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    SPSB4 splA/ryanodine receptor domain and SOCS box containing 4 [ Homo sapiens (human) ]

    Gene ID: 92369, updated on 10-Dec-2024

    Summary

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    Official Symbol
    SPSB4provided by HGNC
    Official Full Name
    splA/ryanodine receptor domain and SOCS box containing 4provided by HGNC
    Primary source
    HGNC:HGNC:30630
    See related
    Ensembl:ENSG00000175093 MIM:611660; AllianceGenome:HGNC:30630
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    SSB4; SSB-4
    Summary
    Enables ubiquitin-like ligase-substrate adaptor activity. Involved in several processes, including positive regulation of protein polyubiquitination; protein ubiquitination; and ubiquitin-dependent protein catabolic process. Located in cytosol. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Low expression observed in reference dataset See more
    Orthologs
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    Genomic context

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    See SPSB4 in Genome Data Viewer
    Location:
    3q23
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (141051347..141148611)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (143798863..143896164)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (140770189..140867453)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ribosomal protein L23a pseudogene 41 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20620 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:140661115-140661962 Neighboring gene solute carrier family 25 member 36 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14772 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:140789226-140789769 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:140789770-140790312 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:140792837-140793422 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:140802197-140802706 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:140805486-140806259 Neighboring gene NANOG hESC enhancer GRCh37_chr3:140821789-140822305 Neighboring gene NANOG hESC enhancer GRCh37_chr3:140923620-140924130 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:140925635-140926136 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14773 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:140978638-140979382 Neighboring gene 2-phosphoxylose phosphatase 1 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_64847 Neighboring gene ribosomal protein L31 pseudogene 21 Neighboring gene uncharacterized LOC124909441 Neighboring gene PHF5A pseudogene 7

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. The E3 Ligases Spsb1 and Spsb4 Regulate RevErbα Degradation and Circadian Period. Mekbib T, et al. J Biol Rhythms, 2019 Dec. PMID 31607207, Free PMC Article
    2. The SPRY domain-containing SOCS box protein 1 (SSB-1) interacts with MET and enhances the hepatocyte growth factor-induced Erk-Elk-1-serum response element pathway. Wang D, et al. J Biol Chem, 2005 Apr 22. PMID 15713673
    3. Genetic risk factors for ischaemic stroke and its subtypes (the METASTROKE collaboration): a meta-analysis of genome-wide association studies. Traylor M, et al. Lancet Neurol, 2012 Nov. PMID 23041239, Free PMC Article
    4. Ubiquitin ligase Siah2 regulates RevErbα degradation and the mammalian circadian clock. DeBruyne JP, et al. Proc Natl Acad Sci U S A, 2015 Oct 6. PMID 26392558, Free PMC Article
    5. Ubiquitin ligase SPSB4 diminishes cell repulsive responses mediated by EphB2. Okumura F, et al. Mol Biol Cell, 2017 Nov 15. PMID 28931592, Free PMC Article

    See all (22) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Our results indicate that the paralogs Spsb1 and Spsb4, but not Spsb2 and Spsb3, can interact with and facilitate RevErbalpha ubiquitination and degradation and regulate circadian clock periodicity.
      Title: The E3 Ligases Spsb1 and Spsb4 Regulate RevErbα Degradation and Circadian Period.
    2. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    Submit: New GeneRIF Correction

    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

    EBI GWAS Catalog

    Description
    Genetic risk factors for ischaemic stroke and its subtypes (the METASTROKE collaboration): a meta-analysis of genome-wide association studies.
    EBI GWAS Catalog
    Shared genetic susceptibility to ischemic stroke and coronary artery disease: a genome-wide analysis of common variants.
    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)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables ubiquitin-like ligase-substrate adaptor activity IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in intracellular signal transduction IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of protein polyubiquitination IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in proteasome-mediated ubiquitin-dependent protein catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein ubiquitination IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in protein ubiquitination IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of circadian rhythm IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in rhythmic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in ubiquitin-dependent protein catabolic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in ubiquitin-dependent protein catabolic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of SCF ubiquitin ligase complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    SPRY domain-containing SOCS box protein 4
    Names
    SPRY domain-containing SOCS box protein SSB-4

    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.

    mRNA and Protein(s)

    1. NM_080862.3 → NP_543138.1  SPRY domain-containing SOCS box protein 4

      See identical proteins and their annotated locations for NP_543138.1

      Status: VALIDATED

      Source sequence(s)
      AC022215, AC108727, AF403029, BC051354, BX376865, CN366621
      Consensus CDS
      CCDS3115.1
      UniProtKB/Swiss-Prot
      Q96A44
      Related
      ENSP00000311609.2, ENST00000310546.3
      Conserved Domains (2) summary
      cd12906
      Location:54 → 227
      SPRY_SOCS1-2-4; SPRY domain in the suppressor of cytokine signaling 1, 2, 4 families (SOCS1, SOCS2, SOCS4)
      cl02533
      Location:232 → 273
      SOCS; SOCS (suppressors of cytokine signaling) box. The SOCS box is found in the C-terminal region of CIS/SOCS family proteins (in combination with a SH2 domain), ASBs (ankyrin repeat-containing proteins with a SOCS box), SSBs (SPRY domain-containing proteins ...

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      141051347..141148611
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017007509.3 → XP_016862998.1  SPRY domain-containing SOCS box protein 4 isoform X1

    RNA

    1. XR_924215.4 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      143798863..143896164
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054348414.1 → XP_054204389.1  SPRY domain-containing SOCS box protein 4 isoform X1

    RNA

    1. XR_008486852.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96A44.1 GenPept UniProtKB/Swiss-Prot:Q96A44

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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