The protein encoded by this gene is a highly conserved, calcium-binding protein, that is preferentially expressed in the liver and kidney. It may have an important role in calcium homeostasis. Studies in rat indicate that this protein may also play a role in aging, as it shows age-associated down-regulation. This gene is part of a gene cluster on chromosome Xp11.3-Xp11.23. Alte... See more...

Aliases for RGN Gene

Aliases for RGN Gene

  • Regucalcin 2 3 4 5
  • Gluconolactonase 2 3 4
  • SMP30 2 3 4
  • RC 2 3 4
  • Senescence Marker Protein 30 3 4
  • GNL 3 4
  • Regucalcin (Senescence Marker Protein-30) 2
  • Epididymis Secretory Protein Li 41 3
  • Senescence Marker Protein-30 2
  • EC 3.1.1.17 4
  • HEL-S-41 3
  • SMP-30 4
  • RGN 5

External Ids for RGN Gene

Previous GeneCards Identifiers for RGN Gene

  • GC0XP045740
  • GC0XP045198
  • GC0XP045983
  • GC0XP046695
  • GC0XP046822
  • GC0XP046937
  • GC0XP044651
  • GC0XP047080
  • GC0XP047083
  • GC0XP047095

Summaries for RGN Gene

Entrez Gene Summary for RGN Gene

  • The protein encoded by this gene is a highly conserved, calcium-binding protein, that is preferentially expressed in the liver and kidney. It may have an important role in calcium homeostasis. Studies in rat indicate that this protein may also play a role in aging, as it shows age-associated down-regulation. This gene is part of a gene cluster on chromosome Xp11.3-Xp11.23. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2013]

GeneCards Summary for RGN Gene

RGN (Regucalcin) is a Protein Coding gene. Diseases associated with RGN include Aging and Hypoascorbemia. Among its related pathways are Carbon metabolism and Pentose and glucuronate interconversions. Gene Ontology (GO) annotations related to this gene include calcium ion binding and gluconolactonase activity.

UniProtKB/Swiss-Prot Summary for RGN Gene

  • Gluconolactonase with low activity towards other sugar lactones, including gulonolactone and galactonolactone. Can also hydrolyze diisopropyl phosphorofluoridate and phenylacetate (in vitro). Calcium-binding protein. Modulates Ca(2+) signaling, and Ca(2+)-dependent cellular processes and enzyme activities (By similarity).

Gene Wiki entry for RGN Gene

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

Genomics for RGN Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for RGN 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
GH0XJ047077 Promoter/Enhancer 1.5 EPDnew Ensembl ENCODE 264.2 +1.5 1526 4.7 CEBPA YY1 FOXA1 SIN3A THAP11 FOXA2 KDM6A RXRA SMAD4 SAP130 RGN HSALNG0137668 HSALNG0137669 lnc-JADE3-2 lnc-JADE3-3 CHST7 RBM10
GH0XJ047143 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 35.6 +67.0 67046 5.2 SP1 NCOR1 ZNF600 ZNF592 POLR2A CEBPA YY1 CTCF CEBPB SMAD5 HSALNG0137677 NDUFB11 RBM10 RGN INE1 RF00017-7776
GH0XJ047091 Enhancer 0.6 Ensembl 43.2 +13.1 13146 1.4 CEBPA SMAD4 RARA BCL6 SOX5 NR2F1 NR2F6 PRDM4 PKNOX1 TCF7 HSALNG0137672 RGN lnc-RGN-1 lnc-NDUFB11-2 RBM10
GH0XJ047297 Enhancer 0.7 Ensembl ENCODE 26.3 +219.3 219277 1.7 ZNF217 CTBP1 E4F1 SMARCE1 DPF2 CREB1 FOS RFX1 RAD21 POLR2A piR-48759-324 RGN ZNF182 RBM10 UBA1 ZNF674-AS1 ENSG00000232009 SNORA11C ZNF81 VEZTP1
GH0XJ047113 Enhancer 0.4 Ensembl 42.9 +34.2 34246 0.4 RAD21 HNF4A CTCF EGR2 lnc-NDUFB11-1 lnc-RGN-2 RGN NDUFB11 RBM10 ENSG00000232009 SNORA11C piR-47162-186 RF00017-7777 lnc-NDUFB11-2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

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

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

Top Transcription factor binding sites by QIAGEN in the RGN gene promoter:
  • AREB6
  • FOXD3
  • FOXO1
  • FOXO1a
  • GR-alpha
  • HSF2
  • NRSF form 1
  • NRSF form 2

Genomic Locations for RGN Gene

Latest Assembly
chrX:47,078,355-47,093,314
(GRCh38/hg38)
Size:
14,960 bases
Orientation:
Plus strand

Previous Assembly
chrX:46,937,842-46,952,712
(GRCh37/hg19 by Entrez Gene)
Size:
14,871 bases
Orientation:
Plus strand

chrX:46,937,775-46,952,712
(GRCh37/hg19 by Ensembl)
Size:
14,938 bases
Orientation:
Plus strand

Genomic View for RGN Gene

Genes around RGN on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for RGN Gene

Proteins for RGN Gene

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

    Protein Symbol:
    Q15493-RGN_HUMAN
    Recommended name:
    Regucalcin
    Protein Accession:
    Q15493
    Secondary Accessions:
    • A4FTW1
    • A8K271
    • Q53FC9
    • Q5JRR5

    Protein attributes for RGN Gene

    Size:
    299 amino acids
    Molecular mass:
    33253 Da
    Cofactor:
    Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
    Cofactor:
    Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
    Cofactor:
    Name=Ca(2+); Xref=ChEBI:CHEBI:29108;
    Cofactor:
    Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
    Quaternary structure:
    • Monomer.

    Three dimensional structures from OCA and Proteopedia for RGN Gene

    Alternative splice isoforms for RGN Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for RGN Gene

Post-translational modifications for RGN Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Antibodies for research

No data available for DME Specific Peptides for RGN Gene

Domains & Families for RGN Gene

Gene Families for RGN Gene

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

Protein Domains for RGN Gene

InterPro:
Blocks:
  • Senescence marker protein-30 (SMP-30)
  • Regucalcin signature
  • SMP-30/Gluconolaconase/LRE-like region

Suggested Antigen Peptide Sequences for RGN Gene

GenScript: Design optimal peptide antigens:
  • Senescence marker protein 30 (RGN_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q15493

UniProtKB/Swiss-Prot:

RGN_HUMAN :
  • Belongs to the SMP-30/CGR1 family.
Family:
  • Belongs to the SMP-30/CGR1 family.
genes like me logo Genes that share domains with RGN: view

Function for RGN Gene

Molecular function for RGN Gene

UniProtKB/Swiss-Prot Function:
Gluconolactonase with low activity towards other sugar lactones, including gulonolactone and galactonolactone. Can also hydrolyze diisopropyl phosphorofluoridate and phenylacetate (in vitro). Calcium-binding protein. Modulates Ca(2+) signaling, and Ca(2+)-dependent cellular processes and enzyme activities (By similarity).
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=D-glucono-1,5-lactone + H2O = D-gluconate + H(+); Xref=Rhea:RHEA:10440, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:16217, ChEBI:CHEBI:18391; EC=3.1.1.17; Evidence={ECO:0000269|PubMed:20329768, ECO:0000269|PubMed:23349732};.
UniProtKB/Swiss-Prot BiophysicochemicalProperties:
Kinetic parameters: KM=2.7 mM for gluconolactone (with Zn(2+) as cofactor) {ECO:0000269|PubMed:20329768}; KM=0.6 mM for gluconolactone (with Mn(2+) as cofactor) {ECO:0000269|PubMed:20329768}; KM=1.3 mM for gluconolactone (with Mg(2+) as cofactor) {ECO:0000269|PubMed:20329768}; KM=3.7 mM for gluconolactone (with Ca(2+) as cofactor) {ECO:0000269|PubMed:20329768};
GENATLAS Biochemistry:
rat calcium binding protein (regucalcin) homolog

Enzyme Numbers (IUBMB) for RGN Gene

Gene Ontology (GO) - Molecular Function for RGN Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004341 gluconolactonase activity IBA,IDA 20329768
GO:0005509 calcium ion binding TAS,ISS --
GO:0008270 zinc ion binding IDA 20329768
GO:0016787 hydrolase activity IEA --
GO:0030234 enzyme regulator activity IEA --
genes like me logo Genes that share ontologies with RGN: view
genes like me logo Genes that share phenotypes with RGN: view

Animal Models for RGN Gene

MGI Knock Outs for RGN:
  • Rgn Rgn<tm1Aish>

miRNA for RGN Gene

miRTarBase miRNAs that target RGN

Inhibitory RNAs for research

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

No data available for Phenotypes From GWAS Catalog , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for RGN Gene

Localization for RGN Gene

Subcellular locations from UniProtKB/Swiss-Prot for RGN Gene

Cytoplasm.

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

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for RGN Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus ISS --
GO:0005737 cytoplasm ISS --
GO:0005829 cytosol IEA --
genes like me logo Genes that share ontologies with RGN: view

Pathways & Interactions for RGN Gene

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

Gene Ontology (GO) - Biological Process for RGN Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001822 kidney development IEA --
GO:0001889 liver development IEA --
GO:0001933 negative regulation of protein phosphorylation IEA --
GO:0006469 negative regulation of protein kinase activity IEA --
GO:0006874 cellular calcium ion homeostasis ISS --
genes like me logo Genes that share ontologies with RGN: view

No data available for SIGNOR curated interactions for RGN Gene

Drugs & Compounds for RGN Gene

(8) Drugs for RGN 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 Phosphate Approved Pharma Target, ligand 0
Calcium phosphate dihydrate Approved Pharma Target 0
Gluconic acid Approved, Investigational Pharma 0
Gluconolactone Approved, Experimental Pharma 0

(9) Additional Compounds for RGN Gene - From: HMDB and Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
6-Hydroxyhexanoic acid
  • 5-Carboxypentanol
  • 5-Hydroxypentanecarboxylic acid
  • 6-Hydroxy caproic acid
  • 6-Hydroxycaproic acid
  • 6-Hydroxyhexanoate
1191-25-9
epsilon-Caprolactone
  • 1,6-Hexanolide
  • 1-Oxa-2-oxocycloheptane
  • 2-Oxacycloheptanone
  • 2-Oxepanone
  • 2-Oxohexamethylene oxide
Gulonic acid
  • Gulonate
  • D-Gulonate
  • D-Gulonic acid
  • L-Gulonate
  • L-Gulonic acid
20246-53-1
L-Gulonolactone
  • gamma-Gulonolactone
  • L-Gulonic acid gamma-lactone
  • L-Gulono-gamma-lactone
  • g-Gulonolactone
  • Γ-gulonolactone
1128-23-0
genes like me logo Genes that share compounds with RGN: view

Transcripts for RGN Gene

mRNA/cDNA for RGN Gene

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

Inhibitory RNAs for research

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

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

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

Relevant External Links for RGN Gene

GeneLoc Exon Structure for
RGN

Expression for RGN Gene

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

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

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

This gene is overexpressed in Adrenal Gland (x10.0) and Liver (x8.9).

Protein differential expression in normal tissues from HIPED for RGN Gene

This gene is overexpressed in Liver, secretome (27.1) and Heart (6.3).

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



Protein tissue co-expression partners for RGN Gene

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

SOURCE GeneReport for Unigene cluster for RGN Gene:

Hs.77854

Evidence on tissue expression from TISSUES for RGN Gene

  • Liver(4.8)
  • Nervous system(4.6)
  • Intestine(4.4)
  • Adrenal gland(3.2)
  • Kidney(2.9)
  • Muscle(2.2)
  • Heart(2.1)
  • Pancreas(2.1)
genes like me logo Genes that share expression patterns with RGN: view

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for RGN Gene

Orthologs for RGN Gene

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

Orthologs for RGN Gene

Organism Taxonomy Gene Similarity Type Details
Cow
(Bos Taurus)
Mammalia RGN 29 30
  • 91.19 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia RGN 29 30
  • 89.63 (n)
OneToOne
Chimpanzee
(Pan troglodytes)
Mammalia RGN 29 30
  • 88.99 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Rgn 29
  • 86.85 (n)
Mouse
(Mus musculus)
Mammalia Rgn 29 16 30
  • 86.51 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia RGN 30
  • 80 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia RGN 30
  • 60 (a)
OneToOne
Chicken
(Gallus gallus)
Aves RGN 29 30
  • 73.47 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia RGN 30
  • 71 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia rgn 29
  • 69.23 (n)
Str.11947 29
African clawed frog
(Xenopus laevis)
Amphibia rgn-A 29
Zebrafish
(Danio rerio)
Actinopterygii rgn 29 30
  • 65.08 (n)
OneToOne
Dr.27166 29
Rainbow Trout
(Oncorhynchus mykiss)
Actinopterygii Omy.9879 29
Fruit Fly
(Drosophila melanogaster)
Insecta regucalcin 29 30 31
  • 48.68 (n)
OneToMany
smp-30 30
  • 33 (a)
OneToMany
K. Lactis Yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0F04301g 29
  • 41.91 (n)
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes YBR053C 29
  • 40.95 (n)
-- 32
-- 32
A. gosspyii yeast
(Eremothecium gossypii)
Saccharomycetes AGOS_ABL098W 29
  • 39.23 (n)
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 30
  • 48 (a)
OneToOne
Bread mold
(Neurospora crassa)
Ascomycetes NCU00326 29
  • 44.24 (n)
Species where no ortholog for RGN was found in the sources mined by GeneCards:
  • 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)
  • 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)
  • 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 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 RGN Gene

ENSEMBL:
Gene Tree for RGN (if available)
TreeFam:
Gene Tree for RGN (if available)
Aminode:
Evolutionary constrained regions (ECRs) for RGN: view image
Alliance of Genome Resources:
Additional Orthologs for RGN

Paralogs for RGN Gene

No data available for Paralogs for RGN Gene

Variants for RGN Gene

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

SNP ID Clinical significance and condition Chr 0X pos Variation AA Info Type
rs148051057 Benign: not provided 47,084,555(+) C/T
NM_152869.4(RGN):c.301C>T (p.Arg101Cys)
MISSENSE
rs188959748 Benign: not provided 47,084,610(+) C/T
NM_152869.4(RGN):c.346+10C>T
INTRON

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for RGN Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

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

Variant ID Type Subtype PubMed ID
esv1734378 CNV insertion 17803354
esv3448339 CNV duplication 20981092
nsv1132239 CNV deletion 24896259
nsv508767 CNV insertion 20534489
nsv513604 CNV insertion 21212237

Variation tolerance for RGN Gene

Residual Variation Intolerance Score: 86.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.74; 32.99% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RGN Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RGN
Leiden Open Variation Database (LOVD)
RGN

SNP Genotyping and Copy Number Assays for research

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

Disorders for RGN Gene

MalaCards: The human disease database

(3) MalaCards diseases for RGN Gene - From: COP and GCD

Disorder Aliases PubMed IDs
aging
hypoascorbemia
  • scurvy
phonagnosia
- elite association - COSMIC cancer census association via MalaCards
Search RGN in MalaCards View complete list of genes associated with diseases

Additional Disease Information for RGN

genes like me logo Genes that share disorders with RGN: view

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

Publications for RGN Gene

  1. Isolation of cDNA clone encoding human homologue of senescence marker protein-30 (SMP30) and its location on the X chromosome. (PMID: 7548213) Fujita T … Maruyama N (Biochimica et biophysica acta 1995) 2 3 4 22
  2. Crystal structure of human senescence marker protein 30: insights linking structural, enzymatic, and physiological functions . (PMID: 20329768) Chakraborti S … Bahnson BJ (Biochemistry 2010) 3 4 22
  3. Transcript heterogeneity of the human gene for Ca2+-binding protein regucalcin. (PMID: 10677570) Misawa H … Yamaguchi M (International journal of molecular medicine 2000) 3 4 22
  4. Structural basis of the γ-lactone-ring formation in ascorbic acid biosynthesis by the senescence marker protein-30/gluconolactonase. (PMID: 23349732) Aizawa S … Senda T (PloS one 2013) 3 4
  5. A strategy for the production of soluble human senescence marker protein-30 in Escherichia coli. (PMID: 20152811) Choi MS … Chilukuri N (Biochemical and biophysical research communications 2010) 3 22

Products for RGN Gene

Sources for RGN Gene