saf4 (SPBC18H10.10c)


Gene Standard Namesaf4 Characterisation Statuspublished
Systematic IDSPBC18H10.10c Feature Typeprotein coding
Synonymscwc16, cwf16 Name Description
Productsplicing associated factor Saf4 Product Size299aa, 34.69 kDa
Genomic Location Chromosome II, 1789159-1786609 (2551nt); CDS:1789046-1788047 (1000nt)

Ensembl Gene Location
GO Biological Process
Term NameCount
mRNA cis splicing, via spliceosome120
Annotation ExtensionEvidenceWith/FromReference
GO Cellular Component
Term NameCount
nucleus2696
Annotation ExtensionEvidenceWith/FromReference
U2-type spliceosomal complex48
Annotation ExtensionEvidenceWith/FromReference
Fission Yeast Phenotype Ontology
Gene Deletion Viability: Viable

Population Phenotype

Term NameAlleleExpressionCount
viable vegetative cell populationsaf4ΔNull3809

Cell Phenotype

Term NameAlleleExpressionCount
viable vegetative cell with normal cell morphologysaf4ΔNull3094
Transcript
Ensembl transcript structure with UTRs, exons and introns

Transcript Structure

Region Coordinates Reference
Exons1789159..1788786, 1788740..1788492, 1788436..1786609
mRNA1789159..1786609
5' UTR1789159..1789047PMID:21511999
CDS1789046..1788786, 1788740..1788492, 1788436..1788047
3' UTR1788046..1786609PMID:21511999
Protein Features

Graphical View

Ensembl protein image with mapped locations of structural domains

Protein Families and Domains

Feature ID Database InterPro Description Start End Count
PF04502 Pfam IPR007590 CWC16 protein 8 211 2
PTHR12111 HMMPANTHER IPR007590 CWC16 protein 6 257 2
PTHR12111:SF2 HMMPANTHER 6 257 1

View domain organization at Pfam

Protein Properties

Ave. residue weight 116.03 Da
Charge 12.50
Isoelectric point 9.86
Molecular weight 34.69 kDa
Number of residues 299
Modifications

Protein Modifications

Term NameResidueCount
O-phospho-L-serineS295 1672
Annotation ExtensionEvidenceResidueReference
experimental evidence S295 PMID:24763107
Sequence
Gene Expression

Quantitative Gene Expression

Protein Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
797.46during GO:0072690PECO:0000005,
PECO:0000014
population wideexperimental evidencePMID:23101633
3633during GO:0072690PECO:0000126,
PECO:0000005
single cellmass spectrometry evidencePMID:24763107

RNA Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
0.34during GO:0072690PECO:0000005,
PECO:0000014
population wideexperimental evidencePMID:23101633
0.22during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000005,
PECO:0000014,
PECO:0000127
population wideexperimental evidencePMID:23101633
Warning
DescriptionQualifierReferenceCount
gene structure updated PMID:21511999433
Species Distribution
DescriptionQualifierReferenceCount
no apparent S. cerevisiae ortholog599
predominantly single copy (one to one)3092
conserved in fungi4603
conserved in eukaryotes4514
conserved in metazoa3424
conserved in vertebrates3399
conserved in eukaryotes only2501
Orthologs

Manually curated orthologous groups

SpeciesGeneDescriptionLinksCount

Orthologs in Compara


Physical Interactions

Source: BioGRID

View all interactions in esyN
View the HCPIN interactions in esyN

Gene Product Evidence Reference
co-purifies withcdc5splicing factor, Prp19 complex subunit Cdc5 Co-purificationPMID:24014766
affinity captured bycwf10U5 snRNP GTPase subunit Cwf10 Affinity Capture-MSPMID:24442611
co-purifies withcwf10U5 snRNP GTPase subunit Cwf10 Co-purificationPMID:24014766
affinity captured bycwf14G10 protein Affinity Capture-MSPMID:24874881
affinity captured bylea1U2 snRNP-associated protein Lea1 (predicted) Affinity Capture-MSPMID:24442611
affinity captured bymtl1TRAMP complex ATP-dependent RNA helicase (predicted) Affinity Capture-MSPMID:24713849
affinity captured bysde2silencing defective protein Sde2 Affinity Capture-MSPMID:25274039
Genetic Interactions

Source: BioGRID

View these interactions in esyN

Gene Product Evidence Reference
negative genetic interaction witharg11N-acetyl-gamma-glutamyl-phosphate reductase/acetylglutamate kinase Negative GeneticPMID:22681890
negative genetic interaction witharg12argininosuccinate synthase Arg12 Negative GeneticPMID:22681890
negative genetic interaction witharg3ornithine carbamoyltransferase Arg3 Negative GeneticPMID:22681890
negative genetic interaction witharg6acetylglutamate synthase Arg6 (predicted) Negative GeneticPMID:22681890
positive genetic interaction withccr4CCR4-Not complex subunit Ccr4 (predicted) Positive GeneticPMID:22681890
negative genetic interaction withcpd1tRNA (m1A) methyltransferase complex catalytic subunit Cpd1 Negative GeneticPMID:22681890
negative genetic interaction withfsv1SNARE Fsv1 Negative GeneticPMID:22681890
negative genetic interaction withint6eIF3e subunit Int6 Negative GeneticPMID:22681890
negative genetic interaction withkin1microtubule affinity-regulating kinase Kin1 Negative GeneticPMID:22681890
negative genetic interaction withlys2homoaconitate hydratase Lys2 Negative GeneticPMID:22681890
negative genetic interaction withlys3saccharopine dehydrogenase Lys3 Negative GeneticPMID:22681890
negative genetic interaction withlys4homocitrate synthase Negative GeneticPMID:22681890
negative genetic interaction withmrpl1mitochondrial ribosomal protein subunit L1 (predicted) Negative GeneticPMID:22681890
positive genetic interaction withnab3poly(A) binding protein Nab3 (predicted) Positive GeneticPMID:22681890
positive genetic interaction withpil2meiotic eisosome BAR domain protein Pil2 Positive GeneticPMID:22681890
negative genetic interaction withplb1phospholipase B homolog Plb1 Negative GeneticPMID:22681890
positive genetic interaction withppk16serine/threonine protein kinase Ppk16 (predicted) Positive GeneticPMID:22681890
positive genetic interaction withpsl1cyclin pho85 family Psl1 (predicted) Positive GeneticPMID:22681890
negative genetic interaction withrpl2660S ribosomal protein L26 (predicted) Negative GeneticPMID:22681890
negative genetic interaction withsaf5splicing factor Saf5 Negative GeneticPMID:22681890
positive genetic interaction withset1histone lysine methyltransferase Set1 Positive GeneticPMID:22681890
negative genetic interaction withSPAC13A11.06pyruvate decarboxylase (predicted) Negative GeneticPMID:22681890
negative genetic interaction withSPAC17H9.13cglutamate 5-kinase (predicted) Negative GeneticPMID:22681890
negative genetic interaction withSPAP8A3.07cphospho-2-dehydro-3-deoxyheptonate aldolase (predicted) Negative GeneticPMID:22681890
negative genetic interaction withSPBC1271.14glutamate N-acetyltransferase (predicted) Negative GeneticPMID:22681890
positive genetic interaction withSPBC24C6.04delta-1-pyrroline-5-carboxylate dehydrogenase (predicted) Positive GeneticPMID:22681890
negative genetic interaction withSPBC25H2.15SSU-rRNA maturation protein Tsr4 homolog 1 (predicted) Negative GeneticPMID:22681890
negative genetic interaction withSPBC365.16conserved protein Negative GeneticPMID:22681890
negative genetic interaction withSPBC725.01aspartate aminotransferase (predicted) Negative GeneticPMID:22681890
negative genetic interaction withSPCC1393.08transcription factor, zf-GATA type (predicted) Negative GeneticPMID:22681890
negative genetic interaction withsty1MAP kinase Sty1 Negative GeneticPMID:22681890
negative genetic interaction withtsf1mitochondrial translation elongation factor EF-Ts Tsf1 Negative GeneticPMID:22681890
positive genetic interaction withvps5retromer complex subunit Vps5 Positive GeneticPMID:22681890
External References
Database Identifier Description
NBRP SPBC18H10.10c Fission yeast strain database, National BioResource Project (Japan)
YOGY SPBC18H10.10c Retrieval of eukaryotic orthologs (Bähler Lab)
BioGrid SPBC18H10.10c BioGRID Interaction Datasets
Expression Viewer SPBC18H10.10c Cell Cycle Expression Profile (Bähler Lab)
Expression Viewer SPBC18H10.10c Meiosis/Sporulation Expression Profies (Bähler Lab)
Expression Viewer SPBC18H10.10c Pheromone response/mating expression profiles (Bähler Lab)
Expression Viewer SPBC18H10.10c Environmental stress expression profiles (Bähler Lab)
Pomb(A) SPBC18H10.10c Polyadenylation Viewer (Gullerova lab)
pombeTV SPBC18H10.10c Transcriptome Viewer (Bähler Lab)
GEO SPBC18H10.10c GEO profiles
PInt SPBC18H10.10c Protein-Protein Interaction Predictor (Bähler Lab)
PeptideAtlas SPBC18H10.10c Peptides identified in tandem mass spectrometry proteomics experiments
SYSGRO SPBC18H10.10c Fission yeast phenotypic data & analysis
Cyclebase SPBC18H10.10c.1 Cell Cycle Data
SPD / RIKEN14/14C08Orfeome Localization Data
UniProtKB/SwissProtO60141Protein saf4
ModBaseO60141Database of comparative protein structure models
STRINGO60141Network display of known and predicted interactions and functional associations
RefSeq PeptideNP_595734splicing associated factor Saf4 (predicted)
RefSeq mRNANM_001021632972h- splicing associated factor Saf4 (predicted) (saf4), mRNA
European Nucleotide ArchiveCAA18407.2ENA Protein Mapping
UniParcUPI000228F49BUniProt Archive

Literature for saf4

Search: Europe PMC or PubMed

Release Version: PomBase:26_53 - 27 May 2015