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

Gene ID: 10946, updated on 6-Jan-2019

Summary

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
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

Genomic context

See SF3A3 in Genome Data Viewer
Location:
1p34.3
Exon count:
17
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 1 NC_000001.11 (37956975..37990110, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (38422647..38456019, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene inositol polyphosphate-5-phosphatase B Neighboring gene RNA, U6 small nuclear 584, pseudogene Neighboring gene uncharacterized LOC105378651 Neighboring gene RNA, U6 small nuclear 510, pseudogene Neighboring gene four and a half LIM domains 3

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

HIV-1 interactions

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 BioSystems

  • Diurnally Regulated Genes with Circadian Orthologs, organism-specific biosystem (from WikiPathways)
    Diurnally Regulated Genes with Circadian Orthologs, organism-specific biosystemHuman genes regulated in the diurnal comparison with orthologues that display circadian regulation in mouse heart and liver (Panda 2002, Storch 2002), and SCN (Panda 2002). The 608 significantly regu...
  • Gene Expression, organism-specific biosystem (from REACTOME)
    Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
  • Processing of Capped Intron-Containing Pre-mRNA, organism-specific biosystem (from REACTOME)
    Processing of Capped Intron-Containing Pre-mRNA, organism-specific biosystemCo-transcriptional pre-mRNA splicing is not obligatory. Pre-mRNA splicing begins co-transcriptionally and often continues post-transcriptionally. Human genes contain an average of nine introns per ge...
  • Spliceosome, organism-specific biosystem (from KEGG)
    Spliceosome, organism-specific biosystemAfter transcription, eukaryotic mRNA precursors contain protein-coding exons and noncoding introns. In the following splicing, introns are excised and exons are joined by a macromolecular complex, th...
  • Spliceosome, conserved biosystem (from KEGG)
    Spliceosome, conserved biosystemAfter transcription, eukaryotic mRNA precursors contain protein-coding exons and noncoding introns. In the following splicing, introns are excised and exons are joined by a macromolecular complex, th...
  • Spliceosome, U2-snRNP, organism-specific biosystem (from KEGG)
    Spliceosome, U2-snRNP, organism-specific biosystemStructural complex; Genetic information processing; Spliceosome
  • Spliceosome, U2-snRNP, conserved biosystem (from KEGG)
    Spliceosome, U2-snRNP, conserved biosystemStructural complex; Genetic information processing; Spliceosome
  • mRNA Processing, organism-specific biosystem (from WikiPathways)
    mRNA Processing, organism-specific biosystemThis process describes the conversion of precursor messenger RNA into mature messenger RNA (mRNA). The pre-mRNA molecule undergoes three main modifications. These modifications are 5' capping, 3' po...
  • mRNA Splicing, organism-specific biosystem (from REACTOME)
    mRNA Splicing, organism-specific biosystemThe process in which excision of introns from the primary transcript of messenger RNA (mRNA) is followed by ligation of the two exon termini exposed by removal of each intron, is called mRNA splicing...
  • mRNA Splicing - Major Pathway, organism-specific biosystem (from REACTOME)
    mRNA Splicing - Major Pathway, organism-specific biosystemThe splicing of pre-mRNA occurs within a large, very dynamic complex, designated the 'spliceosome'. The 50-60S spliceosomes are estimated to be 40-60 nm in diameter, and have molecular weights in the...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

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

General protein information

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)

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_001320830.1NP_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 (3) summary
    pfam11931
    Location:270447
    DUF3449; Domain of unknown function (DUF3449)
    pfam13297
    Location:191250
    Telomere_Sde2_2; Telomere stability C-terminal
    pfam16837
    Location:76151
    SF3A3; Pre-mRNA-splicing factor SF3A3, of SF3a complex, Prp9
  2. NM_006802.4NP_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
    Q12874
    Related
    ENSP00000362110.4, ENST00000373019.4
    Conserved Domains (4) summary
    pfam11931
    Location:323500
    DUF3449; Domain of unknown function (DUF3449)
    pfam12108
    Location:74100
    SF3a60_bindingd; Splicing factor SF3a60 binding domain
    pfam13297
    Location:244303
    Telomere_Sde2_2; Telomere stability C-terminal
    pfam16837
    Location:129204
    SF3A3; Pre-mRNA-splicing factor SF3A3, of SF3a complex, Prp9

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p12 Primary Assembly

    Range
    37956975..37990110 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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