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

Gene ID: 80267, updated on 14-Nov-2024

Summary

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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
mouse all
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Genomic context

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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

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues 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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Pro-Survival Factor EDEM3 Confers Therapy Resistance in Prostate Cancer.
    Title: Pro-Survival Factor EDEM3 Confers Therapy Resistance in Prostate Cancer.
  2. Purified EDEM3 or EDEM1 alone produces determinant oligosaccharide structures from M8B in mammalian glycoprotein ERAD.
    Title: Purified EDEM3 or EDEM1 alone produces determinant oligosaccharide structures from M8B in mammalian glycoprotein ERAD.
  3. Bi-allelic variants in the ER quality-control mannosidase gene EDEM3 cause a congenital disorder of glycosylation.
    Title: Bi-allelic variants in the ER quality-control mannosidase gene EDEM3 cause a congenital disorder of glycosylation.
  4. EDEM3 Domains Cooperate to Perform Its Overall Cell Functioning.
    Title: EDEM3 Domains Cooperate to Perform Its Overall Cell Functioning.
  5. IL8 and EDEM3 gene expression ratio indicates peripheral blood mononuclear cell (PBMC) quality.
    Title: IL8 and EDEM3 gene expression ratio indicates peripheral blood mononuclear cell (PBMC) quality.
  6. the mannose-trimming activity of EDEM3 toward the model misfolded substrate, the glycoprotein T-cell receptor alpha locus (TCRalpha), was reconstituted only when ERp46 had established a covalent interaction with EDEM3
    Title: ER-resident protein 46 (ERp46) triggers the mannose-trimming activity of ER degradation-enhancing α-mannosidase-like protein 3 (EDEM3).
  7. The data corroborated herein suggest that besides ER residents, EDEM3 interacts also with proteins involved in the ERAD cargo recognition and targeting to degradation translocation into the cytosol, including UBA1 and UBA2 ubiquitinating enzymes. In addition, the results indicate that this network of EDEM3 interactors is highly sensitive to interfering with early ER N-glycan processing.
    Title: Inhibition of N-glycan processing modulates the network of EDEM3 interactors.
Submit: New GeneRIF Correction

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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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

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

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

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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 -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)

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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_001319960.2 → NP_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:664 → 789
    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:59 → 498
    Glyco_hydro_47; Glycosyl hydrolase family 47

  2. NM_025191.4 → NP_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:664 → 789
    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:59 → 498
    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_011510012.2 → XP_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:588 → 713
    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:1 → 421
    Glyco_hydro_47; Glycosyl hydrolase family 47

  2. XM_005245499.3 → XP_005245556.1  ER degradation-enhancing alpha-mannosidase-like protein 3 isoform X1

    UniProtKB/TrEMBL
    A0A8I5KTR7
    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:59 → 498
    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_054338869.1 → XP_054194844.1  ER degradation-enhancing alpha-mannosidase-like protein 3 isoform X2

  2. XM_054338868.1 → XP_054194843.1  ER degradation-enhancing alpha-mannosidase-like protein 3 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9BZQ6.2 GenPept UniProtKB/Swiss-Prot:Q9BZQ6

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