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

Gene ID: 25839, updated on 21-Apr-2019

Summary

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
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

Genomic context

See COG4 in Genome Data Viewer
Location:
16q22.1
Exon count:
20
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 16 NC_000016.10 (70480569..70523554, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (70514472..70557457, complement)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene RNA, U6 small nuclear 23, pseudogene Neighboring gene fucose kinase 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

Expression

  • 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

Phenotypes

Associated conditions

Description Tests
Congenital disorder of glycosylation type 2J Compare labs
SAUL-WILSON SYNDROME
MedGen: CN257733 OMIM: 618150 GeneReviews: Not available
not available

NHGRI GWAS Catalog

Description
Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche.
NHGRI GWA Catalog

HIV-1 interactions

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 BioSystems

  • Asparagine N-linked glycosylation, organism-specific biosystem (from REACTOME)
    Asparagine N-linked glycosylation, organism-specific biosystemN-linked glycosylation is the most important form of post-translational modification for proteins synthesized and folded in the Endoplasmic Reticulum (Stanley et al. 2009). An early study in 1999 rev...
  • COPI-mediated anterograde transport, organism-specific biosystem (from REACTOME)
    COPI-mediated anterograde transport, organism-specific biosystemThe ERGIC (ER-to-Golgi intermediate compartment, also known as vesicular-tubular clusters, VTCs) is a stable, biochemically distinct compartment located adjacent to ER exit sites (Ben-Tekaya et al, 2...
  • ER to Golgi Anterograde Transport, organism-specific biosystem (from REACTOME)
    ER to Golgi Anterograde Transport, organism-specific biosystemSecretory cargo destined to be secreted or to arrive at the plasma membrane (PM) leaves the ER via distinct exit sites. This cargo is destined for the Golgi apparatus for further processing.
  • Intra-Golgi and retrograde Golgi-to-ER traffic, organism-specific biosystem (from REACTOME)
    Intra-Golgi and retrograde Golgi-to-ER traffic, organism-specific biosystemThe mammalian Golgi complex, a central hub of both anterograde and retrograde trafficking, is a ribbon of stacked cisterna with biochemically distinct compartments (reviewed in Glick and Nakano, 2009...
  • Intra-Golgi traffic, organism-specific biosystem (from REACTOME)
    Intra-Golgi traffic, organism-specific biosystemThe mammalian Golgi consists of at least three biochemically distinct cisternae, cis-, medial- and trans (reviewed in Szul and Sztul, 2011; Day et al, 2013). The structure and function of the Golgi a...
  • Membrane Trafficking, organism-specific biosystem (from REACTOME)
    Membrane Trafficking, organism-specific biosystemThe secretory membrane system allows a cell to regulate delivery of newly synthesized proteins, carbohydrates, and lipids to the cell surface, a necessity for growth and homeostasis. The system is ma...
  • Metabolism of proteins, organism-specific biosystem (from REACTOME)
    Metabolism of proteins, organism-specific biosystemProtein metabolism comprises the pathways of translation, post-translational modification and protein folding.
  • Post-translational protein modification, organism-specific biosystem (from REACTOME)
    Post-translational protein modification, organism-specific biosystemAfter translation, many newly formed proteins undergo further covalent modifications that alter their functional properties and that are essentially irreversible under physiological conditions in the...
  • Retrograde transport at the Trans-Golgi-Network, organism-specific biosystem (from REACTOME)
    Retrograde transport at the Trans-Golgi-Network, organism-specific biosystemThe trans-Golgi network is the docking site for retrograde cargo from the endolysosomal system and the plasma membrane. Typical cargo includes recycling resident TGN proteins such as TGOLN2 (also kn...
  • Transport to the Golgi and subsequent modification, organism-specific biosystem (from REACTOME)
    Transport to the Golgi and subsequent modification, organism-specific biosystemAt least two mechanisms of transport of proteins from the ER to the Golgi have been described. One is a general flow requiring no export signals (Wieland et al, 1987; Martinez-Menarguez et al, 1999)....
  • Vesicle-mediated transport, organism-specific biosystem (from REACTOME)
    Vesicle-mediated transport, organism-specific biosystemThe transit of proteins and other cargo through the cell requires a cellular transport process in which transported substances are moved in membrane-bounded vesicles. Transported substances are enclo...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • DKFZp586E1519

Gene Ontology Provided by GOA

Function Evidence Code Pubs
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
ER to Golgi vesicle-mediated transport TAS
Traceable Author Statement
more info
 
Golgi organization IMP
Inferred from Mutant Phenotype
more info
PubMed 
Golgi vesicle prefusion complex stabilization IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein transport IEA
Inferred from Electronic Annotation
more info
 
retrograde vesicle-mediated transport, Golgi to ER IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
Golgi membrane TAS
Traceable Author Statement
more info
 
Golgi transport complex IDA
Inferred from Direct Assay
more info
PubMed 
trans-Golgi network membrane TAS
Traceable Author Statement
more info
 

General protein information

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)

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..47986
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    Status: REVIEWED

    Source sequence(s)
    AC106804, AK096557, AL050101, AU125729, BP282697
    Consensus CDS
    CCDS73909.1
    Related
    ENSP00000377236.5, ENST00000393612.8
  2. NM_001365426.1NP_001352355.1  conserved oligomeric Golgi complex subunit 4 isoform 3

    Status: REVIEWED

    Source sequence(s)
    AC106804
  3. NM_015386.3NP_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
    Q9H9E3
    UniProtKB/TrEMBL
    J3KNI1, Q8N8L9
    Related
    ENSP00000315775.5, ENST00000323786.10
    Conserved Domains (2) summary
    pfam08318
    Location:192501
    COG4; COG4 transport protein
    cl19885
    Location:551788
    Sec6; Exocyst complex component Sec6

RNA

  1. NR_158212.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC106804

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000016.10 Reference GRCh38.p12 Primary Assembly

    Range
    70480569..70523554 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011522981.3XP_011521283.1  conserved oligomeric Golgi complex subunit 4 isoform X1

    Conserved Domains (2) summary
    pfam08318
    Location:50359
    COG4; COG4 transport protein
    cl19885
    Location:409646
    Sec6; Exocyst complex component Sec6
  2. XM_024450224.1XP_024305992.1  conserved oligomeric Golgi complex subunit 4 isoform X2

    Conserved Domains (3) summary
    pfam04437
    Location:263449
    RINT1_TIP1; RINT-1 / TIP-1 family
    pfam07393
    Location:358458
    Sec10; Exocyst complex component Sec10
    pfam08318
    Location:20195
    COG4; COG4 transport protein

RNA

  1. XR_933266.2 RNA Sequence

    Related
    ENST00000482252.5
  2. XR_001751889.1 RNA Sequence

  3. XR_933267.1 RNA Sequence

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