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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. GO annotations related to this gene include poly(A) RNA binding and 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

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

Genomics for SF3A1 Gene

Regulatory Elements for SF3A1 Gene

Enhancers for SF3A1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH22G030322 1.6 FANTOM5 ENCODE dbSUPER 13.2 +30.0 30028 8.0 HDGF PKNOX1 WRNIP1 ARID4B SIN3A YY1 TCF12 GLIS2 SP3 SP5 RNF215 CCDC157 CASTOR1 SEC14L3 SF3A1 ENSG00000248751 SEC14L2 ENSG00000249590 LIF OSM
GH22G030390 1.4 Ensembl ENCODE dbSUPER 11 -34.5 -34497 1.4 ELF3 CBX3 ARID4B YBX1 RAD21 ZNF143 FOS MIXL1 THAP11 ZNF654 CASTOR1 TBC1D10A ENSG00000248751 OSM CCDC157 SF3A1 SEC14L3 ENSG00000181123 LIF SEC14L2
GH22G030332 1.1 ENCODE dbSUPER 13.2 +23.9 23887 0.8 HDAC1 PKNOX1 ARNT TCF12 ZNF766 GATA2 CREM CEBPB NCOA1 ZEB2 RNF215 CCDC157 SF3A1 ENSG00000248751 CASTOR1 SEC14L2 ENSG00000249590 LIF SEC14L3 TBC1D10A
GH22G030392 1 ENCODE dbSUPER 11 -36.0 -35961 1.1 BHLHE40 MAX EBF1 RAD21 NR2F2 YY1 EED IKZF1 HNF4G HNF4A CASTOR1 TBC1D10A ENSG00000248751 OSM CCDC157 SF3A1 ENSG00000181123 LIF SEC14L3 SEC14L2
GH22G030190 2 FANTOM5 Ensembl ENCODE dbSUPER 5.1 +161.7 161655 9.1 CREB3L1 ZFP64 DMAP1 FEZF1 YY1 ZNF143 SP3 NFYC TBX21 ZNF610 OSM MTMR3 HORMAD2-AS1 ASCC2 SELENOM SF3A1 SLC35E4 MTFP1 DUSP18 CCDC157
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SF3A1 on UCSC Golden Path with GeneCards custom track

Promoters for SF3A1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000145212 147 2001 HDGF PKNOX1 CREB3L1 ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 SLC30A9

Genomic Location for SF3A1 Gene

Chromosome:
22
Start:
30,331,988 bp from pter
End:
30,356,947 bp from pter
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:
    • 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 Lys55, Lys188, isoforms=2223, isoforms=2251, 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

Protein Domains for SF3A1 Gene

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

No data available for Gene Families for SF3A1 Gene

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.

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

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

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 IBA,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 34 35
  • 99.75 (n)
oppossum
(Monodelphis domestica)
Mammalia SF3A1 35
  • 98 (a)
OneToOne
dog
(Canis familiaris)
Mammalia SF3A1 34 35
  • 91.85 (n)
cow
(Bos Taurus)
Mammalia SF3A1 34 35
  • 91.38 (n)
mouse
(Mus musculus)
Mammalia Sf3a1 34 16 35
  • 90.67 (n)
rat
(Rattus norvegicus)
Mammalia Sf3a1 34
  • 90.16 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia SF3A1 35
  • 74 (a)
OneToOne
chicken
(Gallus gallus)
Aves SF3A1 34 35
  • 81.07 (n)
lizard
(Anolis carolinensis)
Reptilia SF3A1 35
  • 88 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC734097 34
  • 77.54 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.7478 34
zebrafish
(Danio rerio)
Actinopterygii sf3a1 34 34 35
  • 79.04 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP011328 34
  • 62.42 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG16941 36 34 35
  • 61.67 (n)
worm
(Caenorhabditis elegans)
Secernentea prp-21 36 34 35
  • 52.81 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0C03322g 34
  • 41.99 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes PRP21 35 37
  • 29 (a)
OneToOne
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AFR645W 34
rice
(Oryza sativa)
Liliopsida Os.7264 34
sea squirt
(Ciona savignyi)
Ascidiacea CSA.6505 35
  • 52 (a)
OneToOne
bread mold
(Neurospora crassa)
Ascomycetes NCU01913 34
  • 51.65 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes sap114 34
  • 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 Sequence Context AA Info Type
rs765594577 A colorectal cancer sample 30,339,001(+) GGTCC(A/G)GGCCA reference, missense
rs1000043391 -- 30,345,911(+) GAAGG(A/G)ATGGC intron-variant
rs1000053334 -- 30,346,149(+) CATCA(A/G)TACTT intron-variant
rs1000137910 -- 30,346,214(+) CTCCC(C/T)GGGTG intron-variant
rs1000177740 -- 30,339,837(+) TGGCA(C/G)AGTCA 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)

Relevant External Links 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

Relevant External Links for SF3A1

Genetic Association Database (GAD)
SF3A1
Human Genome Epidemiology (HuGE) Navigator
SF3A1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SF3A1

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) Kraemer A. … Bilbe G. (RNA 1995) 2 3 4 22 64
  2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose J.E. … Uhl G.R. (Mol. Med. 2010) 3 46 64
  3. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PMID: 17081983) Olsen J.V. … Mann M. (Cell 2006) 3 4 64
  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 2006) 3 4 64
  5. Immunoaffinity profiling of tyrosine phosphorylation in cancer cells. (PMID: 15592455) Rush J. … Comb M.J. (Nat. Biotechnol. 2005) 3 4 64

Products for SF3A1 Gene

  • Addgene plasmids for SF3A1

Sources for SF3A1 Gene

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