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EDEM3 Gene

protein-coding   GIFtS: 50

GC01M182925
ER degradation enhancer, mannosidase alpha-like 3
(Previous name: chromosome 1 open reading frame 22 )
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database
(Previous symbol: C1orf22)
Services    
(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc , and/or 7Ensembl, 8miRBase)
About This Section

Aliases
C1orf22 2, 3
Descriptions
ER degradation enhancer, mannosidase alpha-like 3 2
ER degradation-enhancing -mannosidase-like protein 3 2
chromosome 1 open reading frame 22 1
External Ids
HGNC: 167871
Entrez Gene: 802672
UniProtKB: Q9BZQ63
Ensembl: ENSG000001164067
Search outside databases for aliases for EDEM3 gene

(According to Entrez Gene, Wikipedia's Gene Wiki,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

EntrezGene summary for EDEM3:
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]

UniProtKB/Swiss-Prot: EDEM3_HUMAN, Q9BZQ6
Function: Involved in endoplasmic reticulum-associated degradation (ERAD). Accelerates the
glycoprotein ERAD by proteasomes. This process depends on mannose-trimming from the N-glycans.
Seems to have alpha 1,2-mannosidase activity (By similarity)

Gene Wiki entry for EDEM3

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 36),
and/or miRBase,
Genomic Views according to UCSC and Ensembl, Transcription factor binding sites according to SABiosciences)
About This Section

Genomic View:
UCSC Golden Path with GeneCards custom track

 Transcription factor binding sites upstream to the EDEM3 gene  

Entrez Gene cytogenetic band: 1q24-q25   Ensembl cytogenetic band:  1q25.3   HGNC cytogenetic band: 1q25

EDEM3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)

GeneLoc gene densities for chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01M182925:     (about GC identifiers)

Start:
182,926,260 bp from pter
End:
182,990,670 bp from pter
Size:
64,411 bases
Orientation:
minus strand
RefSeq DNA sequence:
NC_000001.9  NT_004487.18  
(According to 1UniProtKB, and/or Ensembl, Phosphorylation sites according to 2Phosphosite, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Enzo Life Sciences, Abnova, OriGene and/or, Abcam,
Biochemical Assays by Invitrogen, Millipore, R&D Systems, Cell Signaling Technology, and/or Enzo Life Sciences, Ontologies according to Gene Ontology Consortium 01 Apr 2009 and Entrez Gene, Antibodies by Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Cell Signaling Technology, Abcam, Abnova, and/or Novus Biologicals)
About This Section

UniProtKB/Swiss-Prot: EDEM3_HUMAN, Q9BZQ6 (See protein sequence)
Recommended Name: ER degradation-enhancing alpha-mannosidase-like 3 precursor  
Size: 932 amino acids; 104664 Da
Subcellular location: Endoplasmic reticulum lumen (By similarity)
Secondary accessions: B2RCH6 Q0VGM5 Q5TEZ0 Q9HCW1 Q9UFV7

Post-translational modifications:

  • N-glycosylated (By similarity)1
  • View phosphorylation sites using PhosphoSite2


  • REFSEQ proteins: NP_079467.3  

    ENSEMBL proteins: 
    ENSP00000240560 ENSP00000318147 ENSP00000356482 


    Human Recombinant Proteins 
    Browse Drug Discovery Central at Invitrogen for human recombinant proteins
    Browse Purified and Recombinant Proteins at Millipore
    Browse Human Recombinant Proteins at Sigma-Aldrich  
    Browse R&D Systems for human recombinant proteins
    Browse recombinant and purified proteins available from Enzo Life Sciences
    Recombinant Proteins from Abcam (EDEM3)
    Human Recombinant Proteins from Abnova (C1orf22)
                    Browse Origene for full length recombinant human proteins expressed in human HEK293 cells 

    3 Gene Ontology (GO) cellular component terms (links to tree view):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005783 endoplasmic reticulum IEA--
    GO:0005788 endoplasmic reticulum lumen IEA--
    GO:0016020 membrane IEA--
    About this table

    Antibodies for EDEM3: 
    Browse Antibodies Central at Invitrogen
    Browse Millipore's Extensive Line of Mono- and Polyclonal Antibodies
    Sigma-Aldrich Antibodies for EDEM3
    Browse R&D Systems for Antibodies
    Antibodies from Abcam (EDEM3), each with their AbpromiseSM
    Browse Abnova for Monoclonal and Polyclonal Antibodies
    Search Novus for antibodies for EDEM3

    Assays for EDEM3: 
    Browse Invitrogen for biochemical assays
    Browse Kits and Assays available from Millipore
    Browse R&D Systems for biochemical assays
    Browse biochemical assays available from Enzo Life Sciences

    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    3 InterPro domains/families:
     IPR001382 Glyco_hydro_47
     IPR003137 PA
     IPR000886 ER_targeting_sequence


       GeneDecks  EDEM3 for the domains selected above  
    About GeneDecksing

    Graphical View of Domain Structure for InterPro Entry Q9BZQ6

    ProtoNet protein and cluster: Q9BZQ6

    1 Blocks protein family: IPB001382 Glycosyl hydrolase family 47 signature

    UniProtKB/Swiss-Prot: EDEM3_HUMAN, Q9BZQ6
    Domain: Contains a protease-associated domain (PA) of unknown function
    Similarity: Belongs to the glycosyl hydrolase 47 family
    Similarity: Contains 1 PA (protease associated) domain

    (According to MGI Jun 06 2009, UniProtKB, IUBMB,and/or Genatlas,
    shRNA from OriGene, Sigma-Aldrich, RNAi from Sigma-Aldrich,
    RNAi Products, Clones, and Q-PCR Products from Invitrogen, Millipore, OriGene, and/or Abnova, siRNAs from Applied Biosystems, SYBR primers from OriGene, Cell-based Assays from Millipore, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
    About This Section

    Inhib.
    RNA:
    Invitrogen RNAi Products for gene knock-down (EDEM3)
    Browse for Gene Knock-down Tools from Millipore
    Abnova Chimera RNAi Products for Gene knock-down (C1orf22)
                  OriGene 29mer shRNA kit in GFP-retroviral vector: NM_025191

                  Applied Biosystems Silencer® siRNAs for EDEM3

                  Sigma-Aldrich siRNA for EDEM3  
                         Sigma-Aldrich shRNA for EDEM3  
                         Explore Sigma-Aldrich super-pooled esiRNAs  

    Clones:Invitrogen Clones for EDEM3
    Browse Clones for the Expression of Recombinant Proteins Available from Millipore
                  OriGene GFP tagged cDNA clone in CMV expression vector: NM_025191
                                     Myc/DDK tagged cDNA clone in CMV expression vector: NM_025191
                                     untagged cDNA clones in CMV expression vector (see all 2): NM_025191 

    Primers: Browse Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers
                  OriGene genome-wide validated SYBR primer pairs: NM_025191

    UniProtKB/Swiss-Prot: EDEM3_HUMAN, Q9BZQ6
    Function: Involved in endoplasmic reticulum-associated degradation (ERAD). Accelerates the
    glycoprotein ERAD by proteasomes. This process depends on mannose-trimming from the N-glycans.
    Seems to have alpha 1,2-mannosidase activity (By similarity)

    2 Gene Ontology (GO) molecular function terms (links to tree view):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0004571 mannosyl-oligosaccharide 1,2-alpha-mannosidase activity IEA--
    GO:0005509 calcium ion binding IEA--
    About this table

    (Pathways according to Invitrogen (maps by GeneGo), Millipore, Cell Signaling Technology, Sigma-Aldrich, KEGG and/or UniProtKB,
    Sets of similar genes according to GeneDecks, Proteins Network according to SABiosciences, Interactions according to 1UniProtKB, 2MINT, and/or 3STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
    About This Section



    1 Interacting protein for EDEM3 (ENSP000003564823) via UniProtKB, MINT, and/or STRING
    InteractantInteraction Details
    GeneCardExternal ID(s)
    CANXENSP000002474613STRING (score=.741)
    About this table

    1 Gene Ontology (GO) biological process term (links to tree view):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006986 response to unfolded protein IEA--
    About this table
    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, Sigma-Aldrich, Tocris Bioscience, and/or Novoseek and Drugs according to Enzo Life Sciences and/or PharmGKB)
    About This Section

    Browse drugs & compounds from Enzo Life Sciences
    Browse Small Molecules at Sigma-Aldrich

    Browse Tocris compounds for EDEM3

    (GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 219 Homo sapiens; Jun 2 2009) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView,
    non coding RNAs according to RNAdb,
    ESTs according to GeneTide,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from Invitrogen, Millipore, and/or Abnova,
    siRNAs from Applied Biosystems, Sigma-Aldrich,
    shRNA from Sigma-Aldrich, OriGene,
    Tagged/untagged cDNA clones from OriGene,
    Expression Assays from Applied Biosystems)
    About This Section

    Inhib.
    RNA:
    Invitrogen RNAi Products for gene knock-down (EDEM3)
    Browse for Gene Knock-down Tools from Millipore
    Abnova Chimera RNAi Products for Gene knock-down (C1orf22)
                  OriGene 29mer shRNA kit in GFP-retroviral vector: NM_025191

                  Sigma-Aldrich siRNA for EDEM3  
                         Sigma-Aldrich shRNA for EDEM3  
                         Explore Sigma-Aldrich super-pooled esiRNAs  

    Applied Biosystems Silencer® siRNAs: 

    NM_025191  

    REFSEQ mRNAs for EDEM3 gene: 

    NM_025191.3   

    Applied Biosystems TaqMan ® Gene Expression Assays: 

    NM_025191  

                  OriGene GFP tagged cDNA clone in CMV expression vector: NM_025191
                                     Myc/DDK tagged cDNA clone in CMV expression vector: NM_025191
                                     untagged cDNA clones in CMV expression vector (see all 2): NM_025191 

    Additional cDNA sequence: 

    AF288393.1 AK000945.1 AK225171.1 AK315118.1 AL117441.1 BC016464.1 BC105586.1 BC144149.1 
    BC144150.1 

    8 DOTS entries:

    DT.100779074  DT.113172  DT.100779075  DT.40263182  DT.121374605  DT.95298685  DT.75163364  DT.121374590 

    24/151 AceView cDNA sequences (see all 151 ):

    AI378621 CD723421 AA505824 AI288392 BC016464 BF448323 R98214 AA716418 
    AI289403 BM983602 BM971493 BM789132 BE219441 CK429568 AI474620 AI561130 
    AI522026 AU130604 AK000945 BF002983 AI364612 AA256323 CN483685 BP354408 

    highest scoring ESTs for EDEM3:

    AA182647 AF288393 AI887728 AL037444 BG107025 AA054934 AA055144 AA094801 AA182483 AA182760 

    Unigene Cluster for EDEM3:

    ER degradation enhancer, mannosidase alpha-like 3
    Hs.523811  [show with all ESTs]
    Unigene Representative Sequence: NM_025191


    GeneLoc Exon Structure

    3 Alternative Splicing Database (ASD) splice patterns (SP) for EDEM3

    ExUns: 1a · 1b ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6a · 6b ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20
    SP1:                    -                             -                                                                                       
    SP2:                                                                                                                                          
    SP3:              -     -                                                                                                                     

    About this scheme

    ECgene alternative splicing isoforms for EDEM3

    3 Ensembl transcripts including schematic representations:
    ENST00000240560  ENST00000318130  ENST00000367512  
    (Experimental results according to 1GeneNote and GNF BioGPS,
    probe sets-to-genes annotations according to 2GeneAnnot , 3GeneTide , Sets of similar genes according to GeneDecks, Electronic Northern calculations according to data from UniGene (Build 219 Homo sapiens), SAGE tags according to CGAP, plus additional links to SOURCE, and/or GNF BioGPS, and/or EXPOLDB, and/or UniProtKB,
    Expression Assays from Applied Biosystems )
    About This Section

    EDEM3 expression in normal and diseased human tissues

     Applied Biosystems TaqMan ® Gene Expression Assays for EDEM3

    1 / 2 / 3

    9 probe-sets matching EDEM3 gene


    Affymetrix
    probe-set
    Array  GeneAnnot data GeneNote data GeneTide data
    # genes Sensitivity Specificity Correlation Length Gb_Accession Consensus Uniqueness Score Rank

    65608_at2, 3 U95-C 1 1.00 1.00 0.85 1.40 AI887728 0.80 1.00 0.91 1
    90857_at2, 3 U95-E 1 0.94 1.00 0.67 0.80 AA182647 0.80 1.00 0.91 1

    59633_at2, 3 U95-B 2 0.94 0.97 0.87 0.81 AL037444 0.80 1.00 0.91 1

    223243_s_at2, 3 U133-B 1 1.00 1.00 -- -- BF439488 0.60 1.00 0.82 1

    220926_s_at2, 3 U133-A 1 1.00 1.00 -- -- NM_025191 0.60 1.00 0.82 1

    220342_x_at2, 3 U133-A 1 1.00 1.00 -- -- NM_017992 0.20 1.00 0.72 1

    223243_s_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --

    220926_s_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --

    220342_x_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --
    GeneDecks  EDEM3 for binary patterns associated with the probe-sets selected above  
    About GeneDecksing
    About this table    
    Data from (Publications) and GNF BioGPS
        About these images
    About these images

    CGAP SAGE TAG: AAGAAAGCTC

    SOURCE GeneReport for Unigene cluster: Hs.523811
    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD and/or 5MGI Jun 06 2009, with possible further links to Flybase and/or WormBase, Gene Trees according to Ensembl)
    About This Section


    Orthologs for EDEM3 gene from 5/12 species (see all 12 )
    Organism Gene Locus Description Human
    Similarity
    NCBI accessions
    dog
    (Canis familiaris)
    EDEM31   -- ER degradation enhancer, mannosidase alpha-like 3 95.16(n)
    97.86(a)
    480040  XM_854673.1  XP_859766.1 
    chimpanzee
    (Pan troglodytes)
    EDEM31   -- ER degradation enhancer, mannosidase alpha-like 3 99.74(n)
    99.66(a)
    457578  XM_514054.2  XP_514054.2 
    cow
    (Bos taurus)
    EDEM31   -- ER degradation enhancer, mannosidase alpha-like 3 93.69(n)
    96.62(a)
    519058  XM_597266.3  XP_597266.3 
    rat
    (Rattus norvegicus)
    Edem31   -- ER degradation enhancer, mannosidase alpha-like 3 88.59(n)
    94.48(a)
    289085  XM_222721.4  XP_222721.4 
    mouse
    (Mus musculus)
    Edem31, 5 15
    ER degradation enhancer, mannosidase alpha-like 31, 5 89.06(n)1
    95.38(a)1
    669671  NM_001039644.11  NP_001034733.11 
     AB1883425  AK0036525  (see all 15)
    About this table        Species with no ortholog for EDEM3

    ENSEMBL Gene Tree for EDEM3
    (Paralogs according to 1HomoloGene
    and 2Ensembl, Pseudogenes according to 3Pseudogene.org)
    About This Section

    Paralogs for EDEM3 gene
    EDEM22  EDEM12  

    (According to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, and UniProtKB, Linkage Disequilibrium by HapMap, Genotyping Reagents from Applied Biosystems)
    About This Section


    10/262 NCBI SNPs in EDEM3 are shown (see all 262 )
    (Click for Applied Biosystems TaqMan ® Genotyping Assay)  (see all 69)
    ABGenomic DataTranscription DataAllele Frequencies
    SNP IDValidChr 1 posSequenceRecsAA
    Chg
    TypeMoreRecsAllele
    freq
    PopTotal
    sample
    More
    ------------
    rs94253431,2
    A,C,F,H182930160(+) ATGAAA/CTCTGT 1 I/S mis112Minor allele frequency- C:0.34EU EA WA 1256
    rs10615081,2
    A,C,F,H182928804(-) TGATAG/AAACTG 1 -- ut31 ese310Minor allele frequency- A:0.45MN NA EU EA WA 916
    rs10462391,2
    A,C,F,H182926828(-) TAAAAT/AGAAAA 1 -- ut31 trp38Minor allele frequency- A:0.43MN NA EU EA WA 738
    rs8615751,2
    A,C,F,H182991722(+) AGCAGT/CATTCG 1 -- ng31 tfbs34Minor allele frequency- C:0.49EU EA WA 412
    rs66631781,2
    A,C,F,H182928265(+) TAACTA/GCAATA 1 -- ut317Minor allele frequency- G:0.34NA EU EA WA 534
    --
    rs8615771,2
    C182992244(+) cagtgG/Tctcaa 1 -- ng310--------
    rs8615761,2
    A182992020(+) ATGTCC/TTAATG 1 -- ng310--------
    --
    rs66906031,2
    C182929282(+) CAATGA/GGCAAA 1 -- ut31 ese30--------
    --
    rs94253411,2
    A182925941(+) ATATAA/TAATGT 1 -- ng510--------
    rs37367571,2
    A,C,F,H182944087(+) GCGTCA/GATTGA 1 I/I syn1 ese312Minor allele frequency- G:0.36EA NA EU WA 2434
    About this table

    HapMap Linkage Disequilibrium images for EDEM3 (up to first 250kb)

    (in which this Gene is Involved, According to OMIM, UniProtKB, PharmGKB, Genatlas, GeneTests, Blood group antigen gene mutations by BGMUT, HGMD, GAD, HuGE Navigator, BCGD, and/or TGDB.)
    About This Section

    OMIM: 610214

    (Possibly Related Articles in Doctor's Guide)
    About This Section

      --

    (in PubMed. Associations of this gene to articles via 1Novoseek, 2HGNC, 3Entrez Gene, 4UniProtKB/Swiss-Prot, 5UniProtKB/TrEMBL, 6GAD, and/or 7PharmGKB)
    About This Section

    10/13 PubMed articles for EDEM3 gene (see all 13 ):
    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section

     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)
    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, and/or H-InvDB)
    About This Section

    Entrez Gene: 80267 HGNC: 16787 AceView: C1orf22 Ensembl:ENSG00000116406 euGenes: HUgn80267
    ECgene: EDEM3 H-InvDB: EDEM3
    (According to HUGE)
    About This Section

      --
    (According to ATLAS, HORDE, IMGT, MTDB, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section

      --
    (Available from WIS Yeda, Salk, Tufts)
    About This Section

      --
    (Reagents available from Applied Biosystems, Antibodies and assays by Cell Signaling Technology, Abcam, Novus Biologicals,
    Sigma-Aldrich, R&D Systems, Millipore, Abnova, and/or Invitrogen, Clones available from OriGene,and/or Invitrogen, Drugs and/or compounds by Sigma-Aldrich,
    Enzo Life Sciences, and/or Tocris Bioscience)
    About This Section



    Products for EDEM3:
     TaqMan ® Gene Expression Assays
     TaqMan ® Genotyping Assays
      Free SNP selection tool



      Invitrogen iPath Pathways  Invitrogen BLOCK-iT™ RNAi
      Invitrogen Antibodies  Invitrogen Assays
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      Invitrogen Proteins / Assays / Screening Services  Search Invitrogen catalog for EDEM3-related products

     Millipore Custom Antibody & Bulk Services
     Millipore Preclinical / Clinical Development Services
     Millipore Immunoassay Services
     Millipore Target Screening & Profiling Services


     Predesigned and custom siRNAs for EDEM3 Antibodies for EDEM3
     Explore super-pooled esiRNAs Browse proteins at Sigma-Aldrich
     Lentivirus-delivered shRNAs for EDEM3 Browse small molecules at Sigma-Aldrich
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     Search Novus for antibodies for EDEM3

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