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SF3B4 splicing factor 3b subunit 4 [ Homo sapiens (human) ]

Gene ID: 10262, updated on 6-Jan-2019

Summary

Official Symbol
SF3B4provided by HGNC
Official Full Name
splicing factor 3b subunit 4provided by HGNC
Primary source
HGNC:HGNC:10771
See related
Ensembl:ENSG00000143368 MIM:605593
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
AFD1; Hsh49; SAP49; SF3b49
Summary
This gene encodes one of four subunits of the splicing factor 3B. The protein encoded by this gene cross-links to a region in the pre-mRNA immediately upstream of the branchpoint sequence in pre-mRNA in the prespliceosomal complex A. It also may be involved in the assembly of the B, C and E spliceosomal complexes. In addition to RNA-binding activity, this protein interacts directly and highly specifically with subunit 2 of the splicing factor 3B. This protein contains two N-terminal RNA-recognition motifs (RRMs), consistent with the observation that it binds directly to pre-mRNA. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in testis (RPKM 26.0), bone marrow (RPKM 20.1) and 25 other tissues See more
Orthologs

Genomic context

See SF3B4 in Genome Data Viewer
Location:
1q21.2
Exon count:
6
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 1 NC_000001.11 (149923317..149928252, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (149895209..149901449, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene bolA family member 1 Neighboring gene synaptic vesicle glycoprotein 2A Neighboring gene myotubularin related protein 11 Neighboring gene OTU deubiquitinase 7B

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?

Phenotypes

Associated conditions

Description Tests
Nager syndrome
MedGen: C0265245 OMIM: 154400 GeneReviews: Not available
Compare labs

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated (2014-07-17)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated (2014-07-17)

ClinGen Genome Curation PagePubMed

NHGRI GWAS Catalog

Description
A novel common variant in DCST2 is associated with length in early life and height in adulthood.
NHGRI GWA Catalog
Hundreds of variants clustered in genomic loci and biological pathways affect human height.
NHGRI GWA Catalog
Many sequence variants affecting diversity of adult human height.
NHGRI GWA Catalog

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env Tandem affinity purification and mass spectrometry analysis identify 49kDa subunit 4 of splicing factor 3b (SF3B4), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
Gag-Pol gag-pol Tandem affinity purification and mass spectrometry analysis identify 49kDa subunit 4 of splicing factor 3b (SF3B4), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
Nef nef Tandem affinity purification and mass spectrometry analysis identify 49kDa subunit 4 of splicing factor 3b (SF3B4), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
Pr55(Gag) gag Tandem affinity purification and mass spectrometry analysis identify 49kDa subunit 4 of splicing factor 3b (SF3B4), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
Vpr vpr Interaction of HIV-1 Vpr with SAP145 inhibits SAP145-SAP49 complex formation PubMed
vpr HIV-1 Vpr induces checkpoint activation and G2 arrest by binding to the CUS1 domain of SAP145 and interfering with the functions of the SAP145 and SAP49 proteins, two subunits of the multimeric splicing factor 3b (SF3b) 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...
  • mRNA Splicing - Minor Pathway, organism-specific biosystem (from REACTOME)
    mRNA Splicing - Minor Pathway, organism-specific biosystemThe splicing of a subset of pre-mRNA introns occurs by a second pathway, designated the AT-AC or U12-dependent splicing pathway. AT-AC introns have highly conserved, non-canonical splice sites that ...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC10828

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 
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 
mRNA processing TAS
Traceable Author Statement
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 mRNA splicing, via spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
U12-type spliceosomal complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
U12-type spliceosomal complex IDA
Inferred from Direct Assay
more info
PubMed 
U2-type precatalytic spliceosome IDA
Inferred from Direct Assay
more info
PubMed 
nucleolus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
ribonucleoprotein complex IBA
Inferred from Biological aspect of Ancestor
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 3B subunit 4
Names
SAP 49
SF3b50
pre-mRNA-splicing factor SF3b 49 kDa subunit
spliceosomal protein
spliceosome-associated protein (U2 snRNP)
spliceosome-associated protein 49
splicing factor 3b, subunit 4, 49kD
splicing factor 3b, subunit 4, 49kDa

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_032777.1 RefSeqGene

    Range
    5001..9936
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_005850.5NP_005841.1  splicing factor 3B subunit 4

    See identical proteins and their annotated locations for NP_005841.1

    Status: REVIEWED

    Source sequence(s)
    AI925089, BC004273, DA535996
    Consensus CDS
    CCDS72900.1
    UniProtKB/Swiss-Prot
    Q15427
    UniProtKB/TrEMBL
    B3KUJ0
    Related
    ENSP00000271628.8, ENST00000271628.8
    Conserved Domains (2) summary
    cd12334
    Location:1588
    RRM1_SF3B4; RNA recognition motif 1 in splicing factor 3B subunit 4 (SF3B4) and similar proteins
    cd12335
    Location:99181
    RRM2_SF3B4; RNA recognition motif 2 in splicing factor 3B subunit 4 (SF3B4) and similar proteins

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
    149923317..149928252 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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