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

Summary

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
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

Genomic context

Location:: 19p13.3

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
109.20190905	current	GRCh38.p13 (GCF_000001405.39)	19	NC_000019.10 (2236824..2248655)
105	previous assembly	GRCh37.p13 (GCF_000001405.25)	19	NC_000019.9 (2236816..2248678)

Chromosome 19 - NC_000019.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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

NHGRI GWAS Catalog

Description
A genome-wide association study identifies PLCL2 and AP3D1-DOT1L-SF3A2 as new susceptibility loci for myocardial infarction in Japanese. NHGRI GWA Catalog NHGRI GWA CatalogPubMed

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 BioSystems

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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

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Homology

Orthologs from Annotation Pipeline: 271 organisms have orthologs with human gene SF3A2
Orthologs

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
RNA binding	HDA 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
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	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
positive regulation of neuron projection development	IEA Inferred from Electronic Annotation more info
spliceosomal complex assembly	IBA Inferred from Biological aspect of Ancestor more info	PubMed

Component	Evidence Code	Pubs
U2 snRNP	IBA Inferred from Biological aspect of Ancestor more info	PubMed
U2 snRNP	IDA Inferred from Direct Assay more info	PubMed
U2-type precatalytic spliceosome	IDA Inferred from Direct Assay more info	PubMed
U2-type prespliceosome	IBA Inferred from Biological aspect of Ancestor more info	PubMed
catalytic step 2 spliceosome	IBA Inferred from Biological aspect of Ancestor 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	TAS Traceable Author Statement more info
nucleus	IDA Inferred from Direct Assay more info	PubMed
spliceosomal complex	IDA Inferred from Direct Assay 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)

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

Q15428

UniProtKB/TrEMBL

Q05DF2

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