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

Gene ID: 289085, updated on 11-Apr-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
Ensembl: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
  • 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 mannose trimming 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 ISO
Inferred from Sequence Orthology
more info
  
involved_in mannose trimming involved in glycoprotein ERAD pathway IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within proteasome-mediated ubiquitin-dependent protein catabolic process ISO
Inferred from Sequence Orthology
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 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
    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
    ENSRNOP00000095995.1
    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

    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
    ENSRNOP00000017858.8
    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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