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CALU calumenin [ Homo sapiens (human) ]

Gene ID: 813, updated on 3-May-2020

Summary

Official Symbol
CALUprovided by HGNC
Official Full Name
calumeninprovided by HGNC
Primary source
HGNC:HGNC:1458
See related
Ensembl:ENSG00000128595 MIM:603420
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

Genomic context

See CALU in Genome Data Viewer
Location:
7q32.1
Exon count:
9
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 7 NC_000007.14 (128739359..128773400)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (128379346..128413477)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene family with sequence similarity 71 member F2 Neighboring gene RNA, 5S ribosomal pseudogene 243 Neighboring gene family with sequence similarity 71 member F1 Neighboring gene RNA, 7SL, cytoplasmic 81, pseudogene Neighboring gene blue cone (S) opsin upstream regulatory region Neighboring gene opsin 1, short wave sensitive Neighboring gene tRNA-Pro (anticodon AGG) 2-3

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

NHGRI GWAS Catalog

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

Homology

Clone Names

  • FLJ90608

Gene Ontology Provided by GOA

Function Evidence Code Pubs
calcium ion binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
calcium ion binding IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
biological_process ND
No biological Data available
more info
 
cellular protein metabolic process TAS
Traceable Author Statement
more info
 
post-translational protein modification TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
Golgi apparatus IEA
Inferred from Electronic Annotation
more info
 
endoplasmic reticulum IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
endoplasmic reticulum IDA
Inferred from Direct Assay
more info
 
endoplasmic reticulum lumen TAS
Traceable Author Statement
more info
 
endoplasmic reticulum membrane IEA
Inferred from Electronic Annotation
more info
 
extracellular region IEA
Inferred from Electronic Annotation
more info
 
melanosome IEA
Inferred from Electronic Annotation
more info
 
membrane HDA PubMed 
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)

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/Swiss-Prot
    O43852
    UniProtKB/TrEMBL
    A0A024R755
    Related
    ENSP00000408838.2, ENST00000449187.6
    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/Swiss-Prot
    O43852
    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/Swiss-Prot
    O43852
    Related
    ENSP00000438248.1, ENST00000542996.6
    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
    O43852
    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: Homo sapiens Updated Annotation Release 109.

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000007.14 Reference GRCh38.p13 Primary Assembly

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

mRNA and Protein(s)

  1. XM_017012659.1XP_016868148.1  calumenin isoform X1

    UniProtKB/Swiss-Prot
    O43852
    Related
    ENSP00000417973.1, ENST00000493278.1

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.
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