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S100B Gene(Protein Coding)

S100 Calcium Binding Protein B

GCID:
GC21M046599
GIFtS:
56
Genes Participants
UDN Logo

Aliases for S100B Gene

Aliases for S100B Gene

  • S100 Calcium Binding Protein B 2 3 5
  • S-100 Protein Subunit Beta 3 4
  • S100 Calcium Binding Protein, Beta (Neural) 2
  • S100 Calcium-Binding Protein, Beta (Neural) 3
  • S-100 Calcium-Binding Protein, Beta Chain 3
  • S100 Calcium-Binding Protein B 4
  • S-100 Protein Beta Chain 4
  • Protein S100-B 3
  • S100beta 3
  • S100-B 3
  • S100 3
  • NEF 3

External Ids for S100B Gene

Previous GeneCards Identifiers for S100B Gene

  • GC21M044525
  • GC21M046875
  • GC21M046874
  • GC21M046842
  • GC21M048018
  • GC21M033398

Summaries for S100B Gene

Entrez Gene Summary for S100B Gene

  • The protein encoded by this gene is a member of the S100 family of proteins containing 2 EF-hand calcium-binding motifs. S100 proteins are localized in the cytoplasm and/or nucleus of a wide range of cells, and involved in the regulation of a number of cellular processes such as cell cycle progression and differentiation. S100 genes include at least 13 members which are located as a cluster on chromosome 1q21; however, this gene is located at 21q22.3. This protein may function in Neurite extension, proliferation of melanoma cells, stimulation of Ca2+ fluxes, inhibition of PKC-mediated phosphorylation, astrocytosis and axonal proliferation, and inhibition of microtubule assembly. Chromosomal rearrangements and altered expression of this gene have been implicated in several neurological, neoplastic, and other types of diseases, including Alzheimer's disease, Down's syndrome, epilepsy, amyotrophic lateral sclerosis, melanoma, and type I diabetes. [provided by RefSeq, Jul 2008]

GeneCards Summary for S100B Gene

S100B (S100 Calcium Binding Protein B) is a Protein Coding gene. Diseases associated with S100B include Middle Cerebral Artery Infarction and Amelanotic Melanoma. Among its related pathways are Innate Immune System and Cytosolic sensors of pathogen-associated DNA. Gene Ontology (GO) annotations related to this gene include calcium ion binding and identical protein binding. An important paralog of this gene is S100A1.

UniProtKB/Swiss-Prot for S100B Gene

  • Weakly binds calcium but binds zinc very tightly-distinct binding sites with different affinities exist for both ions on each monomer. Physiological concentrations of potassium ion antagonize the binding of both divalent cations, especially affecting high-affinity calcium-binding sites. Binds to and initiates the activation of STK38 by releasing autoinhibitory intramolecular interactions within the kinase. Interaction with AGER after myocardial infarction may play a role in myocyte apoptosis by activating ERK1/2 and p53/TP53 signaling. Could assist ATAD3A cytoplasmic processing, preventing aggregation and favoring mitochondrial localization. May mediate calcium-dependent regulation on many physiological processes by interacting with other proteins, such as TPR-containing proteins, and modulating their activity.

Tocris Summary for S100B Gene

Gene Wiki entry for S100B Gene

Additional gene information for S100B Gene

No data available for CIViC summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for S100B Gene

Genomics for S100B Gene

Products:

  1. Regulatory Element

GeneHancer (GH) Regulatory Elements for S100B Gene

Promoters and enhancers for S100B 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
GH21I046604 Promoter/Enhancer 1.6 EPDnew Ensembl ENCODE dbSUPER 571.4 -0.7 -705 2 MAX EBF1 ZFHX2 POLR2A EGR1 PRDM10 ZNF600 RUNX3 EGR2 ZNF189 S100B SPATC1L PRMT2
GH21I046632 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 23.8 -30.0 -30008 4.5 HDGF PKNOX1 CLOCK SMAD1 ARNT ARID4B SIN3A DMAP1 ZNF2 ZBTB7B PRMT2 ENSG00000228137 MCM3AP-AS1 DIP2A MCM3AP COL6A1 S100B ENSG00000227438 DSTNP1 SPATC1L
GH21I046620 Enhancer 1.5 FANTOM5 Ensembl ENCODE dbSUPER 21 -16.6 -16643 3.7 ELF3 FOXA2 ARID4B ZSCAN9 RARA SLC30A9 IKZF2 RUNX3 MXD4 ELF1 S100B SPATC1L PRMT2 DIP2A
GH21I046550 Enhancer 0.9 Ensembl ENCODE dbSUPER 32.1 +53.2 53206 3.8 MITF CTCF POLR2A KLF9 REST RUNX3 S100B PRMT2 SPATC1L RNU6-396P DIP2A
GH21I046598 Enhancer 1.2 Ensembl ENCODE dbSUPER 22.8 +5.8 5807 1.5 HDAC1 ELF3 PKNOX1 FOXA2 ARID4B BMI1 RARA ZHX1 KLF11 NR2F2 S100B DIP2A MCM3AP-AS1 RNU6-396P
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around S100B on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the S100B gene promoter:

Genomic Locations for S100B Gene

Genomic Locations for S100B Gene
chr21:46,598,618-46,605,208
(GRCh38/hg38)
Size:
6,591 bases
Orientation:
Minus strand
chr21:48,018,531-48,025,121
(GRCh37/hg19)

Genomic View for S100B Gene

Genes around S100B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
S100B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for S100B Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for S100B Gene

Proteins for S100B Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for S100B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P04271-S100B_HUMAN
    Recommended name:
    Protein S100-B
    Protein Accession:
    P04271
    Secondary Accessions:
    • D3DSN6

    Protein attributes for S100B Gene

    Size:
    92 amino acids
    Molecular mass:
    10713 Da
    Quaternary structure:
    • Dimer of either two alpha chains, or two beta chains, or one alpha and one beta chain. The S100B dimer binds two molecules of STK38. Interacts with CACYBP in a calcium-dependent manner. Interacts with ATAD3A; this interaction probably occurs in the cytosol prior to ATAD3A mitochondrial targeting. Interacts with S100A6. The S100B dimer interacts with two molecules of CAPZA1. Interacts with AGER. Interacts with PPP5C (via TPR repeats); the interaction is calcium-dependent and modulates PPP5C activity.
    Miscellaneous:
    • In addition to metal-ion binding, this protein is involved with the regulation of protein phosphorylation in brain tissue.

    Three dimensional structures from OCA and Proteopedia for S100B Gene

neXtProt entry for S100B Gene

Protein Expression for S100B Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for S100B Gene

No Post-translational modifications

Other Protein References for S100B Gene

ENSEMBL proteins:
REFSEQ proteins:

Protein Products

Assay Products

No data available for DME Specific Peptides for S100B Gene

Domains & Families for S100B Gene

Gene Families for S100B Gene

HGNC:
Human Protein Atlas (HPA):
  • Cancer-related genes
  • Candidate cardiovascular disease genes
  • Predicted intracellular proteins
  • Transporters

Protein Domains for S100B Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for S100B Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

P04271

UniProtKB/Swiss-Prot:

S100B_HUMAN :
  • Belongs to the S-100 family.
Family:
  • Belongs to the S-100 family.
genes like me logo Genes that share domains with S100B: view

Function for S100B Gene

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  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

Molecular function for S100B Gene

GENATLAS Biochemistry:
S100 calcium binding protein,beta polypeptide,neuronal,probably including locus control region LCR-S100B,stimulating GUCY2D at micromolar concentration of Ca2+ for retinal specific activity
UniProtKB/Swiss-Prot Function:
Weakly binds calcium but binds zinc very tightly-distinct binding sites with different affinities exist for both ions on each monomer. Physiological concentrations of potassium ion antagonize the binding of both divalent cations, especially affecting high-affinity calcium-binding sites. Binds to and initiates the activation of STK38 by releasing autoinhibitory intramolecular interactions within the kinase. Interaction with AGER after myocardial infarction may play a role in myocyte apoptosis by activating ERK1/2 and p53/TP53 signaling. Could assist ATAD3A cytoplasmic processing, preventing aggregation and favoring mitochondrial localization. May mediate calcium-dependent regulation on many physiological processes by interacting with other proteins, such as TPR-containing proteins, and modulating their activity.

Phenotypes From GWAS Catalog for S100B Gene

Gene Ontology (GO) - Molecular Function for S100B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005102 receptor binding IEA --
GO:0005509 calcium ion binding NAS,TAS 9519411
GO:0005515 protein binding IPI 3111527
GO:0008270 zinc ion binding ISS --
GO:0042802 identical protein binding IPI 10913138
genes like me logo Genes that share ontologies with S100B: view
genes like me logo Genes that share phenotypes with S100B: view

Animal Models for S100B Gene

MGI Knock Outs for S100B:

Animal Model Products

CRISPR Products

miRNA for S100B Gene

miRTarBase miRNAs that target S100B

Clone Products

  • Addgene plasmids for S100B

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for S100B Gene

Localization for S100B Gene

Subcellular locations from UniProtKB/Swiss-Prot for S100B Gene

Cytoplasm. Nucleus.

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 S100B gene
Compartment Confidence
extracellular 5
nucleus 5
cytosol 4
cytoskeleton 3
plasma membrane 2
mitochondrion 2
golgi apparatus 2
endosome 2
endoplasmic reticulum 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleus (3)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for S100B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001726 ruffle IDA 10913138
GO:0005576 extracellular region TAS --
GO:0005615 extracellular space IEA --
GO:0005634 nucleus IDA,IEA 10913138
GO:0005737 cytoplasm ISS --
genes like me logo Genes that share ontologies with S100B: view

Pathways & Interactions for S100B Gene

genes like me logo Genes that share pathways with S100B: view

Gene Ontology (GO) - Biological Process for S100B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007409 axonogenesis TAS 8202493
GO:0007417 central nervous system development TAS 8202493
GO:0007611 learning or memory ISS --
GO:0007613 memory IEA --
GO:0008283 cell proliferation TAS 8202493
genes like me logo Genes that share ontologies with S100B: view

No data available for SIGNOR curated interactions for S100B Gene

Drugs & Compounds for S100B Gene

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  1. Drug

(66) Drugs for S100B Gene - From: DrugBank, ClinicalTrials, FDA Approved Drugs, HMDB, Tocris, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Olopatadine Approved Pharma Target, other/unknown 0
calcium Approved Nutra Target 0
Calcium Citrate Approved Pharma Target, ligand 0
Calcium Phosphate Approved Pharma Target, ligand 0
Patanase Approved April 2008 Pharma 0

(44) Additional Compounds for S100B Gene - From: Novoseek and Tocris

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
Nogo-66 (1-40)
475221-20-6
PLP (139-151)
122018-58-0

(5) Tocris Compounds for S100B Gene

Compound Action Cas Number
B2 Promotes inclusion formation in Huntington's and Parkinson's diseases 115687-05-3
MOG (35-55) Encephalitogenic myelin oligodendrocyte glycoprotein fragment 149635-73-4
Nogo-66 (1-40) Competitive antagonist for Nogo-66 receptor; promotes neuron regeneration 475221-20-6
PLP (139-151) Encephalitogenic myelin proteolipid fragment 122018-58-0
TCS PrP Inhibitor 13 Antiprion agent; potently inhibits PrP-res accumulation 34320-83-7
genes like me logo Genes that share compounds with S100B: view

Transcripts for S100B Gene

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  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for S100B Gene

(2) REFSEQ mRNAs :
(3) Additional mRNA sequences :
(265) Selected AceView cDNA sequences:
(3) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for S100B Gene

S100 calcium binding protein B:
Representative Sequences:

CRISPR Products

Clone Products

  • Addgene plasmids for S100B

Alternative Splicing Database (ASD) splice patterns (SP) for S100B Gene

ExUns: 1a · 1b · 1c · 1d · 1e ^ 2a · 2b · 2c ^ 3 ^ 4a · 4b · 4c · 4d · 4e
SP1: - -
SP2: -
SP3: - - -
SP4: - - - -
SP5: - -
SP6: -

Relevant External Links for S100B Gene

GeneLoc Exon Structure for
S100B
ECgene alternative splicing isoforms for
S100B

Expression for S100B Gene

Products:

  1. Primer

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for S100B Gene

mRNA expression in normal human tissues for S100B Gene
mRNA expression by GTEx for S100B GenemRNA expression by BioGPS for S100B Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for S100B Gene

This gene is overexpressed in Brain - Spinal cord (cervical c-1) (x17.0) and Brain - Substantia nigra (x6.6).

Protein differential expression in normal tissues from HIPED for S100B Gene

This gene is overexpressed in Spinal cord (35.1), Cerebrospinal fluid (9.0), and Brain (7.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for S100B Gene



NURSA nuclear receptor signaling pathways regulating expression of S100B Gene:

S100B

SOURCE GeneReport for Unigene cluster for S100B Gene:

Hs.422181

mRNA Expression by UniProt/SwissProt for S100B Gene:

P04271-S100B_HUMAN
Tissue specificity: Although predominant among the water-soluble brain proteins, S100 is also found in a variety of other tissues.

Evidence on tissue expression from TISSUES for S100B Gene

  • Nervous system(4.9)
  • Skin(4.8)
  • Blood(3)
  • Eye(2.7)
  • Lymph node(2.5)
  • Spleen(2.5)
  • Heart(2.3)
  • Muscle(2.3)
  • Intestine(2.1)
genes like me logo Genes that share expression patterns with S100B: view

No data available for Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for S100B Gene

Orthologs for S100B Gene

This gene was present in the common ancestor of chordates.

Orthologs for S100B Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia S100B 33 34
  • 98.91 (n)
cow
(Bos Taurus)
 Mammalia S100B 33 34
  • 90.22 (n)
rat
(Rattus norvegicus)
 Mammalia S100b 33
  • 85.87 (n)
mouse
(Mus musculus)
 Mammalia S100b 33 16 34
  • 85.51 (n)
dog
(Canis familiaris)
 Mammalia S100B 33 34
  • 78.62 (n)
platypus
(Ornithorhynchus anatinus)
 Mammalia S100B 34
  • 63 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves S100B 33 34
  • 83.33 (n)
zebrafish
(Danio rerio)
 Actinopterygii s100b 33 34
  • 67.4 (n)
wufq18b10 33
Species where no ortholog for S100B was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for S100B Gene

ENSEMBL:
Gene Tree for S100B (if available)
TreeFam:
Gene Tree for S100B (if available)

Paralogs for S100B Gene

Paralogs for S100B Gene

(22) SIMAP similar genes for S100B Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with S100B: view

Variants for S100B Gene

Sequence variations from dbSNP and Humsavar for S100B Gene

SNP ID Clin Chr 21 pos Variation AA Info Type
rs1000022265 -- 46,598,352(-) C/A/T downstream_transcript_variant
rs1000253369 -- 46,604,046(-) A/G intron_variant
rs1000377048 -- 46,598,498(-) C/T downstream_transcript_variant
rs1001889092 -- 46,603,393(-) G/A intron_variant
rs1001919091 -- 46,606,985(-) T/C upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for S100B Gene

Variant ID Type Subtype PubMed ID
nsv588002 CNV gain 21841781
nsv587999 CNV gain 21841781
nsv528947 CNV gain 19592680
nsv528495 CNV loss 19592680
nsv527542 CNV loss 19592680
nsv470910 CNV gain 18288195
nsv1065227 CNV gain 25217958
nsv1057566 CNV loss 25217958
esv3647173 CNV gain 21293372
esv3647172 CNV loss 21293372
esv3647171 CNV gain 21293372
esv34393 CNV gain 17911159
esv2760700 CNV gain 21179565
esv2758822 CNV gain 17122850
dgv4446n100 CNV gain 25217958
dgv4445n100 CNV gain 25217958
dgv4444n100 CNV gain 25217958
dgv4443n100 CNV gain 25217958
dgv4442n100 CNV gain 25217958
dgv4441n100 CNV gain 25217958

Variation tolerance for S100B Gene

Residual Variation Intolerance Score: 52.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.10; 2.22% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for S100B Gene

Human Gene Mutation Database (HGMD)
S100B
SNPedia medical, phenotypic, and genealogical associations of SNPs for
S100B

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for S100B Gene

Disorders for S100B Gene

MalaCards: The human disease database

(129) MalaCards diseases for S100B Gene - From: HGMD, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
middle cerebral artery infarction
  • infarction middle cerebral artery
amelanotic melanoma
  • melanoma amelanotic
malignant giant cell tumor of soft parts
  • malignant giant cell neoplasm of soft parts
neurofibroma
  • nerve sheath tumors
myxopapillary ependymoma
  • ependymoma myxopapillary
- elite association - COSMIC cancer census association via MalaCards
Search S100B in MalaCards View complete list of genes associated with diseases

Additional Disease Information for S100B

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with S100B: view

No data available for UniProtKB/Swiss-Prot and Genatlas for S100B Gene

Publications for S100B Gene

  1. The calcium-dependent interaction between S100B and the mitochondrial AAA ATPase ATAD3A and the role of this complex in the cytoplasmic processing of ATAD3A. (PMID: 20351179) Gilquin B … Baudier J (Molecular and cellular biology 2010) 3 4 22 58
  2. The calcium binding protein, S100B, is increased in the amniotic fluid of women with intra-amniotic infection/inflammation and preterm labor with intact or ruptured membranes. (PMID: 17624933) Friel LA … Espinoza J (Journal of perinatal medicine 2007) 3 22 25 58
  3. Demonstration of heterodimer formation between S100B and S100A6 in the yeast two-hybrid system and human melanoma. (PMID: 9925766) Yang Q … Marks A (Experimental cell research 1999) 3 4 22 58
  4. Cloning and expression of the human S100 beta gene. (PMID: 2394738) Allore RJ … Marks A (The Journal of biological chemistry 1990) 2 3 4 58
  5. The combination of a genome-wide association study of lymphocyte count and analysis of gene expression data reveals novel asthma candidate genes. (PMID: 22286170) Cusanovich DA … Gilad Y (Human molecular genetics 2012) 3 44 58

Products for S100B Gene