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SF3A1 splicing factor 3a subunit 1 [ Homo sapiens (human) ]

Gene ID: 10291, updated on 7-Apr-2024

Summary

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Official Symbol
SF3A1provided by HGNC
Official Full Name
splicing factor 3a subunit 1provided by HGNC
Primary source
HGNC:HGNC:10765
See related
Ensembl:ENSG00000099995 MIM:605595; AllianceGenome:HGNC:10765
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
PRP21; PRPF21; SAP114; SF3A120
Summary
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]
Expression
Ubiquitous expression in testis (RPKM 34.4), ovary (RPKM 24.5) and 25 other tissues See more
Orthologs
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Genomic context

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See SF3A1 in Genome Data Viewer
Location:
22q12.2
Exon count:
16
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (30331988..30356894, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (30795327..30820234, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (30727977..30752883, complement)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13604 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13605 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18831 Neighboring gene cytosolic arginine sensor for mTORC1 subunit 1 Neighboring gene TBC1 domain family member 10A Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18832 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13606 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:30700665-30701164 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18833 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18834 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18835 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18836 Neighboring gene origin of replication in TBC1D10A Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:30721337-30722286 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13607 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13608 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13609 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:30753765-30754364 Neighboring gene coiled-coil domain containing 157 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:30766725-30767224 Neighboring gene KIAA1656 protein Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13610 Neighboring gene ring finger protein 215

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Identification of a noncanonical RNA binding domain in the U2 snRNP protein SF3A1. Martelly W, et al. RNA, 2019 Nov. PMID 31383795, Free PMC Article
  2. SF3A1 and pancreatic cancer: new evidence for the association of the spliceosome and cancer. Tian J, et al. Oncotarget, 2015 Nov 10. PMID 26498691, Free PMC Article
  3. The Associations between RNA Splicing Complex Gene SF3A1 Polymorphisms and Colorectal Cancer Risk in a Chinese Population. Chen X, et al. PLoS One, 2015. PMID 26079486, Free PMC Article
  4. Stem-loop 4 of U1 snRNA is essential for splicing and interacts with the U2 snRNP-specific SF3A1 protein during spliceosome assembly. Sharma S, et al. Genes Dev, 2014 Nov 15. PMID 25403181, Free PMC Article
  5. 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. Krämer A, et al. RNA, 1995 May. PMID 7489498, Free PMC Article

See all (171) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Structural insights into recognition of SL4, the UUCG stem-loop, of human U1 snRNA by the ubiquitin-like domain, including the C-terminal tail in the SF3A1 subunit of U2 snRNP.
    Title: Structural insights into recognition of SL4, the UUCG stem-loop, of human U1 snRNA by the ubiquitin-like domain, including the C-terminal tail in the SF3A1 subunit of U2 snRNP.
  2. data show that the UBL domain of SF3A1 can function as an RNA binding domain and that mutations in this region may interfere with U1-SL4 binding
    Title: Identification of a noncanonical RNA binding domain in the U2 snRNP protein SF3A1.
  3. Polymorphisms in SF3A1 gene is associated with pancreatic cancer.
    Title: SF3A1 and pancreatic cancer: new evidence for the association of the spliceosome and cancer.
  4. SF3A1 polymorphisms are not associated with Colorectal Cancer Risk.
    Title: The Associations between RNA Splicing Complex Gene SF3A1 Polymorphisms and Colorectal Cancer Risk in a Chinese Population.
  5. the SF3A mRNA splicing complex controls production of a negative regulator of TLR signaling that limits the extent of innate immune activation.
    Title: Limiting of the innate immune response by SF3A-dependent control of MyD88 alternative mRNA splicing.
  6. show that U1-SL4 interacts with the SF3A1 protein of the U2 snRNP
    Title: Stem-loop 4 of U1 snRNA is essential for splicing and interacts with the U2 snRNP-specific SF3A1 protein during spliceosome assembly.
  7. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
  8. SF3a60, 66, and 120, but not SF1, are essential for pre-mRNA splicing
    Title: Human splicing factor SF3a, but not SF1, is essential for pre-mRNA splicing in vivo.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genetics of coronary artery calcification among African Americans, a meta-analysis.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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Replication interactions

Interaction Pubs
Knockdown of splicing factor 3a, subunit 1 (SF3A1) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 PubMed

Protein interactions

Protein Gene Interaction Pubs
Rev rev HIV-1 Rev interacting protein, splicing factor 3a, subunit 1 (SF3A1), is identified by the in-vitro binding experiments involving cytosolic or nuclear extracts from HeLa cells. The interaction of Rev with SF3A1 is increased by RRE PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA binding HDA PubMed 
enables RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables RNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in U2-type prespliceosome assembly IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in U2-type prespliceosome assembly NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in mRNA 3'-splice site recognition TAS
Traceable Author Statement
more info
 PubMed 
involved_in mRNA cis splicing, via spliceosome IEA
Inferred from Electronic Annotation
more info
  
involved_in mRNA processing IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in mRNA splicing, via spliceosome IC
Inferred by Curator
more info
 PubMed 
involved_in mRNA splicing, via spliceosome IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in mRNA splicing, via spliceosome NAS
Non-traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
part_of U2 snRNP IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of U2 snRNP IDA
Inferred from Direct Assay
more info
 PubMed 
part_of U2 snRNP NAS
Non-traceable Author Statement
more info
 PubMed 
part_of U2-type precatalytic spliceosome IDA
Inferred from Direct Assay
more info
 PubMed 
part_of U2-type prespliceosome IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of U2-type prespliceosome IDA
Inferred from Direct Assay
more info
 PubMed 
part_of U2-type spliceosomal complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of U2-type spliceosomal complex IPI
Inferred from Physical Interaction
more info
 PubMed 
part_of catalytic step 2 spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of catalytic step 2 spliceosome IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nuclear speck IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleus NAS
Non-traceable Author Statement
more info
 PubMed 
part_of spliceosomal complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of spliceosomal complex NAS
Non-traceable Author Statement
more info
 PubMed 

General protein information

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Preferred Names
splicing factor 3A subunit 1
Names
SAP 114
pre-mRNA processing 21
pre-mRNA splicing factor SF3a (120 kDa subunit)
spliceosome-associated protein 114
splicing factor 3 subunit 1
splicing factor 3a, subunit 1, 120kD
splicing factor 3a, subunit 1, 120kDa

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_032902.1 RefSeqGene

    Range
    4978..29937
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_622

mRNA and Protein(s)

  1. NM_005877.6 → NP_005868.1  splicing factor 3A subunit 1

    See identical proteins and their annotated locations for NP_005868.1

    Status: REVIEWED

    Source sequence(s)
    AC004997, BC007684, CK300534
    Consensus CDS
    CCDS13875.1
    UniProtKB/Swiss-Prot
    E9PAW1, Q15459
    UniProtKB/TrEMBL
    B4E091
    Related
    ENSP00000215793.7, ENST00000215793.13
    Conserved Domains (4) summary
    smart00648
    Location:50 → 103
    SWAP; Suppressor-of-White-APricot splicing regulator
    cd01800
    Location:704 → 786
    Ubl_SF3a120; ubiquitin-like (Ubl) domain found in splicing factor 3A 120kDa subunit (SF3a120) and similar proteins
    pfam01805
    Location:165 → 215
    Surp; Surp module
    pfam12230
    Location:232 → 472
    PRP21_like_P; Pre-mRNA splicing factor PRP21 like protein

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    30331988..30356894 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    30795327..30820234 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001005409.1: Suppressed sequence

    Description
    NM_001005409.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q15459.1 GenPept UniProtKB/Swiss-Prot:Q15459

Gene LinkOut

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