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Aliases for SF3A3 Gene

Aliases for SF3A3 Gene

  • Splicing Factor 3a Subunit 3 2 3 5
  • Splicing Factor 3a, Subunit 3, 60kDa 2 3
  • Splicing Factor 3a, Subunit 3, 60kD 2 3
  • SAP 61 3 4
  • SF3a60 3 4
  • SAP61 3 4
  • Pre-MRNA Splicing Factor SF3a (60kD) 3
  • Spliceosome Associated Protein 61 3
  • Spliceosome-Associated Protein 61 4
  • Splicing Factor 3A Subunit 3 3
  • PRPF9 3
  • PRP9 3

External Ids for SF3A3 Gene

Previous GeneCards Identifiers for SF3A3 Gene

  • GC01P038261
  • GC01M037458
  • GC01M037835
  • GC01M037826
  • GC01M038091
  • GC01M038195
  • GC01M038422
  • GC01M036540

Summaries for SF3A3 Gene

Entrez Gene Summary for SF3A3 Gene

  • This gene encodes subunit 3 of the splicing factor 3a protein complex. The splicing factor 3a heterotrimer includes subunits 1, 2 and 3 and is necessary for the in vitro conversion of 15S U2 snRNP into an active 17S particle that performs pre-mRNA splicing. Subunit 3 interacts with subunit 1 through its amino-terminus while the zinc finger domain of subunit 3 plays a role in its binding to the 15S U2 snRNP. This gene has a pseudogene on chromosome 20. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2016]

GeneCards Summary for SF3A3 Gene

SF3A3 (Splicing Factor 3a Subunit 3) is a Protein Coding gene. Among its related pathways are mRNA Splicing - Major Pathway and Diurnally Regulated Genes with Circadian Orthologs. Gene Ontology (GO) annotations related to this gene include nucleic acid binding. An important paralog of this gene is SDE2.

UniProtKB/Swiss-Prot for SF3A3 Gene

  • Subunit of the splicing factor SF3A required for A complex assembly formed by the stable binding of U2 snRNP to the branchpoint sequence (BPS) in pre-mRNA. Sequence independent binding of SF3A/SF3B complex upstream of the branch site is essential, it may anchor U2 snRNP to the pre-mRNA. May also be involved in the assembly of the E complex.

Gene Wiki entry for SF3A3 Gene

Additional gene information for SF3A3 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SF3A3 Gene

Genomics for SF3A3 Gene

GeneHancer (GH) Regulatory Elements for SF3A3 Gene

Promoters and enhancers for SF3A3 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01J037994 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 696.5 -10.4 -10417 13.7 HDGF SMAD1 ARNT ARID4B SIN3A ZNF2 YY1 POLR2B ZNF766 E2F8 FHL3 SF3A3 SNIP1 MYCBP C1orf109 FTH1P1 GNL2 MEAF6 UTP11 MTF1
GH01J037988 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE 785.1 +1.1 1134 2.4 ZFP64 FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF143 SP3 SF3A3 GC01P037993 RNU6-510P C1orf109 GNL2 MYCBP FTH1P1 INPP5B FHL3 RSPO1
GH01J038008 Promoter/Enhancer 2.5 EPDnew Ensembl ENCODE dbSUPER 48.6 -22.0 -21989 9.3 CLOCK MLX ZFP64 DMAP1 YY1 SLC30A9 E2F8 ZNF143 SP3 NFYC UTP11 SF3A3 INPP5B SNIP1 C1orf109 RNU6-510P FTH1P1 RSPO1 ENSG00000230955 MTF1
GH01J037513 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 51.9 +476.3 476289 2.6 HDGF PKNOX1 SMAD1 ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 POLR2B MEAF6 SF3A3 GNL2 FTH1P1 DNALI1 INPP5B SNIP1 RPS27P9 YRDC C1orf109
GH01J037552 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 49.1 +437.0 437047 2.1 HDGF PKNOX1 CLOCK SMAD1 ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 SNIP1 C1orf109 SF3A3 GNL2 FTH1P1 YRDC INPP5B CDCA8 ZC3H12A RSPO1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SF3A3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SF3A3 gene promoter:
  • E2F-3a
  • E47
  • E2F
  • E2F-1
  • E2F-2
  • Bach1
  • E2F-4
  • E2F-5
  • C/EBPalpha
  • STAT1

Genomic Locations for SF3A3 Gene

Genomic Locations for SF3A3 Gene
chr1:37,956,975-37,990,921
(GRCh38/hg38)
Size:
33,947 bases
Orientation:
Minus strand
chr1:38,422,647-38,456,593
(GRCh37/hg19)
Size:
33,947 bases
Orientation:
Minus strand

Genomic View for SF3A3 Gene

Genes around SF3A3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SF3A3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SF3A3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SF3A3 Gene

Proteins for SF3A3 Gene

  • Protein details for SF3A3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q12874-SF3A3_HUMAN
    Recommended name:
    Splicing factor 3A subunit 3
    Protein Accession:
    Q12874
    Secondary Accessions:
    • D3DPT5
    • Q15460
    • Q5VT87

    Protein attributes for SF3A3 Gene

    Size:
    501 amino acids
    Molecular mass:
    58849 Da
    Quaternary structure:
    • Identified in the spliceosome C complex. Component of splicing factor SF3A which is composed of three subunits; SF3A3/SAP61, SF3A2/SAP62, SF3A1/SAP114. SF3A associates with the splicing factor SF3B and a 12S RNA unit to form the U2 small nuclear ribonucleoproteins complex (U2 snRNP). Interacts with SF3A1, through its N-terminal region.

    Three dimensional structures from OCA and Proteopedia for SF3A3 Gene

neXtProt entry for SF3A3 Gene

Post-translational modifications for SF3A3 Gene

  • Ubiquitination at isoforms=390 and posLast=201201
  • Modification sites at PhosphoSitePlus

Other Protein References for SF3A3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for SF3A3 Gene

Domains & Families for SF3A3 Gene

Gene Families for SF3A3 Gene

HGNC:
Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins

Protein Domains for SF3A3 Gene

Suggested Antigen Peptide Sequences for SF3A3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q12874

UniProtKB/Swiss-Prot:

SF3A3_HUMAN :
  • Belongs to the SF3A3 family.
Family:
  • Belongs to the SF3A3 family.
genes like me logo Genes that share domains with SF3A3: view

Function for SF3A3 Gene

Molecular function for SF3A3 Gene

UniProtKB/Swiss-Prot Function:
Subunit of the splicing factor SF3A required for A complex assembly formed by the stable binding of U2 snRNP to the branchpoint sequence (BPS) in pre-mRNA. Sequence independent binding of SF3A/SF3B complex upstream of the branch site is essential, it may anchor U2 snRNP to the pre-mRNA. May also be involved in the assembly of the E complex.

Phenotypes From GWAS Catalog for SF3A3 Gene

Gene Ontology (GO) - Molecular Function for SF3A3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding IEA --
GO:0003723 RNA binding IBA --
GO:0005515 protein binding IPI 17098193
GO:0008270 zinc ion binding IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with SF3A3: view
genes like me logo Genes that share phenotypes with SF3A3: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SF3A3

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for SF3A3 Gene

Localization for SF3A3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SF3A3 Gene

Nucleus speckle.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SF3A3 gene
Compartment Confidence
nucleus 5
cytosol 2
peroxisome 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for SF3A3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm TAS --
GO:0005681 spliceosomal complex IDA 9731529
GO:0016607 nuclear speck IEA --
GO:0071013 catalytic step 2 spliceosome IDA 11991638
genes like me logo Genes that share ontologies with SF3A3: view

Pathways & Interactions for SF3A3 Gene

genes like me logo Genes that share pathways with SF3A3: view

Pathways by source for SF3A3 Gene

Gene Ontology (GO) - Biological Process for SF3A3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000375 RNA splicing, via transesterification reactions TAS 7816610
GO:0000389 mRNA 3-splice site recognition TAS 15647371
GO:0000398 mRNA splicing, via spliceosome TAS --
GO:0006397 mRNA processing IMP 15647371
GO:0008380 RNA splicing TAS 7816610
genes like me logo Genes that share ontologies with SF3A3: view

No data available for SIGNOR curated interactions for SF3A3 Gene

Drugs & Compounds for SF3A3 Gene

(1) Drugs for SF3A3 Gene - From: DrugBank

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Phenethyl isothiocyanate Investigational Pharma Target 12
genes like me logo Genes that share compounds with SF3A3: view

Transcripts for SF3A3 Gene

mRNA/cDNA for SF3A3 Gene

Unigene Clusters for SF3A3 Gene

Splicing factor 3a, subunit 3, 60kDa:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SF3A3

Alternative Splicing Database (ASD) splice patterns (SP) for SF3A3 Gene

No ASD Table

Relevant External Links for SF3A3 Gene

GeneLoc Exon Structure for
SF3A3
ECgene alternative splicing isoforms for
SF3A3

Expression for SF3A3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SF3A3 Gene

Protein differential expression in normal tissues from HIPED for SF3A3 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (6.9) and NK cells (6.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SF3A3 Gene



Protein tissue co-expression partners for SF3A3 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SF3A3 Gene:

SF3A3

SOURCE GeneReport for Unigene cluster for SF3A3 Gene:

Hs.77897

mRNA Expression by UniProt/SwissProt for SF3A3 Gene:

Q12874-SF3A3_HUMAN
Tissue specificity: Ubiquitous.

Evidence on tissue expression from TISSUES for SF3A3 Gene

  • Lung(4.5)
  • Nervous system(4.5)
  • Eye(4.3)
  • Liver(4.3)
  • Intestine(2.3)
  • Skin(2.1)
genes like me logo Genes that share expression patterns with SF3A3: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for SF3A3 Gene

Orthologs for SF3A3 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for SF3A3 Gene

Organism Taxonomy Gene Similarity Type Details
dog
(Canis familiaris)
Mammalia -- 34
  • 100 (a)
OneToMany
-- 34
  • 100 (a)
OneToMany
SF3A3 33
  • 92.02 (n)
chimpanzee
(Pan troglodytes)
Mammalia SF3A3 34 33
  • 99.93 (n)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SF3A3 34
  • 99 (a)
OneToOne
cow
(Bos Taurus)
Mammalia SF3A3 34 33
  • 93.21 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Sf3a3 33
  • 91.88 (n)
mouse
(Mus musculus)
Mammalia Sf3a3 16 34 33
  • 91.28 (n)
oppossum
(Monodelphis domestica)
Mammalia -- 34
  • 91 (a)
OneToMany
-- 34
  • 79 (a)
OneToMany
chicken
(Gallus gallus)
Aves SF3A3 34 33
  • 82.57 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SF3A3 34
  • 96 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia sf3a3 33
  • 80.57 (n)
Str.78 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.27314 33
zebrafish
(Danio rerio)
Actinopterygii sf3a3 34 33
  • 79.77 (n)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta noi 34 35 33
  • 62.05 (n)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea T13H5.4 34 35 33
  • 55.96 (n)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes PRP9 36 34
  • 22 (a)
thale cress
(Arabidopsis thaliana)
eudicotyledons ATO 33
  • 52.12 (n)
rice
(Oryza sativa)
Liliopsida Os03g0717600 33
  • 52 (n)
Os.11669 33
corn
(Zea mays)
Liliopsida Zm.6441 33
barley
(Hordeum vulgare)
Liliopsida Hv.3335 33
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 68 (a)
OneToOne
Cin.1167 33
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.1167 33
Species where no ortholog for SF3A3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for SF3A3 Gene

ENSEMBL:
Gene Tree for SF3A3 (if available)
TreeFam:
Gene Tree for SF3A3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SF3A3: view image

Paralogs for SF3A3 Gene

Paralogs for SF3A3 Gene

Pseudogenes.org Pseudogenes for SF3A3 Gene

genes like me logo Genes that share paralogs with SF3A3: view

Variants for SF3A3 Gene

Sequence variations from dbSNP and Humsavar for SF3A3 Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs1000079417 -- 37,991,482(-) T/A upstream_transcript_variant
rs1000129607 -- 37,985,121(-) T/C intron_variant
rs1000169830 -- 37,962,987(-) C/A intron_variant
rs1000238447 -- 37,966,172(-) C/A intron_variant
rs1000295215 -- 37,960,093(-) C/A intron_variant

Structural Variations from Database of Genomic Variants (DGV) for SF3A3 Gene

Variant ID Type Subtype PubMed ID
esv3417422 CNV insertion 20981092
nsv1008462 CNV gain 25217958
nsv822331 CNV loss 20364138
nsv945885 CNV duplication 23825009

Variation tolerance for SF3A3 Gene

Residual Variation Intolerance Score: 19.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.23; 5.09% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SF3A3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SF3A3

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SF3A3 Gene

Disorders for SF3A3 Gene

Additional Disease Information for SF3A3

No disorders were found for SF3A3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for SF3A3 Gene

Publications for SF3A3 Gene

  1. Splicing factor SF3a60 is the mammalian homologue of PRP9 of S.cerevisiae: the conserved zinc finger-like motif is functionally exchangeable in vivo. (PMID: 7816610) Krämer A … Bilbe G (Nucleic acids research 1994) 2 3 4 58
  2. Specific protein-protein interactions between the essential mammalian spliceosome-associated proteins SAP 61 and SAP 114. (PMID: 8022796) Chiara MD … Reed R (Proceedings of the National Academy of Sciences of the United States of America 1994) 2 3 4 58
  3. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory SG … Prigmore E (Nature 2006) 3 4 58
  4. Solution structures of the SURP domains and the subunit-assembly mechanism within the splicing factor SF3a complex in 17S U2 snRNP. (PMID: 17098193) Kuwasako K … Yokoyama S (Structure (London, England : 1993) 2006) 3 4 58
  5. Immunoaffinity profiling of tyrosine phosphorylation in cancer cells. (PMID: 15592455) Rush J … Comb MJ (Nature biotechnology 2005) 3 4 58

Products for SF3A3 Gene

Sources for SF3A3 Gene

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