CALB2 Gene (Protein Coding)

Calbindin 2

GC16P071392
GIFtS:
40
This gene encodes an intracellular calcium-binding protein belonging to the troponin C superfamily. Members of this protein family have six EF-hand domains which bind calcium. This protein plays a role in diverse cellular functions, including message targeting and intracellular calcium buffering. It also functions as a modulator of neuronal excitability, and is a diagnostic mar... See more...

Aliases for CALB2 Gene

Aliases for CALB2 Gene

  • Calbindin 2 2 3 5
  • Calretinin 2 3 4
  • 29 KDa Calbindin 3 4
  • CAB29 3 4
  • CAL2 2 3
  • CR 3 4
  • Testicular Secretory Protein Li 8 3
  • Calbindin 2, 29kDa (Calretinin) 2
  • Calbindin 2, (29kD, Calretinin) 3
  • Calbindin D29K 3
  • CALB2 5

External Ids for CALB2 Gene

Previous GeneCards Identifiers for CALB2 Gene

  • GC16P062284
  • GC16P072115
  • GC16P071128
  • GC16P071168
  • GC16P069950
  • GC16P057160

Summaries for CALB2 Gene

Entrez Gene Summary for CALB2 Gene

  • This gene encodes an intracellular calcium-binding protein belonging to the troponin C superfamily. Members of this protein family have six EF-hand domains which bind calcium. This protein plays a role in diverse cellular functions, including message targeting and intracellular calcium buffering. It also functions as a modulator of neuronal excitability, and is a diagnostic marker for some human diseases, including Hirschsprung disease and some cancers. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jun 2010]

GeneCards Summary for CALB2 Gene

CALB2 (Calbindin 2) is a Protein Coding gene. Diseases associated with CALB2 include Adenomatoid Tumor and Sertoli-Leydig Cell Tumor. Gene Ontology (GO) annotations related to this gene include calcium ion binding. An important paralog of this gene is CALB1.

UniProtKB/Swiss-Prot Summary for CALB2 Gene

  • Calretinin is a calcium-binding protein which is abundant in auditory neurons.

Gene Wiki entry for CALB2 Gene

Additional gene information for CALB2 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for CALB2 Gene

Genomics for CALB2 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for CALB2 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
GH16J071358 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE CraniofacialAtlas 600.7 +1.0 983 3 CTCF HNRNPL IKZF1 BACH1 LARP7 ZNF143 ZNF24 REST RAD21 POLR2A CALB2 ATXN1L LOC105371332 TLE7
GH16J071425 Promoter/Enhancer 1.4 Ensembl ENCODE 10.5 +67.8 67788 1.8 HNRNPL GATAD2A TEAD4 PRDM10 ZNF629 TFE3 SOX13 IKZF1 NFKBIZ KDM1A LINC02136 TRM-CAT2-1 ZNF23 ZNF19 DHX38 SF3B3 ENSG00000247324 PHLPP2 ATXN1L IST1
GH16J071492 Enhancer 1 Ensembl ENCODE 10.1 +133.6 133588 5.8 LEF1 CTCF JUND MTA2 PKNOX1 ZNF24 DPF2 HDAC1 SOX6 FOXJ2 ZNF23 SF3B3 DHX38 ZNF19 ENSG00000247324 TAT CALB2 VAC14 TAT-AS1 PHLPP2
GH16J070803 Promoter/Enhancer 1 Ensembl ENCODE 8.8 -553.4 -553407 3.4 POLR2A CEBPB CBX3 NFE2 ZNF316 JUN FOS ZNF318 MAFK TRIM24 ENSG00000262890 MN297380 CALB2 VAC14 ENSG00000261777 lnc-IL34-3 HYDIN
GH16J071413 Enhancer 0.8 ENCODE 10.6 +54.2 54200 0.2 GATAD2A CTCF IKZF1 REST RAD21 TRIM22 BRCA1 EGR1 SMC3 MYC ENSG00000247324 ZNF23 CALB2 ZNF19 ENSG00000262120 lnc-CALB2-5 LINC02136 LOC105371332 TLE7
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CALB2 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for CALB2

Top Transcription factor binding sites by QIAGEN in the CALB2 gene promoter:
  • AML1a
  • c-Myc
  • CREB
  • LyF-1
  • Max1
  • MIF-1
  • MyoD
  • POU3F2
  • POU3F2 (N-Oct-5a)
  • POU3F2 (N-Oct-5b)

Genomic Locations for CALB2 Gene

Genomic Locations for CALB2 Gene
chr16:71,358,713-71,390,438
(GRCh38/hg38)
Size:
31,726 bases
Orientation:
Plus strand
chr16:71,392,616-71,424,341
(GRCh37/hg19)
Size:
31,726 bases
Orientation:
Plus strand

Genomic View for CALB2 Gene

Genes around CALB2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CALB2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CALB2 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for CALB2 Gene

Proteins for CALB2 Gene

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  • Protein details for CALB2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P22676-CALB2_HUMAN
    Recommended name:
    Calretinin
    Protein Accession:
    P22676
    Secondary Accessions:
    • A8K4Y1
    • Q53HD2
    • Q96BK4

    Protein attributes for CALB2 Gene

    Size:
    271 amino acids
    Molecular mass:
    31540 Da
    Quaternary structure:
    No Data Available

neXtProt entry for CALB2 Gene

Protein Expression for CALB2 Gene

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

Post-translational modifications for CALB2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for CALB2 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for CALB2 Gene

Domains & Families for CALB2 Gene

Gene Families for CALB2 Gene

HGNC:
Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins
  • Transporters

Protein Domains for CALB2 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for CALB2 Gene

GenScript: Design optimal peptide antigens:
  • 29 kDa calbindin (CALB2_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P22676

UniProtKB/Swiss-Prot:

CALB2_HUMAN :
  • Belongs to the calbindin family.
Family:
  • Belongs to the calbindin family.
genes like me logo Genes that share domains with CALB2: view

Function for CALB2 Gene

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  2. CRISPR
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Molecular function for CALB2 Gene

UniProtKB/Swiss-Prot Function:
Calretinin is a calcium-binding protein which is abundant in auditory neurons.
GENATLAS Biochemistry:
calbindin (29kDa),vitamin D dependent calcium binding protein 2,from the intestine

Phenotypes From GWAS Catalog for CALB2 Gene

Gene Ontology (GO) - Molecular Function for CALB2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding IEA,IBA 21873635
GO:0046872 metal ion binding IEA --
GO:0099534 calcium ion binding involved in regulation of presynaptic cytosolic calcium ion concentration IEA --
genes like me logo Genes that share ontologies with CALB2: view
genes like me logo Genes that share phenotypes with CALB2: view

Animal Models for CALB2 Gene

MGI Knock Outs for CALB2:

Animal Model Products

CRISPR Products

miRNA for CALB2 Gene

miRTarBase miRNAs that target CALB2

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CALB2

Clone Products

  • Addgene plasmids for CALB2

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for CALB2 Gene

Localization for CALB2 Gene

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 CALB2 gene
Compartment Confidence
cytosol 5
cytoskeleton 4
nucleus 4
plasma membrane 3
extracellular 2
mitochondrion 2
endoplasmic reticulum 2
endosome 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (4)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for CALB2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005623 cell IEA --
GO:0005634 nucleus IEA,IBA 21873635
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol IDA --
GO:0005921 gap junction IEA --
genes like me logo Genes that share ontologies with CALB2: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for CALB2 Gene

Pathways & Interactions for CALB2 Gene

PathCards logo

SuperPathways for CALB2 Gene

No Data Available

Gene Ontology (GO) - Biological Process for CALB2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0051480 regulation of cytosolic calcium ion concentration IBA 21873635
GO:0099509 regulation of presynaptic cytosolic calcium ion concentration IBA 21873635
GO:1900271 regulation of long-term synaptic potentiation IBA 21873635
genes like me logo Genes that share ontologies with CALB2: view

No data available for Pathways by source and SIGNOR curated interactions for CALB2 Gene

Drugs & Compounds for CALB2 Gene

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  1. Drug

(25) Drugs for CALB2 Gene - From: DrugBank, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Calcium citrate Approved, Investigational Pharma Target, ligand 0
Calcium levulinate Approved, Experimental Pharma Target, agonist 0
Calcium Phosphate Approved Pharma Target, ligand 0
Calcium phosphate dihydrate Approved Pharma Target 0
Calcium Nutra 6556

(12) Additional Compounds for CALB2 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with CALB2: view

Transcripts for CALB2 Gene

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  1. CRISPR
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  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for CALB2 Gene

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

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CALB2

Clone Products

  • Addgene plasmids for CALB2

Alternative Splicing Database (ASD) splice patterns (SP) for CALB2 Gene

No ASD Table

Relevant External Links for CALB2 Gene

GeneLoc Exon Structure for
CALB2

Expression for CALB2 Gene

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  1. Primer
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mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for CALB2 Gene

mRNA expression in normal human tissues for CALB2 Gene
mRNA expression by GTEx for CALB2 GenemRNA expression by BioGPS for CALB2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CALB2 Gene

This gene is overexpressed in Brain - Hypothalamus (x11.9), Adipose - Visceral (Omentum) (x4.4), Brain - Cerebellum (x4.3), and Brain - Cerebellar Hemisphere (x4.2).

Protein differential expression in normal tissues from HIPED for CALB2 Gene

This gene is overexpressed in Testis (29.9), Nasopharynx (10.2), and Fetal testis (7.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for CALB2 Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for CALB2

SOURCE GeneReport for Unigene cluster for CALB2 Gene:

Hs.106857

mRNA Expression by UniProt/SwissProt for CALB2 Gene:

P22676-CALB2_HUMAN
Tissue specificity: Brain.

Evidence on tissue expression from TISSUES for CALB2 Gene

  • Nervous system(4.9)
  • Intestine(4.5)
  • Eye(3.1)
  • Kidney(2.8)
  • Lung(2.8)
  • Adrenal gland(2.7)
  • Muscle(2.5)
  • Skin(2.5)
  • Blood(2.4)
  • Heart(2.4)
  • Lymph node(2)
genes like me logo Genes that share expression patterns with CALB2: view

No data available for Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for CALB2 Gene

Orthologs for CALB2 Gene

This gene was present in the common ancestor of animals.

Orthologs for CALB2 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia CALB2 31
  • 99 (a)
 OneToOne
Dog
(Canis familiaris)
 Mammalia CALB2 30 31
  • 93.68 (n)
 OneToOne
Platypus
(Ornithorhynchus anatinus)
 Mammalia CALB2 31
  • 93 (a)
 OneToOne
Cow
(Bos Taurus)
 Mammalia CALB2 30 31
  • 91.39 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Calb2 30
  • 91.14 (n)
Mouse
(Mus musculus)
 Mammalia Calb2 30 17 31
  • 91.02 (n)
 OneToOne
Oppossum
(Monodelphis domestica)
 Mammalia CALB2 31
  • 84 (a)
 OneToOne
Chicken
(Gallus gallus)
 Aves CALB2 30 31
  • 81.04 (n)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia calb2 30
  • 72.68 (n)
Zebrafish
(Danio rerio)
 Actinopterygii calb2a 30 31
  • 73.36 (n)
 OneToMany
calb2b 31
  • 72 (a)
 OneToMany
-- 30
Rainbow Trout
(Oncorhynchus mykiss)
 Actinopterygii Omy.698 30
Fruit Fly
(Drosophila melanogaster)
 Insecta Cbp53E 31 32
  • 41 (a)
 OneToMany
Species where no ortholog for CALB2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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)
  • 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)
  • 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 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)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for CALB2 Gene

ENSEMBL:
Gene Tree for CALB2 (if available)
TreeFam:
Gene Tree for CALB2 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CALB2: view image

Paralogs for CALB2 Gene

Paralogs for CALB2 Gene

(3) SIMAP similar genes for CALB2 Gene using alignment to 4 proteins:

  • CALB2_HUMAN
  • A6NER6_HUMAN
  • H3BMN5_HUMAN
  • H3BN14_HUMAN
genes like me logo Genes that share paralogs with CALB2: view

Variants for CALB2 Gene

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Additional dbSNP identifiers (rs#s) for CALB2 Gene

Structural Variations from Database of Genomic Variants (DGV) for CALB2 Gene

Variant ID Type Subtype PubMed ID
esv2640068 CNV insertion 19546169
esv3417792 CNV duplication 20981092
esv3582293 CNV loss 25503493
esv3638971 CNV gain 21293372
nsv572949 CNV loss 21841781
nsv7285 OTHER inversion 18451855

Variation tolerance for CALB2 Gene

Residual Variation Intolerance Score: 29.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.87; 79.42% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CALB2 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
CALB2

SNP Genotyping and Copy Number Assay Products

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 CALB2 Gene

Disorders for CALB2 Gene

MalaCards: The human disease database

(154) MalaCards diseases for CALB2 Gene - From: DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
adenomatoid tumor
  • adenomatoid tumour
sertoli-leydig cell tumor
  • sertoli-leydig cell tumors
sertoli cell tumor
  • tubular androblastoma
adenofibroma
sarcomatoid mesothelioma
  • malignant fibrous mesothelioma
- elite association - COSMIC cancer census association via MalaCards
Search CALB2 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for CALB2

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with CALB2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CALB2 Gene

Publications for CALB2 Gene

  1. Heterozygosity of SNP513 in intron 9 of the human calretinin gene (CALB2) is a risk factor for colon cancer. (PMID: 18214032) Vonlanthen S … Schwaller B (Anticancer research 2007) 3 23 41
  2. Structure of the human brain calcium-binding protein calretinin and its expression in bacteria. (PMID: 2001709) Parmentier M … Lefort A (European journal of biochemistry 1991) 3 4 23
  3. The human calbindin D28k (CALB1) and calretinin (CALB2) genes are located at 8q21.3----q22.1 and 16q22----q23, respectively, suggesting a common duplication with the carbonic anhydrase isozyme loci. (PMID: 1906795) Parmentier M … Mattei MG (Cytogenetics and cell genetics 1991) 2 3 23
  4. A bipartite butyrate-responsive element in the human calretinin (CALB2) promoter acts as a repressor in colon carcinoma cells but not in mesothelioma cells. (PMID: 19998412) Häner K … Schwaller B (Journal of cellular biochemistry 2010) 3 23
  5. In vitro and in vivo characterization of highly purified human mesothelioma derived cells. (PMID: 20175889) Melotti A … Corte G (BMC cancer 2010) 3 23

ExternalLinks

View latest publications for CALB2 gene in Mastermind

Products for CALB2 Gene

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Sources for CALB2 Gene