Aliases for SPSB1 Gene

Aliases for SPSB1 Gene

  • SplA/Ryanodine Receptor Domain And SOCS Box Containing 1 2 3 5
  • SSB-1 2 3 4
  • SPRY Domain-Containing SOCS Box Protein 1 3 4
  • SSB1 3 4
  • SPRY Domain-Containing SOCS Box Protein SSB-1 3
  • Novel SPRY Domain Containing Protein 3
  • SPSB1 5

External Ids for SPSB1 Gene

Previous GeneCards Identifiers for SPSB1 Gene

  • GC01P009288
  • GC01P009352
  • GC01P008547

Summaries for SPSB1 Gene

GeneCards Summary for SPSB1 Gene

SPSB1 (SplA/Ryanodine Receptor Domain And SOCS Box Containing 1) is a Protein Coding gene. Diseases associated with SPSB1 include Congenital Muscular Dystrophy-Dystroglycanopathy A7. Among its related pathways are Class I MHC mediated antigen processing and presentation and Innate Immune System. An important paralog of this gene is SPSB4.

UniProtKB/Swiss-Prot Summary for SPSB1 Gene

  • 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 (PubMed:15601820, PubMed:21199876). Negatively regulates nitric oxide (NO) production and limits cellular toxicity in activated macrophages by mediating the ubiquitination and proteasomal degradation of NOS2 (PubMed:21199876). Acts as a bridge which links NOS2 with the ECS E3 ubiquitin ligase complex components ELOC and CUL5 (PubMed:21199876).

Gene Wiki entry for SPSB1 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SPSB1 Gene

Genomics for SPSB1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SPSB1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01J009291 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 255.7 +1.1 1095 5.1 SP1 ZNF600 IKZF1 ZSCAN16 POLR2A NFIC ZIC2 ZBTB10 PLRG1 FOXA1 SPSB1 SLC45A1 RERE-AS1 HE855948 SLC25A33 HSALNG0000677
GH01J009347 Promoter/Enhancer 0.6 EPDnew Ensembl 250.2 +54.9 54907 0.4 ATF2 SPSB1 GPR157 lnc-GPR157-6 piR-43105-004 SLC25A33 HSALNG0000677
GH01J009274 Enhancer 1.2 FANTOM5 ENCODE dbSUPER 9.3 -17.2 -17230 1.3 SP1 NCOR1 ZNF600 JUND NFIC ZIC2 BCL11A SIN3A SAP130 IRF4 HSALNG0000691 SPSB1 H6PD SLC25A33 piR-60181 HSALNG0000677
GH01J009278 Enhancer 1.1 ENCODE CraniofacialAtlas dbSUPER 6.9 -12.5 -12545 3.8 CEBPA ZIC2 BHLHE40 NR2C1 MAX SAP130 ETV4 RARA TEAD3 TBP SPSB1 SLC2A5 H6PD PIK3CD piR-32670-001 HSALNG0000677
GH01J009268 Enhancer 0.9 Ensembl CraniofacialAtlas dbSUPER 6.9 -22.6 -22641 2.3 ZNF600 SMC3 ZBTB48 CTCF KLF1 ZNF692 ZBTB17 PRDM10 USF1 ZBTB20 H6PD SPSB1 lnc-H6PD-2 piR-60181 HSALNG0000691 HSALNG0000677
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SPSB1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SPSB1

Top Transcription factor binding sites by QIAGEN in the SPSB1 gene promoter:
  • AML1a
  • C/EBPbeta
  • Egr-2
  • GATA-1
  • S8
  • SEF-1 (1)
  • STAT1
  • STAT1alpha
  • STAT1beta
  • Zic3

Genomic Locations for SPSB1 Gene

Latest Assembly
chr1:9,292,894-9,369,532
(GRCh38/hg38)
Size:
76,639 bases
Orientation:
Plus strand

Previous Assembly
chr1:9,352,953-9,429,591
(GRCh37/hg19 by Entrez Gene)
Size:
76,639 bases
Orientation:
Plus strand

chr1:9,352,939-9,429,591
(GRCh37/hg19 by Ensembl)
Size:
76,653 bases
Orientation:
Plus strand

Genomic View for SPSB1 Gene

Genes around SPSB1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SPSB1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SPSB1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SPSB1 Gene

Proteins for SPSB1 Gene

  • Protein details for SPSB1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96BD6-SPSB1_HUMAN
    Recommended name:
    SPRY domain-containing SOCS box protein 1
    Protein Accession:
    Q96BD6
    Secondary Accessions:
    • A2A275
    • Q59FA1
    • Q5TIH9
    • Q9BRY9
    • Q9H6C5

    Protein attributes for SPSB1 Gene

    Size:
    273 amino acids
    Molecular mass:
    30942 Da
    Quaternary structure:
    • Component of the probable ECS(SPSB1) E3 ubiquitin-protein ligase complex which contains CUL5, RNF7/RBX2, Elongin BC complex and SPSB1 (PubMed:15601820). Interacts with CUL5, RNF7, ELOB and ELOC (PubMed:15601820). Directly interacts with MET tyrosine kinase domain in the presence and in the absence of HGF, however HGF treatment has a positive effect on this interaction (PubMed:15713673). When phosphorylated, interacts with RASA1 without affecting its stability (PubMed:15713673). Interacts (via B30.2/SPRY domain) with PAWR; this interaction is direct and occurs in association with the Elongin BC complex (PubMed:17189197, PubMed:20561531). Interacts with NOS2 (PubMed:21199876). Interacts with EPHB2 (PubMed:28931592).
    SequenceCaution:
    • Sequence=BAD92796.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for SPSB1 Gene

neXtProt entry for SPSB1 Gene

Post-translational modifications for SPSB1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SPSB1 Gene

No data available for DME Specific Peptides for SPSB1 Gene

Domains & Families for SPSB1 Gene

Gene Families for SPSB1 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for SPSB1 Gene

InterPro:
Blocks:
  • G-protein beta WD-40 repeat signature
  • SOCS protein, C-terminal

Suggested Antigen Peptide Sequences for SPSB1 Gene

GenScript: Design optimal peptide antigens:
  • SPRY domain-containing SOCS box protein 1 (SPSB1_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q96BD6

UniProtKB/Swiss-Prot:

SPSB1_HUMAN :
  • The SOCS box domain mediates the interaction with the Elongin BC complex, an adapter module in different E3 ubiquitin ligase complexes (By similarity). Essential for its ability to link NOS2 and the ECS E3 ubiquitin ligase complex components ELOC and CUL5.
  • Belongs to the SPSB family.
Domain:
  • The SOCS box domain mediates the interaction with the Elongin BC complex, an adapter module in different E3 ubiquitin ligase complexes (By similarity). Essential for its ability to link NOS2 and the ECS E3 ubiquitin ligase complex components ELOC and CUL5.
  • The B30.2/SPRY domain is involved in MET and PAWR binding (PubMed:15713673, PubMed:20561531).
Family:
  • Belongs to the SPSB family.
genes like me logo Genes that share domains with SPSB1: view

Function for SPSB1 Gene

Molecular function for SPSB1 Gene

UniProtKB/Swiss-Prot Function:
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 (PubMed:15601820, PubMed:21199876). Negatively regulates nitric oxide (NO) production and limits cellular toxicity in activated macrophages by mediating the ubiquitination and proteasomal degradation of NOS2 (PubMed:21199876). Acts as a bridge which links NOS2 with the ECS E3 ubiquitin ligase complex components ELOC and CUL5 (PubMed:21199876).

Phenotypes From GWAS Catalog for SPSB1 Gene

Gene Ontology (GO) - Molecular Function for SPSB1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 20561531
GO:1990756 protein binding, bridging involved in substrate recognition for ubiquitination IPI 21199876
genes like me logo Genes that share ontologies with SPSB1: view
genes like me logo Genes that share phenotypes with SPSB1: view

Animal Models for research

  • Taconic Biosciences Mouse Models for SPSB1

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SPSB1

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for SPSB1 Gene

Localization for SPSB1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SPSB1 Gene

Cytoplasm. Cytoplasm, cytosol. Note=Exhibits a diffuse cytosolic localization. {ECO:0000269 PubMed:21199876}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SPSB1 gene
Compartment Confidence
cytosol 5
mitochondrion 2
nucleus 2
plasma membrane 1
extracellular 1
cytoskeleton 1
endosome 1
golgi apparatus 1
peroxisome 0

Gene Ontology (GO) - Cellular Components for SPSB1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol TAS --
GO:0019005 SCF ubiquitin ligase complex IBA 21873635
genes like me logo Genes that share ontologies with SPSB1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for SPSB1 Gene

Pathways & Interactions for SPSB1 Gene

genes like me logo Genes that share pathways with SPSB1: view

UniProtKB/Swiss-Prot Q96BD6-SPSB1_HUMAN

  • Pathway: Protein modification; protein ubiquitination.

Gene Ontology (GO) - Biological Process for SPSB1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000209 protein polyubiquitination TAS --
GO:0006511 ubiquitin-dependent protein catabolic process IDA 21199876
GO:0016567 protein ubiquitination IEA,IDA 21199876
GO:0043161 proteasome-mediated ubiquitin-dependent protein catabolic process IBA 21873635
GO:0043687 post-translational protein modification TAS --
genes like me logo Genes that share ontologies with SPSB1: view

No data available for SIGNOR curated interactions for SPSB1 Gene

Drugs & Compounds for SPSB1 Gene

No Compound Related Data Available

Transcripts for SPSB1 Gene

mRNA/cDNA for SPSB1 Gene

1 REFSEQ mRNAs :
9 NCBI additional mRNA sequence :
4 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SPSB1

Alternative Splicing Database (ASD) splice patterns (SP) for SPSB1 Gene

No ASD Table

Relevant External Links for SPSB1 Gene

GeneLoc Exon Structure for
SPSB1

Expression for SPSB1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SPSB1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for SPSB1 Gene

This gene is overexpressed in Breast (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for SPSB1 Gene



Protein tissue co-expression partners for SPSB1 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SPSB1

SOURCE GeneReport for Unigene cluster for SPSB1 Gene:

Hs.8261

Evidence on tissue expression from TISSUES for SPSB1 Gene

  • Nervous system(4.6)
  • Muscle(2.4)
genes like me logo Genes that share expression patterns with SPSB1: view

Primer products for research

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for SPSB1 Gene

Orthologs for SPSB1 Gene

This gene was present in the common ancestor of animals.

Orthologs for SPSB1 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia SPSB1 29 30
  • 99.39 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia SPSB1 30
  • 98 (a)
OneToOne
Dog
(Canis familiaris)
Mammalia SPSB1 29 30
  • 91.45 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia SPSB1 29 30
  • 91.45 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Spsb1 29 16 30
  • 88.64 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Spsb1 29
  • 88.16 (n)
Platypus
(Ornithorhynchus anatinus)
Mammalia SPSB1 30
  • 67 (a)
OneToOne
Chicken
(Gallus gallus)
Aves SPSB1 29 30
  • 80.95 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia SPSB1 30
  • 92 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia spsb1 29
  • 75.09 (n)
Str.16969 29
African clawed frog
(Xenopus laevis)
Amphibia nszf-e326-prov 29
Zebrafish
(Danio rerio)
Actinopterygii spsb1 29 30
  • 74.24 (n)
OneToOne
Rainbow Trout
(Oncorhynchus mykiss)
Actinopterygii Omy.7541 29
Fruit Fly
(Drosophila melanogaster)
Insecta gus 30
  • 70 (a)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.8004 30
  • 48 (a)
OneToMany
Species where no ortholog for SPSB1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for SPSB1 Gene

ENSEMBL:
Gene Tree for SPSB1 (if available)
TreeFam:
Gene Tree for SPSB1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SPSB1: view image
Alliance of Genome Resources:
Additional Orthologs for SPSB1

Paralogs for SPSB1 Gene

Paralogs for SPSB1 Gene

(3) SIMAP similar genes for SPSB1 Gene using alignment to 2 proteins:

  • SPSB1_HUMAN
  • A2A276_HUMAN
genes like me logo Genes that share paralogs with SPSB1: view

Variants for SPSB1 Gene

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for SPSB1 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for SPSB1 Gene

Variant ID Type Subtype PubMed ID
dgv12e212 CNV gain 25503493
dgv13e212 CNV gain 25503493
dgv16n100 CNV gain 25217958
dgv17n100 CNV gain 25217958
dgv2e55 CNV gain 17911159
dgv3n27 CNV gain 19166990
dgv96n54 CNV gain 21841781
dgv97n54 CNV gain 21841781
esv1000068 CNV insertion 20482838
esv2201511 CNV deletion 18987734
esv2743574 CNV deletion 23290073
esv2743586 CNV deletion 23290073
esv2750845 CNV gain 17911159
esv2763409 CNV gain 21179565
esv3577722 CNV loss 25503493
esv3585168 CNV gain 21293372
esv3585169 CNV gain 21293372
nsv464172 CNV loss 19166990
nsv520191 CNV gain 19592680
nsv545350 CNV gain 21841781
nsv545362 CNV loss 21841781
nsv832092 CNV loss 17160897

Variation tolerance for SPSB1 Gene

Residual Variation Intolerance Score: 16.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.53; 11.55% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SPSB1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SPSB1
Leiden Open Variation Database (LOVD)
SPSB1

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SPSB1 Gene

Disorders for SPSB1 Gene

MalaCards: The human disease database

(1) MalaCards diseases for SPSB1 Gene - From: COP

Disorder Aliases PubMed IDs
congenital muscular dystrophy-dystroglycanopathy a7
  • congenital muscular dystrophy-dystroglycanopathy with brain and eye anomalies type a7
- elite association - COSMIC cancer census association via MalaCards
Search SPSB1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for SPSB1

Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with SPSB1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SPSB1 Gene

Publications for SPSB1 Gene

  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. (PMID: 15713673) Wang D … Wu G (The Journal of biological chemistry 2005) 2 3 4 22
  2. Ubiquitin ligase SPSB4 diminishes cell repulsive responses mediated by EphB2. (PMID: 28931592) Okumura F … Kamura T (Molecular biology of the cell 2017) 3 4
  3. Genome-wide association analysis implicates the involvement of eight loci with response to tocilizumab for the treatment of rheumatoid arthritis. (PMID: 22491018) Wang J … Platt A (The pharmacogenomics journal 2013) 3 40
  4. Regulation of inducible nitric-oxide synthase by the SPRY domain- and SOCS box-containing proteins. (PMID: 21199876) Nishiya T … Miwa S (The Journal of biological chemistry 2011) 3 4
  5. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 40

Products for SPSB1 Gene

Sources for SPSB1 Gene