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RGN regucalcin [ Homo sapiens (human) ]

Gene ID: 9104, updated on 5-Mar-2024

Summary

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Official Symbol
RGNprovided by HGNC
Official Full Name
regucalcinprovided by HGNC
Primary source
HGNC:HGNC:9989
See related
Ensembl:ENSG00000130988 MIM:300212; AllianceGenome:HGNC:9989
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
RC; GNL; SMP30; HEL-S-41
Summary
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]
Expression
Biased expression in liver (RPKM 68.0), adrenal (RPKM 65.2) and 11 other tissues See more
Orthologs
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Genomic context

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See RGN in Genome Data Viewer
Location:
Xp11.3
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (47078443..47093313)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (46485437..46503065)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (46937842..46952712)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 1545 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29578 Neighboring gene Sharpr-MPRA regulatory region 4088 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20797 Neighboring gene jade family PHD finger 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29579 Neighboring gene Sharpr-MPRA regulatory region 7060 Neighboring gene RNA, U6 small nuclear 1189, pseudogene Neighboring gene uncharacterized LOC105373193 Neighboring gene uncharacterized LOC107985720 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29580 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29581 Neighboring gene RNA, U12 small nuclear 2, pseudogene

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. Senescence in oral lichen planus as assessed by the immunohistochemical evaluation of senescence marker protein-30 (Regucalcin). Peter CD, et al. Indian J Pathol Microbiol, 2023 Jan-Mar. PMID 36656203
  2. Functional pleiotropy of calcium binding protein Regucalcin in signaling and diseases. Danish M, et al. Cell Signal, 2023 Feb. PMID 36442591
  3. Senescence marker protein30 protects lens epithelial cells against oxidative damage by restoring mitochondrial function. Teng H, et al. Bioengineered, 2022 May. PMID 35615975, Free PMC Article
  4. Overexpression of regucalcin blocks the migration, invasion, and bone metastatic activity of human prostate cancer cells: Crosstalk between cancer cells and bone cells. Yamaguchi M, et al. Prostate, 2022 Jun. PMID 35365850
  5. Prolonged survival of renal cancer patients is concomitant with a higher regucalcin gene expression in tumor tissues: Overexpression of regucalcin suppresses the growth of human renal cell carcinoma cells in vitro. Yamaguchi M, et al. Int J Oncol, 2019 Jan. PMID 30387835, Free PMC Article

See all (69) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Regucalcin downregulation in human cancer.
    Title: Regucalcin downregulation in human cancer.
  2. Uroplakin 1a Interacts with Regucalcin and Proteasome Subunit Beta 1.
    Title: Uroplakin 1a Interacts with Regucalcin and Proteasome Subunit Beta 1.
  3. The inflammatory macrophages repress the growth of bone metastatic human prostate cancer cells via TNF-alpha and IL-6 signaling: Involvement of cell signaling regulator regucalcin.
    Title: The inflammatory macrophages repress the growth of bone metastatic human prostate cancer cells via TNF-α and IL-6 signaling: Involvement of cell signaling regulator regucalcin.
  4. Senescence in oral lichen planus as assessed by the immunohistochemical evaluation of senescence marker protein-30 (Regucalcin).
    Title: Senescence in oral lichen planus as assessed by the immunohistochemical evaluation of senescence marker protein-30 (Regucalcin).
  5. Functional pleiotropy of calcium binding protein Regucalcin in signaling and diseases.
    Title: Functional pleiotropy of calcium binding protein Regucalcin in signaling and diseases.
  6. Senescence marker protein30 protects lens epithelial cells against oxidative damage by restoring mitochondrial function.
    Title: Senescence marker protein30 protects lens epithelial cells against oxidative damage by restoring mitochondrial function.
  7. Overexpression of regucalcin blocks the migration, invasion, and bone metastatic activity of human prostate cancer cells: Crosstalk between cancer cells and bone cells.
    Title: Overexpression of regucalcin blocks the migration, invasion, and bone metastatic activity of human prostate cancer cells: Crosstalk between cancer cells and bone cells.
  8. Senescence Marker Protein 30 (SMP30): A Novel Pan-Species Diagnostic Marker for the Histopathological Diagnosis of Breast Cancer in Humans and Animals.
    Title: Senescence Marker Protein 30 (SMP30): A Novel Pan-Species Diagnostic Marker for the Histopathological Diagnosis of Breast Cancer in Humans and Animals.
  9. Results demonstrate that RGN is epigenetically modified in non-small cell lung cancer (NSCLC) tissues. A high expression of RGN on the RNA level was positively correlated with patients' survival in adenocarcinomas. Also, high expression of Regucalcin seems to be protective in never smokers.
    Title: Live and let die: epigenetic modifications of Survivin and Regucalcin in non-small cell lung cancer tissues contribute to malignancy.
  10. In vitro experiments on colonic epithelial cells showed that stable SMP30 expression inhibited but that SMP30 siRNA expression increased TNF-alpha-induced apoptosis. SMP30 inhibition decreased Nrf2 mRNA expression levels (p<0.0001), but SMP30 overexpression increased Nrf2 mRNA expression levels (p=0.0495).
    Title: Senescence marker protein 30 protects intestinal epithelial cells against inflammation-induced cell death by enhancing Nrf2 activity.
Submit: New GeneRIF Correction See all GeneRIFs (48)

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)

Genotypes

Pathways from PubChem

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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 IDA
Inferred from Direct Assay
more info
 PubMed 
enables calcium ion binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables enzyme regulator activity IEA
Inferred from Electronic Annotation
more info
  
enables gluconolactonase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables gluconolactonase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables zinc ion binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in L-ascorbic acid biosynthetic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in intracellular calcium ion homeostasis ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in kidney development IEA
Inferred from Electronic Annotation
more info
  
involved_in liver regeneration IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of DNA biosynthetic process IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of DNA catabolic process IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of RNA biosynthetic process IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of apoptotic process IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of bone development IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of epithelial cell proliferation IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of flagellated sperm motility IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of nitric oxide biosynthetic process IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of protein phosphorylation IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of ATP-dependent activity ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of fatty acid biosynthetic process IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of glucose metabolic process IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of proteolysis involved in protein catabolic process IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of triglyceride biosynthetic process IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of calcium-mediated signaling ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in spermatogenesis IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in cytoplasm ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in nucleus ISS
Inferred from Sequence or Structural Similarity
more info
  

General protein information

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Preferred Names
regucalcin
Names
epididymis secretory protein Li 41
gluconolactonase
senescence marker protein 30
NP_001269777.1
NP_001269778.1
NP_004674.1
NP_690608.1
XP_006724630.1
XP_006724631.1
XP_016885443.1
XP_054184061.1
XP_054184062.1
XP_054184063.1

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_001282848.2 → NP_001269777.1  regucalcin isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate splice site in the 5' coding region and initiates translation at a downstream start codon, compared to variant 2. It encodes isoform 2, which has a shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    BC058880, HY260443
    UniProtKB/Swiss-Prot
    Q15493
    Conserved Domains (2) summary
    pfam08450
    Location:1 → 211
    SGL; SMP-30/Gluconolaconase/LRE-like region
    sd00039
    Location:150 → 186
    7WD40; WD40 repeat [structural motif]

  2. NM_001282849.2 → NP_001269778.1  regucalcin isoform 3

    See identical proteins and their annotated locations for NP_001269778.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks an alternate in-frame exon in the 5' coding region, compared to variant 2. It encodes isoform 3, which is shorter than isoform 1.
    Source sequence(s)
    BC050371, HY260443
    Consensus CDS
    CCDS75968.1
    UniProtKB/Swiss-Prot
    Q15493
    Related
    ENSP00000406568.1, ENST00000457380.5
    Conserved Domains (2) summary
    pfam08450
    Location:16 → 192
    SGL; SMP-30/Gluconolaconase/LRE-like region
    sd00039
    Location:58 → 95
    7WD40; WD40 repeat [structural motif]

  3. NM_004683.6 → NP_004674.1  regucalcin isoform 1

    See identical proteins and their annotated locations for NP_004674.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) differs in the 5' UTR compared to variant 2. Variants 1 and 2 encode the same isoform (1).
    Source sequence(s)
    AK290136, HY260443
    Consensus CDS
    CCDS14272.1
    UniProtKB/Swiss-Prot
    A4FTW1, A8K271, Q15493, Q53FC9, Q5JRR5
    UniProtKB/TrEMBL
    V9HWF8
    Related
    ENSP00000253303.4, ENST00000352078.8
    Conserved Domains (1) summary
    pfam08450
    Location:16 → 264
    SGL; SMP-30/Gluconolaconase/LRE-like region

  4. NM_152869.4 → NP_690608.1  regucalcin isoform 1

    See identical proteins and their annotated locations for NP_690608.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) represents the longest transcript. Variants 1 and 2 encode the same isoform (1).
    Source sequence(s)
    BC050371, D31815, HY260443
    Consensus CDS
    CCDS14272.1
    UniProtKB/Swiss-Prot
    A4FTW1, A8K271, Q15493, Q53FC9, Q5JRR5
    UniProtKB/TrEMBL
    V9HWF8
    Related
    ENSP00000380365.1, ENST00000397180.6
    Conserved Domains (1) summary
    pfam08450
    Location:16 → 264
    SGL; SMP-30/Gluconolaconase/LRE-like region

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

  1. NC_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    47078443..47093313
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017029954.3 → XP_016885443.1  regucalcin isoform X2

    Conserved Domains (1) summary
    COG3386
    Location:1 → 181
    YvrE; Sugar lactone lactonase YvrE [Carbohydrate transport and metabolism]

  2. XM_006724567.3 → XP_006724630.1  regucalcin isoform X1

    See identical proteins and their annotated locations for XP_006724630.1

    UniProtKB/Swiss-Prot
    Q15493
    Conserved Domains (2) summary
    pfam08450
    Location:16 → 192
    SGL; SMP-30/Gluconolaconase/LRE-like region
    sd00039
    Location:58 → 95
    7WD40; WD40 repeat [structural motif]

  3. XM_006724568.3 → XP_006724631.1  regucalcin isoform X2

    Conserved Domains (1) summary
    COG3386
    Location:1 → 181
    YvrE; Sugar lactone lactonase YvrE [Carbohydrate transport and metabolism]

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    46485437..46503065
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054328087.1 → XP_054184062.1  regucalcin isoform X2

  2. XM_054328086.1 → XP_054184061.1  regucalcin isoform X1

  3. XM_054328088.1 → XP_054184063.1  regucalcin isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q15493.1 GenPept UniProtKB/Swiss-Prot:Q15493

Gene LinkOut

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Chemical Information
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