FB2022_03, released June 9, 2022

Gene: Dmel\Cog4

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General Information
Symbol
Dmel\Cog4
Species
D. melanogaster
Name
Component of oligomeric golgi complex 4
Annotation Symbol
CG7456
Feature Type
protein_coding_gene
FlyBase ID
FBgn0032258
Gene Model Status
Current
Stock Availability
6 publicly available
Gene Summary
Required for normal Golgi function. (UniProt, Q95TN4)
Contribute a Gene Snapshot for this gene.
All Summaries
Key Links
Genomic Location
Cytogenetic map
31F1-31F1
Sequence location
Recombination map
2-43
RefSeq locus
NT_033779 REGION:10485538..10488622
Sequence
Get Decorated FASTA
Genomic Maps
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
NCBI
UCSC
Ensembl
PopFly
Function
GO Summary Ribbons
Gene Ontology (GO) Annotations (5 terms)
Molecular Function (0 terms)
There is no information supporting a Molecular Function term for this gene. (Based on a review of available data on: 2015-09-15 )
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (0 terms)
Biological Process (4 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (4 terms)
CV Term
Evidence
References
involved_in Golgi organization
inferred from biological aspect of ancestor with PANTHER:PTN000613642
(assigned by GO_Central )
(Gaudet et al., 2011)
inferred from sequence or structural similarity with UniProtKB:Q9H9E3
(FlyBase Curators, 2008-)
involved_in Golgi vesicle prefusion complex stabilization
inferred from biological aspect of ancestor with PANTHER:PTN000613642
(assigned by GO_Central )
(Gaudet et al., 2011)
involved_in intra-Golgi vesicle-mediated transport
inferred from sequence or structural similarity with SGD:S000006309
(FlyBase Curators, 2008-)
involved_in retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum
inferred from biological aspect of ancestor with PANTHER:PTN000613642
(assigned by GO_Central )
(Gaudet et al., 2011)
Cellular Component (1 term)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
part_of Golgi transport complex
inferred from direct assay
(Gillingham et al., 2014)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
part_of Golgi transport complex
inferred from biological aspect of ancestor with PANTHER:PTN000613642
(assigned by GO_Central )
(Gaudet et al., 2011)
inferred from sequence or structural similarity with HGNC:18620
(FlyBase Curators, 2008-)
Gene Group (FlyBase)
Protein Family (UniProt)
Belongs to the COG4 family. (Q95TN4)
Protein Signatures (InterPro)
Summaries
Gene Group (FlyBase)
CONSERVED OLIGOMERIC GOLGI COMPLEX -
The conserved oligomeric Golgi (COG) complex is a multi-subunit tethering complex of the CATCHR family that functions as a vesicular tether during retrograde intra-Golgi trafficking. (Adapted from PMID:23839779).
Protein Function (UniProtKB)
Required for normal Golgi function.
(UniProt, Q95TN4)
Gene Model and Products
Number of Transcripts
1
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\Cog4 for information on other features

To submit a correction to a gene model please use the Contact FlyBase form

Protein Domains (via Pfam)
Isoform displayed:
Pfam protein domains
InterPro name
classification
start
end
Protein Domains (via SMART)
Isoform displayed:
SMART protein domains
InterPro name
classification
start
end
Structure New Section
Protein 3D structure   (Predicted by AlphaFold)   (AlphaFold entry Q95TN4)

If you don't see the viewer to the right, refresh your browser.
Model Confidence:
  • Very high (pLDDT > 90)
  • Confident (90 > pLDDT > 70)
  • Low (70 > pLDDT > 50)
  • Very low (pLDDT < 50)

AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Some regions with low pLDDT may be unstructured in isolation.

Comments on Gene Model

Gene model reviewed during 5.48

Sequence Ontology: Class of Gene
nuclear_gene
protein_coding_gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
Cog4-RA
FBtr0080038
NM_135569
2666
776
Additional Transcript Data and Comments
Reported size (kB)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
UniProt
RefSeq ID
GenBank
Cog4-PA
FBpp0079628
87.7
776
5.64
Q95TN4
NP_609413
AAF52963
Polypeptides with Identical Sequences

There is only one protein coding transcript and one polypeptide associated with this gene

Additional Polypeptide Data and Comments
Reported size (kDa)
Comments
External Data
Subunit Structure (UniProtKB)

Component of the conserved oligomeric Golgi complex which is composed of eight different subunits and is required for normal Golgi morphology and localization.

(UniProt, Q95TN4)
Crossreferences
InterPro - A database of protein families, domains and functional sites
Linkouts
Sequences Consistent with the Gene Model
Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\Cog4 using the Feature Mapper tool.

External Data
Crossreferences
Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
Linkouts
Expression Data
Expression Summary Ribbons
Colored tiles in ribbon indicate that the Fly Cell Atlas project found the gene expressed in that cell type. Darker colors mean that more cells of that cell type express the gene:
 low
high 
Colorless tiles indicate that there is no scRNAseq data for the gene in that cell type.
Colored tiles in ribbon indicate that expression data (RNA and/or protein) has been curated by FlyBase for that anatomical location. Colorless tiles indicate that there is no curated data for that location.
Colored tiles in the ribbon indicate the average RNA expression level of the gene at the indicated stages:
 low
high 
as determined by RNA-seq (RPKM) using whole organism samples modENCODE, Brown et al., 2014. For complete stage-specific expression data, view the modENCODE Development RNA-Seq section under High-Throughput Expression below.
Transcript Expression
Polypeptide Expression
mass spectroscopy
Stage
Tissue/Position (including subcellular localization)
Reference
adult stage
adult head
(Aradska et al., 2015)
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
part_of Golgi transport complex
inferred from direct assay
(Gillingham et al., 2014)
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\Cog4 in GBrowse 2
RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region
Bulk Downloads
RNA-Seq RPKM values for all genes
Reference
See Gelbart and Emmert, 2013 for analysis details and data files for all genes.
Developmental Proteome: Life Cycle
Developmental Proteome: Embryogenesis
External Data and Images
Linkouts
BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
Flygut - An atlas of the Drosophila adult midgut
Images
FlyExpress - Embryonic expression images (BDGP data)
  • Stages(s) 1-3
  • Stages(s) 4-6
  • Stages(s) 7-8
  • Stages(s) 11-12
  • Stages(s) 13-16
FlyBase Wiki
Image Based Resources
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 2 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 7 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Cog4
Transgenic constructs containing regulatory region of Cog4
Aberrations (Deficiencies and Duplications) ( 1 )
Inferred from experimentation ( 1 )
Gene disrupted in
Df(2L)Exel7048
(Ryder, 2004.4.26)
Inferred from location ( 0 )
Alleles Representing Disease-Implicated Variants
Phenotypes
For more details about a specific phenotype click on the relevant allele symbol.
Phenotype manifest in
Allele
Orthologs
Downloads
Download All DIOPT Orthologs
Human Orthologs (via DIOPT v8.0)
Homo sapiens (Human) (1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
eggNOG
Hieranoid
Homologene
Inparanoid
Isobase
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
RoundUp
TreeFam
ZFIN
Alignment
Complementation?
Transgene?
Hsap\COG4
14 of 15
Yes
Yes
1  
Model Organism Orthologs (via DIOPT v8.0)
Mus musculus (laboratory mouse) (1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
eggNOG
Hieranoid
Homologene
Inparanoid
Isobase
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
RoundUp
TreeFam
ZFIN
Alignment
Complementation?
Transgene?
Mmus\Cog4
13 of 15
Yes
Yes
Rattus norvegicus (Norway rat) (1)
Rnor\Cog4
13 of 13
Yes
Yes
Xenopus tropicalis (Western clawed frog) (1)
Xtro\cog4
9 of 12
Yes
Yes
Danio rerio (Zebrafish) (1)
Drer\cog4
14 of 15
Yes
Yes
Caenorhabditis elegans (Nematode, roundworm) (1)
Cele\cogc-4
12 of 15
Yes
Yes
Arabidopsis thaliana (thale-cress) (1)
Atha\AT4G01395
8 of 9
Yes
Yes
Saccharomyces cerevisiae (Brewer's yeast) (1)
Scer\COG4
12 of 15
Yes
Yes
Schizosaccharomyces pombe (Fission yeast) (1)
Spom\cog4
10 of 12
Yes
Yes
Other Organism Orthologs (via OrthoDB)
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v8.0)
Drosophila melanogaster (Fruit fly) (1)
Gene Symbol
Score
Source
Compara
eggNOG
Homologene
Inparanoid
Isobase
OrthoDB
OrthoFinder
orthoMCL
Panther
RoundUp
Alignment
CG43322
2 of 10
Human Disease Associations
FlyBase Human Disease Model Reports
    Disease Model Summary Ribbon
    Disease Ontology (DO) Annotations
    Models Based on Experimental Evidence ( 0 )
    Allele
    Disease
    Evidence
    References
    Potential Models Based on Orthology ( 2 )
    Modifiers Based on Experimental Evidence ( 0 )
    Allele
    Disease
    Interaction
    References
    Disease Associations of Human Orthologs (via DIOPT v8.0 and OMIM)
    Note that ortholog calls supported by only 1 or 2 algorithms (DIOPT score < 3) are not shown.
    Homo sapiens (Human)
    Gene name
    Score
    OMIM
    OMIM Phenotype
    DO term
    Complementation?
    Transgene?
    COG4; component of oligomeric golgi complex 4
    14 of 15
    606976
     
    Functional Complementation Data
    Functional complementation data is computed by FlyBase using a combination of the orthology data obtained from DIOPT and OrthoDB and the allele-level genetic interaction data curated from the literature.
    Interactions
    Summary of Physical Interactions
    esyN Network Diagram
    Show neighbor-neighbor interactions:
    Select Layout:
    Legend:
    Protein
    RNA
    Selected Interactor(s)
    Interactions Browser
    View in Interactions Browser
    Please see the Physical Interaction reports below for full details
    protein-protein
    Physical Interaction
    Assay
    References
    Cog4 - CG12241
    experimental knowledge based
    (Guruharsha et al., 2011)
    Cog4 - CG3511
    experimental knowledge based
    (Guruharsha et al., 2011)
    Cog4 - Rsph3
    two hybrid
    (Hu et al., 2017.6.13)
    Summary of Genetic Interactions
    esyN Network Diagram
    Starting gene(s)
    Interaction type
    Interacting gene(s)
    Reference
    Starting gene(s)
    Interaction type
    Interacting gene(s)
    Reference
    External Data
    Subunit Structure (UniProtKB)
    Component of the conserved oligomeric Golgi complex which is composed of eight different subunits and is required for normal Golgi morphology and localization.
    (UniProt, Q95TN4 )
    Linkouts
    BioGRID - A database of protein and genetic interactions.
    DroID - A comprehensive database of gene and protein interactions.
    MIST (protein-protein) - An integrated Molecular Interaction Database
    Pathways
    Signaling Pathways (FlyBase)
    Metabolic Pathways
    FlyMet - A comprehensive tissue-specific metabolomics resource for Drosophila.
    External Data
    Linkouts
    Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
    Genomic Location and Detailed Mapping Data
    Chromosome (arm)
    2L
    Recombination map
    2-43
    Cytogenetic map
    31F1-31F1
    Sequence location
    FlyBase Computed Cytological Location
    Cytogenetic map
    Evidence for location
    31F1-31F1
    Limits computationally determined from genome sequence between P{lacW}KdelRk00311 and P{lacW}l(2)k09116k09116&P{lacW}Fatpk10307
    Experimentally Determined Cytological Location
    Cytogenetic map
    Notes
    References
    Experimentally Determined Recombination Data
    Location

    2-43

    (FlyBase, 2016)

    2-35.5

    (Comeron et al., 2012)
    Left of (cM)
    Right of (cM)
    Notes
    Stocks and Reagents
    Stocks (6)
    Genomic Clones (20)
    cDNA Clones (122)
     

    Please Note This section lists cDNAs and ESTs that fall within the genomic extent of the gene model, which may include cDNAs and ESTs of genes within introns, or of overlapping genes. Please see GBrowse for alignment of the cDNAs and ESTs to the gene model.

    cDNA clones, fully sequenced
    BDGP DGC clones
    Other clones
    Drosophila Genomics Resource Center cDNA clones

    For each fully sequenced cDNA the DGRC maintains various forms of the cDNA (e.g tagged or untagged) in several different host vectors for subsequent cloning and expression in Drosophila and Drosophila cell lines.

    cDNA Clones, End Sequenced (ESTs)
    BDGP DGC clones
    Other clones
    RNAi and Array Information
    Linkouts
    DRSC - Results frm RNAi screens
    GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
    Antibody Information
    Laboratory Generated Antibodies
     
    Commercially Available Antibodies
     
    Other Information
    Relationship to Other Genes
    Source for database identify of

    Source for identity of: Cog4 CG7456

    (Gillingham et al., 2014)
    Source for database merge of
    Additional comments
    Other Comments
    Origin and Etymology
    Discoverer
    Etymology
    Identification
    External Crossreferences and Linkouts ( 35 )
    Sequence Crossreferences
    NCBI Gene - Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.
    GenBank Nucleotide - A collection of sequences from several sources, including GenBank, RefSeq, TPA, and PDB.
    GenBank Protein - A collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB.
    RefSeq - A comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein.
    UniProt/GCRP - The gene-centric reference proteome (GCRP) provides a 1:1 mapping between genes and UniProt accessions in which a single 'canonical' isoform represents the product(s) of each protein-coding gene.
    UniProt/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information
    Other crossreferences
    AlphaFold DB - AlphaFold provides open access to protein structure predictions for the human proteome and other key proteins of interest, to accelerate scientific research.
    BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
    Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
    DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
    EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
    Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
    FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
    FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
    Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
    Flygut - An atlas of the Drosophila adult midgut
    FlyMet - A comprehensive tissue-specific metabolomics resource for Drosophila.
    GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
    iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
    InterPro - A database of protein families, domains and functional sites
    KEGG Genes - Molecular building blocks of life in the genomic space.
    MARRVEL_MODEL - MARRVEL (model organism gene)
    modMine - A data warehouse for the modENCODE project
    Linkouts
    BioGRID - A database of protein and genetic interactions.
    DroID - A comprehensive database of gene and protein interactions.
    DRSC - Results frm RNAi screens
    FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
    FlyMine - An integrated database for Drosophila genomics
    MIST (protein-protein) - An integrated Molecular Interaction Database
    Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
    Synonyms and Secondary IDs (3)
    Datasets (0)
    Study focus (0)
    Experimental Role
    Project
    Project Type
    Title
    Study result (0)
    Result
    Result Type
    Title
    References (32)