CALB2 calbindin 2 [Homo sapiens (human)] - Gene

Summary

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

Location:: 16q22.2

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	16	NC_000016.10 (71358723..71390433)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	16	NC_060940.1 (77174637..77207658)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	16	NC_000016.9 (71392626..71424336)

Chromosome 16 - NC_000016.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

"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.
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.
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.
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.
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.
CLDN15 is a novel diagnostic marker for malignant pleural mesothelioma.
Title: CLDN15 is a novel diagnostic marker for malignant pleural mesothelioma.
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.
Determinants of plasma calretinin in patients with malignant pleural mesothelioma.
Title: Determinants of plasma calretinin in patients with malignant pleural mesothelioma.
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.
Expression of calretinin in odontogenic keratocysts and basal cell carcinomas: A study of sporadic and Gorlin-Goltz syndrome-related cases.
Title: Expression of calretinin in odontogenic keratocysts and basal cell carcinomas: A study of sporadic and Gorlin-Goltz syndrome-related cases.

Submit: New GeneRIF Correction See all GeneRIFs (78)

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

SHGC-147616 (e-PCR)
- UniSTS:175915

SHGC-11961 (e-PCR)
- UniSTS:36694

D16S681 (e-PCR)
- UniSTS:54945

GDB:180914 (e-PCR)
- UniSTS:155119

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)

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
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

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_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000016.10 Reference GRCh38.p14 Primary Assembly

Range

71358723..71390433

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GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

NW_013171813.1 Reference GRCh38.p14 PATCHES

Range

226200..257930

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GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

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

NM_007087.2: Suppressed sequence

Description

NM_007087.2: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.