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    SPSB3 splA/ryanodine receptor domain and SOCS box containing 3 [ Homo sapiens (human) ]

    Gene ID: 90864, updated on 10-Dec-2024

    Summary

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    Official Symbol
    SPSB3provided by HGNC
    Official Full Name
    splA/ryanodine receptor domain and SOCS box containing 3provided by HGNC
    Primary source
    HGNC:HGNC:30629
    See related
    Ensembl:ENSG00000162032 MIM:611659; AllianceGenome:HGNC:30629
    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
    SSB3; C16orf31
    Summary
    Enables ubiquitin-like ligase-substrate adaptor activity. Involved in several processes, including negative regulation of cGAS/STING signaling pathway; negative regulation of epithelial to mesenchymal transition; and protein K48-linked ubiquitination. Part of Cul5-RING ubiquitin ligase complex. Is active in nucleus. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in skin (RPKM 23.4), spleen (RPKM 22.6) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SPSB3 in Genome Data Viewer
    Location:
    16p13.3
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (1776712..1782571, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (1792547..1798407, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (1826713..1832572, complement)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene mitogen-activated protein kinase 8 interacting protein 3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7000 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7001 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10236 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7002 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10237 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7003 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7004 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7005 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7006 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:1824057-1824845 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:1825681-1826181 Neighboring gene mitochondrial ribosomal protein S34 Neighboring gene NME/NM23 nucleoside diphosphate kinase 3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7007 Neighboring gene essential meiotic structure-specific endonuclease subunit 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10238 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7008 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:1833677-1833903 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:1836968-1837136 Neighboring gene NUBP iron-sulfur cluster assembly factor 2, cytosolic Neighboring gene insulin like growth factor binding protein acid labile subunit

    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. SPSB3 targets SNAIL for degradation in GSK-3β phosphorylation-dependent manner and regulates metastasis. Liu Y, et al. Oncogene, 2018 Feb 8. PMID 29059170
    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. The CRL5-SPSB3 ubiquitin ligase targets nuclear cGAS for degradation. Xu P, et al. Nature, 2024 Mar. PMID 38418882, Free PMC Article
    4. Regulation of inducible nitric-oxide synthase by the SPRY domain- and SOCS box-containing proteins. Nishiya T, et al. J Biol Chem, 2011 Mar 18. PMID 21199876, Free PMC Article
    5. Use of genome-wide expression data to mine the "Gray Zone" of GWA studies leads to novel candidate obesity genes. Naukkarinen J, et al. PLoS Genet, 2010 Jun 3. PMID 20532202, Free PMC Article

    See all (25) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The CRL5-SPSB3 ubiquitin ligase targets nuclear cGAS for degradation.
      Title: The CRL5-SPSB3 ubiquitin ligase targets nuclear cGAS for degradation.
    2. Low SPSB3 expression is associated with lymph node metastasis in Ovarian and esophageal squamous cell carcinoma.
      Title: SPSB3 targets SNAIL for degradation in GSK-3β phosphorylation-dependent manner and regulates metastasis.
    3. Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
      Title: Use of genome-wide expression data to mine the "Gray Zone" of GWA studies leads to novel candidate obesity genes.
    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

    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 IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in negative regulation of cGAS/STING signaling pathway IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of epithelial to mesenchymal transition 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 proteasome-mediated ubiquitin-dependent protein catabolic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in protein K48-linked ubiquitination IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of Cul5-RING ubiquitin ligase complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of SCF ubiquitin ligase complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    is_active_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    SPRY domain-containing SOCS box protein 3
    Names
    SPRY domain-containing SOCS box protein SSB-3

    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_001324081.1 → NP_001311010.1  SPRY domain-containing SOCS box protein 3

      Status: VALIDATED

      Source sequence(s)
      AC012180
      Consensus CDS
      CCDS32365.1
      UniProtKB/Swiss-Prot
      D3DU78, Q49A96, Q6PJ21, Q86X18, Q8WXK5, Q96IE6, Q96RY2
      Related
      ENSP00000301717.4, ENST00000301717.8
      Conserved Domains (2) summary
      cd03717
      Location:273 → 312
      SOCS_SOCS_like; SOCS (suppressors of cytokine signaling) box of SOCS-like proteins. The CIS/SOCS family of proteins is characterized by the presence of a C-terminal SOCS box and a central SH2 domain. These intracellular proteins regulate the responses of immune cells to ...
      cd12876
      Location:104 → 286
      SPRY_SOCS3; SPRY domain in the suppressor of cytokine signaling 3 (SOCS3) family

    2. NM_080861.4 → NP_543137.2  SPRY domain-containing SOCS box protein 3

      See identical proteins and their annotated locations for NP_543137.2

      Status: VALIDATED

      Source sequence(s)
      AK074190, BI768095, BM836743
      Consensus CDS
      CCDS32365.1
      UniProtKB/Swiss-Prot
      D3DU78, Q49A96, Q6PJ21, Q86X18, Q8WXK5, Q96IE6, Q96RY2
      Related
      ENSP00000457206.1, ENST00000566339.6
      Conserved Domains (2) summary
      cd03717
      Location:273 → 312
      SOCS_SOCS_like; SOCS (suppressors of cytokine signaling) box of SOCS-like proteins. The CIS/SOCS family of proteins is characterized by the presence of a C-terminal SOCS box and a central SH2 domain. These intracellular proteins regulate the responses of immune cells to ...
      cd12876
      Location:104 → 286
      SPRY_SOCS3; SPRY domain in the suppressor of cytokine signaling 3 (SOCS3) family

    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_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      1776712..1782571 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005255673.6 → XP_005255730.1  SPRY domain-containing SOCS box protein 3 isoform X1

      Conserved Domains (2) summary
      cd03717
      Location:328 → 367
      SOCS_SOCS_like; SOCS (suppressors of cytokine signaling) box of SOCS-like proteins. The CIS/SOCS family of proteins is characterized by the presence of a C-terminal SOCS box and a central SH2 domain. These intracellular proteins regulate the responses of immune cells to ...
      cd12876
      Location:159 → 341
      SPRY_SOCS3; SPRY domain in the suppressor of cytokine signaling 3 (SOCS3) family

    2. XM_047434866.1 → XP_047290822.1  SPRY domain-containing SOCS box protein 3 isoform X2

      UniProtKB/Swiss-Prot
      D3DU78, Q49A96, Q6PJ21, Q86X18, Q8WXK5, Q96IE6, Q96RY2
      Related
      ENST00000564709.5

    3. XM_047434867.1 → XP_047290823.1  SPRY domain-containing SOCS box protein 3 isoform X3

      UniProtKB/TrEMBL
      B7Z7H9

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      1792547..1798407 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054314318.1 → XP_054170293.1  SPRY domain-containing SOCS box protein 3 isoform X1

    2. XM_054314319.1 → XP_054170294.1  SPRY domain-containing SOCS box protein 3 isoform X3

      UniProtKB/TrEMBL
      B7Z7H9
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6PJ21.2 GenPept UniProtKB/Swiss-Prot:Q6PJ21

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