | IPR009287 | Transcription initiation Spt4 |
| InterPro | IPR022800 | Spt4/RpoE2 zinc finger |
| InterPro | IPR029040 | RNA polymerase subunit RPABC4/transcription elongation factor Spt4 |
| PFam | PF06093 | Spt4/RpoE2 zinc finger |
| Superfamily | SSF63393 | RNA polymerase subunit RPABC4/transcription elongation factor Spt4 |
| PMID | Title | Authors | DOI/Link |
|---|---|---|---|
| 12368864 | Genome sequence of the human malaria parasite Plasmodium falciparum. | Gardner MJ, Hall N, ..., Barrell B | 10.1038/nature01097 |
| 23181666 | Organellar proteomics reveals hundreds of novel nuclear proteins in the malariaparasite Plasmodium falciparum. | Oehring SC, Woodcroft BJ, ..., Voss TS | 10.1186/gb-2012-13-11-r108 |
| 32017676 | The chromatin bound proteome of the human malaria parasite | Batugedara G, Lu XM, ..., Le Roch KG | 10.1099/mgen.0.000327 |