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Aliases for EDEM3 Gene

Aliases for EDEM3 Gene

  • ER Degradation Enhancing Alpha-Mannosidase Like Protein 3 2 3 5
  • ER Degradation Enhancer, Mannosidase Alpha-Like 3 2 3
  • Alpha-1,2-Mannosidase EDEM3 3 4
  • C1orf22 3 4
  • ER Degradation-Enhancing Alpha-Mannosidase-Like Protein 3 3
  • ER Degradation-Enhancing -Mannosidase-Like Protein 3 3
  • ER Degradation-Enhancing Alpha-Mannosidase-Like 3 3
  • Chromosome 1 Open Reading Frame 22 2
  • EC 3.2.1.113 4

External Ids for EDEM3 Gene

Previous HGNC Symbols for EDEM3 Gene

  • C1orf22

Previous GeneCards Identifiers for EDEM3 Gene

  • GC01M182925
  • GC01M155896

Summaries for EDEM3 Gene

Entrez Gene Summary for EDEM3 Gene

  • 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]

GeneCards Summary for EDEM3 Gene

EDEM3 (ER Degradation Enhancing Alpha-Mannosidase Like Protein 3) is a Protein Coding gene. Among its related pathways are Protein processing in endoplasmic reticulum and Transport to the Golgi and subsequent modification. GO annotations related to this gene include calcium ion binding and glycoprotein endo-alpha-1,2-mannosidase activity. An important paralog of this gene is EDEM1.

UniProtKB/Swiss-Prot for EDEM3 Gene

  • Involved in endoplasmic reticulum-associated degradation (ERAD). Accelerates the glycoprotein ERAD by proteasomes, by catalyzing mannose trimming from Man8GlcNAc2 to Man7GlcNAc2 in the N-glycans. Seems to have alpha 1,2-mannosidase activity (By similarity).

Gene Wiki entry for EDEM3 Gene

Additional gene information for EDEM3 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for EDEM3 Gene

Genomics for EDEM3 Gene

Regulatory Elements for EDEM3 Gene

Enhancers for EDEM3 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH01H184744 1.4 Ensembl ENCODE dbSUPER 22.5 +8.4 8401 3.2 HDAC1 PKNOX1 ATF1 FOXA2 TBL1XR1 BMI1 ZNF766 GATA2 FOS ATF7 EDEM3 FAM129A GC01M184689
GH01H184752 1.4 FANTOM5 ENCODE 20 +0.5 497 3.5 HDGF PKNOX1 FOXA2 ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF766 EDEM3 SWT1 GC01M184689
GH01H184836 1.3 Ensembl ENCODE dbSUPER 15.4 -83.0 -82966 3.3 GTF2F1 TBP NFIB JUN ZSCAN4 MAX BMI1 RAD21 RFX5 CTBP1 FAM129A EDEM3 RNF2 RNU7-13P GC01P184860
GH01H185374 1.4 FANTOM5 Ensembl ENCODE 12.8 -621.3 -621297 3.1 PKNOX1 STAT1 ZNF740 ETV1 TSC22D4 DPF2 ZNF354B GABPA BCL11A ZNF341 IVNS1ABP EDEM3 TPR RNU7-183P C1orf27 FAM129A SWT1 LOC100422414 RNF2 TRMT1L
GH01H184663 1 Ensembl ENCODE 16.1 +90.7 90728 0.9 CTCF ZBTB40 ZNF2 RAD21 CC2D1A GLIS2 PATZ1 SMC3 ZNF143 KLF8 EDEM3 LOC105371648 GC01P184689
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around EDEM3 on UCSC Golden Path with GeneCards custom track

Promoters for EDEM3 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000017039 213 2601 HDGF PKNOX1 FOXA2 ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF766

Genomic Locations for EDEM3 Gene

Genomic Locations for EDEM3 Gene
chr1:184,690,231-184,754,913
(GRCh38/hg38)
Size:
64,683 bases
Orientation:
Minus strand
chr1:184,659,365-184,724,047
(GRCh37/hg19)

Genomic View for EDEM3 Gene

Genes around EDEM3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
EDEM3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for EDEM3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for EDEM3 Gene

Proteins for EDEM3 Gene

  • Protein details for EDEM3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9BZQ6-EDEM3_HUMAN
    Recommended name:
    ER degradation-enhancing alpha-mannosidase-like protein 3
    Protein Accession:
    Q9BZQ6
    Secondary Accessions:
    • B2RCH6
    • B7ZLZ2
    • Q0VGM5
    • Q5TEZ0
    • Q7L2Y5
    • Q9HCW1
    • Q9UFV7

    Protein attributes for EDEM3 Gene

    Size:
    932 amino acids
    Molecular mass:
    104664 Da
    Cofactor:
    Name=Ca(2+); Xref=ChEBI:CHEBI:29108;
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=AAG60613.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=BAG37573.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for EDEM3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for EDEM3 Gene

Post-translational modifications for EDEM3 Gene

  • Ubiquitination at isoforms=2435
  • Glycosylation at posLast=118118, posLast=195195, posLast=504504, isoforms=2511, posLast=810810, isoforms=2814, and isoforms=2900
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for EDEM3 Gene

Domains & Families for EDEM3 Gene

Gene Families for EDEM3 Gene

Human Protein Atlas (HPA):
  • Enzymes
  • Predicted intracellular proteins
  • Predicted secreted proteins

Protein Domains for EDEM3 Gene

Suggested Antigen Peptide Sequences for EDEM3 Gene

Graphical View of Domain Structure for InterPro Entry

Q9BZQ6

UniProtKB/Swiss-Prot:

EDEM3_HUMAN :
  • Contains a protease-associated domain (PA) of unknown function.
  • Belongs to the glycosyl hydrolase 47 family.
Domain:
  • Contains a protease-associated domain (PA) of unknown function.
Family:
  • Belongs to the glycosyl hydrolase 47 family.
genes like me logo Genes that share domains with EDEM3: view

Function for EDEM3 Gene

Molecular function for EDEM3 Gene

UniProtKB/Swiss-Prot CatalyticActivity:
Hydrolysis of the terminal (1->2)-linked alpha-D-mannose residues in the oligo-mannose oligosaccharide Man(9)(GlcNAc)(2).
UniProtKB/Swiss-Prot Function:
Involved in endoplasmic reticulum-associated degradation (ERAD). Accelerates the glycoprotein ERAD by proteasomes, by catalyzing mannose trimming from Man8GlcNAc2 to Man7GlcNAc2 in the N-glycans. Seems to have alpha 1,2-mannosidase activity (By similarity).

Enzyme Numbers (IUBMB) for EDEM3 Gene

Phenotypes From GWAS Catalog for EDEM3 Gene

Gene Ontology (GO) - Molecular Function for EDEM3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004571 mannosyl-oligosaccharide 1,2-alpha-mannosidase activity TAS --
GO:0005509 calcium ion binding IEA --
GO:0016787 hydrolase activity IEA --
GO:0016798 hydrolase activity, acting on glycosyl bonds IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with EDEM3: view

Phenotypes for EDEM3 Gene

genes like me logo Genes that share phenotypes with EDEM3: view

miRNA for EDEM3 Gene

miRTarBase miRNAs that target EDEM3

Clone Products

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for EDEM3 Gene

Localization for EDEM3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for EDEM3 Gene

Endoplasmic reticulum lumen.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for EDEM3 gene
Compartment Confidence
endoplasmic reticulum 5
mitochondrion 3
cytosol 2
extracellular 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Endoplasmic reticulum (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for EDEM3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005783 endoplasmic reticulum IBA --
GO:0005788 endoplasmic reticulum lumen IEA --
GO:0016020 membrane IEA --
GO:0044322 endoplasmic reticulum quality control compartment TAS --
genes like me logo Genes that share ontologies with EDEM3: view

Pathways & Interactions for EDEM3 Gene

genes like me logo Genes that share pathways with EDEM3: view

UniProtKB/Swiss-Prot Q9BZQ6-EDEM3_HUMAN

  • Pathway: Protein modification; protein glycosylation.

Gene Ontology (GO) - Biological Process for EDEM3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006486 protein glycosylation IEA --
GO:0006491 N-glycan processing IBA --
GO:0006516 glycoprotein catabolic process IEA --
GO:0006986 response to unfolded protein IEA --
GO:0008152 metabolic process IEA --
genes like me logo Genes that share ontologies with EDEM3: view

No data available for SIGNOR curated interactions for EDEM3 Gene

Drugs & Compounds for EDEM3 Gene

No Compound Related Data Available

Transcripts for EDEM3 Gene

Unigene Clusters for EDEM3 Gene

ER degradation enhancer, mannosidase alpha-like 3:
Representative Sequences:

Clone Products

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

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: - -

Relevant External Links for EDEM3 Gene

GeneLoc Exon Structure for
EDEM3
ECgene alternative splicing isoforms for
EDEM3

Expression for EDEM3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for EDEM3 Gene

Protein differential expression in normal tissues from HIPED for EDEM3 Gene

This gene is overexpressed in Stomach (38.3) and Pancreas (7.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for EDEM3 Gene



NURSA nuclear receptor signaling pathways regulating expression of EDEM3 Gene:

EDEM3

SOURCE GeneReport for Unigene cluster for EDEM3 Gene:

Hs.523811

Evidence on tissue expression from TISSUES for EDEM3 Gene

  • Nervous system(4.4)
  • Liver(4.3)
  • Lung(4.2)
genes like me logo Genes that share expression patterns with EDEM3: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for EDEM3 Gene

Orthologs for EDEM3 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for EDEM3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia EDEM3 33 34
  • 99.68 (n)
dog
(Canis familiaris)
Mammalia EDEM3 33 34
  • 95.06 (n)
cow
(Bos Taurus)
Mammalia EDEM3 33 34
  • 93.61 (n)
mouse
(Mus musculus)
Mammalia Edem3 33 16 34
  • 89 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia EDEM3 34
  • 89 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Edem3 33
  • 88.54 (n)
oppossum
(Monodelphis domestica)
Mammalia EDEM3 34
  • 88 (a)
OneToOne
chicken
(Gallus gallus)
Aves EDEM3 33 34
  • 80.72 (n)
lizard
(Anolis carolinensis)
Reptilia EDEM3 34
  • 84 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia edem3 33
  • 73.86 (n)
zebrafish
(Danio rerio)
Actinopterygii EDEM3 34
  • 69 (a)
OneToOne
edem3 33
  • 66.21 (n)
fruit fly
(Drosophila melanogaster)
Insecta Edem2 33 34
  • 54.8 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP008749 33
  • 53.54 (n)
worm
(Caenorhabditis elegans)
Secernentea ZC506.1 33 34
  • 55.93 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes MNL1 34
  • 27 (a)
OneToMany
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.2482 33
Species where no ortholog for EDEM3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for EDEM3 Gene

ENSEMBL:
Gene Tree for EDEM3 (if available)
TreeFam:
Gene Tree for EDEM3 (if available)

Paralogs for EDEM3 Gene

Paralogs for EDEM3 Gene

(6) SIMAP similar genes for EDEM3 Gene using alignment to 4 proteins:

genes like me logo Genes that share paralogs with EDEM3: view

Variants for EDEM3 Gene

Sequence variations from dbSNP and Humsavar for EDEM3 Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type
rs1000063763 -- 184,735,482(+) CCCAT(G/T)AGATG intron-variant
rs1000096989 -- 184,692,004(+) GAAAT(C/T)AGGTT nc-transcript-variant, utr-variant-3-prime
rs1000126681 -- 184,691,741(+) TTTTT(A/T)GACGA nc-transcript-variant, utr-variant-3-prime
rs1000135027 -- 184,738,100(+) AACAT(C/T)TGTCA intron-variant
rs1000149178 -- 184,705,379(+) GATGA(A/T)GAATA intron-variant

Structural Variations from Database of Genomic Variants (DGV) for EDEM3 Gene

Variant ID Type Subtype PubMed ID
nsv832048 CNV loss 17160897
nsv832037 CNV gain 17160897
nsv508053 OTHER sequence alteration 20534489
nsv1009529 CNV loss 25217958
esv2720195 CNV deletion 23290073
esv2720184 CNV deletion 23290073
dgv478n100 CNV loss 25217958

Variation tolerance for EDEM3 Gene

Residual Variation Intolerance Score: 15.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.47; 64.24% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for EDEM3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
EDEM3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for EDEM3 Gene

Disorders for EDEM3 Gene

Relevant External Links for EDEM3

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
EDEM3

No disorders were found for EDEM3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for EDEM3 Gene

Publications for EDEM3 Gene

  1. EDEM2 initiates mammalian glycoprotein ERAD by catalyzing the first mannose trimming step. (PMID: 25092655) Ninagawa S … Mori K (The Journal of cell biology 2014) 3 4 60
  2. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory SG … Prigmore E (Nature 2006) 3 4 60
  3. A novel stress-induced EDEM variant regulating endoplasmic reticulum-associated glycoprotein degradation. (PMID: 15579471) Olivari S … Molinari M (The Journal of biological chemistry 2005) 2 3 60
  4. Human EDEM2, a novel homolog of family 47 glycosidases, is involved in ER-associated degradation of glycoproteins. (PMID: 15537790) Mast SW … Moremen KW (Glycobiology 2005) 2 3 60
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 60

Products for EDEM3 Gene

Sources for EDEM3 Gene

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