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    CALU calumenin [ Homo sapiens (human) ]

    Gene ID: 813, updated on 5-May-2024

    Summary

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    Official Symbol
    CALUprovided by HGNC
    Official Full Name
    calumeninprovided by HGNC
    Primary source
    HGNC:HGNC:1458
    See related
    Ensembl:ENSG00000128595 MIM:603420; AllianceGenome:HGNC:1458
    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
    The product of this gene is a calcium-binding protein localized in the endoplasmic reticulum (ER) and it is involved in such ER functions as protein folding and sorting. This protein belongs to a family of multiple EF-hand proteins (CERC) that include reticulocalbin, ERC-55, and Cab45 and the product of this gene. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Oct 2008]
    Expression
    Ubiquitous expression in heart (RPKM 44.6), placenta (RPKM 44.1) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    7q32.1
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (128739359..128773400)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (130051503..130085553)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (128379413..128413454)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene golgi associated RAB2 interactor 1A Neighboring gene MED14-independent group 3 enhancer GRCh37_chr7:128341516-128342715 Neighboring gene RNA, 5S ribosomal pseudogene 243 Neighboring gene uncharacterized LOC124901825 Neighboring gene golgi associated RAB2 interactor 1B Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18612 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18613 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26603 Neighboring gene RNA, 7SL, cytoplasmic 81, pseudogene Neighboring gene blue cone (S) opsin upstream regulatory region Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18614 Neighboring gene opsin 1, short wave sensitive Neighboring gene tRNA-Pro (anticodon AGG) 2-3 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:128431137-128431405 Neighboring gene coiled-coil domain containing 136

    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. Calumenin contributes to ER-Ca(2+) homeostasis in bronchial epithelial cells expressing WT and F508del mutated CFTR and to F508del-CFTR retention. Philippe R, et al. Cell Calcium, 2017 Mar. PMID 28189267
    2. CALU polymorphism A29809G affects calumenin availability involving vascular calcification. Jover E, et al. J Mol Cell Cardiol, 2015 May. PMID 25823396
    3. CALU A29809G polymorphism in coronary atherothrombosis: Implications for coronary calcification and prognosis. Hernández-Romero D, et al. Ann Med, 2010 Sep. PMID 20673165
    4. A polymorphism in the VKORC1 regulator calumenin predicts higher warfarin dose requirements in African Americans. Voora D, et al. Clin Pharmacol Ther, 2010 Apr. PMID 20200517, Free PMC Article
    5. Human calumenin localizes to the secretory pathway and is secreted to the medium. Vorum H, et al. Exp Cell Res, 1999 May 1. PMID 10222138

    See all (157) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Establishment of a CALU, AURKA, and MCM2 gene panel for discrimination of metastasis from primary colon and lung cancers.
      Title: Establishment of a CALU, AURKA, and MCM2 gene panel for discrimination of metastasis from primary colon and lung cancers.
    2. Replacing Leu with Gly (L150G) in Calu1 enables the protein to adopt a structural fold even in the Ca(2+) free form. The fourth (of seven) EF-hand of HsCalu1 nucleates the structural fold of the protein depending on the switch residue (Gly or Leu).
      Title: The Differential Response to Ca(2+) from Vertebrate and Invertebrate Calumenin Is Governed by a Single Amino Acid Residue.
    3. The Calumenin modulates Sarco/Endoplasmic reticulumCa2+ATPase (SERCA) pump activity without drastically affecting ER-Ca(2+) concentration.
      Title: Calumenin contributes to ER-Ca(2+) homeostasis in bronchial epithelial cells expressing WT and F508del mutated CFTR and to F508del-CFTR retention.
    4. irradiated tumor cells were observed to significantly up-regulate the expression of calcium-binding proteins CALM1, CALU, and RCN1, suggesting important roles for these mediators in promoting irradiated tumor cell survival during hypoxia
      Title: Irradiation of Epithelial Carcinoma Cells Upregulates Calcium-Binding Proteins That Promote Survival under Hypoxic Conditions.
    5. Calu-15, a novel isoform of Calu with phosphorylation-dependent nuclear localization, has a critical role in promoting filopodia formation and cell migration by upregulating the GDF-15 transcription.
      Title: Calumenin-15 facilitates filopodia formation by promoting TGF-β superfamily cytokine GDF-15 transcription.
    6. Results provide direct evidence for the involvement of CALU and LGALS3BP as potential negative regulators in the virus-triggered induction of the typeI interferons.
      Title: Quantitative Proteomics Reveals the Roles of Peroxisome-associated Proteins in Antiviral Innate Immune Responses.
    7. Results show that OSBPL5 and CALU were expressed at higher levels in the lung tissues of metastasis-positive cases than that in the metastasis-negative cases suggesting they can promote invasiveness of lung cancer cells.
      Title: Identification and evaluation of metastasis-related proteins, oxysterol binding protein-like 5 and calumenin, in lung tumors.
    8. CALU polymorphism A29809G affects calumenin availability involving vascular calcification
      Title: CALU polymorphism A29809G affects calumenin availability involving vascular calcification.
    9. Calumenin is characterized as a charged protein exhibiting close similarity with intrinsically disordered proteins and is hypothesized to regulate F508del-CFTR folding by electrostatic effects.
      Title: Biophysical characterisation of calumenin as a charged F508del-CFTR folding modulator.
    10. Calumenin is a new CFTR chaperone.
      Title: Proteomic identification of calumenin as a G551D-CFTR associated protein.
    Submit: New GeneRIF Correction See all GeneRIFs (19)

    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

    EBI GWAS Catalog

    Description
    Genome-wide association study of primary tooth eruption identifies pleiotropic loci associated with height and craniofacial distances.
    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 calumenin (CALU) 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

    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

    Clone Names

    • FLJ90608

    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 protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    Component Evidence Code Pubs
    located_in Golgi apparatus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in endoplasmic reticulum IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    		  
    located_in endoplasmic reticulum lumen TAS
    Traceable Author Statement
    more info
    		  
    located_in endoplasmic reticulum membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in extracellular region IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in melanosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in membrane HDA PubMed 
    located_in sarcoplasmic reticulum lumen IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    calumenin
    Names
    IEF SSP 9302
    crocalbin-like protein
    multiple EF-hand protein

    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.

    Genomic

    1. NG_033110.1 RefSeqGene

      Range
      5068..39109
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001130674.3 → NP_001124146.1  calumenin isoform b precursor

      See identical proteins and their annotated locations for NP_001124146.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) has an alternate in-frame exon, compared to variant 1. The resulting isoform (b) is of the same length but has a different internal segment, compared to isoform a.
      Source sequence(s)
      AC024952, AF345637, BF438624, HM002611
      Consensus CDS
      CCDS47703.1
      UniProtKB/TrEMBL
      B3KNG6
      Related
      ENSP00000408838.2, ENST00000449187.7
      Conserved Domains (1) summary
      cd16228
      Location:37 → 299
      EFh_CREC_Calumenin; EF-hand, calcium binding motif, found in calumenin

    2. NM_001199671.2 → NP_001186600.1  calumenin isoform c precursor

      See identical proteins and their annotated locations for NP_001186600.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) has an additional exon in the 5' region, introducing an in-frame upstream AUG start codon, compared to variant 1. The resulting isoform (c) has a longer N-terminus, compared to isoform a.
      Source sequence(s)
      AC024952, AK056338, BF438624, HM002604
      Consensus CDS
      CCDS56506.1
      UniProtKB/TrEMBL
      B3KQF5
      Related
      ENSP00000420381.1, ENST00000479257.5
      Conserved Domains (1) summary
      cd16228
      Location:45 → 307
      EFh_CREC_Calumenin; EF-hand, calcium binding motif, found in calumenin

    3. NM_001199672.2 → NP_001186601.1  calumenin isoform d precursor

      See identical proteins and their annotated locations for NP_001186601.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) has an additional exon in the 5' region, introducing an in-frame upstream AUG start codon, and has an alternate in-frame coding exon, compared to variant 1. The resulting isoform (d) has a longer N-terminus and a different internal segment, compared to isoform a.
      Source sequence(s)
      AC024952, AK056338, BF438624, HM002605, HM002606
      Consensus CDS
      CCDS56507.1
      UniProtKB/TrEMBL
      B3KNG6
      Related
      ENSP00000438248.1, ENST00000542996.7
      Conserved Domains (1) summary
      cd16228
      Location:45 → 307
      EFh_CREC_Calumenin; EF-hand, calcium binding motif, found in calumenin

    4. NM_001199673.2 → NP_001186602.1  calumenin isoform e precursor

      See identical proteins and their annotated locations for NP_001186602.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) lacks a coding exon in the 3' region, resulting in frame-shift, compared to variant 1. The resulting isoform (e) has a shorter and different C-terminus, compared to isoform a.
      Source sequence(s)
      AC024952, BC013383, BF438624, HM002611
      Consensus CDS
      CCDS56508.1
      UniProtKB/Swiss-Prot
      O43852
      Related
      ENSP00000442110.1, ENST00000535011.6
      Conserved Domains (2) summary
      cd15899
      Location:37 → 65
      EFh_CREC; EF-hand motif [structural motif]
      cl25354
      Location:37 → 223
      EFh_CREC; EF-hand, calcium binding motif, found in CREC-EF hand family

    5. NM_001219.5 → NP_001210.1  calumenin isoform a precursor

      See identical proteins and their annotated locations for NP_001210.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the predominant isoform (a).
      Source sequence(s)
      AC024952, AK074862, BF438624, HM002604
      Consensus CDS
      CCDS5805.1
      UniProtKB/Swiss-Prot
      B3KPG9, D6QS48, D6QS49, D6QS50, D6QS51, D6QS52, D6QS53, D6QS54, D6QS55, D6QS56, D6QS57, D6QS58, D6QS59, F5H1Q9, F5H879, O43852, O60456, Q6FHB9, Q96RL3, Q9NR43
      UniProtKB/TrEMBL
      B3KQF5, Q6IAW5
      Related
      ENSP00000249364.4, ENST00000249364.9
      Conserved Domains (1) summary
      cd16228
      Location:37 → 299
      EFh_CREC_Calumenin; EF-hand, calcium binding motif, found in calumenin

    RNA

    1. NR_074086.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (7) lacks two consecutive exons in the 5' region, compared to variant 1. This variant is represented as non-coding due to the presence of an upstream ORF that is predicted to interfere with translation of the primary ORF; translation of the upstream ORF renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC024952, BC013383, BF438624, HM002616

    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_000007.14 Reference GRCh38.p14 Primary Assembly

      Range
      128739359..128773400
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060931.1 Alternate T2T-CHM13v2.0

      Range
      130051503..130085553
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001199674.1: Suppressed sequence

      Description
      NM_001199674.1: This RefSeq was permanently suppressed because it is now thought that this transcript does not encode a protein.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O43852.2 GenPept UniProtKB/Swiss-Prot:O43852

    Gene LinkOut

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

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