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    Edem3 ER degradation enhancing alpha-mannosidase like protein 3 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 289085, updated on 18-Sep-2024

    Summary

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    Official Symbol
    Edem3provided by RGD
    Official Full Name
    ER degradation enhancing alpha-mannosidase like protein 3provided by RGD
    Primary source
    RGD:1561496
    See related
    EnsemblRapid:ENSRNOG00000028358 AllianceGenome:RGD:1561496
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    RGD1561496
    Summary
    Predicted to enable mannosyl-oligosaccharide 1,2-alpha-mannosidase activity. Predicted to be involved in mannose trimming involved in glycoprotein ERAD pathway. Predicted to act upstream of or within glycoprotein catabolic process and proteasome-mediated ubiquitin-dependent protein catabolic process. Predicted to be located in endoplasmic reticulum lumen. Human ortholog(s) of this gene implicated in congenital disorder of glycosylation type II. Orthologous to human EDEM3 (ER degradation enhancing alpha-mannosidase like protein 3). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Kidney (RPKM 158.0), Adrenal (RPKM 146.6) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Edem3 in Genome Data Viewer
    Location:
    13q21
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 13 NC_086031.1 (66403022..66470496)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 13 NC_051348.1 (63858282..63920538)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 13 NC_005112.4 (69135095..69197708)

    Chromosome 13 - NC_086031.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC134481627 Neighboring gene niban apoptosis regulator 1 Neighboring gene ribosomal protein L23A like 9 Neighboring gene uncharacterized LOC120096277 Neighboring gene similar to human chromosome 1 open reading frame 21 Neighboring gene uncharacterized LOC108352552

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. EDEM3, a soluble EDEM homolog, enhances glycoprotein endoplasmic reticulum-associated degradation and mannose trimming. Hirao K, et al. J Biol Chem, 2006 Apr 7. PMID 16431915
    2. EDEM2 initiates mammalian glycoprotein ERAD by catalyzing the first mannose trimming step. Ninagawa S, et al. J Cell Biol, 2014 Aug 4. PMID 25092655, Free PMC Article
    3. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables calcium ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables mannosyl-oligosaccharide 1,2-alpha-mannosidase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables mannosyl-oligosaccharide 1,2-alpha-mannosidase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in ERAD pathway ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in carbohydrate metabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in endoplasmic reticulum unfolded protein response IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within glycoprotein catabolic process ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in mannoprotein catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in mannoprotein catabolic process ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in mannose trimming involved in glycoprotein ERAD pathway IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within proteasome-mediated ubiquitin-dependent protein catabolic process ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in ubiquitin-dependent glycoprotein ERAD pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in endoplasmic reticulum IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in endoplasmic reticulum lumen ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in endoplasmic reticulum quality control compartment IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    ER degradation-enhancing alpha-mannosidase-like protein 3
    Names
    ER degradation enhancer, mannosidase alpha-like 3
    ER degradation-enhancing alpha-mannosidase-like 3
    NP_001178600.1
    XP_006250047.2
    XP_006250048.2
    XP_017454191.2
    XP_038946376.1
    XP_038946377.1
    XP_038946378.1
    XP_063128169.1

    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_001191671.1 → NP_001178600.1  ER degradation-enhancing alpha-mannosidase-like protein 3 precursor

      Status: PROVISIONAL

      Source sequence(s)
      JAXUCZ010000013
      Related
      ENSRNOP00000104197.1, ENSRNOT00000127738.1
      Conserved Domains (2) summary
      cd02126
      Location:665 → 790
      PA_EDEM3_like; PA_EDEM3_like: protease associated domain (PA) domain-containing EDEM3-like proteins. This group contains various PA domain-containing proteins similar to mouse EDEM3 (ER-degradation-enhancing mannosidase-like 3 protein). EDEM3 contains a region, similar ...
      pfam01532
      Location:60 → 499
      Glyco_hydro_47; Glycosyl hydrolase family 47

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086031.1 Reference GRCr8

      Range
      66403022..66470496
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039090448.2 → XP_038946376.1  ER degradation-enhancing alpha-mannosidase-like protein 3 isoform X1

      Conserved Domains (2) summary
      cd02126
      Location:666 → 791
      PA_EDEM3_like; protease associated domain (PA) domain-containing EDEM3-like proteins. This group contains various PA domain-containing proteins similar to mouse EDEM3 (ER-degradation-enhancing mannosidase-like 3 protein). EDEM3 contains a region, similar to Class I ...
      pfam01532
      Location:60 → 499
      Glyco_hydro_47; Glycosyl hydrolase family 47

    2. XM_006249985.4 → XP_006250047.2  ER degradation-enhancing alpha-mannosidase-like protein 3 isoform X3

      UniProtKB/TrEMBL
      A0A8I6AKY3
      Related
      ENSRNOP00000109021.1, ENSRNOT00000128784.1
      Conserved Domains (2) summary
      cd02126
      Location:666 → 791
      PA_EDEM3_like; protease associated domain (PA) domain-containing EDEM3-like proteins. This group contains various PA domain-containing proteins similar to mouse EDEM3 (ER-degradation-enhancing mannosidase-like 3 protein). EDEM3 contains a region, similar to Class I ...
      pfam01532
      Location:60 → 499
      Glyco_hydro_47; Glycosyl hydrolase family 47

    3. XM_039090449.2 → XP_038946377.1  ER degradation-enhancing alpha-mannosidase-like protein 3 isoform X4

      Conserved Domains (2) summary
      cd02126
      Location:647 → 772
      PA_EDEM3_like; protease associated domain (PA) domain-containing EDEM3-like proteins. This group contains various PA domain-containing proteins similar to mouse EDEM3 (ER-degradation-enhancing mannosidase-like 3 protein). EDEM3 contains a region, similar to Class I ...
      pfam01532
      Location:60 → 499
      Glyco_hydro_47; Glycosyl hydrolase family 47

    4. XM_006249986.4 → XP_006250048.2  ER degradation-enhancing alpha-mannosidase-like protein 3 isoform X6

      Related
      ENSRNOP00000017858.9, ENSRNOT00000017858.9
      Conserved Domains (2) summary
      cd02126
      Location:647 → 772
      PA_EDEM3_like; protease associated domain (PA) domain-containing EDEM3-like proteins. This group contains various PA domain-containing proteins similar to mouse EDEM3 (ER-degradation-enhancing mannosidase-like 3 protein). EDEM3 contains a region, similar to Class I ...
      pfam01532
      Location:60 → 499
      Glyco_hydro_47; Glycosyl hydrolase family 47

    5. XM_017598702.3 → XP_017454191.2  ER degradation-enhancing alpha-mannosidase-like protein 3 isoform X2

      UniProtKB/TrEMBL
      D4AB70
      Related
      ENSRNOP00000095995.2, ENSRNOT00000115520.2
      Conserved Domains (2) summary
      cd02126
      Location:665 → 790
      PA_EDEM3_like; protease associated domain (PA) domain-containing EDEM3-like proteins. This group contains various PA domain-containing proteins similar to mouse EDEM3 (ER-degradation-enhancing mannosidase-like 3 protein). EDEM3 contains a region, similar to Class I ...
      pfam01532
      Location:60 → 499
      Glyco_hydro_47; Glycosyl hydrolase family 47

    6. XM_039090450.2 → XP_038946378.1  ER degradation-enhancing alpha-mannosidase-like protein 3 isoform X5

      Conserved Domains (2) summary
      cd02126
      Location:646 → 771
      PA_EDEM3_like; protease associated domain (PA) domain-containing EDEM3-like proteins. This group contains various PA domain-containing proteins similar to mouse EDEM3 (ER-degradation-enhancing mannosidase-like 3 protein). EDEM3 contains a region, similar to Class I ...
      pfam01532
      Location:60 → 499
      Glyco_hydro_47; Glycosyl hydrolase family 47

    7. XM_063272099.1 → XP_063128169.1  ER degradation-enhancing alpha-mannosidase-like protein 3 isoform X7

    Nucleotide Protein Strain
    Heading Accession and Version

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