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    EDEM3 ER degradation enhancing alpha-mannosidase like protein 3 [ Homo sapiens (human) ]

    Gene ID: 80267, updated on 3-Dec-2024

    Summary

    Official Symbol
    EDEM3provided by HGNC
    Official Full Name
    ER degradation enhancing alpha-mannosidase like protein 3provided by HGNC
    Primary source
    HGNC:HGNC:16787
    See related
    Ensembl:ENSG00000116406 MIM:610214; AllianceGenome:HGNC:16787
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    CDG2V; C1orf22
    Summary
    Quality control in the endoplasmic reticulum (ER) ensures that only properly folded proteins are retained in the cell through recognition and degradation of misfolded or unassembled proteins. EDEM3 belongs to a group of proteins that accelerate degradation of misfolded glycoproteins in the ER (Hirao et al., 2006 [PubMed 16431915]).[supplied by OMIM, Mar 2008]
    Expression
    Ubiquitous expression in stomach (RPKM 15.9), colon (RPKM 13.5) and 25 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See EDEM3 in Genome Data Viewer
    Location:
    1q25.3
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (184690237..184754858, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (184053426..184118046, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (184659371..184723992, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904468 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2235 Neighboring gene uncharacterized LOC105371648 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2236 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2237 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2238 Neighboring gene uncharacterized LOC105371649 Neighboring gene uncharacterized LOC107985238 Neighboring gene niban apoptosis regulator 1 Neighboring gene RNA, U7 small nuclear 13 pseudogene

    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

    Associated conditions

    Description Tests
    Congenital disorder of glycosylation, type 2v
    MedGen: C5561971 OMIM: 619493 GeneReviews: Not available
    Compare labs

    EBI GWAS Catalog

    Description
    GWAS identifies novel SLE susceptibility genes and explains the association of the HLA region.
    EBI GWAS Catalog
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    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 ER degradation enhancer, mannosidase alpha-like 3 (EDEM3) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed
    Envelope surface glycoprotein gp160, precursor env HIV-1 gp160 interacts with EDEM3; predicted interaction to be within the endoplasmic reticulum and function as chaperone for endoplasmic reticulum-associated degradation PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    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 IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables mannosyl-oligosaccharide 1,2-alpha-mannosidase activity TAS
    Traceable Author Statement
    more info
     
    Process Evidence Code Pubs
    involved_in ERAD pathway IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in carbohydrate metabolic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in endoplasmic reticulum mannose trimming IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in endoplasmic reticulum unfolded protein response IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in mannoprotein catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in mannoprotein catabolic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in protein glycosylation IEA
    Inferred from Electronic Annotation
    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 IEA
    Inferred from Electronic Annotation
    more info
     
    located_in endoplasmic reticulum quality control compartment TAS
    Traceable Author Statement
    more info
     
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    ER degradation-enhancing alpha-mannosidase-like protein 3
    Names
    ER degradation enhancer, mannosidase alpha-like 3
    ER degradation-enhancing -mannosidase-like protein 3
    ER degradation-enhancing alpha-mannosidase-like 3
    alpha-1,2-mannosidase EDEM3
    NP_001306889.1
    NP_079467.3
    XP_005245556.1
    XP_011508314.1
    XP_054194843.1
    XP_054194844.1

    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.

    mRNA and Protein(s)

    1. NM_001319960.2NP_001306889.1  ER degradation-enhancing alpha-mannosidase-like protein 3 isoform 1 precursor

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AI521228, AL096819, BC016464, BC144149, DA724785
      Consensus CDS
      CCDS91128.1
      UniProtKB/TrEMBL
      A0A8I5KTR7, A0A8J8YX80
      Related
      ENSP00000356482.4, ENST00000367512.8
      Conserved Domains (2) summary
      cd02126
      Location:664789
      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:59498
      Glyco_hydro_47; Glycosyl hydrolase family 47
    2. NM_025191.4NP_079467.3  ER degradation-enhancing alpha-mannosidase-like protein 3 isoform 2 precursor

      See identical proteins and their annotated locations for NP_079467.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
      Source sequence(s)
      AF288393, AI521228, AL096819, BC016464, DA724785
      Consensus CDS
      CCDS1363.2
      UniProtKB/Swiss-Prot
      B2RCH6, B7ZLZ2, Q0VGM5, Q5TEZ0, Q7L2Y5, Q9BZQ6, Q9HCW1, Q9UFV7
      UniProtKB/TrEMBL
      A0A8I5KTR7
      Related
      ENSP00000318147.7, ENST00000318130.13
      Conserved Domains (2) summary
      cd02126
      Location:664789
      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:59498
      Glyco_hydro_47; Glycosyl hydrolase family 47

    RNA

    1. NR_135118.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) uses an alternate splice junction compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AI521228, AL096819, BC016464, BC144150, DA724785

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      184690237..184754858 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011510012.2XP_011508314.1  ER degradation-enhancing alpha-mannosidase-like protein 3 isoform X2

      UniProtKB/TrEMBL
      A0A8I5KWI4
      Related
      ENSP00000509571.1, ENST00000687113.1
      Conserved Domains (2) summary
      cd02126
      Location:588713
      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:1421
      Glyco_hydro_47; Glycosyl hydrolase family 47
    2. XM_005245499.3XP_005245556.1  ER degradation-enhancing alpha-mannosidase-like protein 3 isoform X1

      UniProtKB/TrEMBL
      A0A8I5KTR7
      Conserved Domains (2) summary
      cd02126
      Location:665790
      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:59498
      Glyco_hydro_47; Glycosyl hydrolase family 47

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      184053426..184118046 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054338869.1XP_054194844.1  ER degradation-enhancing alpha-mannosidase-like protein 3 isoform X2

      UniProtKB/TrEMBL
      A0A8I5KWI4
    2. XM_054338868.1XP_054194843.1  ER degradation-enhancing alpha-mannosidase-like protein 3 isoform X1

      UniProtKB/TrEMBL
      A0A8I5KTR7