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

Gene ID: 10262, updated on 7-Apr-2024

Summary

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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; AllianceGenome:HGNC:10771
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
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Genomic context

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See SF3B4 in Genome Data Viewer
Location:
1q21.2
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (149923317..149927803, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (149047800..149055723, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (149895209..149899695, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1664 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:149881729-149882230 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:149882231-149882730 Neighboring gene bolA family member 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1290 Neighboring gene synaptic vesicle glycoprotein 2A Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1665 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1666 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:149908038-149908562 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1667 Neighboring gene myotubularin related protein 11 Neighboring gene OTU deubiquitinase 7B Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:149981420-149982302 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1292 Neighboring gene uncharacterized LOC124904413 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:149989091-149989750 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:149989751-149990408 Neighboring gene ribosomal protein L6 pseudogene 31

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. The Role of Splicing Factor SF3B4 in Congenital Diseases and Tumors. Yan L, et al. Discov Med, 2021 Nov-Dec. PMID 35220998
  2. Nager syndrome in patient lacking acrofacial dysostosis: Expanding the phenotypic spectrum of SF3B4-related disease. Cadieux-Dion M, et al. Am J Med Genet A, 2021 May. PMID 33559401
  3. Component of splicing factor SF3b plays a key role in translational control of polyribosomes on the endoplasmic reticulum. Ueno T, et al. Proc Natl Acad Sci U S A, 2019 May 7. PMID 31004060, Free PMC Article
  4. SF3B4 as an early-stage diagnostic marker and driver of hepatocellular carcinoma. Shen Q, et al. BMB Rep, 2018 Feb. PMID 29397868, Free PMC Article
  5. A synonymous splicing mutation in the SF3B4 gene segregates in a family with highly variable Nager syndrome. Cassina M, et al. Eur J Hum Genet, 2017 Feb. PMID 27966544, Free PMC Article

See all (159) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. SETDB1 promotes progression through upregulation of SF3B4 expression and regulates the immunity in ovarian cancer.
    Title: SETDB1 promotes progression through upregulation of SF3B4 expression and regulates the immunity in ovarian cancer.
  2. SF3B4 promotes Twist1 expression and clear cell renal cell carcinoma progression by facilitating the export of KLF 16 mRNA from the nucleus to the cytoplasm.
    Title: SF3B4 promotes Twist1 expression and clear cell renal cell carcinoma progression by facilitating the export of KLF 16 mRNA from the nucleus to the cytoplasm.
  3. SF3B4 Depletion Retards the Growth of A549 Non-Small Cell Lung Cancer Cells via UBE4B-Mediated Regulation of p53/p21 and p27 Expression.
    Title: SF3B4 Depletion Retards the Growth of A549 Non-Small Cell Lung Cancer Cells via UBE4B-Mediated Regulation of p53/p21 and p27 Expression.
  4. SF3B4 promotes ovarian cancer progression by regulating alternative splicing of RAD52.
    Title: SF3B4 promotes ovarian cancer progression by regulating alternative splicing of RAD52.
  5. The Role of Splicing Factor SF3B4 in Congenital Diseases and Tumors.
    Title: The Role of Splicing Factor SF3B4 in Congenital Diseases and Tumors.
  6. Enabled homolog (ENAH) regulated by RNA binding protein splicing factor 3b subunit 4 (SF3B4) exacerbates the proliferation, invasion and migration of hepatocellular carcinoma cells via Notch signaling pathway.
    Title: Enabled homolog (ENAH) regulated by RNA binding protein splicing factor 3b subunit 4 (SF3B4) exacerbates the proliferation, invasion and migration of hepatocellular carcinoma cells via Notch signaling pathway.
  7. Nager syndrome in patient lacking acrofacial dysostosis: Expanding the phenotypic spectrum of SF3B4-related disease.
    Title: Nager syndrome in patient lacking acrofacial dysostosis: Expanding the phenotypic spectrum of SF3B4-related disease.
  8. Publicly available data from paired normal and tumor tissues in hepatocellular carcinoma (HCC) and results from patients with HCC suggest that SRSF3 and SF3B4 possess an inverse relationship. SRSF3 is a key molecule for determining SF3B4 levels in HCC cells
    Title: SRSF3 Depletion Leads to an Increase in SF3B4 Expression in SNU-368 HCC Cells.
  9. A unique system comprising a p180-SF3b4-mRNA complex facilitates the selective assembly of polyribosomes on the endoplasmic reticulum.
    Title: Component of splicing factor SF3b plays a key role in translational control of polyribosomes on the endoplasmic reticulum.
  10. MiRNA-133b not only regulates the endogenous expression of SF3B4 but also modulates SF3B4-mediated AS efficiency in HCC tumorigenesis.
    Title: SF3B4 is regulated by microRNA-133b and promotes cell proliferation and metastasis in hepatocellular carcinoma.
Submit: New GeneRIF Correction See all GeneRIFs (25)

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

Associated conditions

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

EBI GWAS Catalog

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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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 PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC10828

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA binding HDA PubMed 
enables RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables splicing factor binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in RNA splicing TAS
Traceable Author Statement
more info
 PubMed 
involved_in RNA splicing, via transesterification reactions TAS
Traceable Author Statement
more info
 PubMed 
involved_in U2-type prespliceosome assembly NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in mRNA processing TAS
Traceable Author Statement
more info
 PubMed 
involved_in mRNA splicing, via spliceosome IC
Inferred by Curator
more info
 PubMed 
involved_in mRNA splicing, via spliceosome IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in mRNA splicing, via spliceosome NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in positive regulation of mRNA splicing, via spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
part_of U12-type spliceosomal complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of U12-type spliceosomal complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of U2 snRNP IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of U2 snRNP NAS
Non-traceable Author Statement
more info
 PubMed 
part_of U2-type precatalytic spliceosome IDA
Inferred from Direct Assay
more info
 PubMed 
part_of U2-type spliceosomal complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of U2-type spliceosomal complex IPI
Inferred from Physical Interaction
more info
 PubMed 
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleus NAS
Non-traceable Author Statement
more info
 PubMed 
part_of spliceosomal complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of spliceosomal complex NAS
Non-traceable Author Statement
more info
 PubMed 

General protein information

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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)

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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.

Genomic

  1. NG_032777.2 RefSeqGene

    Range
    5000..9486
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_005850.5 → NP_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, Q5SZ63
    UniProtKB/TrEMBL
    Q53FG6
    Related
    ENSP00000271628.8, ENST00000271628.9
    Conserved Domains (2) summary
    cd12334
    Location:15 → 88
    RRM1_SF3B4; RNA recognition motif 1 (RRM1) found in splicing factor 3B subunit 4 (SF3B4) and similar proteins
    cd12335
    Location:99 → 181
    RRM2_SF3B4; RNA recognition motif 2 (RRM2) found in splicing factor 3B subunit 4 (SF3B4) and similar proteins

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    149923317..149927803 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    149047800..149055723 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054333793.1 → XP_054189768.1  splicing factor 3B subunit 4 isoform X1

    UniProtKB/Swiss-Prot
    Q15427, Q5SZ63
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q15427.1 GenPept UniProtKB/Swiss-Prot:Q15427

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