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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

SPSB4 Gene

protein-coding   GIFtS: 52
GCID: GC03P140770

splA/ryanodine receptor domain and SOCS box containing 4

 Explore 1 disease affiliated with
SPSB4 via our new
 Human Malady Compendium 
Biological research products
for SPSB4
    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section

Aliases
SplA/Ryanodine Receptor Domain And SOCS Box Containing 41 2
SSB-41 2 3
SSB42 3 5
SPRY Domain-Containing SOCS Box Protein 42
SPRY Domain-Containing SOCS Box Protein SSB-42

External Ids:    HGNC: 306301   Entrez Gene: 923692   Ensembl: ENSG000001750937   OMIM: 6116605   UniProtKB: Q96A443   

Export aliases for SPSB4 gene to outside databases

Previous GC identifers: GC03P142253 GC03P138145


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

UniProtKB/Swiss-Prot: SPSB4_HUMAN, Q96A44
Function: Probable 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




(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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000003.11  NC_018914.1  NT_005612.16  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the SPSB4 gene promoter:
         NF-1/L   NF-1   Spz1   Lmo2   HSF1 (long)   XBP-1   Nkx6-1   HSF1short   Ik-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSPSB4 promoter sequence
   Search SABiosciences Chromatin IP Primers for SPSB4

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat SPSB4


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

Entrez Gene cytogenetic band: 3q23   Ensembl cytogenetic band:  3q23   HGNC cytogenetic band: 3q23

SPSB4 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SPSB4 gene location

GeneLoc information about chromosome 3         GeneLoc Exon Structure

GeneLoc location for GC03P140770:  view genomic region     (about GC identifiers)

Start:
140,770,244 bp from pter      End:
140,867,453 bp from pter
Size:
97,210 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, 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, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: SPSB4_HUMAN, Q96A44 (See protein sequence)
Recommended Name: SPRY domain-containing SOCS box protein 4  
Size: 273 amino acids; 30179 Da
Subunit: Interacts with PARW (By similarity). Probable component of the ECS(SPSB4) E3 ubiquitin-protein ligase complex
which contains CUL5, RNF7/RBX2, Elongin BC complex and SPSB4. Interacts with MET
Subcellular location: Cytoplasm (Probable)
1 PDB 3D structure from and Proteopedia for SPSB4:
2V24 (3D)    

Explore the universe of human proteins at neXtProt for SPSB4: NX_Q96A44

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q96A44

  • SPSB4 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_543138.1  
    ENSEMBL proteins: 
     ENSP00000311609   ENSP00000422034  
    Reactome Protein details: Q96A44
    Human Recombinant Protein Products: 
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    Uscn Proteins for SPSB4

    Gene Ontology (GO): 1 cellular component term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005737cytoplasm IEA--


    SPSB4 for ontologies           About GeneDecksing



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    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    SPSB4 for domains           About GeneDecksing

    5 InterPro domains/families:
     IPR001496 SOCS_C
     IPR018355 SPla/RYanodine_receptor_subgr
     IPR001870 B30.2/SPRY
     IPR008985 ConA-like_lec_gl_sf
     IPR003877 SPRY_rcpt

    Graphical View of Domain Structure for InterPro Entry Q96A44

    ProtoNet protein and cluster: Q96A44

    1 Blocks protein family: IPB001496 SOCS protein

    UniProtKB/Swiss-Prot: SPSB4_HUMAN, Q96A44
    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


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section

    Function Summary:

         UniProtKB/Swiss-Prot: SPSB4_HUMAN, Q96A44
    Function: Probable 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

    miRNA
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    hsa-miR-4307 hsa-miR-15a hsa-miR-29a hsa-miR-632 hsa-miR-424 hsa-miR-23a hsa-miR-15b hsa-miR-1298
    SwitchGear 3'UTR luciferase reporter plasmidSPSB4 3' UTR sequence
    Inhib. RNA
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    Gene Ontology (GO): 1 molecular function term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding IPI19159283


    SPSB4 for ontologies           About GeneDecksing



    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, 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 Mar 2013 via Entrez Gene).
    About This Section

    Unified GeneCards pathways  About this table 
    See pathways by source

    Super-pathwaycontained gene-specific pathways
    1Antigen processing: Ubiquitination & Proteasome degradation
    Antigen processing: Ubiquitination & Proteasome degradation1.00
    Polyubiquitination of substrate0.75
    Class I MHC mediated antigen processing & presentation0.83
    2Immune System
    Immune System1.00
    Adaptive Immune System0.59

    Pathway sources
    See GeneCards unified pathways
    Show all pathways


    5        Reactome Pathways for SPSB4
        Antigen processing: Ubiquitination & Proteasome degradation
    Polyubiquitination of substrate
    Adaptive Immune System
    Class I MHC mediated antigen processing & presentation
    Immune System


    UniProtKB/Swiss-Prot: SPSB4_HUMAN, Q96A44
    Pathway: Protein modification; protein ubiquitination


    SPSB4 for pathways           About GeneDecksing

    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for SPSB4

    STRING Interaction Network Preview (showing 5 interactants - click image to see 8)

    5/9 Interacting proteins for SPSB4 (Q96A441, 3 ENSP000003116094) via UniProtKB, MINT, STRING, and/or I2D (see all 9)

    InteractantInteraction Details
    GeneCardExternal ID(s)
    TCEB1Q153691, 3, ENSP000002848114EBI-2323233,EBI-301231 I2D: score=2 STRING: ENSP00000284811
    NOS2P352283, ENSP000003272514I2D: score=1 STRING: ENSP00000327251
    RNF7Q9UBF63, ENSP000002734804I2D: score=1 STRING: ENSP00000273480
    TCEB2Q153703, ENSP000002623064I2D: score=1 STRING: ENSP00000262306
    CUL5Q930343I2D: score=1 
    About this table

    Gene Ontology (GO): 2 biological process terms (GO ID links to tree view):    About this table

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


    SPSB4 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for SPSB4
    Search CenterWatch for drugs/clinical trials and news about SPSB4 

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 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,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for SPSB4 gene: 
    NM_080862.1  

    Unigene Cluster for SPSB4:

    SplA/ryanodine receptor domain and SOCS box containing 4
    Hs.655112  [show with all ESTs]
    Unigene Representative Sequence: BC051354
    4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000310546(uc003ett.3 uc010hum.3) ENST00000508126 ENST00000508828
    ENST00000507895

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    hsa-miR-4307 hsa-miR-15a hsa-miR-29a hsa-miR-632 hsa-miR-424 hsa-miR-23a hsa-miR-15b hsa-miR-1298
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    Additional cDNA sequence: 

    AF086345.1 AF403029.1 AK056147.1 AK056367.1 BC008324.1 BC051354.1 

    4 DOTS entries:

    DT.97791370  DT.100684548  DT.309089  DT.433213 

    24/46 AceView cDNA sequences (see all 46):

    BM929361 AW293029 AA757366 CR613017 AA581737 CR593903 AI369332 BU848703 
    BE261590 AA308601 AF086345 AA581718 AA405968 BX351403 BC008324 AA405736 
    BG826825 AF403029 AK056367 BE041628 BX112094 BG829052 AI953088 NM_080862 

    GeneLoc Exon Structure

    3 Alternative Splicing Database (ASD) splice patterns (SP) for SPSB4    About this scheme

    ExUns: 1 ^ 2a · 2b ^ 3 ^ 4 ^ 5 ^ 6
    SP1:                    -     -               
    SP2:                    -     -     -         
    SP3:                                          


    ECgene alternative splicing isoforms for SPSB4

    (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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    SPSB4 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: GGGGCAGCCT

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)

    About this image

    SPSB4 expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    1 LifeMap In Vivo Development Anatomical Compartment/Cell 
    Tissue Anatomical Compartment CellCategory (developmental path)
    Head MesenchymeBranchial Arch 1Cranial Neural Crest CellsNeural Crest
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization

    See SPSB4 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for SPSB4

    SOURCE GeneReport for Unigene cluster: Hs.655112
        SABiosciences Expression via Pathway-Focused PCR Array including SPSB4: 
              Ubiquitin Ligases in human mouse rat

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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SPSB4

    (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)
    About This Section

    This gene was present in the common ancestor of animals.

    Orthologs for SPSB4 gene from 5/19 species (see all 19)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    chicken
    (Gallus gallus)
    Aves SPSB41 splA/ryanodine receptor domain and SOCS box containing more 71.31(n)
    81.32(a)
      429129  XM_426685.2  XP_426685.2 
    lizard
    (Anolis carolinensis)
    Reptilia SPSB46
    --
    77(a)
    1 ↔ 1
    GL343404.1(646828-647666)
    zebrafish
    (Danio rerio)
    Actinopterygii nszf-e3262 nszf-e326 73.91(n)   335778  CF996573.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta gus1 gustavus 58.21(n)
    69.49(a)
      35478  NM_136314.3  NP_610158.3 
    worm
    (Caenorhabditis elegans)
    Secernentea spsb-11 Protein SPSB-1 57.83(n)
    58.5(a)
      266876  NM_064920.3  NP_497321.3 


    ENSEMBL Gene Tree for SPSB4 (if available)
    TreeFam Gene Tree for SPSB4 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for SPSB4 gene
    SPSB22  FBXO452  SPSB12  
    18/32 SIMAP similar genes for SPSB4 using alignment to 2 protein entries:     SPSB4_HUMAN (see all proteins) (see all similar genes):
    COX7A2    IPO7    ZNF568    SPSB1    TMEM67    CES4A
    THADA    IFT122    TGFBR3    DAPK2    NDUFS7    NSD1
    SENP7    ZNF23    ZNHIT3    C19orf25    C19orf47    CNOT2

    SPSB4 for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, 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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    3 NCBI SNPs in SPSB4 are shown     About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 3 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs673917981,2
    C--138148669(+) AAAAA-/AAAAAA 1 -- int11Minor allele frequency- A:0.00NA 2
    rs711514101,2
    C--140780581(-) AAAAA-/AGAAAG 1 -- int11Minor allele frequency- A:0.00NA 2
    rs716278981,2
    ----140830196(+) CTTGCT/-TTTTT 1 -- int11Minor allele frequency- -:0.50NA 2

    HapMap Linkage Disequilibrium report for SPSB4 (140770244 - 140867453 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 1 variation for SPSB4
         1 CNV: 63605

    SABiosciences Cancer Mutation PCR Assays
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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.)
    About This Section

    SPSB4 for disorders           About GeneDecksing

    OMIM gene information: 611660    OMIM disorders: --

    1 disease for SPSB4:    About MalaCards
    brucellosis

    Human Genome Epidemiology (HuGE) Navigator: SPSB4 (1 document)

    Export disorders for SPSB4 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)
    About This Section

    PubMed articles for SPSB4 gene, integrated from 9 sources (see all 13):
    (articles sorted by number of sources associating them with SPSB4)
        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. (2005)
    2. 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. (2004)
    3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    4. VHL-box and SOCS-box domains determine binding specificity for Cul2- Rbx1 and Cul5-Rbx2 modules of ubiquitin ligases. (PubMed id 15601820)1, 2 Kamura T.... Nakayama K.I. (2004)
    5. The SOCS box: a tale of destruction and degradation. (PubMed id 12076535)1, 3 Kile B.T....Hilton D.J. (2002)
    6. Regulation of inducible nitric-oxide synthase by the SPRY domain- and SOCS box-containing proteins. (PubMed id 21199876)1 Nishiya T....Miwa S. (2011)
    7. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)1 Rose J.E....Uhl G.R. (2010)
    8. The SPRY domain-containing SOCS box protein SPSB2 tar gets iNOS for proteasomal degradation. (PubMed id 20603330)1 Kuang Z....Nicholson S.E. (2010)
    9. Structural basis for Par-4 recognition by the SPRY do main- and SOCS box-containing proteins SPSB1, SPSB2, and SPSB4. (PubMed id 20561531)1 Filippakopoulos P....Bullock A.N. (2010)
    10. Array MAPPIT: high-throughput interactome analysis in mammalian cells. (PubMed id 19159283)1 Lievens S....Tavernier J. (2009)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 92369 HGNC: 30630 AceView: SSB4 Ensembl:ENSG00000175093 euGenes: HUgn92369
    ECgene: SPSB4 H-InvDB: SPSB4

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for SPSB4 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 SPSB4 gene:
    Search GeneIP for patents involving SPSB4

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