This gene encodes a calcium-binding protein that is abundant in neutrophils and macrophages. In the absence of divalent cation, this protein localizes to the cytosolic fraction; with magnesium alone, it partitions with the granule fraction; and in the presence of magnesium and calcium, it associates with both the granule and membrane fractions. Alternative splicing and use of a... See more...

Aliases for GCA Gene

Aliases for GCA Gene

  • Grancalcin 2 3 4 5
  • Grancalcin, EF-Hand Calcium-Binding Protein 2 3
  • GCL 3 4
  • Grancalcin, EF-Hand Calcium Binding Protein 2
  • Grancalcin, Penta-EF-Hand Protein 3

External Ids for GCA Gene

Previous GeneCards Identifiers for GCA Gene

  • GC02P161254
  • GC02P161728
  • GC02P163164
  • GC02P163403
  • GC02P163026
  • GC02P162908
  • GC02P155082

Summaries for GCA Gene

Entrez Gene Summary for GCA Gene

  • This gene encodes a calcium-binding protein that is abundant in neutrophils and macrophages. In the absence of divalent cation, this protein localizes to the cytosolic fraction; with magnesium alone, it partitions with the granule fraction; and in the presence of magnesium and calcium, it associates with both the granule and membrane fractions. Alternative splicing and use of alternative promoters results in multiple transcript variants. [provided by RefSeq, Aug 2016]

GeneCards Summary for GCA Gene

GCA (Grancalcin) is a Protein Coding gene. Diseases associated with GCA include Retinitis Pigmentosa 19. Among its related pathways are Innate Immune System. Gene Ontology (GO) annotations related to this gene include calcium ion binding and protein heterodimerization activity. An important paralog of this gene is SRI.

UniProtKB/Swiss-Prot Summary for GCA Gene

  • Calcium-binding protein that may play a role in the adhesion of neutrophils to fibronectin. May play a role in the formation of focal adhesions.

Gene Wiki entry for GCA Gene

Additional gene information for GCA Gene

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

Genomics for GCA Gene

GeneHancer (GH) Regulatory Elements for GCA Gene

Promoters and enhancers for GCA 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
GH02J162316 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 500.7 -0.7 -673 5.4 EP300 RXRA ZBTB40 ZNF217 CTCF SIN3A POLR2G SP1 ZFX POLR2A GCA IFIH1 NONHSAG029692.2 ENSG00000226121 FAP lnc-FAP-3
GH02J162343 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 512.6 +26.1 26108 4.2 ZNF217 EP300 TCF12 POLR2G SP1 PHF8 POLR2A ZBTB26 SAP30 RFX1 GCA IFIH1 FAP piR-46501-057 RF00998-078
GH02J162342 Promoter 0.4 Ensembl 12.8 +23.7 23708 0.2 HLF IFIH1 GCA piR-46501-057 RF00998-078
GH02J162478 Enhancer 0.6 FANTOM5 Ensembl 5.9 +160.0 160022 0.8 FOS STAT1 MYC STAT3 GCA piR-48049-041 RF00001-177 RNA5SP109 KCNH7
GH02J162277 Enhancer 0.3 Ensembl 5.4 -40.9 -40892 0.6 CREB1 SPI1 FAP GCA LOC105373724 lnc-FAP-3 IFIH1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around GCA on UCSC Golden Path with GeneCards custom track

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

Top Transcription factor binding sites by QIAGEN in the GCA gene promoter:
  • ATF6
  • c-Rel
  • C/EBPalpha
  • Nkx3-1 v4
  • p53
  • POU3F2
  • POU3F2 (N-Oct-5a)
  • POU3F2 (N-Oct-5b)
  • STAT1

Genomic Locations for GCA Gene

Genomic Locations for GCA Gene
chr2:162,318,793-162,379,989
(GRCh38/hg38)
Size:
61,197 bases
Orientation:
Plus strand
chr2:163,175,350-163,228,105
(GRCh37/hg19)
Size:
52,756 bases
Orientation:
Plus strand

Genomic View for GCA Gene

Genes around GCA on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for GCA Gene

Proteins for GCA Gene

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

    Protein Symbol:
    P28676-GRAN_HUMAN
    Recommended name:
    Grancalcin
    Protein Accession:
    P28676
    Secondary Accessions:
    • B2R5X3
    • Q53TB5
    • Q59EP3

    Protein attributes for GCA Gene

    Size:
    217 amino acids
    Molecular mass:
    24010 Da
    Quaternary structure:
    • Homodimer. Interacts with SRI and LCP1.
    Miscellaneous:
    • This protein has been shown to bind calcium with high affinity.
    SequenceCaution:
    • Sequence=BAD93005.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for GCA Gene

neXtProt entry for GCA Gene

Post-translational modifications for GCA Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for GCA Gene

Domains & Families for GCA Gene

Gene Families for GCA Gene

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

Protein Domains for GCA Gene

Suggested Antigen Peptide Sequences for GCA Gene

GenScript: Design optimal peptide antigens:
  • Grancalcin (GRAN_HUMAN)
genes like me logo Genes that share domains with GCA: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for GCA Gene

Function for GCA Gene

Molecular function for GCA Gene

UniProtKB/Swiss-Prot Function:
Calcium-binding protein that may play a role in the adhesion of neutrophils to fibronectin. May play a role in the formation of focal adhesions.

Phenotypes From GWAS Catalog for GCA Gene

Gene Ontology (GO) - Molecular Function for GCA Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding IDA 11717497
GO:0005515 protein binding IPI 25416956
GO:0042803 protein homodimerization activity IPI 11717497
GO:0046872 metal ion binding IEA --
GO:0046982 protein heterodimerization activity IPI 12804766
genes like me logo Genes that share ontologies with GCA: view
genes like me logo Genes that share phenotypes with GCA: view

Animal Models for GCA Gene

MGI Knock Outs for GCA:
  • Gca Gca<tm1Roes>

Animal Model Products

CRISPR Products

miRNA for GCA Gene

miRTarBase miRNAs that target GCA

Clone Products

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

Localization for GCA Gene

Subcellular locations from UniProtKB/Swiss-Prot for GCA Gene

Cytoplasm. Cytoplasmic granule membrane; Peripheral membrane protein; Cytoplasmic side. Note=Primarily cytosolic in the absence of calcium or magnesium ions. Relocates to granules and other membranes in response to elevated calcium and magnesium levels. {ECO:0000269 PubMed:1737748}.

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

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (3)
  • Plasma membrane (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for GCA Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region TAS --
GO:0005737 cytoplasm TAS 1530588
GO:0005829 cytosol IDA --
GO:0005886 plasma membrane IDA,TAS --
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with GCA: view

Pathways & Interactions for GCA Gene

PathCards logo

SuperPathways for GCA Gene

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

Pathways by source for GCA Gene

Gene Ontology (GO) - Biological Process for GCA Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0043312 neutrophil degranulation TAS --
GO:0061025 membrane fusion TAS 1530588
genes like me logo Genes that share ontologies with GCA: view

No data available for SIGNOR curated interactions for GCA Gene

Drugs & Compounds for GCA Gene

(20) Drugs for GCA Gene - From: DrugBank, ClinicalTrials, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Calcium Approved Nutra 7884
Calcium Citrate Approved, Investigational Pharma Target, ligand 0
Calcium Phosphate Approved Pharma Target, ligand 0
Calcium phosphate dihydrate Approved Pharma Target 0
Prednisone Approved, Vet_approved Pharma 1684

(3) Additional Compounds for GCA Gene - From: Novoseek

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

Transcripts for GCA Gene

mRNA/cDNA for GCA Gene

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

CRISPR Products

Clone Products

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

ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3 ^ 4a · 4b ^ 5a · 5b ^ 6 ^ 7a · 7b · 7c ^ 8a · 8b · 8c ^ 9
SP1: - - -
SP2: - - - -
SP3: - -
SP4: -
SP5:
SP6: - - - - - - - - - -
SP7:

Relevant External Links for GCA Gene

GeneLoc Exon Structure for
GCA

Expression for GCA Gene

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

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

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

This gene is overexpressed in Whole Blood (x30.1).

Protein differential expression in normal tissues from HIPED for GCA Gene

This gene is overexpressed in Neutrophil (14.3) and Saliva (6.9).

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



Protein tissue co-expression partners for GCA Gene

- Elite partner

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

SOURCE GeneReport for Unigene cluster for GCA Gene:

Hs.377894

mRNA Expression by UniProt/SwissProt for GCA Gene:

P28676-GRAN_HUMAN
Tissue specificity: Detected in neutrophils and macrophages (at protein level). Highly expressed in bone marrow.

Evidence on tissue expression from TISSUES for GCA Gene

  • Nervous system(4.8)
  • Blood(4.6)
  • Bone marrow(2.2)
  • Intestine(2.1)
  • Spleen(2)
genes like me logo Genes that share expression patterns with GCA: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for GCA Gene

Orthologs for GCA Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for GCA Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia GCA 31 30
  • 99.08 (n)
OneToOne
dog
(Canis familiaris)
Mammalia GCA 31 30
  • 88.84 (n)
OneToOne
cow
(Bos Taurus)
Mammalia GCA 31 30
  • 88.7 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Gca 17 31 30
  • 83.72 (n)
rat
(Rattus norvegicus)
Mammalia Gca 30
  • 82.49 (n)
oppossum
(Monodelphis domestica)
Mammalia GCA 31
  • 77 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia GCA 31
  • 70 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia GCA 31
  • 71 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia gca 30
  • 72.61 (n)
Str.15515 30
African clawed frog
(Xenopus laevis)
Amphibia Xl.16710 30
zebrafish
(Danio rerio)
Actinopterygii zgc:92027 30
  • 66.5 (n)
GCA 31
  • 63 (a)
OneToOne
Dr.5366 30
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.2717 30
fruit fly
(Drosophila melanogaster)
Insecta CG17765 31
  • 31 (a)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes PEF1 31
  • 15 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 34 (a)
OneToMany
Species where no ortholog for GCA was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • 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 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 GCA Gene

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

Paralogs for GCA Gene

(10) SIMAP similar genes for GCA Gene using alignment to 6 proteins:

  • GRAN_HUMAN
  • C9JIZ3_HUMAN
  • C9JV47_HUMAN
  • C9JWQ8_HUMAN
  • H7BXD5_HUMAN
  • H7C2Z6_HUMAN
genes like me logo Genes that share paralogs with GCA: view

Variants for GCA Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for GCA Gene

SNP ID Clinical significance and condition Chr 02 pos Variation AA Info Type
rs17783344 - p.Ser80Ala

Additional dbSNP identifiers (rs#s) for GCA Gene

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

Variant ID Type Subtype PubMed ID
nsv1160878 CNV deletion 26073780
nsv583520 CNV loss 21841781
nsv955278 CNV duplication 24416366

Variation tolerance for GCA Gene

Residual Variation Intolerance Score: 69.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.54; 64.81% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for GCA Gene

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

SNP Genotyping and Copy Number Assay Products

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

Disorders for GCA Gene

MalaCards: The human disease database

(1) MalaCards diseases for GCA Gene - From: DISEASES

Disorder Aliases PubMed IDs
retinitis pigmentosa 19
  • rp19
- elite association - COSMIC cancer census association via MalaCards
Search GCA in MalaCards View complete list of genes associated with diseases

Additional Disease Information for GCA

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 GCA: view

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

Publications for GCA Gene

  1. The PEF family proteins sorcin and grancalcin interact in vivo and in vitro. (PMID: 12804766) Hansen C … Berchtold MW (FEBS letters 2003) 2 3 4 23 54
  2. Molecular cloning and characterization of grancalcin, a novel EF-hand calcium-binding protein abundant in neutrophils and monocytes. (PMID: 1737748) Boyhan A … Segal AW (The Journal of biological chemistry 1992) 2 3 4 23 54
  3. Isolation and characterization of grancalcin, a novel 28 kDa EF-hand calcium-binding protein from human neutrophils. (PMID: 1530588) Teahan CG … Segal AW (The Biochemical journal 1992) 2 3 4 23 54
  4. Structure of Ca(2+)-loaded human grancalcin. (PMID: 11717497) Jia J … Cygler M (Acta crystallographica. Section D, Biological crystallography 2001) 3 4 23 54
  5. Biochemical characterization of the penta-EF-hand protein grancalcin and identification of L-plastin as a binding partner. (PMID: 11279160) Lollike K … Cox JA (The Journal of biological chemistry 2001) 3 4 23 54

Products for GCA Gene

Sources for GCA Gene