Human Gene EDEM3 (ENST00000318130.13_11) from GENCODE V47lift37
  Description: ER degradation enhancing alpha-mannosidase like protein 3, transcript variant 2 (from RefSeq NM_025191.4)
Gencode Transcript: ENST00000318130.13_11
Gencode Gene: ENSG00000116406.20_19
Transcript (Including UTRs)
   Position: hg19 chr1:184,659,371-184,723,992 Size: 64,622 Total Exon Count: 20 Strand: -
Coding Region
   Position: hg19 chr1:184,663,197-184,723,780 Size: 60,584 Coding Exon Count: 20 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:184,659,371-184,723,992)mRNA (may differ from genome)Protein (932 aa)
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-  Comments and Description Text from UniProtKB
  ID: EDEM3_HUMAN
DESCRIPTION: RecName: Full=ER degradation-enhancing alpha-mannosidase-like 3; Flags: Precursor;
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).
SUBCELLULAR LOCATION: Endoplasmic reticulum lumen (By similarity).
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.
SEQUENCE CAUTION: Sequence=AAG60613.1; Type=Erroneous initiation; Sequence=BAG37573.1; Type=Erroneous initiation;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


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

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 11.27 RPKM in Cells - Cultured fibroblasts
Total median expression: 323.20 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 -98.80212-0.466 Picture PostScript Text
3' UTR -888.803826-0.232 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
IPR003137 - Protease-assoc_domain

Pfam Domains:
PF01532 - Glycosyl hydrolase family 47
PF02225 - PA domain

SCOP Domains:
48208 - Six-hairpin glycosidases
48225 - Seven-hairpin glycosidases
52025 - PA domain

ModBase Predicted Comparative 3D Structure on Q9BZQ6
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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 orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
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-  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
GO:0016787 hydrolase activity
GO:0046872 metal ion binding

Biological Process:
GO:0006486 protein glycosylation
GO:0006491 N-glycan processing
GO:0006516 glycoprotein catabolic process
GO:0006986 response to unfolded protein
GO:0030968 endoplasmic reticulum unfolded protein response
GO:0043161 proteasome-mediated ubiquitin-dependent protein catabolic process
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
  AL117441 - Homo sapiens mRNA; cDNA DKFZp434N126 (from clone DKFZp434N126).
AF288393 - Homo sapiens C1orf22 mRNA, complete cds.
AK023095 - Homo sapiens cDNA FLJ13033 fis, clone NT2RP3001126.
BC144149 - Homo sapiens cDNA clone MGC:177686 IMAGE:9052669, complete cds.
BC144150 - Homo sapiens cDNA clone IMAGE:9052670.
AK315118 - Homo sapiens cDNA, FLJ96081.
BC160020 - Synthetic construct Homo sapiens clone IMAGE:100063956, MGC:193135 EDEM3 protein (EDEM3) mRNA, encodes complete protein.
AB385131 - Synthetic construct DNA, clone: pF1KB5599, Homo sapiens EDEM3 gene for ER degradation-enhancing alpha-mannosidase-like 3, complete cds, without stop codon, in Flexi system.
AK225171 - Homo sapiens mRNA for hypothetical protein LOC80267 variant, clone: CBR06182.
BC016464 - Homo sapiens ER degradation enhancer, mannosidase alpha-like 3, mRNA (cDNA clone IMAGE:4152945), partial cds.
JD309174 - Sequence 290198 from Patent EP1572962.
JD378917 - Sequence 359941 from Patent EP1572962.
JD084107 - Sequence 65131 from Patent EP1572962.
JD562849 - Sequence 543873 from Patent EP1572962.
JD304969 - Sequence 285993 from Patent EP1572962.
JD113008 - Sequence 94032 from Patent EP1572962.
JD506551 - Sequence 487575 from Patent EP1572962.
JD130942 - Sequence 111966 from Patent EP1572962.
JD559811 - Sequence 540835 from Patent EP1572962.
JD503927 - Sequence 484951 from Patent EP1572962.
JD360219 - Sequence 341243 from Patent EP1572962.
JD298923 - Sequence 279947 from Patent EP1572962.
JD435257 - Sequence 416281 from Patent EP1572962.
JD083792 - Sequence 64816 from Patent EP1572962.
JD509410 - Sequence 490434 from Patent EP1572962.
JD247892 - Sequence 228916 from Patent EP1572962.
JD280114 - Sequence 261138 from Patent EP1572962.
JD296301 - Sequence 277325 from Patent EP1572962.
JD234883 - Sequence 215907 from Patent EP1572962.
AK000945 - Homo sapiens cDNA FLJ10083 fis, clone HEMBA1002084.
JD040086 - Sequence 21110 from Patent EP1572962.
JD224022 - Sequence 205046 from Patent EP1572962.
JD045867 - Sequence 26891 from Patent EP1572962.
JD269192 - Sequence 250216 from Patent EP1572962.
JD130154 - Sequence 111178 from Patent EP1572962.
JD188296 - Sequence 169320 from Patent EP1572962.
KJ903295 - Synthetic construct Homo sapiens clone ccsbBroadEn_12689 EDEM3 gene, encodes complete protein.
JD483714 - Sequence 464738 from Patent EP1572962.
JD451433 - Sequence 432457 from Patent EP1572962.
JD155658 - Sequence 136682 from Patent EP1572962.
JD535272 - Sequence 516296 from Patent EP1572962.
JD246009 - Sequence 227033 from Patent EP1572962.
JD142894 - Sequence 123918 from Patent EP1572962.
JD346016 - Sequence 327040 from Patent EP1572962.
JD277323 - Sequence 258347 from Patent EP1572962.
JD309732 - Sequence 290756 from Patent EP1572962.
BC105586 - Homo sapiens ER degradation enhancer, mannosidase alpha-like 3, mRNA (cDNA clone IMAGE:4693089), complete cds.
BC070173 - Homo sapiens cDNA clone IMAGE:4694193, with apparent retained intron.
JD377576 - Sequence 358600 from Patent EP1572962.
JD537235 - Sequence 518259 from Patent EP1572962.

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

Protein Q9BZQ6 (Reactome details) participates in the following event(s):

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: B2RCH6, B7ZLZ2, C1orf22, EDEM3_HUMAN, ENST00000318130.1, ENST00000318130.10, ENST00000318130.11, ENST00000318130.12, ENST00000318130.2, ENST00000318130.3, ENST00000318130.4, ENST00000318130.5, ENST00000318130.6, ENST00000318130.7, ENST00000318130.8, ENST00000318130.9, NM_025191, Q0VGM5, Q5TEZ0, Q7L2Y5, Q9BZQ6, Q9HCW1, Q9UFV7, uc317qkj.1, uc317qkj.2
UCSC ID: ENST00000318130.13_11
RefSeq Accession: NM_025191.4
Protein: Q9BZQ6 (aka EDEM3_HUMAN)

-  Gene Model Information
  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.