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

    Gene ID: 10291, updated on 28-Oct-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
    mouse all
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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_2024_08 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (30331988..30356894, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (30795327..30820234, complement)
    RS_2024_09 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 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. 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
    3. 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
    4. 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
    5. 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

    See all (194) 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_2024_08

    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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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