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ERGIC3 ERGIC and golgi 3 [ Homo sapiens (human) ]

Gene ID: 51614, updated on 11-Apr-2024

Summary

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Official Symbol
ERGIC3provided by HGNC
Official Full Name
ERGIC and golgi 3provided by HGNC
Primary source
HGNC:HGNC:15927
See related
Ensembl:ENSG00000125991 MIM:616971; AllianceGenome:HGNC:15927
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
Erv46; CGI-54; C2orf47; PRO0989; C20orf47; NY-BR-84; SDBCAG84; dJ477O4.2
Summary
Predicted to be involved in endoplasmic reticulum to Golgi vesicle-mediated transport and retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum. Located in membrane. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in thyroid (RPKM 113.7), testis (RPKM 112.2) and 25 other tissues See more
Orthologs
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Genomic context

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See ERGIC3 in Genome Data Viewer
Location:
20q11.22
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (35542078..35557634)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (37262891..37278470)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (34129827..34145405)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene centrosomal protein 250 Neighboring gene CEP250 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17785 Neighboring gene chromosome 20 open reading frame 173 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17786 Neighboring gene ribosomal protein L36 pseudogene 4 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:34145795-34145976 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:34146815-34147316 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:34147317-34147816 Neighboring gene fer-1 like family member 4 (pseudogene) Neighboring gene ReSE screen-validated silencer GRCh37_chr20:34164928-34165090 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:34176389-34176889 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:34177977-34178478 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:34178479-34178978 Neighboring gene ribosomal protein L37 pseudogene 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:34187074-34187574 Neighboring gene uncharacterized LOC124904891 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12860

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Transcriptome changes in ERGIC3-knockdown hepatocellular carcinoma cells: ERGIC3 is a novel immune function related gene. Liu M, et al. PeerJ, 2022. PMID 35602902, Free PMC Article
  2. Identification and characterization of endoplasmic reticulum-associated protein, ERp43. Nishikawa M, et al. Gene, 2007 Jan 15. PMID 17020792
  3. Endoplasmic reticulum-Golgi intermediate compartment protein 3 knockdown suppresses lung cancer through endoplasmic reticulum stress-induced autophagy. Hong SH, et al. Oncotarget, 2016 Oct 4. PMID 27588471, Free PMC Article
  4. ERGIC3, which is regulated by miR-203a, is a potential biomarker for non-small cell lung cancer. Lin QH, et al. Cancer Sci, 2015 Oct. PMID 26177443, Free PMC Article
  5. 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, et al. J Biol Chem, 2013 Feb 8. PMID 23212913, Free PMC Article

See all (50) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Transcriptome changes in ERGIC3-knockdown hepatocellular carcinoma cells: ERGIC3 is a novel immune function related gene.
    Title: Transcriptome changes in ERGIC3-knockdown hepatocellular carcinoma cells: ERGIC3 is a novel immune function related gene.
  2. MARCH2 reduced secretion of alpha1-antitrypsin and haptoglobin, and coexpression of the ubiquitination-resistant ERGIC3 variant largely restored their secretion, suggesting that MARCH2-mediated ERGIC3 ubiquitination is the major cause of the decrease in trafficking of ERGIC3-binding secretory proteins.
    Title: The E3 ubiquitin ligase MARCH2 regulates ERGIC3-dependent trafficking of secretory proteins.
  3. these data showed that knockdown of ERGIC3 triggers endoplasmic reticulum stress-induced autophagic cancer cell death
    Title: Endoplasmic reticulum-Golgi intermediate compartment protein 3 knockdown suppresses lung cancer through endoplasmic reticulum stress-induced autophagy.
  4. Results showed that miR-203a downregulation induced ERGIC3 overexpression in non-small cell lung cancer cells.
    Title: ERGIC3, which is regulated by miR-203a, is a potential biomarker for non-small cell lung cancer.
  5. ERGIC3 may play an active role in the development and progression of lung cancer.
    Title: Suppression subtractive hybridization identified differentially expressed genes in lung adenocarcinoma: ERGIC3 as a novel lung cancer-related gene.
  6. 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).
    Title: 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).
  7. Plays important roles in cell growth and endoplasmic reticulum stress-induced cell death.
    Title: Identification and characterization of endoplasmic reticulum-associated protein, ERp43.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Biological, clinical and population relevance of 95 loci for blood lipids.
EBI GWAS Catalog
Discovery and refinement of loci associated with lipid levels.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp160, precursor env HIV-1 gp160 interacts with ERGIC3; predicted interaction to be within the endoplasmic reticulum to Golgi transport PubMed
env HIV-1 gp160 is identified to have a physical interaction with ERGIC and golgi 3 (ERGIC3) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in endoplasmic reticulum to Golgi vesicle-mediated transport IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in endoplasmic reticulum to Golgi vesicle-mediated transport IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of intracellular protein transport IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum NAS
Non-traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
is_active_in COPII-coated ER to Golgi transport vesicle IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in Golgi apparatus IEA
Inferred from Electronic Annotation
more info
  
is_active_in Golgi membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in endoplasmic reticulum IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in endoplasmic reticulum membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in endoplasmic reticulum membrane IEA
Inferred from Electronic Annotation
more info
  
located_in endoplasmic reticulum-Golgi intermediate compartment membrane IEA
Inferred from Electronic Annotation
more info
  
located_in membrane HDA PubMed 
part_of retrograde transporter complex, Golgi to ER IPI
Inferred from Physical Interaction
more info
 PubMed 
part_of transporter complex IPI
Inferred from Physical Interaction
more info
 PubMed 

General protein information

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Preferred Names
endoplasmic reticulum-Golgi intermediate compartment protein 3
Names
endoplasmic reticulum-localized protein ERp43
serologically defined breast cancer antigen 84
serologically defined breast cancer antigen NY-BR-84

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_015966.3 → NP_057050.1  endoplasmic reticulum-Golgi intermediate compartment protein 3 isoform b

    See identical proteins and their annotated locations for NP_057050.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a.
    Source sequence(s)
    AF077030
    Consensus CDS
    CCDS13257.1
    UniProtKB/Swiss-Prot
    Q5JWS3, Q6ZWP7, Q9H276, Q9P1L3, Q9Y282
    UniProtKB/TrEMBL
    A2TJK5, Q5JWS0
    Related
    ENSP00000341358.2, ENST00000348547.7
    Conserved Domains (2) summary
    pfam07970
    Location:145 → 363
    COPIIcoated_ERV; Endoplasmic reticulum vesicle transporter
    pfam13850
    Location:7 → 97
    ERGIC_N; Endoplasmic Reticulum-Golgi Intermediate Compartment (ERGIC)

  2. NM_198398.2 → NP_938408.1  endoplasmic reticulum-Golgi intermediate compartment protein 3 isoform a

    See identical proteins and their annotated locations for NP_938408.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).
    Source sequence(s)
    AL161963, BU528333
    Consensus CDS
    CCDS13258.1
    UniProtKB/TrEMBL
    Q5JWS0
    Related
    ENSP00000349970.4, ENST00000357394.8
    Conserved Domains (2) summary
    pfam07970
    Location:145 → 368
    COPIIcoated_ERV; Endoplasmic reticulum vesicle transporter
    pfam13850
    Location:7 → 97
    ERGIC_N; Endoplasmic Reticulum-Golgi Intermediate Compartment (ERGIC)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    35542078..35557634
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    37262891..37278470
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9Y282.1 GenPept UniProtKB/Swiss-Prot:Q9Y282

Gene LinkOut

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