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    RGN regucalcin [ Homo sapiens (human) ]

    Gene ID: 9104, updated on 14-Nov-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
    mouse all
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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_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (47078443..47093313)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (46485437..46503065)
    RS_2024_09 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 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?
    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)

    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 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 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_2024_08

    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

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

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