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    CALB2 calbindin 2 [ Homo sapiens (human) ]

    Gene ID: 794, updated on 10-Dec-2024

    Summary

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    Official Symbol
    CALB2provided by HGNC
    Official Full Name
    calbindin 2provided by HGNC
    Primary source
    HGNC:HGNC:1435
    See related
    Ensembl:ENSG00000172137 MIM:114051; AllianceGenome:HGNC:1435
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    CR; CAL2; CAB29
    Summary
    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]
    Expression
    Biased expression in fat (RPKM 72.8), testis (RPKM 20.4) and 4 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See CALB2 in Genome Data Viewer
    Location:
    16q22.2
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (71358723..71390433)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (77174637..77207658)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (71392626..71424336)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC102723786 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7675 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7676 Neighboring gene cap methyltransferase 2 Neighboring gene uncharacterized LOC102725168 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr16:71371582-71372781 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:71392357-71393322 Neighboring gene Sharpr-MPRA regulatory region 14967 Neighboring gene uncharacterized LOC105371332 Neighboring gene Sharpr-MPRA regulatory region 5468 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr16:71420497-71421047 Neighboring gene hESC enhancers GRCh37_chr16:71421048-71421598 and GRCh37_chr16:71421599-71422149 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_43990 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:71423333-71423878 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:71445925-71446426 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11071 Neighboring gene long intergenic non-protein coding RNA 2136 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:71459785-71460285 Neighboring gene tRNA-Met (anticodon CAT) 2-1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Calbindin 2 (CALB2) regulates 5-fluorouracil sensitivity in colorectal cancer by modulating the intrinsic apoptotic pathway. Stevenson L, et al. PLoS One, 2011. PMID 21629658, Free PMC Article
    2. SV40-induced expression of calretinin protects mesothelial cells from asbestos cytotoxicity and may be a key factor contributing to mesothelioma pathogenesis. Henzi T, et al. Am J Pathol, 2009 Jun. PMID 19435792, Free PMC Article
    3. Calretinin: modulator of neuronal excitability. Camp AJ, et al. Int J Biochem Cell Biol, 2009 Nov. PMID 19450707
    4. Calretinin: diagnostic utility in the female genital tract. Portugal R, et al. Adv Anat Pathol, 2009 Mar. PMID 19550372
    5. Calretinin immunohistochemistry: a simple and efficient tool to diagnose Hirschsprung disease. Guinard-Samuel V, et al. Mod Pathol, 2009 Oct. PMID 19648883

    See all (104) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Expression of Calretinin in the Cecal Muscularis Interna: Observation and Hypothetical Relevance to Appendicitis.
      Title: Expression of Calretinin in the Cecal Muscularis Interna: Observation and Hypothetical Relevance to Appendicitis.
    2. "Deciduoid" Change in Uterine Leiomyomas in Pregnancy: Aberrant Expression of Sex Cord Markers Inhibin and Calretinin.
      Title: "Deciduoid" Change in Uterine Leiomyomas in Pregnancy: Aberrant Expression of Sex Cord Markers Inhibin and Calretinin.
    3. Serum Calretinin and Genetic Variability as a Prognostic and Predictive Factor in Malignant Mesothelioma.
      Title: Serum Calretinin and Genetic Variability as a Prognostic and Predictive Factor in Malignant Mesothelioma.
    4. All-Ion Monitoring-Directed Low-Abundance Protein Quantification Reveals CALB2 as a Key Promoter in Hepatocellular Carcinoma Metastasis.
      Title: All-Ion Monitoring-Directed Low-Abundance Protein Quantification Reveals CALB2 as a Key Promoter in Hepatocellular Carcinoma Metastasis.
    5. Increasing Trend of Calretinin-Positive Mucosal Innervation from Aganglionic Zone toward Transition Zone in Hirschsprung's Disease.
      Title: Increasing Trend of Calretinin-Positive Mucosal Innervation from Aganglionic Zone toward Transition Zone in Hirschsprung's Disease.
    6. Expression of Calretinin, Marker of Mesothelial Differentiation, in Pancreatic Ductal Adenocarcinoma: A Potential Diagnostic Pitfall.", trans "Expression of Calretinin, Marker of Mesothelial Differentiation, in Pancreatic Ductal Adenocarcinoma: A Potential Diagnostic Pitfall.
      Title: Expression of Calretinin, Marker of Mesothelial Differentiation, in Pancreatic Ductal Adenocarcinoma: A Potential Diagnostic Pitfall.
    7. CLDN15 is a novel diagnostic marker for malignant pleural mesothelioma.
      Title: CLDN15 is a novel diagnostic marker for malignant pleural mesothelioma.
    8. LncRNA CALB2 sponges miR-30b-3p to promote odontoblast differentiation of human dental pulp stem cells via up-regulating RUNX2.
      Title: LncRNA CALB2 sponges miR-30b-3p to promote odontoblast differentiation of human dental pulp stem cells via up-regulating RUNX2.
    9. Determinants of plasma calretinin in patients with malignant pleural mesothelioma.
      Title: Determinants of plasma calretinin in patients with malignant pleural mesothelioma.
    10. Whole-genome sequencing of African Americans implicates differential genetic architecture in inflammatory bowel disease.
      Title: Whole-genome sequencing of African Americans implicates differential genetic architecture in inflammatory bowel disease.
    Submit: New GeneRIF Correction See all GeneRIFs (79)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables calcium ion binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables calcium ion binding involved in regulation of presynaptic cytosolic calcium ion concentration IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in regulation of long-term synaptic potentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of presynaptic cytosolic calcium ion concentration IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytosol IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in dendrite IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in gap junction IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in parallel fiber to Purkinje cell synapse IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in synapse IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in terminal bouton IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    calretinin
    Names
    29 kDa calbindin
    calbindin 2, (29kD, calretinin)
    calbindin D29K
    testicular secretory protein Li 8

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001740.5 → NP_001731.2  calretinin isoform 1

      See identical proteins and their annotated locations for NP_001731.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (isoform 1), which has also been designated as the full-length isoform.
      Source sequence(s)
      AK222495
      Consensus CDS
      CCDS10899.1
      UniProtKB/Swiss-Prot
      A8K4Y1, P22676, Q53HD2, Q96BK4
      UniProtKB/TrEMBL
      A0A140VK08, H3BN14
      Related
      ENSP00000307508.4, ENST00000302628.9
      Conserved Domains (2) summary
      cd00051
      Location:111 → 180
      EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...
      pfam13499
      Location:113 → 180
      EF-hand_7; EF-hand domain pair

    2. NM_007088.4 → NP_009019.1  calretinin isoform 22k

      See identical proteins and their annotated locations for NP_009019.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (CALB2c) lacks an alternate segment in the 3' coding region, which results in a frameshift and an early stop codon, compared to variant 1. The resulting protein (isoform 22k) has a shorter and distinct C-terminus, compared to isoform 1. There are no publicly available transcripts supporting this variant; it is represented based on data in PMID:7607211.
      Source sequence(s)
      AK222495
      UniProtKB/TrEMBL
      A6NER6
      Related
      ENSP00000340294.5, ENST00000349553.9
      Conserved Domains (2) summary
      cd00051
      Location:111 → 179
      EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...
      pfam13499
      Location:113 → 176
      EF-hand_7; EF-hand domain pair

    RNA

    1. NR_027910.3 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (CALB2b) lacks an alternate internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD). This variant was described by Schwaller et al (PMID: 7607211), and proposed to encode a 20kDa isoform, but this protein has not been shown to be expressed in vivo.
      Source sequence(s)
      AK222495

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      71358723..71390433
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 PATCHES

    Genomic

    1. NW_013171813.1 Reference GRCh38.p14 PATCHES

      Range
      226200..257930
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      77174637..77207658
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_007087.2: Suppressed sequence

      Description
      NM_007087.2: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P22676.2 GenPept UniProtKB/Swiss-Prot:P22676

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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