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

Gene ID: 80267, updated on 1-Jun-2020

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
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
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

Genomic context

See EDEM3 in Genome Data Viewer
Location:
1q25.3
Exon count:
21
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (184690237..184754907, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (184659625..184724041, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene chromosome 1 open reading frame 21 Neighboring gene uncharacterized LOC107985236 Neighboring gene uncharacterized LOC105371648 Neighboring gene uncharacterized LOC105371649 Neighboring gene uncharacterized LOC107985238 Neighboring gene niban apoptosis regulator 1

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

Phenotypes

NHGRI GWAS Catalog

Description
GWAS identifies novel SLE susceptibility genes and explains the association of the HLA region.
NHGRI GWA Catalog
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
NHGRI GWA 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

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
calcium ion binding IEA
Inferred from Electronic Annotation
more info
 
mannosyl-oligosaccharide 1,2-alpha-mannosidase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
Process Evidence Code Pubs
mannose trimming involved in glycoprotein ERAD pathway IMP
Inferred from Mutant Phenotype
more info
PubMed 
mannose trimming involved in glycoprotein ERAD pathway TAS
Traceable Author Statement
more info
 
protein glycosylation IEA
Inferred from Electronic Annotation
more info
 
response to unfolded protein IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
endoplasmic reticulum lumen IEA
Inferred from Electronic Annotation
more info
 
endoplasmic reticulum quality control compartment TAS
Traceable Author Statement
more info
 
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_011508315.1
XP_011508316.1
XP_016857886.1
XP_016857887.1

NCBI Reference Sequences (RefSeq)

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
    UniProtKB/Swiss-Prot
    Q9BZQ6
    Related
    ENSP00000356482.3, ENST00000367512.7
    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
    Q9BZQ6
    UniProtKB/TrEMBL
    A0A024R931
    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: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

    Range
    184690237..184754907 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    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
  2. XM_017002397.1XP_016857886.1  ER degradation-enhancing alpha-mannosidase-like protein 3 isoform X3

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

    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
  4. XM_011510014.3XP_011508316.1  ER degradation-enhancing alpha-mannosidase-like protein 3 isoform X5

    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
  5. XM_011510013.3XP_011508315.1  ER degradation-enhancing alpha-mannosidase-like protein 3 isoform X4

    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
  6. XM_017002398.1XP_016857887.1  ER degradation-enhancing alpha-mannosidase-like protein 3 isoform X6

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