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

Gene ID: 8175, updated on 7-Apr-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
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Genomic context

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Location:
19p13.3
Exon count:
9
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (2236824..2248655)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (2210388..2222298)
105.20220307 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. 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
  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. Correspondence between a mammalian spliceosome component and an essential yeast splicing factor. Bennett M, et al. Science, 1993 Oct 1. PMID 8211113
  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 (106) 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)

Genotypes

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_2023_10

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

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

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