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    CALU calumenin [ Homo sapiens (human) ]

    Gene ID: 813, updated on 17-Jun-2024

    Summary

    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See CALU in Genome Data Viewer
    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

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

    Description
    Genome-wide association study of primary tooth eruption identifies pleiotropic loci associated with height and craniofacial distances.
    EBI GWAS Catalog

    HIV-1 interactions

    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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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

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

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001130674.3NP_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:37299
      EFh_CREC_Calumenin; EF-hand, calcium binding motif, found in calumenin
    2. NM_001199671.2NP_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:45307
      EFh_CREC_Calumenin; EF-hand, calcium binding motif, found in calumenin
    3. NM_001199672.2NP_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:45307
      EFh_CREC_Calumenin; EF-hand, calcium binding motif, found in calumenin
    4. NM_001199673.2NP_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:3765
      EFh_CREC; EF-hand motif [structural motif]
      cl25354
      Location:37223
      EFh_CREC; EF-hand, calcium binding motif, found in CREC-EF hand family
    5. NM_001219.5NP_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:37299
      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.