Human Gene EDEM2 (uc002xbo.2) Description and Page Index
  Description: Homo sapiens ER degradation enhancer, mannosidase alpha-like 2 (EDEM2), transcript variant 1, mRNA.
RefSeq Summary (NM_018217): In the endoplasmic reticulum (ER), misfolded proteins are retrotranslocated to the cytosol and degraded by the proteasome in a process known as ER-associated degradation (ERAD). EDEM2 belongs to a family of proteins involved in ERAD of glycoproteins (Mast et al., 2005 [PubMed 15537790]).[supplied by OMIM, Mar 2008].
Transcript (Including UTRs)
   Position: hg19 chr20:33,703,160-33,735,161 Size: 32,002 Total Exon Count: 11 Strand: -
Coding Region
   Position: hg19 chr20:33,703,236-33,735,061 Size: 31,826 Coding Exon Count: 11 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr20:33,703,160-33,735,161)mRNA (may differ from genome)Protein (578 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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neXtProtOMIMPubMedReactomeStanford SOURCETreefam
UniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: EDEM2_HUMAN
DESCRIPTION: RecName: Full=ER degradation-enhancing alpha-mannosidase-like 2; Flags: Precursor;
FUNCTION: Involved in endoplasmic reticulum-associated degradation (ERAD) that targets misfolded glycoproteins for degradation in an N-glycan-dependent manner. It lacks mannosidase activity. Extracts misfolded glycoproteins, but not glycoproteins undergoing productive folding, from the calnexin cycle.
SUBCELLULAR LOCATION: Secreted. Endoplasmic reticulum lumen.
TISSUE SPECIFICITY: Expressed ubiquitously in all tissues tested with slightly higher levels detected in small intestine and peripheral blood leukocytes and weakest levels in brain and skeletal muscle.
INDUCTION: Up-regulated by the unfolded protein response (UPR) via the XBP1 transcription factor.
PTM: Glycosylated.
SIMILARITY: Belongs to the glycosyl hydrolase 47 family.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): EDEM2
CDC HuGE Published Literature: EDEM2
Positive Disease Associations: Protein C
Related Studies:
  1. Protein C
    Weihong Tang et al. Blood 2010, Genome-wide association study identifies novel loci for plasma levels of protein C: the ARIC study., Blood. [PubMed 20802025]

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 16.82 RPKM in Spleen
Total median expression: 371.59 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -46.30100-0.463 Picture PostScript Text
3' UTR -7.2676-0.096 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR001382 - Glyco_hydro_47

Pfam Domains:
PF01532 - Glycosyl hydrolase family 47

SCOP Domains:
48225 - Seven-hairpin glycosidases

ModBase Predicted Comparative 3D Structure on Q9BV94
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserGenome BrowserGenome BrowserGenome BrowserNo ortholog
Gene DetailsGene Details Gene DetailsGene Details 
Gene SorterGene Sorter Gene SorterGene Sorter 
 RGDEnsemblFlyBaseWormBase 
 Protein SequenceProtein SequenceProtein SequenceProtein Sequence 
 AlignmentAlignmentAlignmentAlignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003824 catalytic activity
GO:0004571 mannosyl-oligosaccharide 1,2-alpha-mannosidase activity
GO:0005509 calcium ion binding

Biological Process:
GO:0006491 N-glycan processing
GO:0006986 response to unfolded protein
GO:0030968 endoplasmic reticulum unfolded protein response
GO:0036509 trimming of terminal mannose on B branch
GO:0036510 trimming of terminal mannose on C branch
GO:0036511 trimming of first mannose on A branch
GO:0036512 trimming of second mannose on A branch
GO:0097466 glycoprotein ERAD pathway
GO:1904154 positive regulation of retrograde protein transport, ER to cytosol
GO:1904382 mannose trimming involved in glycoprotein ERAD pathway

Cellular Component:
GO:0005783 endoplasmic reticulum
GO:0005788 endoplasmic reticulum lumen
GO:0016020 membrane
GO:0044322 endoplasmic reticulum quality control compartment


-  Descriptions from all associated GenBank mRNAs
  AK296878 - Homo sapiens cDNA FLJ60292 complete cds, highly similar to ER degradation-enhancingalpha-mannosidase-like 2 precursor.
AF086313 - Homo sapiens full length insert cDNA clone ZD52B10.
BC016184 - Homo sapiens ER degradation enhancer, mannosidase alpha-like 2, mRNA (cDNA clone MGC:23193 IMAGE:4860424), complete cds.
AY358580 - Homo sapiens clone DNA56870 C20orf31 (UNQ573) mRNA, complete cds.
BC001371 - Homo sapiens ER degradation enhancer, mannosidase alpha-like 2, mRNA (cDNA clone MGC:935 IMAGE:3051376), complete cds.
AK293583 - Homo sapiens cDNA FLJ56055 complete cds, highly similar to ER degradation-enhancingalpha-mannosidase-like 2 precursor.
AK096016 - Homo sapiens cDNA FLJ38697 fis, clone KIDNE2001979.
AK298794 - Homo sapiens cDNA FLJ56127 complete cds, highly similar to ER degradation-enhancingalpha-mannosidase-like 2 precursor.
AK023931 - Homo sapiens cDNA FLJ13869 fis, clone THYRO1001287, weakly similar to MANNOSYL-OLIGOSACCHARIDE ALPHA-1,2-MANNOSIDASE (EC 3.2.1.113).
AY007088 - Homo sapiens clone TCCCIA00097 mRNA sequence.
AK300212 - Homo sapiens cDNA FLJ55524 complete cds, highly similar to ER degradation-enhancingalpha-mannosidase-like 2 precursor.
AK303816 - Homo sapiens cDNA FLJ61531 complete cds, highly similar to ER degradation-enhancingalpha-mannosidase-like 2 precursor.
AK001645 - Homo sapiens cDNA FLJ10783 fis, clone NT2RP4000417, weakly similar to MANNOSYL-OLIGOSACCHARIDE ALPHA-1,2-MANNOSIDASE (EC 3.2.1.113).
KJ899181 - Synthetic construct Homo sapiens clone ccsbBroadEn_08575 EDEM2 gene, encodes complete protein.
CR457266 - Homo sapiens full open reading frame cDNA clone RZPDo834C046D for gene C20orf31, chromosome 20 open reading frame 31; complete cds, incl. stopcodon.
CU674674 - Synthetic construct Homo sapiens gateway clone IMAGE:100017714 5' read EDEM2 mRNA.
JD464282 - Sequence 445306 from Patent EP1572962.
JD337994 - Sequence 319018 from Patent EP1572962.
JD187558 - Sequence 168582 from Patent EP1572962.
JD370544 - Sequence 351568 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9BV94 (Reactome details) participates in the following event(s):

R-HSA-901024 MAN1B1 hydrolyses 1,2-linked mannose (a branch)
R-HSA-901036 MAN1B1 hydrolyses a second 1,2-linked mannose (a branch)
R-HSA-901039 MAN1B1 hydrolyses 1,2-linked mannose (c branch)
R-HSA-901074 MAN1B1,EDEM2 hydrolyse 1,2-linked mannose (b branch)
R-HSA-901032 ER Quality Control Compartment (ERQC)
R-HSA-901042 Calnexin/calreticulin cycle
R-HSA-532668 N-glycan trimming in the ER and Calnexin/Calreticulin cycle
R-HSA-446203 Asparagine N-linked glycosylation
R-HSA-597592 Post-translational protein modification
R-HSA-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: B4DTG9, C20orf31, C20orf49, EDEM2_HUMAN, NM_018217, NP_060687, Q6GU33, Q6IA89, Q6UWZ4, Q9BV94, Q9H4U0, Q9H886, Q9NTL9, Q9NVE6, UNQ573/PRO1135
UCSC ID: uc002xbo.2
RefSeq Accession: NM_018217
Protein: Q9BV94 (aka EDEM2_HUMAN)
CCDS: CCDS13247.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_018217.2
exon count: 11CDS single in 3' UTR: no RNA size: 1918
ORF size: 1737CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3532.00frame shift in genome: no % Coverage: 99.74
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.