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

    Gene ID: 51614, updated on 27-Nov-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
    Involved in endoplasmic reticulum to Golgi vesicle-mediated transport and positive regulation of intracellular protein transport. Located in membrane. Part of retrograde transporter complex, Golgi to ER. Biomarker of lung adenocarcinoma. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in thyroid (RPKM 113.7), testis (RPKM 112.2) and 25 other tissues See more
    Orthologs
    mouse all
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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_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (35542078..35557634)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (37262891..37278470)
    RS_2024_09 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. Identification and characterization of endoplasmic reticulum-associated protein, ERp43. Nishikawa M, et al. Gene, 2007 Jan 15. PMID 17020792
    2. 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
    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 (57) 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)

    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
    		  
    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-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_2024_08

    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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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