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SF3A3 splicing factor 3a subunit 3 [ Homo sapiens (human) ]

Gene ID: 10946, updated on 7-Apr-2024

Summary

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Official Symbol
SF3A3provided by HGNC
Official Full Name
splicing factor 3a subunit 3provided by HGNC
Primary source
HGNC:HGNC:10767
See related
Ensembl:ENSG00000183431 MIM:605596; AllianceGenome:HGNC:10767
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
PRP9; PRPF9; SAP61; SF3a60
Summary
This gene encodes subunit 3 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 3 interacts with subunit 1 through its amino-terminus while the zinc finger domain of subunit 3 plays a role in its binding to the 15S U2 snRNP. This gene has a pseudogene on chromosome 20. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2016]
Expression
Ubiquitous expression in bone marrow (RPKM 22.5), lymph node (RPKM 20.6) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
1p34.3
Exon count:
17
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (37956975..37990022, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (37823865..37857205, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (38422647..38455694, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene inositol polyphosphate-5-phosphatase B Neighboring gene uncharacterized LOC124904043 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 778 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:38396367-38396866 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 683 Neighboring gene uncharacterized LOC105378651 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:38412547-38413076 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:38414283-38414956 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 780 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 781 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:38456307-38456852 Neighboring gene Sharpr-MPRA regulatory region 8264 Neighboring gene RNA, U6 small nuclear 510, pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:38463160-38464081 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:38465171-38465958 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:38465959-38466746 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:38469196-38470004 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 684 Neighboring gene four and a half LIM domains 3

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. Oncogenic translation directs spliceosome dynamics revealing an integral role for SF3A3 in breast cancer. Cieśla M, et al. Mol Cell, 2021 Apr 1. PMID 33662273
  2. CircSCAP interacts with SF3A3 to inhibit the malignance of non-small cell lung cancer by activating p53 signaling. Chen D, et al. J Exp Clin Cancer Res, 2022 Apr 1. PMID 35365208, Free PMC Article
  3. Specific inhibition of transcriptional activity of the constitutive androstane receptor (CAR) by the splicing factor SF3a3. Yun HJ, et al. Biol Chem, 2008 Oct. PMID 18713018
  4. Solution structures of the SURP domains and the subunit-assembly mechanism within the splicing factor SF3a complex in 17S U2 snRNP. Kuwasako K, et al. Structure, 2006 Nov. PMID 17098193
  5. Splicing factor SF3a60 is the mammalian homologue of PRP9 of S.cerevisiae: the conserved zinc finger-like motif is functionally exchangeable in vivo. Krämer A, et al. Nucleic Acids Res, 1994 Dec 11. PMID 7816610, Free PMC Article

See all (146) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. CircSCAP interacts with SF3A3 to inhibit the malignance of non-small cell lung cancer by activating p53 signaling.
    Title: CircSCAP interacts with SF3A3 to inhibit the malignance of non-small cell lung cancer by activating p53 signaling.
  2. Oncogenic translation directs spliceosome dynamics revealing an integral role for SF3A3 in breast cancer.
    Title: Oncogenic translation directs spliceosome dynamics revealing an integral role for SF3A3 in breast cancer.
  3. The interaction between CSR1 and SF3A3 led to migration of SF3A3 from nucleus to cytoplasm. The cytoplasmic redistribution of SF3A3 significantly reduced the splicing efficiency of epidermal growth factor receptor and platelet-derived growth factor receptor.
    Title: Cellular stress response 1 down-regulates the expression of epidermal growth factor receptor and platelet-derived growth factor receptor through inactivation of splicing factor 3A3.
  4. SF3a3 functions as a co-repressor of Constitutive Androstane Receptor transcriptional activity, in addition to its canonical function.
    Title: Specific inhibition of transcriptional activity of the constitutive androstane receptor (CAR) by the splicing factor SF3a3.
  5. 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

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 3 (SF3A3), is identified by the in-vitro binding experiments involving cytosolic or nuclear extracts from HeLa cells. The interaction of Rev with SF3A3 is increased by RRE PubMed
retropepsin gag-pol HIV-1 PR is identified to have a physical interaction with splicing factor 3a, subunit 3 (SF3A3) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses 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 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 RNA splicing, via transesterification reactions TAS
Traceable Author Statement
more info
 PubMed 
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 IBA
Inferred from Biological aspect of Ancestor
more info
  
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 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 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 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 IBA
Inferred from Biological aspect of Ancestor
more info
  
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 3
Names
SAP 61
pre-mRNA splicing factor SF3a (60kD)
spliceosome associated protein 61
splicing factor 3a, subunit 3, 60kD
splicing factor 3a, subunit 3, 60kDa

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_001320830.2 → NP_001307759.1  splicing factor 3A subunit 3 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks alternate in-frame exons in the 5' coding region, compared to variant 1. The encoded isoform (2) is shorter, compared to isoform 1.
    Source sequence(s)
    AK301424, AL603790, BM455074, BM702776, DA835019
    UniProtKB/TrEMBL
    B4DW90
    Conserved Domains (2) summary
    COG5188
    Location:77 → 448
    PRP9; Splicing factor 3a, subunit 3 [RNA processing and modification]
    pfam11931
    Location:270 → 447
    DUF3449; Domain of unknown function (DUF3449)

  2. NM_006802.4 → NP_006793.1  splicing factor 3A subunit 3 isoform 1

    See identical proteins and their annotated locations for NP_006793.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AL603790, BC002395, BC011523, BM702776
    Consensus CDS
    CCDS428.1
    UniProtKB/Swiss-Prot
    D3DPT5, Q12874, Q15460, Q5VT87
    UniProtKB/TrEMBL
    A8K566, A8K7V1, B3KY12, Q53HM6
    Related
    ENSP00000362110.4, ENST00000373019.5
    Conserved Domains (2) summary
    COG5188
    Location:2 → 501
    PRP9; Splicing factor 3a, subunit 3 [RNA processing and modification]
    pfam11931
    Location:323 → 500
    DUF3449; Domain of unknown function (DUF3449)

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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    37956975..37990022 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    37823865..37857205 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q12874.1 GenPept UniProtKB/Swiss-Prot:Q12874

Gene LinkOut

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