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    SF3A2 splicing factor 3a subunit 2 [ Homo sapiens (human) ]

    Gene ID: 8175, updated on 27-Nov-2024

    Summary

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    Official Symbol
    SF3A2provided by HGNC
    Official Full Name
    splicing factor 3a subunit 2provided by HGNC
    Primary source
    HGNC:HGNC:10766
    See related
    Ensembl:ENSG00000104897 MIM:600796; AllianceGenome:HGNC:10766
    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
    PRP11; SAP62; PRPF11; SF3a66
    Summary
    This gene encodes subunit 2 of the splicing factor 3a protein complex. The splicing factor 3a heterotrimer includes subunits 1, 2 and 3 and is necessary for the in vitro conversion of 15S U2 snRNP into an active 17S particle that performs pre-mRNA splicing. Subunit 2 interacts with subunit 1 through its amino-terminus while the single zinc finger domain of subunit 2 plays a role in its binding to the 15S U2 snRNP. Subunit 2 may also function independently of its RNA splicing function as a microtubule-binding protein. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in testis (RPKM 28.5), ovary (RPKM 22.4) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SF3A2 in Genome Data Viewer
    Location:
    19p13.3
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (2236824..2248655)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (2210388..2222298)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (2236823..2248654)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene pleckstrin homology domain containing J1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:2234553-2235132 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:2235135-2235743 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9774 Neighboring gene microRNA 1227 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:2236352-2236960 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9775 Neighboring gene microRNA 6789 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:2239731-2240468 Neighboring gene Sharpr-MPRA regulatory region 2271 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:2242682-2242879 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:2243337-2243914 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:2245579-2246079 Neighboring gene AMH 5' regulatory region Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9776 Neighboring gene microRNA 4321 Neighboring gene anti-Mullerian hormone Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13668 Neighboring gene junctional sarcoplasmic reticulum protein 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13669

    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. The pre-mRNA-splicing factor SF3a66 functions as a microtubule-binding and -bundling protein. Takenaka K, et al. Biochem J, 2004 Aug 15. PMID 15142036, Free PMC Article
    2. Correspondence between a mammalian spliceosome component and an essential yeast splicing factor. Bennett M, et al. Science, 1993 Oct 1. PMID 8211113
    3. Structural/functional properties of a mammalian multi-component structure containing all major spliceosomal small nuclear ribonucleoprotein particles. Moraitou M, et al. Biochem J, 1998 May 15. PMID 9576861, Free PMC Article
    4. Combined biochemical and electron microscopic analyses reveal the architecture of the mammalian U2 snRNP. Krämer A, et al. J Cell Biol, 1999 Jun 28. PMID 10385517, Free PMC Article
    5. A role for Cajal bodies in the final steps of U2 snRNP biogenesis. Nesic D, et al. J Cell Sci, 2004 Sep 1. PMID 15316075

    See all (130) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The results indicate that Sf3A2 and Prp31 directly regulate interactions among kinetochores, spindle microtubules and the Ndc80 complex in both Drosophila and human cells.
      Title: Splicing factors Sf3A2 and Prp31 have direct roles in mitotic chromosome segregation.
    2. A genome-wide association study identifies PLCL2 and AP3D1-DOT1L-SF3A2 as new susceptibility loci for myocardial infarction in Japanese
      Title: A genome-wide association study identifies PLCL2 and AP3D1-DOT1L-SF3A2 as new susceptibility loci for myocardial infarction in Japanese.
    3. 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.
    4. 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
    A genome-wide association study identifies PLCL2 and AP3D1-DOT1L-SF3A2 as new susceptibility loci for myocardial infarction in Japanese.
    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)

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Rev rev HIV-1 Rev interacting protein, splicing factor 3a, subunit 2 (SF3A2), is identified by the in-vitro binding experiments involving cytosolic or nuclear extracts from HeLa cells. The interaction of Rev with SF3A2 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 protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    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 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 
    involved_in positive regulation of neuron projection development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in spliceosomal complex assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    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 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 IEA
    Inferred from Electronic Annotation
    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 2
    Names
    SAP 62
    pre-mRNA splicing factor SF3A, subunit 2
    spliceosome associated protein 62
    splicing factor 3a, subunit 2, 66kD
    splicing factor 3a, subunit 2, 66kDa

    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.

    mRNA and Protein(s)

    1. NM_007165.5 → NP_009096.2  splicing factor 3A subunit 2

      See identical proteins and their annotated locations for NP_009096.2

      Status: REVIEWED

      Source sequence(s)
      BC009903, BC015804, BG325385
      Consensus CDS
      CCDS12084.1
      UniProtKB/Swiss-Prot
      B2RBU1, D6W605, O75245, Q15428
      Related
      ENSP00000221494.3, ENST00000221494.10
      Conserved Domains (2) summary
      COG5246
      Location:1 → 217
      PRP11; Splicing factor 3a, subunit 2 [RNA processing and modification]
      PRK07764
      Location:302 → 427
      PRK07764; DNA polymerase III subunits gamma and tau; Validated

    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_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      2236824..2248655
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      2210388..2222298
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q15428.2 GenPept UniProtKB/Swiss-Prot:Q15428

    Gene LinkOut

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