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EDEM1 ER degradation enhancing alpha-mannosidase like protein 1 [ Homo sapiens (human) ]

Gene ID: 9695, updated on 27-Nov-2024

Summary

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Official Symbol
EDEM1provided by HGNC
Official Full Name
ER degradation enhancing alpha-mannosidase like protein 1provided by HGNC
Primary source
HGNC:HGNC:18967
See related
Ensembl:ENSG00000134109 MIM:607673; AllianceGenome:HGNC:18967
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
EDEM
Summary
Enables mannosyl-oligosaccharide 1,2-alpha-mannosidase activity and misfolded protein binding activity. Involved in positive regulation of retrograde protein transport, ER to cytosol; protein targeting to ER; and proteolysis involved in protein catabolic process. Located in aggresome and endoplasmic reticulum quality control compartment. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Ubiquitous expression in bone marrow (RPKM 22.7), lymph node (RPKM 21.0) and 25 other tissues See more
Orthologs
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Genomic context

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See EDEM1 in Genome Data Viewer
Location:
3p26.1
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (5187707..5219958)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (5181638..5213889)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (5229392..5261643)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene CD24 pseudogene 5 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14023 Neighboring gene uncharacterized LOC124906212 Neighboring gene Sharpr-MPRA regulatory region 5688 Neighboring gene Sharpr-MPRA regulatory region 5493 Neighboring gene ARF like GTPase 8B Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19376 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19377 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19378 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19379 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14024 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14026 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14025 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19380 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14027 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19381 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19382 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19383 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19384 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr3:5255069-5255570 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:5264003-5264559 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:5264560-5265115 Neighboring gene NANOG hESC enhancer GRCh37_chr3:5274159-5274668 Neighboring gene RNA, 7SL, cytoplasmic 553, pseudogene Neighboring gene microRNA 4790

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
  • 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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Related articles in PubMed

  1. Basal autophagy is involved in the degradation of the ERAD component EDEM1. Le Fourn V, et al. Cell Mol Life Sci, 2009 Apr. PMID 19266160, Free PMC Article
  2. EDEM accelerates ERAD by preventing aberrant dimer formation of misfolded alpha1-antitrypsin. Hosokawa N, et al. Genes Cells, 2006 May. PMID 16629899
  3. Alterations of EDEM1 functions enhance ATF6 pro-survival signaling. Papaioannou A, et al. FEBS J, 2018 Nov. PMID 30281916
  4. A single point mutation in ricin A-chain increases toxin degradation and inhibits EDEM1-dependent ER retrotranslocation. Sokołowska I, et al. Biochem J, 2011 Jun 1. PMID 21388347
  5. Endoplasmic reticulum degradation-enhancing α-mannosidase-like protein 1 targets misfolded HLA-B27 dimers for endoplasmic reticulum-associated degradation. Guiliano DB, et al. Arthritis Rheumatol, 2014 Nov. PMID 25132672, Free PMC Article

See all (54) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. EDEM1 Regulates Amyloid Precursor Protein (APP) Metabolism and Amyloid-beta Production.
    Title: EDEM1 Regulates Amyloid Precursor Protein (APP) Metabolism and Amyloid-β Production.
  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. Cleavage and degradation of EDEM1 promotes coxsackievirus B3 replication via ATF6a-mediated unfolded protein response signalling.
    Title: Cleavage and degradation of EDEM1 promotes coxsackievirus B3 replication via ATF6a-mediated unfolded protein response signalling.
  4. EDEM1 Drives Misfolded Protein Degradation via ERAD and Exploits ER-Phagy as Back-Up Mechanism When ERAD Is Impaired.
    Title: EDEM1 Drives Misfolded Protein Degradation via ERAD and Exploits ER-Phagy as Back-Up Mechanism When ERAD Is Impaired.
  5. A somatic variant of EDEM1 (N198I) alters ATF6 signaling and provides a selective advantage to the transforming cells and results in hepatocellular carcinoma.
    Title: Alterations of EDEM1 functions enhance ATF6 pro-survival signaling.
  6. EDEM1 employs different binding modalities to interact with ERAD clients and ER quality control (ERQC) machinery partners and some of these properties are shared with its homologues EDEM2 and EDEM3.
    Title: EDEM1's mannosidase-like domain binds ERAD client proteins in a redox-sensitive manner and possesses catalytic activity.
  7. EDEM1 colocalizes with the selective autophagy cargo receptors p62/SQSTM1, neighbor of BRCA1 gene 1 (NBR1) and autophagy-linked FYVE (Alfy) protein, and becomes engulfed by autophagic isolation membranes.
    Title: ERADication of EDEM1 occurs by selective autophagy and requires deglycosylation by cytoplasmic peptide N-glycanase.
  8. Endoplasmic reticulum degradation-enhancing alpha-mannosidase-like protein 1 targets misfolded HLA-B27 dimers for endoplasmic reticulum-associated degradation.
    Title: Endoplasmic reticulum degradation-enhancing α-mannosidase-like protein 1 targets misfolded HLA-B27 dimers for endoplasmic reticulum-associated degradation.
  9. miR-581 promotes hepatitis B virus surface antigen expression by targeting Dicer and EDEM1 in HepG2 cells.
    Title: MicroRNA-581 promotes hepatitis B virus surface antigen expression by targeting Dicer and EDEM1.
  10. EDEM1 associates with lifespan in animal models, although not humans.
    Title: Identification of genes promoting skin youthfulness by genome-wide association study.
Submit: New GeneRIF Correction See all GeneRIFs (25)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ51559, FLJ51560, KIAA0212

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables calcium ion binding IEA
Inferred from Electronic Annotation
more info
  
NOT enables mannosyl-oligosaccharide 1,2-alpha-mannosidase activity IDA
Inferred from Direct Assay
more info
 PubMed 
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
  
enables misfolded protein binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables misfolded protein binding IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in ERAD pathway IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in ERAD pathway ISS
Inferred from Sequence or Structural Similarity
more info
  
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 mannoprotein catabolic process IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of retrograde protein transport, ER to cytosol IGI
Inferred from Genetic Interaction
more info
 PubMed 
involved_in positive regulation of retrograde protein transport, ER to cytosol IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in protein targeting to ER IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in ubiquitin-dependent protein catabolic process IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in aggresome IDA
Inferred from Direct Assay
more info
  
located_in endoplasmic reticulum IDA
Inferred from Direct Assay
more info
 PubMed 
located_in endoplasmic reticulum IMP
Inferred from Mutant Phenotype
more info
 PubMed 
located_in endoplasmic reticulum membrane ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in endoplasmic reticulum quality control compartment IDA
Inferred from Direct Assay
more info
 PubMed 
located_in endoplasmic reticulum quality control compartment TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
ER degradation-enhancing alpha-mannosidase-like protein 1
Names
ER degradation enhancer, mannosidase alpha-like 1
ER degradation-enhancing alpha-mannosidase-like 1
NP_055489.1
XP_011532574.1
XP_047305220.1
XP_047305221.1
XP_047305222.1
XP_047305223.1
XP_054204483.1
XP_054204484.1
XP_054204485.1
XP_054204486.1
XP_054204487.1

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_014674.3 → NP_055489.1  ER degradation-enhancing alpha-mannosidase-like protein 1

    See identical proteins and their annotated locations for NP_055489.1

    Status: VALIDATED

    Source sequence(s)
    AC026202, AK292643, BC019088, CN364698
    Consensus CDS
    CCDS33686.1
    UniProtKB/Swiss-Prot
    A8K9C8, B4DXP3, Q92611
    Related
    ENSP00000256497.4, ENST00000256497.9
    Conserved Domains (1) summary
    pfam01532
    Location:137 → 582
    Glyco_hydro_47; Glycosyl hydrolase family 47

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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    5187707..5219958
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011534272.3 → XP_011532574.1  ER degradation-enhancing alpha-mannosidase-like protein 1 isoform X3

    See identical proteins and their annotated locations for XP_011532574.1

    Conserved Domains (1) summary
    pfam01532
    Location:16 → 422
    Glyco_hydro_47; Glycosyl hydrolase family 47

  2. XM_047449264.1 → XP_047305220.1  ER degradation-enhancing alpha-mannosidase-like protein 1 isoform X1

    Related
    ENST00000465369.5

  3. XM_047449265.1 → XP_047305221.1  ER degradation-enhancing alpha-mannosidase-like protein 1 isoform X2

  4. XM_047449266.1 → XP_047305222.1  ER degradation-enhancing alpha-mannosidase-like protein 1 isoform X4

  5. XM_047449267.1 → XP_047305223.1  ER degradation-enhancing alpha-mannosidase-like protein 1 isoform X4

RNA

  1. XR_007095771.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    5181638..5213889
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054348510.1 → XP_054204485.1  ER degradation-enhancing alpha-mannosidase-like protein 1 isoform X3

  2. XM_054348508.1 → XP_054204483.1  ER degradation-enhancing alpha-mannosidase-like protein 1 isoform X1

  3. XM_054348509.1 → XP_054204484.1  ER degradation-enhancing alpha-mannosidase-like protein 1 isoform X2

  4. XM_054348512.1 → XP_054204487.1  ER degradation-enhancing alpha-mannosidase-like protein 1 isoform X4

  5. XM_054348511.1 → XP_054204486.1  ER degradation-enhancing alpha-mannosidase-like protein 1 isoform X4

RNA

  1. XR_008486860.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q92611.1 GenPept UniProtKB/Swiss-Prot:Q92611

Gene LinkOut

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