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Aliases for SF3A1 Gene

Aliases for SF3A1 Gene

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

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. Among its related pathways are mRNA Splicing - Major Pathway and Gene Expression. Gene Ontology (GO) annotations related to this gene include RNA binding.

UniProtKB/Swiss-Prot for SF3A1 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 SF3A1 Gene

Additional gene information for SF3A1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SF3A1 Gene

Genomics for SF3A1 Gene

GeneHancer (GH) Regulatory Elements for SF3A1 Gene

Promoters and enhancers for SF3A1 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
GH22I030355 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 550.8 +0.4 436 2.6 HDGF PKNOX1 ARID4B SIN3A FEZF1 DMAP1 ZNF2 IRF4 YY1 SLC30A9 CCDC157 SF3A1 RNF215 CASTOR1 SEC14L6 TBC1D10A
GH22I030234 Promoter/Enhancer 2.8 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 54.2 +110.2 110217 24.6 PKNOX1 ARID4B SIN3A ZNF2 ZBTB7B ZNF416 ZNF143 FOS ZNF263 SP5 LIF LOC91370 TUG1 SF3A1 EWSR1 MORC2 PES1 RNF215 TBC1D10A ENSG00000272689
GH22I030415 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 31.1 -64.5 -64492 11.6 MLX FEZF1 DMAP1 YBX1 IRF4 YY1 SLC30A9 ZNF213 ZNF143 SP3 RNF215 ENSG00000272689 ENSG00000273350 MTFP1 RNU6-564P TUG1 SF3A1 TBC1D10A SEC14L3 PES1
GH22I029600 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 34.1 +753.6 753649 4.7 HDGF PKNOX1 ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 ZNF766 E2F8 NF2 GC22P029604 GC22P029605 GC22P029606 SF3A1 THOC5 EWSR1 CCDC117 NIPSNAP1 UQCR10
GH22I029552 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 31.2 +802.6 802606 3.5 HDGF PKNOX1 SMAD1 ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 THOC5 EWSR1 SF3A1 TBC1D10A NIPSNAP1 ENSG00000272858 RNF215 CCDC117 RHBDD3 LOC91370
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SF3A1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SF3A1 gene promoter:

Genomic Locations for SF3A1 Gene

Genomic Locations for SF3A1 Gene
chr22:30,331,988-30,356,947
(GRCh38/hg38)
Size:
24,960 bases
Orientation:
Minus strand
chr22:30,727,977-30,752,936
(GRCh37/hg19)

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:
    • 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 SF3A3.

    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 posLast=5555, posLast=188188, isoforms=2223, posLast=251251, isoforms=2419, isoforms=2467, and posLast=708708

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

Suggested Antigen Peptide Sequences for SF3A1 Gene

GenScript: Design optimal peptide antigens:

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:
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 SF3A1 Gene

Gene Ontology (GO) - Molecular Function for SF3A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding IDA,IEA 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

Clone Products

  • Addgene plasmids 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

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
plasma membrane 2
peroxisome 2
cytosol 2

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 --
GO:0005654 nucleoplasm TAS --
GO:0005681 spliceosomal complex IDA 9731529
GO:0005684 U2-type spliceosomal complex IDA 10882114
GO:0005686 U2 snRNP IDA 23793891
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:0000381 regulation of alternative mRNA splicing, via spliceosome IBA --
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
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

Unigene Clusters for SF3A1 Gene

Splicing factor 3a, subunit 1, 120kDa:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids 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
ECgene alternative splicing isoforms for
SF3A1

Expression for SF3A1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP 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, PaxDb, MaxQB, and MOPED for SF3A1 Gene



Protein tissue co-expression partners for SF3A1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SF3A1 Gene:

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(4.5)
  • Blood(4.4)
  • Kidney(3)
  • Eye(2.9)
  • Lung(2.9)
  • Skin(2.9)
  • Adrenal gland(2.6)
  • Bone marrow(2.6)
  • Gall bladder(2.6)
  • Heart(2.6)
  • Intestine(2.6)
  • Lymph node(2.6)
  • Muscle(2.6)
  • Pancreas(2.6)
  • Stomach(2.6)
  • Thyroid gland(2.6)
genes like me logo Genes that share expression patterns with SF3A1: view

Primer Products

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 33 34
  • 99.75 (n)
oppossum
(Monodelphis domestica)
Mammalia SF3A1 34
  • 98 (a)
OneToOne
dog
(Canis familiaris)
Mammalia SF3A1 33 34
  • 91.85 (n)
cow
(Bos Taurus)
Mammalia SF3A1 33 34
  • 91.38 (n)
mouse
(Mus musculus)
Mammalia Sf3a1 33 16 34
  • 90.67 (n)
rat
(Rattus norvegicus)
Mammalia Sf3a1 33
  • 90.16 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia SF3A1 34
  • 74 (a)
OneToOne
chicken
(Gallus gallus)
Aves SF3A1 33 34
  • 81.07 (n)
lizard
(Anolis carolinensis)
Reptilia SF3A1 34
  • 88 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC734097 33
  • 77.54 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.7478 33
zebrafish
(Danio rerio)
Actinopterygii sf3a1 33 33 34
  • 79.04 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP011328 33
  • 62.42 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG16941 35 33 34
  • 61.67 (n)
worm
(Caenorhabditis elegans)
Secernentea prp-21 35 33 34
  • 52.81 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0C03322g 33
  • 41.99 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes PRP21 34 36
  • 29 (a)
OneToOne
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AFR645W 33
rice
(Oryza sativa)
Liliopsida Os.7264 33
sea squirt
(Ciona savignyi)
Ascidiacea CSA.6505 34
  • 52 (a)
OneToOne
bread mold
(Neurospora crassa)
Ascomycetes NCU01913 33
  • 51.65 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes sap114 33
  • 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 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)

Paralogs for SF3A1 Gene

No data available for Paralogs for SF3A1 Gene

Variants for SF3A1 Gene

Sequence variations from dbSNP and Humsavar for SF3A1 Gene

SNP ID Clin Chr 22 pos Variation AA Info Type
rs765594577 A colorectal cancer sample 30,339,001(-) G/A coding_sequence_variant, missense_variant
rs1000043391 -- 30,345,911(-) G/A intron_variant
rs1000053334 -- 30,346,149(-) G/A intron_variant
rs1000137910 -- 30,346,214(-) T/C intron_variant
rs1000177740 -- 30,339,837(-) G/C intron_variant

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

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

Disorders for SF3A1 Gene

Additional Disease Information for SF3A1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for SF3A1 Gene.

No data available for MalaCards , 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 22 58
  2. 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 44 58
  3. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PMID: 17081983) Olsen JV … Mann M (Cell 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 SF3A1 Gene

Sources for SF3A1 Gene

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