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Clgn calmegin [ Mus musculus (house mouse) ]

Gene ID: 12745, updated on 1-Mar-2024

Summary

Official Symbol
Clgnprovided by MGI
Official Full Name
calmeginprovided by MGI
Primary source
MGI:MGI:107472
See related
Ensembl:ENSMUSG00000002190 AllianceGenome:MGI:107472
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
Cln; A2/6; 4930459O04Rik
Summary
This gene belongs to the calreticulin family, which includes calreticulin, calnexin, and calmegin, and encodes a calcium-binding molecular chaperone specifically expressed in pachytene stage male germ cells. It is required for the proper folding of newly synthesized membrane proteins in the endoplasmic reticulum including those critical for sperm migration from the uterus into the oviduct and sperm adhesion to and penetration of the zona pellucida. This gene plays a key role in spermatogenesis and male infertility. Alternative splice variants exist for this gene. [provided by RefSeq, Jul 2016]
Expression
Biased expression in testis adult (RPKM 55.5), cerebellum adult (RPKM 3.2) and 1 other tissue See more
Orthologs
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Genomic context

See Clgn in Genome Data Viewer
Location:
8 C2; 8 39.97 cM
Exon count:
17
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 8 NC_000074.7 (84116454..84155181)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 8 NC_000074.6 (83389790..83428552)

Chromosome 8 - NC_000074.7Genomic Context describing neighboring genes Neighboring gene MGAT4 family, member C Neighboring gene cofilin 1, non-muscle pseudogene Neighboring gene STARR-seq mESC enhancer starr_22081 Neighboring gene predicted gene, 32377 Neighboring gene STARR-positive B cell enhancer mm9_chr8:85966309-85966610 Neighboring gene short coiled-coil protein Neighboring gene pescadillo homolog pseudogene

Genomic regions, transcripts, and products

Expression

  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Targeted (2)  1 citation
  • Endonuclease-mediated (2) 

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables calcium ion binding IBA
Inferred from Biological aspect of Ancestor
more info
 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables protein folding chaperone IMP
Inferred from Mutant Phenotype
more info
PubMed 
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
 
acts_upstream_of_or_within binding of sperm to zona pellucida IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within cell differentiation IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within meiotic cell cycle IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within multicellular organism development IEA
Inferred from Electronic Annotation
more info
 
involved_in protein folding IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in protein folding IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within protein-containing complex assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within single fertilization IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of_or_within spermatogenesis IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
located_in endoplasmic reticulum ISO
Inferred from Sequence Orthology
more info
 
is_active_in endoplasmic reticulum membrane IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in membrane IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
calmegin
Names
MEG 1 antigen
calnexin-T

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_001329627.1NP_001316556.1  calmegin isoform 1 precursor

    Status: REVIEWED

    Source sequence(s)
    AC155304, AK019534, AW456491, BY100733
    Consensus CDS
    CCDS22452.1
    UniProtKB/Swiss-Prot
    P52194, Q80YU3, Q9D2K5
    Related
    ENSMUSP00000002259.7, ENSMUST00000002259.13
    Conserved Domains (1) summary
    pfam00262
    Location:62429
    Calreticulin; Calreticulin family
  2. NM_001329680.1NP_001316609.1  calmegin isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an internal exon which results in a distinct 5' UTR and the use of a downstream translation start site compared to transcript variant 1. The encoded isoform has a shorter N-terminus compared to isoform (2).
    Source sequence(s)
    AC155304, AW456491
    Conserved Domains (1) summary
    pfam00262
    Location:1251
    Calreticulin; Calreticulin family
  3. NM_009904.4NP_034034.2  calmegin isoform 1 precursor

    See identical proteins and their annotated locations for NP_034034.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1). Both variants 1 and 2 encode the same protein.
    Source sequence(s)
    AC155304, AW456491, BC050767, BY100733
    Consensus CDS
    CCDS22452.1
    UniProtKB/Swiss-Prot
    P52194, Q80YU3, Q9D2K5
    Related
    ENSMUSP00000105457.3, ENSMUST00000109831.3
    Conserved Domains (1) summary
    pfam00262
    Location:62429
    Calreticulin; Calreticulin family

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000074.7 Reference GRCm39 C57BL/6J

    Range
    84116454..84155181
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011248296.4XP_011246598.1  calmegin isoform X1

    See identical proteins and their annotated locations for XP_011246598.1

    Conserved Domains (1) summary
    pfam00262
    Location:66433
    Calreticulin; Calreticulin family
  2. XM_011248298.4XP_011246600.1  calmegin isoform X2

    See identical proteins and their annotated locations for XP_011246600.1

    UniProtKB/Swiss-Prot
    P52194, Q80YU3, Q9D2K5
    Conserved Domains (1) summary
    pfam00262
    Location:62429
    Calreticulin; Calreticulin family
  3. XM_030243276.2XP_030099136.1  calmegin isoform X4

    Conserved Domains (1) summary
    pfam00262
    Location:1251
    Calreticulin; Calreticulin family
  4. XM_006530636.4XP_006530699.1  calmegin isoform X3

    Conserved Domains (1) summary
    pfam00262
    Location:2346
    Calreticulin; Calreticulin family
  5. XM_017312554.2XP_017168043.1  calmegin isoform X4

    Conserved Domains (1) summary
    pfam00262
    Location:1251
    Calreticulin; Calreticulin family
  6. XM_030243275.1XP_030099135.1  calmegin isoform X3

    Conserved Domains (1) summary
    pfam00262
    Location:2346
    Calreticulin; Calreticulin family
  7. XM_011248297.3XP_011246599.1  calmegin isoform X1

    See identical proteins and their annotated locations for XP_011246599.1

    Conserved Domains (1) summary
    pfam00262
    Location:66433
    Calreticulin; Calreticulin family