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

    Gene ID: 10262, updated on 17-Jun-2024

    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; 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
    NEW
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    Genomic context

    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

    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 Functions

    What'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

    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

    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 PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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 
    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

    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)

    NEW Try the new Transcript table

    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_005850.5NP_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, Q5SZ63
      UniProtKB/TrEMBL
      Q53FG6
      Related
      ENSP00000271628.8, ENST00000271628.9
      Conserved Domains (2) summary
      cd12334
      Location:1588
      RRM1_SF3B4; RNA recognition motif 1 (RRM1) found in splicing factor 3B subunit 4 (SF3B4) and similar proteins
      cd12335
      Location:99181
      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_054333793.1XP_054189768.1  splicing factor 3B subunit 4 isoform X1

      UniProtKB/Swiss-Prot
      Q15427, Q5SZ63
      UniProtKB/TrEMBL
      Q53FG6