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ERGIC3 (ERGIC and golgi 3)

Written2014-09Mingsong Wu, Yi Cao
Department of Cell Biology, Genetics, Zunyi Medical University, Guizhou Zunyi 563000, China (MW); Laboratory of Molecular, Experimental Pathology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China (YC)

Abstract Review on ERGIC3, with data on DNA/RNA, on the protein encoded and where the gene is implicated.

Keywords ERGIC3; Erv46.

(Note : for Links provided by Atlas : click)

Identity

Alias_namesSDBCAG84
C20orf47
serologically defined breast cancer antigen 84
chromosome 20 open reading frame 47
Alias_symbol (synonym)CGI-54
PRO0989
NY-BR-84
Erv46
Other aliasdJ477O4.2
HGNC (Hugo) ERGIC3
LocusID (NCBI) 51614
Atlas_Id 42222
Location 20q11.22  [Link to chromosome band 20q11]
Location_base_pair Starts at 35542029 and ends at 35557634 bp from pter ( according to hg19-Feb_2009)  [Mapping ERGIC3.png]
Local_order ERGIC3 is located on the forward strand of chromosome 20 at 20q11.22 (figure 1.A). It is between base pairs 35542029-35557634 (figure 1.B) and is composed of 15606 nucleotides encoding 13 or 14 exons (figure 2). NCBI gene ID is 51614.
 
  Figure 1. ERGIC3 chromosomal localization (A) (adapted from GeneCards) and the ERGIC3 gene maps on chromosome 20q11.22 (B). The red line is the location of ERGIC3 on chromosome 20 (chr20).
Fusion genes
(updated 2017)
Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
BAZ2A (12q13.3) / ERGIC3 (20q11.22)ERGIC3 (20q11.22) / ERGIC3 (20q11.22)ERGIC3 (20q11.22) / H2AFZ (4q23)
POLR3E (16p12.2) / ERGIC3 (20q11.22)
Note According to hg38/GRCh38-Dec_2013: (GRCh38)
- ERGIC3 at chr20: 35542029-35557634 (NM_198398) endoplasmic reticulum-Golgi intermediate compartment protein 3 isoform 1
- ERGIC3 at chr20: 35542029-35557634 (NM_015966) endoplasmic reticulum-Golgi intermediate compartment protein 3 isoform 2

DNA/RNA

Note According to hg38/GRCh38-Dec_2013:(GRCh38)
- Start: chr20: 35542029 bp from pter
- End: chr20:35557634 bp from pter
- Size: 15606 bases
- Orientation: forward strand.
 
  Figure 2. The transcript variants and coding sequence (CDS) of ERGIC3.
Transcription Two alternatively spliced transcript variants encoding different isoforms have been demonstrated for this gene.
Isoform 1 transcript is 1383 bases (RefSeq: NM_198398.1), which is comprised of 14 exons and coding the longer isoform (Figure 2).
Isoform 2 represents the shorter 1368 bases, RefSeq: NM_015966.2, which is comprised of 13 exons and coding the shorter isoform (Figure 2). The open reading frame (ORF) is shifted because the variant is not spliced. Therefore, compared to isoform 1 the protein is shorter.
Pseudogene No observed pseudogenes.

Protein

Note Human ERGIC3 protein is a type II transmembrane protein containing two external membrane areas (1~19, 368~383), two transmembrane areas (20~42, 341~362), as well as a endoplasmic reticulum lumen area (43~344) from amino acid residues (figure 3). Human ERGIC3 consists of 383 amino acid with the molecular mass 43.2 kD and the value of theoretical isoelectric point 5.68, (Geng et al., 2014). ERGIC3 protein contains two conserved domains, ERGIC_N and COPIIcoated_ERV (figure 3) which are localized to the early secretory pathway and are involved in protein maturation and processing in the endoplasmic reticulum and/or sorting into COPII vesicles for transport to the Golgi (Otte et al., 2001). There are 2 glycosylation sites in the N241, N266 (figure 3).
 
  Figure 3. The domains of ERGIC3 protein (adapted from NCBI). aa: amino acid; posttrans. modifi.: posttranslational modification. TM: transmembrane domain.
Description 388 aa (Accession: NM_198398.1, NP_938408 ) isoform 1; 383 aa (Accession: NM_015966.2, NP_057050.1). isoform 2. ERGIC3 belongs to the family of the ER vesicle (Erv) proteins (Otte et al., 2001). ERGIC3 interacts with ERGIC2 (Welsh et al., 2006) and ERGIC1 (Breuza et al., 2004) and forms a heterotrimeric protein complex. Both isoforms contain ERGIC_N domain and COPIIcoated_ERV domain (figure 3) which is conserved from fungi to humans. ERGIC3 works in close on junction with ERGIC2 and together they form a complex which cycles between the endoplasmic reticulum and cis-Golgi network. Both are integral membrane proteins with two membrane spanning segments each, short N- and C-terminal tails expose to the cytosol, and large central luminal domains (figure 3) (Welsh et al., 2006).
Expression In normal human tissues, ERGIC3 is found in some epitheial cells such as liver, pancreas, stomach, intestine, and so on, but is undetected in lung, cerebral cortex, cerebellum, heart, spleen, thymus, muscle (Lin, 2014). In human tumor tissues, ERGIC3 is highly expressed in lung cancer, hepatocellular carcinoma, pancreatic carcinoma, gastric carcinoma, colon cancer, esophagus cancer, but is negative in osteosarcoma, chondrosarcoma, and fibrosarcoma by immunohistochemical (IHC) staining (Lin, 2014). In addtion, ERGIC3 is highly expressed in the spinal cord and kidney of mouse (Nishikawa et al., 2007).
Localisation ERGIC3 mainly localizes to endoplasmic reticulum, endoplasmic reticulum-golgi intermediate compartment (ERGIC) and cis-Golgi network, (Breuza et al., 2004; Orci et al., 2003; Wu et al., 2013).
Function The precise function of ERGIC3 is presently unclear, especially in mammal cells. There is a strong interaction between ERGIC3 and ERGIC2 so as to form a heteromer complex which exerting its biological function. The complex may be involved in : 1) the sorting of some secretory molecules during vesiclar transport (Belden and Barlowe, 2001; Otte and Barlowe, 2004) due to the hydrophobic signals present on both C-terminal tails of the ERGIC3-ERGIC2 complex control sorting into COPII vesicles for anterograde transport, and retrieval from the Golgi is mediated by a COPI binding KKxx motif on ERGIC3 (Otte and Barlowe, 2002) ; 2) protein folding and glycoprotein processing in the endoplasmic reticulum and cis- Golgi network (Nishikawa et al., 2007; Welsh et al., 2006). Glucosidase II is not transported into COPII vesicles in vitro as well as cells lacking a cycling ERGIC3-ERGIC2 complex have a mild glycoprotein processing defect and a partial loss of glucosidase (Leah, 2006) inhibiting endoplasmic reticulum stress (ERS)-induced cell death by tunicamycin in HEK-293 cells (Nishikawa et al., 2007).
Homology ERGIC3 is highly conserved in species. The amino acid sequence is at least 98% among 8 vertebrates, human, pongo, macaca, ailuropoda, myotis, bovini, mus, heterocephalus. There is only one change in amino acid (T164) between human and pongo, 2 changes in amino acid (T112, W170) between human and macaca (Geng et al., 2014).

Mutations

Note No observed mutation sites.

Implicated in

Note
  
Entity Non-small cell lung cancer (NSCLC)
Note ERGIC3 is highly up-regulated in NSCLC. A study (Wu et al., 2013) demonstrated that ERGIC3 was positive in 89% of NSCLCs while ERGIC3 was not detected in normal bronchial epithelial cells and alveolar cells. Moreover, the positive rate of lung adenocarcinoma was higher than that of lung squamous cell carcinoma, and the positive rate of poorly differentiated NSCLCs was higher than that of the well and moderately differentiated NSCLCs. The study suggested that ERGIC3 may be a potential biomarker for lung cancer. Additionally, the over-expression of ERGIC3 promotes the cell proliferation, migration, and invasion in NSLCs (Wu et al., 2013).
  
  
Entity Hepatocellular carcinoma (HCC)
Note ERGIC3 was up-regulated in HCC. The over-expression of ERGIC3 modulates the epithelial to mesenchymal transition (EMT), and increases the cell proliferation, migration, and invasion in HCCs (Zhang et al., 2013). Furthermore, ERGIC3 expression is regulated by MiR-490-3p (Zhang et al., 2013).
  

Bibliography

Proteomics of endoplasmic reticulum-Golgi intermediate compartment (ERGIC) membranes from brefeldin A-treated HepG2 cells identifies ERGIC-32, a new cycling protein that interacts with human Erv46.
Breuza L, Halbeisen R, Jeno P, Otte S, Barlowe C, Hong W, Hauri HP.
J Biol Chem. 2004 Nov 5;279(45):47242-53. Epub 2004 Aug 11.
PMID 15308636
 
Construction of prokaryotic expression vector with hERGIC3 gene and the bioinformatics analysists of hERGIC3 protein.
Geng N, Wu M, Zheng X, Liu X, Li X.
J mod med health.2014;30:2404-2406.
 
Preparation and identification of ERGIC3 monoclonal antibody and preliminary application research.
Lin Q.
Beijing: Graduate University of Chinese Academy of Sciences. 2014.
 
Identification and characterization of endoplasmic reticulum-associated protein, ERp43.
Nishikawa M, Kira Y, Yabunaka Y, Inoue M.
Gene. 2007 Jan 15;386(1-2):42-51. Epub 2006 Aug 25.
PMID 17020792
 
Mammalian Erv46 localizes to the endoplasmic reticulum-Golgi intermediate compartment and to cis-Golgi cisternae.
Orci L, Ravazzola M, Mack GJ, Barlowe C, Otte S.
Proc Natl Acad Sci U S A. 2003 Apr 15;100(8):4586-91. Epub 2003 Mar 27.
PMID 12663859
 
The Erv41p-Erv46p complex: multiple export signals are required in trans for COPII-dependent transport from the ER.
Otte S, Barlowe C.
EMBO J. 2002 Nov 15;21(22):6095-104.
PMID 12426381
 
Erv41p and Erv46p: new components of COPII vesicles involved in transport between the ER and Golgi complex.
Otte S, Belden WJ, Heidtman M, Liu J, Jensen ON, Barlowe C.
J Cell Biol. 2001 Feb 5;152(3):503-18.
PMID 11157978
 
Genetic and molecular interactions of the Erv41p-Erv46p complex involved in transport between the endoplasmic reticulum and Golgi complex.
Welsh LM, Tong AH, Boone C, Jensen ON, Otte S.
J Cell Sci. 2006 Nov 15;119(Pt 22):4730-40. Epub 2006 Oct 31.
PMID 17077122
 
Suppression subtractive hybridization identified differentially expressed genes in lung adenocarcinoma: ERGIC3 as a novel lung cancer-related gene.
Wu M, Tu T, Huang Y, Cao Y.
BMC Cancer. 2013 Feb 1;13:44. doi: 10.1186/1471-2407-13-44.
PMID 23374247
 
miR-490-3p modulates cell growth and epithelial to mesenchymal transition of hepatocellular carcinoma cells by targeting endoplasmic reticulum-Golgi intermediate compartment protein 3 (ERGIC3).
Zhang LY, Liu M, Li X, Tang H.
J Biol Chem. 2013 Feb 8;288(6):4035-47. doi: 10.1074/jbc.M112.410506. Epub 2012 Dec 4.
PMID 23212913
 

Citation

This paper should be referenced as such :
Mingsong Wu, Yi Cao
ERGIC3 (ERGIC and golgi 3)
Atlas Genet Cytogenet Oncol Haematol. 2015;19(8):499-502.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/ERGIC3ID42222ch20q11.html


External links

Nomenclature
HGNC (Hugo)ERGIC3   15927
Cards
AtlasERGIC3ID42222ch20q11
Entrez_Gene (NCBI)ERGIC3  51614  ERGIC and golgi 3
AliasesC20orf47; C2orf47; CGI-54; Erv46; 
NY-BR-84; PRO0989; SDBCAG84; dJ477O4.2
GeneCards (Weizmann)ERGIC3
Ensembl hg19 (Hinxton)ENSG00000125991 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000125991 [Gene_View]  chr20:35542029-35557634 [Contig_View]  ERGIC3 [Vega]
ICGC DataPortalENSG00000125991
TCGA cBioPortalERGIC3
AceView (NCBI)ERGIC3
Genatlas (Paris)ERGIC3
WikiGenes51614
SOURCE (Princeton)ERGIC3
Genetics Home Reference (NIH)ERGIC3
Genomic and cartography
GoldenPath hg38 (UCSC)ERGIC3  -     chr20:35542029-35557634 +  20q11.22   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)ERGIC3  -     20q11.22   [Description]    (hg19-Feb_2009)
EnsemblERGIC3 - 20q11.22 [CytoView hg19]  ERGIC3 - 20q11.22 [CytoView hg38]
Mapping of homologs : NCBIERGIC3 [Mapview hg19]  ERGIC3 [Mapview hg38]
OMIM616971   
Gene and transcription
Genbank (Entrez)AF077030 AF091085 AF116614 AF151812 AF308298
RefSeq transcript (Entrez)NM_015966 NM_198398
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)ERGIC3
Cluster EST : UnigeneHs.472558 [ NCBI ]
CGAP (NCI)Hs.472558
Alternative Splicing GalleryENSG00000125991
Gene ExpressionERGIC3 [ NCBI-GEO ]   ERGIC3 [ EBI - ARRAY_EXPRESS ]   ERGIC3 [ SEEK ]   ERGIC3 [ MEM ]
Gene Expression Viewer (FireBrowse)ERGIC3 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)51614
GTEX Portal (Tissue expression)ERGIC3
Human Protein AtlasENSG00000125991-ERGIC3 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ9Y282   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ9Y282  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ9Y282
Splice isoforms : SwissVarQ9Y282
PhosPhoSitePlusQ9Y282
Domains : Interpro (EBI)Erv_C   
Domain families : Pfam (Sanger)COPIIcoated_ERV (PF07970)   
Domain families : Pfam (NCBI)pfam07970   
Conserved Domain (NCBI)ERGIC3
DMDM Disease mutations51614
Blocks (Seattle)ERGIC3
SuperfamilyQ9Y282
Human Protein Atlas [tissue]ENSG00000125991-ERGIC3 [tissue]
Peptide AtlasQ9Y282
HPRD15306
IPIIPI00006438   IPI00552115   IPI00446875   IPI00383663   IPI00644136   IPI00552465   IPI01012929   IPI00853517   IPI00853202   IPI00472099   
Protein Interaction databases
DIP (DOE-UCLA)Q9Y282
IntAct (EBI)Q9Y282
FunCoupENSG00000125991
BioGRIDERGIC3
STRING (EMBL)ERGIC3
ZODIACERGIC3
Ontologies - Pathways
QuickGOQ9Y282
Ontology : AmiGOendoplasmic reticulum membrane  Golgi apparatus  membrane  integral component of membrane  vesicle-mediated transport  endoplasmic reticulum-Golgi intermediate compartment membrane  
Ontology : EGO-EBIendoplasmic reticulum membrane  Golgi apparatus  membrane  integral component of membrane  vesicle-mediated transport  endoplasmic reticulum-Golgi intermediate compartment membrane  
NDEx NetworkERGIC3
Atlas of Cancer Signalling NetworkERGIC3
Wikipedia pathwaysERGIC3
Orthology - Evolution
OrthoDB51614
GeneTree (enSembl)ENSG00000125991
Phylogenetic Trees/Animal Genes : TreeFamERGIC3
HOVERGENQ9Y282
HOGENOMQ9Y282
Homologs : HomoloGeneERGIC3
Homology/Alignments : Family Browser (UCSC)ERGIC3
Gene fusions - Rearrangements
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerERGIC3 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)ERGIC3
dbVarERGIC3
ClinVarERGIC3
1000_GenomesERGIC3 
Exome Variant ServerERGIC3
ExAC (Exome Aggregation Consortium)ENSG00000125991
GNOMAD BrowserENSG00000125991
Genetic variants : HAPMAP51614
Genomic Variants (DGV)ERGIC3 [DGVbeta]
DECIPHERERGIC3 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisERGIC3 
Mutations
ICGC Data PortalERGIC3 
TCGA Data PortalERGIC3 
Broad Tumor PortalERGIC3
OASIS PortalERGIC3 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICERGIC3  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDERGIC3
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch ERGIC3
DgiDB (Drug Gene Interaction Database)ERGIC3
DoCM (Curated mutations)ERGIC3 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)ERGIC3 (select a term)
intoGenERGIC3
NCG5 (London)ERGIC3
Cancer3DERGIC3(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM616971   
Orphanet
MedgenERGIC3
Genetic Testing Registry ERGIC3
NextProtQ9Y282 [Medical]
TSGene51614
GENETestsERGIC3
Target ValidationERGIC3
Huge Navigator ERGIC3 [HugePedia]
snp3D : Map Gene to Disease51614
BioCentury BCIQERGIC3
ClinGenERGIC3
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD51614
Chemical/Pharm GKB GenePA38050
Clinical trialERGIC3
Miscellaneous
canSAR (ICR)ERGIC3 (select the gene name)
Probes
Litterature
PubMed20 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineERGIC3
EVEXERGIC3
GoPubMedERGIC3
iHOPERGIC3
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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