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SPSB3 Gene

protein-coding   GIFtS: 50
GCID: GC16M001826

SplA/Ryanodine Receptor Domain And SOCS Box Containing 3

(Previous name: chromosome 16 open reading frame 31)
(Previous symbol: C16orf31)
  Search for SPSB3
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
SplA/Ryanodine Receptor Domain And SOCS Box Containing 31 2     SPRY Domain-Containing SOCS Box Protein 32
C16orf311 2 3     SPRY Domain-Containing SOCS Box Protein SSB-32
SSB32 3 5     SSB-33
Chromosome 16 Open Reading Frame 311     

External Ids:    HGNC: 306291   Entrez Gene: 908642   Ensembl: ENSG000001620327   OMIM: 6116595   UniProtKB: Q6PJ213   

Export aliases for SPSB3 gene to outside databases

Previous GC identifer: GC16M001768


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for SPSB3 Gene:
SPSB3 (splA/ryanodine receptor domain and SOCS box containing 3) is a protein-coding gene.

UniProtKB/Swiss-Prot: SPSB3_HUMAN, Q6PJ21
Function: May be a substrate recognition component of a SCF-like ECS (Elongin BC-CUL2/5-SOCS-box protein) E3
ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of
target proteins (By similarity)




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000016.9  NT_010393.17  NC_018927.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the SPSB3 gene promoter:
         STAT1   Pax-5   STAT4   STAT1beta   Olf-1   STAT1alpha   YY1   CP2   STAT2   STAT3   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSPSB3 promoter sequence
   Search Chromatin IP Primers for SPSB3

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SPSB3


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 16p13.3   Ensembl cytogenetic band:  16p13.3   HGNC cytogenetic band: 16p13.3

SPSB3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SPSB3 gene location

GeneLoc information about chromosome 16         GeneLoc Exon Structure

GeneLoc location for GC16M001826:  view genomic region     (about GC identifiers)

Start:
1,826,713 bp from pter      End:
1,843,701 bp from pter
Size:
16,989 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: SPSB3_HUMAN, Q6PJ21 (See protein sequence)
Recommended Name: SPRY domain-containing SOCS box protein 3  
Size: 355 amino acids; 39376 Da
Subunit: Interacts with MET
Sequence caution: Sequence=AAH41897.1; Type=Miscellaneous discrepancy; Note=Intron retention; Sequence=AAK61293.1;
Type=Erroneous gene model prediction;
Secondary accessions: D3DU78 Q49A96 Q86X18 Q8WXK5 Q96IE6 Q96RY2

Explore the universe of human proteins at neXtProt for SPSB3: NX_Q6PJ21

Explore proteomics data for SPSB3 at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys142
  • Modification sites at PhosphoSitePlus

  • See SPSB3 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_543137.2  
    ENSEMBL proteins: 
     ENSP00000457206   ENSP00000301717   ENSP00000455098  

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    4 InterPro protein domains:
     IPR001870 B30.2/SPRY
     IPR003877 SPRY_rcpt
     IPR001496 SOCS_C
     IPR008985 ConA-like_lec_gl_sf

    Graphical View of Domain Structure for InterPro Entry Q6PJ21

    ProtoNet protein and cluster: Q6PJ21

    1 Blocks protein domain: IPB001496 SOCS protein

    UniProtKB/Swiss-Prot: SPSB3_HUMAN, Q6PJ21
    Domain: The SOCS box domain mediates the interaction with the Elongin BC complex, an adapter module in different
    E3 ubiquitin ligase complexes (By similarity)
    Similarity: Belongs to the SPSB family
    Similarity: Contains 1 B30.2/SPRY domain
    Similarity: Contains 1 SOCS box domain


    Find genes that share domains with SPSB3           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: SPSB3_HUMAN, Q6PJ21
    Function: May be a substrate recognition component of a SCF-like ECS (Elongin BC-CUL2/5-SOCS-box protein) E3
    ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of
    target proteins (By similarity)

         Gene Ontology (GO): 1 molecular function term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding ----
         
    Find genes that share ontologies with SPSB3           About GenesLikeMe


    Phenotypes:
         2 GenomeRNAi human phenotypes for SPSB3:
     Decreased Salmonella enterica   Increased gamma-H2AX phosphory 

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for SPSB3
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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    cytosol2
    nucleus2
    mitochondrion1
    peroxisome1

    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    UniProtKB/Swiss-Prot: SPSB3_HUMAN, Q6PJ21
    Pathway: Protein modification; protein ubiquitination

        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for SPSB3
    Interactions:

        Search GeneGlobe Interaction Network for SPSB3

    STRING Interaction Network Preview (showing 3 interactants - click image to see more details)

    3 Interacting proteins for SPSB3 (Q6PJ213 ENSP000003017174) via UniProtKB, MINT, STRING, and/or I2D

    InteractantInteraction Details
    GeneCardExternal ID(s)
    TCEB1Q153693, ENSP000002848114I2D: score=1 STRING: ENSP00000284811
    METENSP000003172724STRING: ENSP00000317272
    ENSG00000232960ENSP000003955464STRING: ENSP00000395546
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    Gene Ontology (GO): 2 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0016567protein ubiquitination IEA--
    GO:0035556intracellular signal transduction IEA--

    Find genes that share ontologies with SPSB3           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for SPSB3



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for SPSB3 gene: 
    NM_080861.3  

    Unigene Cluster for SPSB3:

    SplA/ryanodine receptor domain and SOCS box containing 3
    Hs.592080  [show with all ESTs]
    Unigene Representative Sequence: BC041897
    12 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000566339(uc002cmu.3) ENST00000564709(uc002cmt.3) ENST00000569380(uc010uvm.2)
    ENST00000567868 ENST00000563741 ENST00000301717 ENST00000563668 ENST00000563705
    ENST00000569769 ENST00000565550 ENST00000564070 ENST00000568416
    miRNA
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    Inhib. RNA
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      QuantiTect SYBR Green Assays in human, mouse, rat SPSB3
      QuantiFast Probe-based Assays in human, mouse, rat SPSB3

    Additional mRNA sequence: 

    AF403028.1 AK074190.1 AK302041.1 BC007588.1 BC024244.1 BC035065.1 BC041897.1 BC047441.1 
    BC065515.1 

    18 DOTS entries:

    DT.446875  DT.100820574  DT.100820578  DT.97854693  DT.100820565  DT.75157124  DT.100763039  DT.100820559 
    DT.100820560  DT.120716774  DT.100820580  DT.120716731  DT.453906  DT.95266595  DT.91752999  DT.95266587 
    DT.95266597  DT.95266583 

    Selected AceView cDNA sequences (see all 35):

    CR608229 CR598252 CR596537 CR610957 NM_080861 CR622113 CR609820 CR612312 
    CR595592 CR592259 CR611923 CR594533 BC065515 CR590538 BC041897 CR604082 
    CR594897 CR605628 CR624932 BC007588 CR591468 CR601897 AF403028 CR617347 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    SPSB3 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: CTGTCAGCGG
    SPSB3 Expression
    About this image

    SPSB3 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    SPSB3 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.592080
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    In Situ
    Assay Products:
     

     
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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of animals.

    Orthologs for SPSB3 gene from Selected species (see all 12)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Spsb31 , 5 splA/ryanodine receptor domain and SOCS box containing more1, 5 83.62(n)1
    89.55(a)1
      17 (12.53 cM)5
    790431  NM_027141.21  NP_081417.21 
     248866435 
    chicken
    (Gallus gallus)
    Aves SPSB31 splA/ryanodine receptor domain and SOCS box containing more 78.25(n)
    81.92(a)
      416401  XM_414716.4  XP_414716.3 
    lizard
    (Anolis carolinensis)
    Reptilia SPSB36
    splA/ryanodine receptor domain and SOCS box contai...
    77(a)
    1 ↔ 1
    AAWZ02038659(1772-10216)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia spsb31 splA/ryanodine receptor domain and SOCS box containing more 71.01(n)
    75.35(a)
      550104  NM_001017350.2  NP_001017350.1 
    zebrafish
    (Danio rerio)
    Actinopterygii spsb3a1 splA/ryanodine receptor domain and SOCS box containing more 68.17(n)
    69.49(a)
      796171  NM_001123008.1  NP_001116480.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG105161 CG10516 49.52(n)
    39.92(a)
      39738  NM_140562.2  NP_648819.2 


    ENSEMBL Gene Tree for SPSB3 (if available)
    TreeFam Gene Tree for SPSB3 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for SPSB3 gene

    Find genes that share paralogs with SPSB3           About GenesLikeMe


    1 Pseudogenes.org Pseudogene for SPSB3
    PGOHUM00000262924


    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for SPSB3 (see all 186)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 16 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1479376921,2
    --1826748(+) GCAGTC/TCTTTA 1 -- ut310--------
    rs1417501411,2
    --1826750(+) AGTCCA/TTTAAG 1 -- ut310--------
    rs1817567831,2
    C--1826775(+) GCAGCC/TGCTGA 1 -- ut310--------
    rs1873610481,2
    --1826858(+) TCCTCA/GCAGCC 1 -- ut310--------
    rs1177138141,2
    F--1826901(+) TCCCCA/TCCCAG 1 -- ut311Minor allele frequency- T:0.02EA 120
    rs1908643181,2
    --1826914(+) CAGCAG/TCAGAG 1 -- ut310--------
    rs1823467351,2
    --1826915(+) AGCAGC/GAGAGG 1 -- ut310--------
    rs1132222681,2
    C,F--1826967(+) AGCAAG/CAGATG 1 -- ut311Minor allele frequency- C:0.50CSA 2
    rs138891,2
    C,F,H--1827002(+) AACTCC/TGCCCT 1 -- ut31 ese32Minor allele frequency- T:0.02MN NA 304
    rs1457081691,2
    --1827004(+) CTCCGC/TCCTGG 1 -- ut310--------

    HapMap Linkage Disequilibrium report for SPSB3 (1826713 - 1843701 bp)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for SPSB3 (see all 18):    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2422427CNV Duplication17116639
    nsv904954CNV Loss21882294
    dgv2541n71CNV Loss21882294
    nsv457336CNV Loss19166990
    dgv2540n71CNV Loss21882294
    nsv905017CNV Loss21882294
    dgv2539n71CNV Loss21882294
    nsv905034CNV Loss21882294
    nsv518641CNV Loss19592680
    dgv2542n71CNV Loss21882294

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing SPSB3
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 611659    OMIM disorders: --


    Find genes that share disorders with SPSB3           About GenesLikeMe

    Genetic Association Database (GAD): SPSB3
    Human Genome Epidemiology (HuGE) Navigator: SPSB3 (1 document)

    Export disorders for SPSB3 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for SPSB3 gene, integrated from 10 sources (see all 13):
    (articles sorted by number of sources associating them with SPSB3)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. 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. (PubMed id 15713673)1, 2, 9 Wang D.... Wu G. (J. Biol. Chem. 2005)
    2. Use of genome-wide expression data to mine the &quot;Gray Zone&quot; of GWA studies leads to novel candidate obesity genes. (PubMed id 20532202)1, 4 Naukkarinen J....Peltonen L. (PLoS Genet. 2010)
    3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    4. The SOCS box: a tale of destruction and degradation. (PubMed id 12076535)1, 3 Kile B.T....Hilton D.J. (Trends Biochem. Sci. 2002)
    5. Sequence, structure and pathology of the fully annotated terminal 2 Mb of the short arm of human chromosome 16. (PubMed id 11157797)1, 2 Daniels R.J....Higgs D.R. (Hum. Mol. Genet. 2001)
    6. Quantitative analysis of HSP90-client interactions reveals principles of substrate recognition. (PubMed id 22939624)1 Taipale M....Lindquist S. (Cell 2012)
    7. Toward an understanding of the protein interaction network of the human liver. (PubMed id 21988832)1 Wang J....Yang X. (Mol. Syst. Biol. 2011)
    8. Regulation of inducible nitric-oxide synthase by the SPRY domain- and SOCS box-containing proteins. (PubMed id 21199876)1 Nishiya T....Miwa S. (J. Biol. Chem. 2011)
    9. A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles. (PubMed id 21890473)1 Wagner S.A....Choudhary C. (amp 2011)
    10. Dynamics of cullin-RING ubiquitin ligase network revealed by systematic quantitative proteomics. (PubMed id 21145461)1 Bennett E.J....Harper J.W. (Cell 2010)

    (in PubMed, OMIM, and NCBI Bookshelf)
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      Query String
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      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 90864 HGNC: 30629 AceView: SSB3 Ensembl:ENSG00000162032 euGenes: HUgn90864
    ECgene: SPSB3 H-InvDB: SPSB3

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for SPSB3 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for SPSB3 gene:
    Search GeneIP for patents involving SPSB3

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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