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

    Gene ID: 9695, updated on 14-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
    mouse all
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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 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. 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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