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

Gene ID: 90864, updated on 2-Nov-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, Nov 2024]
Expression
Ubiquitous expression in skin (RPKM 23.4), spleen (RPKM 22.6) and 25 other tissues See more
Orthologs
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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: HPA RNA-seq normal tissues 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. 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 Variation Viewer (GRCh37.p13)

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

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

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

Gene LinkOut

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