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SF3A1 splicing factor 3a, subunit 1, 120kDa [ Homo sapiens (human) ]

Gene ID: 10291, updated on 6-Jul-2014
Official Symbol
SF3A1provided by HGNC
Official Full Name
splicing factor 3a, subunit 1, 120kDaprovided by HGNC
Primary source
HGNC:10765
See related
Ensembl:ENSG00000099995; HPRD:06903; MIM:605595; Vega:OTTHUMG00000151005
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 subunit 1 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 1 belongs to the SURP protein family; named for the SURP (also called SWAP or Suppressor-of-White-APricot) motifs that are thought to mediate RNA binding. Subunit 1 has tandemly repeated SURP motifs in its amino-terminal half while its carboxy-terminal half contains a proline-rich region and a ubiquitin-like domain. Binding studies with truncated subunit 1 derivatives demonstrated that the two SURP motifs are necessary for binding to subunit 3 while contacts with subunit 2 may occur through sequences carboxy-terminal to the SURP motifs. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]
See SF3A1 in Epigenomics, MapViewer
Location:
22q12.2
Exon count :
16
Annotation release Status Assembly Chr Location
106 current GRCh38 (GCF_000001405.26) 22 NC_000022.11 (30331988..30356924, 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 GATS protein-like 3 Neighboring gene TBC1 domain family, member 10A Neighboring gene coiled-coil domain containing 157 Neighboring gene KIAA1656 protein Neighboring gene ring finger protein 215

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

NHGRI GWAS Catalog

Description
Genetics of coronary artery calcification among African Americans, a meta-analysis.
NHGRI GWA Catalog

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, p19 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 Protein Interaction Database

  • 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 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...
  • 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...
Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
RNA binding IDA
Inferred from Direct Assay
more info
PubMed 
poly(A) RNA binding IDA
Inferred from Direct Assay
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
RNA splicing TAS
Traceable Author Statement
more info
 
gene expression TAS
Traceable Author Statement
more info
 
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-type spliceosomal complex IDA
Inferred from Direct Assay
more info
PubMed 
catalytic step 2 spliceosome IDA
Inferred from Direct Assay
more info
PubMed 
NOT nucleolus IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IDA
Inferred from Direct Assay
more info
 
spliceosomal complex IDA
Inferred from Direct Assay
more info
PubMed 
Preferred Names
splicing factor 3A subunit 1
Names
splicing factor 3A subunit 1
SAP 114
pre-mRNA processing 21
splicing factor 3 subunit 1
spliceosome-associated protein 114
splicing factor 3a, subunit 1, 120kD
pre-mRNA splicing factor SF3a (120 kDa subunit)

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 

    Range
    5001..29937
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001005409.1NP_001005409.1  splicing factor 3A subunit 1 isoform 2

    See proteins identical to NP_001005409.1

    Status: REVIEWED

    Description
    Transcript Variant: Transcript variant 2 uses two alternative splice sites in the coding region, compared to transcript variant 1. Variant 2 encodes isoform 2, which is shorter than isoform 1.
    Source sequence(s)
    AI681052, AU100212, AV750569, BC001976, BF965438, BI827130, BQ212479, BQ223575, BQ437843, BQ447452, CA440158
    Consensus CDS
    CCDS46684.1
    UniProtKB/Swiss-Prot
    Q15459
    Related
    ENSP00000390336, ENST00000439242
    Conserved Domains (3) summary
    cd01800
    Location:653728
    Blast Score: 375
    SF3a120_C; Ubiquitin-like domain of Mammalian splicing factor SF3a_120
    smart00648
    Location:50103
    Blast Score: 247
    SWAP; Suppressor-of-White-APricot splicing regulator
    pfam12230
    Location:157407
    Blast Score: 371
    PRP21_like_P; Pre-mRNA splicing factor PRP21 like protein
  2. NM_005877.4NP_005868.1  splicing factor 3A subunit 1 isoform 1

    See proteins identical to NP_005868.1

    Status: REVIEWED

    Description
    Transcript Variant: Transcript variant 1 encodes isoform 1, which is longer than isoform 2.
    Source sequence(s)
    AI681052, AU100212, AV750569, BC001976, BF965438, BQ212479, BQ223575, BQ437843, BQ447452, CA440158
    Consensus CDS
    CCDS13875.1
    UniProtKB/Swiss-Prot
    Q15459
    Related
    ENSP00000215793, OTTHUMP00000198919, ENST00000215793, OTTHUMT00000320916
    Conserved Domains (3) summary
    cd01800
    Location:718793
    Blast Score: 376
    SF3a120_C; Ubiquitin-like domain of Mammalian splicing factor SF3a_120
    smart00648
    Location:50103
    Blast Score: 248
    SWAP; Suppressor-of-White-APricot splicing regulator
    pfam12230
    Location:222472
    Blast Score: 370
    PRP21_like_P; Pre-mRNA splicing factor PRP21 like protein

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 106

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

Reference GRCh38 Primary Assembly

Genomic

  1. NC_000022.11 

    Range
    30331988..30356924
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate HuRef

Genomic

  1. AC_000154.1 

    Range
    13689762..13714601
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate CHM1_1.1

Genomic

  1. NC_018933.2 

    Range
    30687097..30712033
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

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