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    COG4 component of oligomeric golgi complex 4 [ Homo sapiens (human) ]

    Gene ID: 25839, updated on 2-Nov-2024

    Summary

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    Official Symbol
    COG4provided by HGNC
    Official Full Name
    component of oligomeric golgi complex 4provided by HGNC
    Primary source
    HGNC:HGNC:18620
    See related
    Ensembl:ENSG00000103051 MIM:606976; AllianceGenome:HGNC:18620
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    COD1; CDG2J; SWILS
    Summary
    The protein encoded by this gene is a component of an oligomeric protein complex involved in the structure and function of the Golgi apparatus. Defects in this gene may be a cause of congenital disorder of glycosylation type IIj. Two transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Aug 2010]
    Expression
    Ubiquitous expression in testis (RPKM 19.4), skin (RPKM 14.3) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See COG4 in Genome Data Viewer
    Location:
    16q22.1
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (70480567..70523554, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (76291598..76334735, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (70514470..70557457, complement)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903708 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:70500319-70500820 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:70500821-70501320 Neighboring gene fucose kinase Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:70504733-70505668 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11064 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11065 Neighboring gene Sharpr-MPRA regulatory region 8991 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11066 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:70558263-70559000 Neighboring gene small nucleolar RNA, C/D box 111B Neighboring gene splicing factor 3b subunit 3 Neighboring gene small nucleolar RNA, C/D box 111

    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 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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    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Growth in individuals with Saul-Wilson syndrome.
      Title: Growth in individuals with Saul-Wilson syndrome.
    2. A specific heterozygous COG4 substitution as the molecular basis of Saul-Wilson syndrome.
      Title: A Recurrent De Novo Heterozygous COG4 Substitution Leads to Saul-Wilson Syndrome, Disrupted Vesicular Trafficking, and Altered Proteoglycan Glycosylation.
    3. TMEM-COG4, COG7 and COG8 subunits restore endogenous COG localization to the Golgi membranes
      Title: Membrane detachment is not essential for COG complex function.
    4. A novel R729W missense mutation in COG4 was associated with the congenital disorder of glycosylation type II.
      Title: Golgi function and dysfunction in the first COG4-deficient CDG type II patient.
    5. The 1.9 A crystal structure of a Cog4 C-terminal fragment, was determined. Arg 729 is found to occupy a key position at the center of a salt bridge network, thereby stabilizing Cog4's small C-terminal domain.
      Title: Structural basis for a human glycosylation disorder caused by mutation of the COG4 gene.
    6. Study shows that the SM protein, Sly1, interacts directly with the conserved oligomeric Golgi (COG) tethering complex; Sly1-COG interaction is mediated by the Cog4 subunit, which also interacts with Syntaxin 5 through a different binding site.
      Title: Direct interaction between the COG complex and the SM protein, Sly1, is required for Golgi SNARE pairing.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche.
    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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    Replication interactions

    Interaction Pubs
    Knockdown of component of oligomeric golgi complex 4 (COG4) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • DKFZp586E1519

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in Golgi organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in Golgi organization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in glycosylation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in protein transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in retrograde transport, vesicle recycling within Golgi 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 IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in Golgi membrane NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in Golgi membrane TAS
    Traceable Author Statement
    more info
    		  
    part_of Golgi transport complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of Golgi transport complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of Golgi transport complex NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in trans-Golgi network membrane TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    conserved oligomeric Golgi complex subunit 4
    Names
    COG complex subunit 4
    complexed with Dor1p
    conserved oligomeric Golgi complex protein 4

    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.

    Genomic

    1. NG_027529.1 RefSeqGene

      Range
      5001..47984
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001195139.2 → NP_001182068.2  conserved oligomeric Golgi complex subunit 4 isoform 2

      Status: REVIEWED

      Source sequence(s)
      AC106804, AK096557, AL050101, AU125729, BP282697
      Consensus CDS
      CCDS73909.2
      UniProtKB/TrEMBL
      A0A6I8PIQ6, Q6PIW8
      Related
      ENSP00000501405.1, ENST00000674443.1

    2. NM_001365426.1 → NP_001352355.1  conserved oligomeric Golgi complex subunit 4 isoform 3

      Status: REVIEWED

      Source sequence(s)
      AC106804
      UniProtKB/TrEMBL
      Q8N8L9

    3. NM_015386.3 → NP_056201.2  conserved oligomeric Golgi complex subunit 4 isoform 1

      Status: REVIEWED

      Source sequence(s)
      AK096557, AL050101, AU125729, BP282697
      Consensus CDS
      CCDS10892.2
      UniProtKB/Swiss-Prot
      B4DMN8, C9JS23, Q96D40, Q9BRF0, Q9BVZ2, Q9H5Y4, Q9H9E3, Q9Y3W3
      UniProtKB/TrEMBL
      J3KNI1
      Related
      ENSP00000315775.5, ENST00000323786.10
      Conserved Domains (2) summary
      pfam08318
      Location:192 → 501
      COG4; COG4 transport protein
      cl19885
      Location:551 → 788
      Sec6; Exocyst complex component Sec6

    RNA

    1. NR_158212.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC106804
      Related
      ENST00000703108.1

    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_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      70480567..70523554 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      76291598..76334735 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_145818.1: Suppressed sequence

      Description
      NM_145818.1: This RefSeq record was removed by NCBI staff. Contact info@ncbi.nlm.nih.gov for further information.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9H9E3.3 GenPept UniProtKB/Swiss-Prot:Q9H9E3

    Gene LinkOut

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

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