This gene encodes a subunit of the splicing factor 3a protein complex. The splicing factor 3a heterotrimer is a component of the mature U2 small nuclear ribonucleoprotein particle (snRNP). U2 small nuclear ribonucleoproteins play a critical role in spliceosome assembly and pre-mRNA splicing. [provided by RefSeq, Aug 2014] See more...

Aliases for SF3A1 Gene

Aliases for SF3A1 Gene

  • Splicing Factor 3a Subunit 1 2 3 5
  • SAP114 2 3 4
  • Splicing Factor 3a, Subunit 1, 120kDa 2 3
  • Splicing Factor 3a, Subunit 1, 120kD 2 3
  • Spliceosome-Associated Protein 114 3 4
  • Splicing Factor 3A Subunit 1 3 4
  • SAP 114 3 4
  • SF3a120 2 4
  • PRPF21 2 3
  • Pre-MRNA Splicing Factor SF3a (120 KDa Subunit) 3
  • Splicing Factor 3 Subunit 1 3
  • Pre-MRNA Processing 21 3
  • SF3A120 3
  • PRP21 3
  • SF3A1 5
  • Prp21 2

External Ids for SF3A1 Gene

Previous GeneCards Identifiers for SF3A1 Gene

  • GC22M027424
  • GC22M029052
  • GC22M029054
  • GC22M030727
  • GC22M013689

Summaries for SF3A1 Gene

Entrez Gene Summary for SF3A1 Gene

  • This gene encodes a subunit of the splicing factor 3a protein complex. The splicing factor 3a heterotrimer is a component of the mature U2 small nuclear ribonucleoprotein particle (snRNP). U2 small nuclear ribonucleoproteins play a critical role in spliceosome assembly and pre-mRNA splicing. [provided by RefSeq, Aug 2014]

GeneCards Summary for SF3A1 Gene

SF3A1 (Splicing Factor 3a Subunit 1) is a Protein Coding gene. Diseases associated with SF3A1 include Retinitis Pigmentosa 61 and Colorectal Cancer. Among its related pathways are Gene Expression and mRNA Splicing - Major Pathway. Gene Ontology (GO) annotations related to this gene include RNA binding.

UniProtKB/Swiss-Prot Summary for SF3A1 Gene

  • Involved in pre-mRNA splicing as a component of the splicing factor SF3A complex that contributes to the assembly of the 17S U2 snRNP, and the subsequent assembly of the pre-spliceosome 'E' complex and the pre-catalytic spliceosome 'A' complex (PubMed:10882114, PubMed:11533230). Involved in pre-mRNA splicing as a component of pre-catalytic spliceosome 'B' complexes (PubMed:29360106, PubMed:30315277).

Gene Wiki entry for SF3A1 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SF3A1 Gene

Genomics for SF3A1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SF3A1 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SF3A1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SF3A1

Top Transcription factor binding sites by QIAGEN in the SF3A1 gene promoter:
  • AP-2alpha
  • AP-2alphaA
  • E47
  • HNF-3beta
  • Nkx2-5
  • Olf-1
  • p53
  • POU2F1
  • POU2F1a

Genomic Locations for SF3A1 Gene

Genomic Locations for SF3A1 Gene
chr22:30,331,988-30,356,919
(GRCh38/hg38)
Size:
24,932 bases
Orientation:
Minus strand
chr22:30,727,977-30,752,936
(GRCh37/hg19)
Size:
24,960 bases
Orientation:
Minus strand

Genomic View for SF3A1 Gene

Genes around SF3A1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SF3A1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SF3A1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SF3A1 Gene

Proteins for SF3A1 Gene

  • Protein details for SF3A1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q15459-SF3A1_HUMAN
    Recommended name:
    Splicing factor 3A subunit 1
    Protein Accession:
    Q15459
    Secondary Accessions:
    • E9PAW1

    Protein attributes for SF3A1 Gene

    Size:
    793 amino acids
    Molecular mass:
    88886 Da
    Quaternary structure:
    • Component of splicing factor SF3A which is composed of three subunits; SF3A3/SAP61, SF3A2/SAP62 and SF3A1/SAP114 (PubMed:10882114, PubMed:11533230, PubMed:21349847). SF3A1 functions as scaffold that interacts directly with both SF3A2 and SF3A3 (PubMed:11533230, PubMed:21349847, PubMed:17098193). SF3A associates with the splicing factor SF3B and a 12S RNA unit to form the mature 17S U2 small nuclear ribonucleoprotein complex (17S U2 snRNP) (PubMed:10882114, PubMed:11533230). Identified in the spliceosome 'E' complex, a precursor of the spliceosome 'A' complex (PubMed:10882114). Identified in the spliceosome 'A' and 'B' complexes (PubMed:10882114, PubMed:29360106, PubMed:30315277). Identified in the spliceosome 'C' complex (PubMed:11991638).

    Three dimensional structures from OCA and Proteopedia for SF3A1 Gene

    Alternative splice isoforms for SF3A1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SF3A1 Gene

Post-translational modifications for SF3A1 Gene

  • Ubiquitination at Lys55, Lys80, Lys188, Lys223, Lys251, Lys419, Lys467, and Lys708
  • Modification sites at PhosphoSitePlus

Other Protein References for SF3A1 Gene

No data available for DME Specific Peptides for SF3A1 Gene

Domains & Families for SF3A1 Gene

Gene Families for SF3A1 Gene

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

Protein Domains for SF3A1 Gene

InterPro:
Blocks:
  • Ubiquitin domain
  • SWAP/Surp
ProtoNet:

Suggested Antigen Peptide Sequences for SF3A1 Gene

GenScript: Design optimal peptide antigens:
  • Spliceosome-associated protein 114 (SF3A1_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q15459

UniProtKB/Swiss-Prot:

SF3A1_HUMAN :
  • SURP motif 2 mediates direct binding to SF3A3.
Domain:
  • SURP motif 2 mediates direct binding to SF3A3.
genes like me logo Genes that share domains with SF3A1: view

Function for SF3A1 Gene

Molecular function for SF3A1 Gene

UniProtKB/Swiss-Prot Function:
Involved in pre-mRNA splicing as a component of the splicing factor SF3A complex that contributes to the assembly of the 17S U2 snRNP, and the subsequent assembly of the pre-spliceosome 'E' complex and the pre-catalytic spliceosome 'A' complex (PubMed:10882114, PubMed:11533230). Involved in pre-mRNA splicing as a component of pre-catalytic spliceosome 'B' complexes (PubMed:29360106, PubMed:30315277).

Phenotypes From GWAS Catalog for SF3A1 Gene

Gene Ontology (GO) - Molecular Function for SF3A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding IEA,IDA 10882114
GO:0005515 protein binding IPI 10976766
genes like me logo Genes that share ontologies with SF3A1: view
genes like me logo Genes that share phenotypes with SF3A1: view

Animal Model Products

CRISPR Products

miRNA for SF3A1 Gene

miRTarBase miRNAs that target SF3A1

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SF3A1

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for SF3A1 Gene

Localization for SF3A1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SF3A1 Gene

Nucleus. 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 SF3A1 gene
Compartment Confidence
nucleus 5
cytosol 3
plasma membrane 2
extracellular 1
cytoskeleton 1
mitochondrion 1
peroxisome 1
endoplasmic reticulum 1
endosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear speckles (4)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SF3A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA,IDA 10882114
GO:0005654 nucleoplasm TAS --
GO:0005681 spliceosomal complex IDA 9731529
GO:0005684 U2-type spliceosomal complex IDA 10882114
GO:0005686 U2 snRNP IDA 10882114
genes like me logo Genes that share ontologies with SF3A1: view

Pathways & Interactions for SF3A1 Gene

genes like me logo Genes that share pathways with SF3A1: view

Pathways by source for SF3A1 Gene

1 KEGG pathway for SF3A1 Gene

Gene Ontology (GO) - Biological Process for SF3A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000389 mRNA 3'-splice site recognition TAS 15647371
GO:0000398 mRNA splicing, via spliceosome TAS --
GO:0006396 RNA processing IEA --
GO:0006397 mRNA processing IMP 15647371
GO:0008380 RNA splicing IEA --
genes like me logo Genes that share ontologies with SF3A1: view

No data available for SIGNOR curated interactions for SF3A1 Gene

Drugs & Compounds for SF3A1 Gene

No Compound Related Data Available

Transcripts for SF3A1 Gene

mRNA/cDNA for SF3A1 Gene

2 REFSEQ mRNAs :
18 NCBI additional mRNA sequence :
10 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SF3A1

Alternative Splicing Database (ASD) splice patterns (SP) for SF3A1 Gene

ExUns: 1a · 1b ^ 2a · 2b ^ 3a · 3b ^ 4a · 4b ^ 5 ^ 6a · 6b ^ 7 ^ 8 ^ 9a · 9b ^ 10 ^ 11 ^ 12a · 12b · 12c ^ 13 ^ 14a · 14b ^ 15 ^ 16a · 16b ^
SP1: -
SP2: -
SP3: -
SP4: - - -
SP5:
SP6:
SP7: - - - - - - - - - - - - - -
SP8:
SP9:
SP10:

ExUns: 17 ^ 18
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:

Relevant External Links for SF3A1 Gene

GeneLoc Exon Structure for
SF3A1

Expression for SF3A1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SF3A1 Gene

Protein differential expression in normal tissues from HIPED for SF3A1 Gene

This gene is overexpressed in Lymph node (14.5) and Peripheral blood mononuclear cells (8.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SF3A1 Gene



Protein tissue co-expression partners for SF3A1 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SF3A1

SOURCE GeneReport for Unigene cluster for SF3A1 Gene:

Hs.406277

mRNA Expression by UniProt/SwissProt for SF3A1 Gene:

Q15459-SF3A1_HUMAN
Tissue specificity: Ubiquitously expressed.

Evidence on tissue expression from TISSUES for SF3A1 Gene

  • Nervous system(4.8)
  • Liver(4.6)
  • Blood(4.6)
  • Skin(3.6)
  • Kidney(3.5)
  • Lung(3.3)
  • Bone marrow(3.2)
  • Intestine(3.1)
  • Muscle(3.1)
  • Heart(3)
  • Lymph node(2.9)
  • Eye(2.9)
  • Pancreas(2.9)
  • Thyroid gland(2.9)
  • Adrenal gland(2.6)
  • Gall bladder(2.6)
  • Stomach(2.6)
  • Spleen(2.3)
genes like me logo Genes that share expression patterns with SF3A1: 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 SF3A1 Gene

Orthologs for SF3A1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for SF3A1 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia SF3A1 30 31
  • 99.75 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia SF3A1 31
  • 98 (a)
OneToOne
Dog
(Canis familiaris)
Mammalia SF3A1 30 31
  • 91.85 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia SF3A1 30 31
  • 91.38 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Sf3a1 30 17 31
  • 90.67 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Sf3a1 30
  • 90.16 (n)
Platypus
(Ornithorhynchus anatinus)
Mammalia SF3A1 31
  • 74 (a)
OneToOne
Chicken
(Gallus gallus)
Aves SF3A1 30 31
  • 81.07 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia SF3A1 31
  • 88 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia LOC734097 30
  • 77.54 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.7478 30
Zebrafish
(Danio rerio)
Actinopterygii sf3a1 30 30 31
  • 79.04 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP011328 30
  • 62.42 (n)
Fruit Fly
(Drosophila melanogaster)
Insecta CG16941 30 31 32
  • 61.67 (n)
OneToOne
Worm
(Caenorhabditis elegans)
Secernentea prp-21 30 31 32
  • 52.81 (n)
OneToOne
K. Lactis Yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0C03322g 30
  • 41.99 (n)
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes PRP21 31 33
  • 29 (a)
OneToOne
A. gosspyii yeast
(Eremothecium gossypii)
Saccharomycetes AGOS_AFR645W 30
Rice
(Oryza sativa)
Liliopsida Os.7264 30
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.6505 31
  • 52 (a)
OneToOne
Bread mold
(Neurospora crassa)
Ascomycetes NCU01913 30
  • 51.65 (n)
Fission Yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes sap114 30
  • 49.57 (n)
Species where no ortholog for SF3A1 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • 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 Vase (Ciona intestinalis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for SF3A1 Gene

ENSEMBL:
Gene Tree for SF3A1 (if available)
TreeFam:
Gene Tree for SF3A1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SF3A1: view image

Paralogs for SF3A1 Gene

No data available for Paralogs for SF3A1 Gene

Variants for SF3A1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SF3A1 Gene

SNP ID Clinical significance and condition Chr 22 pos Variation AA Info Type
777682 Benign: not provided 30,344,925(-) C/G INTRON_VARIANT
rs765594577 A colorectal cancer sample p.Arg511Trp

Additional dbSNP identifiers (rs#s) for SF3A1 Gene

Structural Variations from Database of Genomic Variants (DGV) for SF3A1 Gene

Variant ID Type Subtype PubMed ID
esv1167139 CNV deletion 17803354
esv2724134 CNV deletion 23290073
esv2724135 CNV deletion 23290073
esv2724136 CNV deletion 23290073
esv3234984 CNV deletion 24192839
esv3558050 CNV deletion 23714750
esv996703 CNV deletion 20482838
nsv1064350 CNV gain 25217958
nsv1066179 CNV gain 25217958
nsv1110864 OTHER inversion 24896259
nsv3593 CNV deletion 18451855
nsv829171 CNV loss 20364138
nsv834174 CNV gain+loss 17160897

Variation tolerance for SF3A1 Gene

Residual Variation Intolerance Score: 14.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.58; 30.51% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SF3A1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SF3A1

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SF3A1 Gene

Disorders for SF3A1 Gene

MalaCards: The human disease database

(2) MalaCards diseases for SF3A1 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
retinitis pigmentosa 61
  • rp61
colorectal cancer
  • crc
- elite association - COSMIC cancer census association via MalaCards
Search SF3A1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for SF3A1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with SF3A1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SF3A1 Gene

Publications for SF3A1 Gene

  1. Mammalian splicing factor SF3a120 represents a new member of the SURP family of proteins and is homologous to the essential splicing factor PRP21p of Saccharomyces cerevisiae. (PMID: 7489498) Krämer A … Bilbe G (RNA (New York, N.Y.) 1995) 2 3 4 23
  2. Domains in human splicing factors SF3a60 and SF3a66 required for binding to SF3a120, assembly of the 17S U2 snRNP, and prespliceosome formation. (PMID: 11533230) Nesic D … Krämer A (Molecular and cellular biology 2001) 3 4 23
  3. Structure of the human activated spliceosome in three conformational states. (PMID: 29360106) Zhang X … Shi Y (Cell research 2018) 3 4
  4. Interaction domains and nuclear targeting signals in subunits of the U2 small nuclear ribonucleoprotein particle-associated splicing factor SF3a. (PMID: 21349847) Huang CJ … Krämer A (The Journal of biological chemistry 2011) 3 4
  5. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 41

Products for SF3A1 Gene

Sources for SF3A1 Gene