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SF3A1 splicing factor 3a subunit 1 [ Homo sapiens (human) ]

Gene ID: 10291, updated on 12-Jan-2019

Summary

Official Symbol
SF3A1provided by HGNC
Official Full Name
splicing factor 3a subunit 1provided by HGNC
Primary source
HGNC:HGNC:10765
See related
Ensembl:ENSG00000099995 MIM:605595
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
PRP21; PRPF21; SAP114; SF3A120
Summary
This gene encodes a subunit of the splicing factor 3a protein complex. The splicing factor 3a heterotrimer is a component of the mature U2 small nuclear ribonucleoprotein particle (snRNP). U2 small nuclear ribonucleoproteins play a critical role in spliceosome assembly and pre-mRNA splicing. [provided by RefSeq, Aug 2014]
Expression
Ubiquitous expression in testis (RPKM 34.4), ovary (RPKM 24.5) and 25 other tissues See more
Orthologs

Genomic context

See SF3A1 in Genome Data Viewer
Location:
22q12.2
Exon count:
16
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 22 NC_000022.11 (30331988..30356947, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (30727977..30752931, complement)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene cytosolic arginine sensor for mTORC1 subunit 1 Neighboring gene TBC1 domain family member 10A Neighboring gene origin of replication in TBC1D10A Neighboring gene coiled-coil domain containing 157 Neighboring gene KIAA1656 protein Neighboring gene ring finger protein 215

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

Replication interactions

Interaction Pubs
Knockdown of splicing factor 3a, subunit 1 (SF3A1) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 PubMed

Protein interactions

Protein Gene Interaction Pubs
Rev rev HIV-1 Rev interacting protein, splicing factor 3a, subunit 1 (SF3A1), is identified by the in-vitro binding experiments involving cytosolic or nuclear extracts from HeLa cells. The interaction of Rev with SF3A1 is increased by RRE PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • 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 
RNA binding IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
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
 
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 
U2-type prespliceosome IDA
Inferred from Direct Assay
more info
PubMed 
U2-type spliceosomal complex IDA
Inferred from Direct Assay
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 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 IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
splicing factor 3A subunit 1
Names
SAP 114
pre-mRNA processing 21
pre-mRNA splicing factor SF3a (120 kDa subunit)
spliceosome-associated protein 114
splicing factor 3 subunit 1
splicing factor 3a, subunit 1, 120kD
splicing factor 3a, subunit 1, 120kDa

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.

Genomic

  1. NG_032902.1 RefSeqGene

    Range
    4978..29937
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_622

mRNA and Protein(s)

  1. NM_005877.6NP_005868.1  splicing factor 3A subunit 1

    See identical proteins and their annotated locations for NP_005868.1

    Status: REVIEWED

    Source sequence(s)
    AC004997, BC007684, CK300534
    Consensus CDS
    CCDS13875.1
    UniProtKB/Swiss-Prot
    Q15459
    UniProtKB/TrEMBL
    A0A024R1K8
    Related
    ENSP00000215793.7, ENST00000215793.12
    Conserved Domains (4) summary
    cd01800
    Location:718793
    SF3a120_C; Ubiquitin-like domain of Mammalian splicing factor SF3a_120
    smart00648
    Location:50103
    SWAP; Suppressor-of-White-APricot splicing regulator
    pfam01805
    Location:165215
    Surp; Surp module
    pfam12230
    Location:232472
    PRP21_like_P; Pre-mRNA splicing factor PRP21 like protein

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_000022.11 Reference GRCh38.p12 Primary Assembly

    Range
    30331988..30356947 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001005409.1: Suppressed sequence

    Description
    NM_001005409.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
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