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    COG5 component of oligomeric golgi complex 5 [ Homo sapiens (human) ]

    Gene ID: 10466, updated on 27-Nov-2024

    Summary

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    Official Symbol
    COG5provided by HGNC
    Official Full Name
    component of oligomeric golgi complex 5provided by HGNC
    Primary source
    HGNC:HGNC:14857
    See related
    Ensembl:ENSG00000164597 MIM:606821; AllianceGenome:HGNC:14857
    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
    CDG2I; GTC90; GOLTC1
    Summary
    The protein encoded by this gene is one of eight proteins (Cog1-8) which form a Golgi-localized complex (COG) required for normal Golgi morphology and function. The encoded protein is organized with conserved oligomeric Golgi complex components 6, 7 and 8 into a sub-complex referred to as lobe B. Alternative splicing results in multiple transcript variants. Mutations in this gene result in congenital disorder of glycosylation type 2I.[provided by RefSeq, Jan 2011]
    Expression
    Ubiquitous expression in thyroid (RPKM 12.7), prostate (RPKM 10.2) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See COG5 in Genome Data Viewer
    Location:
    7q22.3
    Exon count:
    23
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (107201372..107563920, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (108517426..108879966, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (106841817..107204365, complement)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26490 Neighboring gene phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit gamma Neighboring gene CRISPRi-validated cis-regulatory element chr7.4040 Neighboring gene CRISPRi-validated cis-regulatory element chr7.4041 Neighboring gene CRISPRi-validated cis-regulatory element chr7.4042 Neighboring gene CRISPRi-validated cis-regulatory element chr7.4045 Neighboring gene CRISPRi-validated cis-regulatory element chr7.4046 Neighboring gene CRISPRi-validated cis-regulatory element chr7.4048 Neighboring gene CRISPRi-validated cis-regulatory element chr7.4050 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:106681203-106681414 Neighboring gene Sharpr-MPRA regulatory region 8060 Neighboring gene PRKAR2B antisense RNA 1 Neighboring gene Sharpr-MPRA regulatory region 12069 Neighboring gene protein kinase cAMP-dependent type II regulatory subunit beta Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr7:106792322-106793521 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:106808976-106809549 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18537 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18538 Neighboring gene uncharacterized LOC124901720 Neighboring gene uncharacterized LOC124901721 Neighboring gene HMG-box transcription factor 1 Neighboring gene MPRA-validated peak6677 silencer Neighboring gene NANOG hESC enhancer GRCh37_chr7:107031303-107031825 Neighboring gene MPRA-validated peak6680 silencer Neighboring gene ribosomal protein L37a pseudogene 6 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:107148389-107148890 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:107148891-107149390 Neighboring gene G protein-coupled receptor 22 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:107204244-107204454 Neighboring gene DUS4L-BCAP29 readthrough Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18539 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr7:107204943-107206142 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18540 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26493 Neighboring gene uncharacterized LOC124901856 Neighboring gene dihydrouridine synthase 4 like Neighboring gene B cell receptor associated protein 29

    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. Deficiency in COG5 causes a moderate form of congenital disorders of glycosylation. Paesold-Burda P, et al. Hum Mol Genet, 2009 Nov 15. PMID 19690088
    2. Purification and characterization of a novel 13 S hetero-oligomeric protein complex that stimulates in vitro Golgi transport. Walter DM, et al. J Biol Chem, 1998 Nov 6. PMID 9792665
    3. The familial mediterranean fever protein interacts and colocalizes with a putative Golgi transporter. Chen X, et al. Proc Soc Exp Biol Med, 2000 May. PMID 10782044
    4. Fusion of HMGA2 to COG5 in uterine leiomyoma. Velagaleti GV, et al. Cancer Genet Cytogenet, 2010 Oct 1. PMID 20804914
    5. A genome-wide association study identifies an osteoarthritis susceptibility locus on chromosome 7q22. Kerkhof HJ, et al. Arthritis Rheum, 2010 Feb. PMID 20112360, Free PMC Article

    See all (52) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Fetal glycosylation defect due to ALG3 and COG5 variants detected via amniocentesis: Complex glycosylation defect with embryonic lethal phenotype.
      Title: Fetal glycosylation defect due to ALG3 and COG5 variants detected via amniocentesis: Complex glycosylation defect with embryonic lethal phenotype.
    2. COG5 variants lead to complex early onset retinal degeneration, upregulation of PERK and DNA damage.
      Title: COG5 variants lead to complex early onset retinal degeneration, upregulation of PERK and DNA damage.
    3. Targeted silencing of components of lobe B of the COG complex, namely COG5, COG6, COG7 and COG8, inhibited HIV-1 replication
      Title: Target silencing of components of the conserved oligomeric Golgi complex impairs HIV-1 replication.
    4. Cog5-Cog7 crystal structure reveals interactions essential for the function of a multisubunit tethering complex.
      Title: Cog5-Cog7 crystal structure reveals interactions essential for the function of a multisubunit tethering complex.
    5. In conclusion, we find that GDF5, but not COG5 or MCF2L, influence the extent of radiographic damage in knee osteoarthritis
      Title: Genetic contribution to radiographic severity in osteoarthritis of the knee.
    6. Meta-analysis and genome-wide association study of gene-disease association. (HuGE Navigator)
      Title: Meta-analysis of genome-wide association studies confirms a susceptibility locus for knee osteoarthritis on chromosome 7q22.
    7. Report on a uterine leiomyoma with a novel HMGA2 fusion gene in a 44-year-old woman.
      Title: Fusion of HMGA2 to COG5 in uterine leiomyoma.
    8. Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
      Title: A genome-wide association study identifies an osteoarthritis susceptibility locus on chromosome 7q22.
    9. Sec34 is implicated in traffic from the endoplasmic reticulum to the Golgi and exists in a complex with GTC-90 and ldlBp
      Title: Sec34 is implicated in traffic from the endoplasmic reticulum to the Golgi and exists in a complex with GTC-90 and ldlBp.
    10. COG5- and COG7 subunits play distinctive roles in controlling Golgi structure and function
      Title: Genetic analysis of the subunit organization and function of the conserved oligomeric golgi (COG) complex: studies of COG5- and COG7-deficient mammalian cells.
    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
    A genome-wide association study identifies an osteoarthritis susceptibility locus on chromosome 7q22.
    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)

    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

    • FLJ41732, FLJ44289

    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 Golgi organization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in glycosylation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within inter-Golgi cisterna vesicle-mediated transport IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in intra-Golgi vesicle-mediated transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in intra-Golgi vesicle-mediated transport NAS
    Non-traceable Author Statement
    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 
    Component Evidence Code Pubs
    located_in Golgi apparatus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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 membrane HDA PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    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 5
    Names
    13S golgi transport complex 1 90 kDa subunit
    COG complex subunit 5
    conserved oligomeric Golgi complex protein 5

    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_028095.2 RefSeqGene

      Range
      5595..368143
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001161520.2 → NP_001154992.2  conserved oligomeric Golgi complex subunit 5 isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 3' UTR and lacks a portion of the 3' coding region, compared to variant 1. The encoded isoform (3) is shorter and has a distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AC004492, AK022835, AK314270, BC068540
      Consensus CDS
      CCDS55152.2
      UniProtKB/TrEMBL
      A0AAA9X2X8, A0AAG2TF56
      Related
      ENSP00000377228.3, ENST00000393603.7
      Conserved Domains (1) summary
      pfam10392
      Location:35 → 158
      COG5; Golgi transport complex subunit 5

    2. NM_001379511.1 → NP_001366440.1  conserved oligomeric Golgi complex subunit 5 isoform 4

      Status: REVIEWED

      Source sequence(s)
      AC002381, AC004492, AC004855
      UniProtKB/Swiss-Prot
      A4D0R6, A4D0R7, O14555, O95008, Q6NUL5, Q9UP83
      Conserved Domains (1) summary
      pfam10392
      Location:35 → 158
      COG5; Golgi transport complex subunit 5

    3. NM_001379512.1 → NP_001366441.1  conserved oligomeric Golgi complex subunit 5 isoform 5

      Status: REVIEWED

      Source sequence(s)
      AC002381, AC004492, AC004855
      UniProtKB/TrEMBL
      A0AAG2TDC7
      Conserved Domains (1) summary
      pfam10392
      Location:35 → 158
      COG5; Golgi transport complex subunit 5

    4. NM_001379513.1 → NP_001366442.1  conserved oligomeric Golgi complex subunit 5 isoform 6

      Status: REVIEWED

      Source sequence(s)
      AC002381, AC004492, AC004855
      UniProtKB/Swiss-Prot
      A4D0R6, A4D0R7, O14555, O95008, Q6NUL5, Q9UP83
      Conserved Domains (1) summary
      pfam10392
      Location:35 → 158
      COG5; Golgi transport complex subunit 5

    5. NM_001379514.1 → NP_001366443.1  conserved oligomeric Golgi complex subunit 5 isoform 7

      Status: REVIEWED

      Source sequence(s)
      AC002381, AC004492, AC004855
      UniProtKB/Swiss-Prot
      A4D0R6, A4D0R7, O14555, O95008, Q6NUL5, Q9UP83
      Conserved Domains (1) summary
      pfam10392
      Location:35 → 158
      COG5; Golgi transport complex subunit 5

    6. NM_001379515.1 → NP_001366444.1  conserved oligomeric Golgi complex subunit 5 isoform 8

      Status: REVIEWED

      Source sequence(s)
      AC002381, AC004492
      Conserved Domains (2) summary
      pfam10392
      Location:35 → 158
      COG5; Golgi transport complex subunit 5
      cl00549
      Location:481 → 559
      ABC_membrane; ABC transporter transmembrane region

    7. NM_001379516.1 → NP_001366445.1  conserved oligomeric Golgi complex subunit 5 isoform 9

      Status: REVIEWED

      Source sequence(s)
      AC002381, AC004492, AC004855
      Conserved Domains (1) summary
      cl22951
      Location:35 → 81
      Vps51; Vps51/Vps67

    8. NM_006348.5 → NP_006339.4  conserved oligomeric Golgi complex subunit 5 isoform 1

      Status: REVIEWED

      Source sequence(s)
      AC002381, AC004492, AC004855
      Consensus CDS
      CCDS5742.2
      UniProtKB/Swiss-Prot
      A4D0R6, A4D0R7, O14555, O95008, Q6NUL5, Q9UP83
      Related
      ENSP00000297135.4, ENST00000297135.9
      Conserved Domains (1) summary
      pfam10392
      Location:35 → 158
      COG5; Golgi transport complex subunit 5

    9. NM_181733.4 → NP_859422.3  conserved oligomeric Golgi complex subunit 5 isoform 2

      Status: REVIEWED

      Source sequence(s)
      AC002381, AC004492, AC004855
      Consensus CDS
      CCDS5743.2
      UniProtKB/TrEMBL
      A0AAA9X096, A0AAG2TDC7
      Related
      ENSP00000334703.3, ENST00000347053.8
      Conserved Domains (1) summary
      pfam10392
      Location:35 → 158
      COG5; Golgi transport complex subunit 5

    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_000007.14 Reference GRCh38.p14 Primary Assembly

      Range
      107201372..107563920 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_024446634.2 → XP_024302402.2  conserved oligomeric Golgi complex subunit 5 isoform X1

    Reference GRCh38.p14 PATCHES

    Genomic

    1. NW_017852930.1 Reference GRCh38.p14 PATCHES

      Range
      46894..409575 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054332128.1 → XP_054188103.1  conserved oligomeric Golgi complex subunit 5 isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060931.1 Alternate T2T-CHM13v2.0

      Range
      108517426..108879966 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054357090.1 → XP_054213065.1  conserved oligomeric Golgi complex subunit 5 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9UP83.4 GenPept UniProtKB/Swiss-Prot:Q9UP83

    Gene LinkOut

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

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