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    CLGN calmegin [ Homo sapiens (human) ]

    Gene ID: 1047, updated on 3-Nov-2024

    Summary

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    Official Symbol
    CLGNprovided by HGNC
    Official Full Name
    calmeginprovided by HGNC
    Primary source
    HGNC:HGNC:2060
    See related
    Ensembl:ENSG00000153132 MIM:601858; AllianceGenome:HGNC:2060
    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
    Summary
    Calmegin is a testis-specific endoplasmic reticulum chaperone protein. CLGN may play a role in spermatogeneisis and infertility. [provided by RefSeq, Jul 2008]
    Expression
    Biased expression in testis (RPKM 66.0), heart (RPKM 22.6) and 2 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See CLGN in Genome Data Viewer
    Location:
    4q31.1
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (140388453..140427648, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (143708226..143747412, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (141309607..141348802, complement)

    Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene short coiled-coil protein Neighboring gene SCOC antisense RNA 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:141237061-141237740 Neighboring gene NADH:ubiquinone oxidoreductase subunit B4 pseudogene 9 Neighboring gene OCT4 hESC enhancer GRCh37_chr4:141294483-141294984 Neighboring gene ribosomal protein L14 pseudogene 3 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:141334799-141335364 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21935 Neighboring gene MGAT4 family member D Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:141418967-141419468 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:141419469-141419968 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15710 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15711 Neighboring gene ELMO domain containing 2

    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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    Related articles in PubMed

    1. Glycan specificity of a testis-specific lectin chaperone calmegin and effects of hydrophobic interactions. Sakono M, et al. Biochim Biophys Acta, 2014 Sep. PMID 24769397
    2. Cloning and characterization of the human Calmegin gene encoding putative testis-specific chaperone. Tanaka H, et al. Gene, 1997 Dec 19. PMID 9434179
    3. Coordinated transcriptional regulation of calmegin,a testis-specific molecular chaperon, by histone deacetylase and CpG methyltransferase. Kim DH, et al. Exp Mol Med, 2005 Oct 31. PMID 16264275
    4. Molecular cloning of a novel Ca(2+)-binding protein (calmegin) specifically expressed during male meiotic germ cell development. Watanabe D, et al. J Biol Chem, 1994 Mar 11. PMID 8126001
    5. The putative chaperone calmegin is required for sperm fertility. Ikawa M, et al. Nature, 1997 Jun 5. PMID 9177349

    See all (69) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. In gene-based analysis CLGN1 represented one of a cluster of genes, which interacted with sodium to influence Blood Pressure.
      Title: Genome-Wide Gene-Sodium Interaction Analyses on Blood Pressure: The Genetic Epidemiology Network of Salt-Sensitivity Study.
    2. Although their similarity in carbohydrate binding specificities is high, there seems to be some differences in the mode of substrate recognition between calmegin and calnexin.
      Title: Glycan specificity of a testis-specific lectin chaperone calmegin and effects of hydrophobic interactions.
    3. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    4. calmegin expression is regulated by histone deacetylase and CpG methyltransferase in a coordinative way
      Title: Coordinated transcriptional regulation of calmegin,a testis-specific molecular chaperon, by histone deacetylase and CpG methyltransferase.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Genome-wide association with select biomarker traits in the Framingham Heart Study.
    EBI GWAS Catalog

    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

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp120 env HIV-1 gp120 is identified to have a physical interaction with calmegin (CLGN) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed
    Envelope surface glycoprotein gp160, precursor env HIV-1 gp160 interacts with CLGN; predicted interaction to be within the endoplasmic reticulum PubMed
    env HIV-1 gp160 is identified to have a physical interaction with calmegin (CLGN) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed

    Go to the HIV-1, Human Interaction Database

    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 protein folding chaperone IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables unfolded protein binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in ERAD pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in binding of sperm to zona pellucida IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in protein folding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein-containing complex assembly IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in single fertilization TAS
    Traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in endoplasmic reticulum membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nuclear envelope IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    calmegin
    Names
    testis tissue sperm-binding protein Li 79P

    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_001130675.2 → NP_001124147.1  calmegin precursor

      See identical proteins and their annotated locations for NP_001124147.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) contains an extra exon in the 5' UTR, compared to variant 1.
      Source sequence(s)
      AL045602, BC028357, D86322, DC396076
      Consensus CDS
      CCDS3751.1
      UniProtKB/Swiss-Prot
      B3KS90, B4DXV8, D3DNY8, O14967
      UniProtKB/TrEMBL
      A0A140VKG2, A8K454
      Related
      ENSP00000392782.1, ENST00000414773.5
      Conserved Domains (1) summary
      pfam00262
      Location:62 → 429
      Calreticulin; Calreticulin family

    2. NM_004362.3 → NP_004353.1  calmegin precursor

      See identical proteins and their annotated locations for NP_004353.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) is the shorter transcript. Both variants 1 and 2 encode the same protein.
      Source sequence(s)
      BC028357, D86322, DC396076
      Consensus CDS
      CCDS3751.1
      UniProtKB/Swiss-Prot
      B3KS90, B4DXV8, D3DNY8, O14967
      UniProtKB/TrEMBL
      A0A140VKG2, A8K454
      Related
      ENSP00000326699.5, ENST00000325617.10
      Conserved Domains (1) summary
      pfam00262
      Location:62 → 429
      Calreticulin; Calreticulin family

    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_000004.12 Reference GRCh38.p14 Primary Assembly

      Range
      140388453..140427648 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060928.1 Alternate T2T-CHM13v2.0

      Range
      143708226..143747412 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O14967.1 GenPept UniProtKB/Swiss-Prot:O14967

    Gene LinkOut

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

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