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Aliases for COG4 Gene

Aliases for COG4 Gene

  • Component Of Oligomeric Golgi Complex 4 2 3 4 5
  • COG Complex Subunit 4 3 4
  • Conserved Oligomeric Golgi Complex Protein 4 3
  • Conserved Oligomeric Golgi Complex Subunit 4 3
  • Complexed With Dor1p 3
  • CDG2J 3
  • COD1 3

External Ids for COG4 Gene

Previous GeneCards Identifiers for COG4 Gene

  • GC16M061216
  • GC16M070934
  • GC16M070249
  • GC16M070290
  • GC16M069071
  • GC16M056346

Summaries for COG4 Gene

Entrez Gene Summary for COG4 Gene

  • 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]

GeneCards Summary for COG4 Gene

COG4 (Component Of Oligomeric Golgi Complex 4) is a Protein Coding gene. Diseases associated with COG4 include Congenital Disorder Of Glycosylation, Type Iij and Congenital Disorder Of Glycosylation, Type Ii. Among its related pathways are Golgi-to-ER retrograde transport and Retrograde transport at the Trans-Golgi-Network.

UniProtKB/Swiss-Prot for COG4 Gene

  • Required for normal Golgi function. Plays a role in SNARE-pin assembly and Golgi-to-ER retrograde transport via its interaction with SCFD1.

Gene Wiki entry for COG4 Gene

Additional gene information for COG4 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for COG4 Gene

Genomics for COG4 Gene

Regulatory Elements for COG4 Gene

Enhancers for COG4 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH16H070426 2.1 FANTOM5 Ensembl ENCODE dbSUPER 22.3 +92.6 92614 8 MLX ZFP64 FEZF1 DMAP1 YBX1 YY1 SP3 MEF2D SSRP1 GLIS1 SF3B3 DDX19B NONOP1 COG4 PDPR PDXDC2P-NPIPB14P NFAT5 LOC400541 ST3GAL2 NPIPB14P
GH16H070436 1.4 ENCODE dbSUPER 24.2 +85.4 85425 3 HDGF PKNOX1 ARNT ARID4B SIN3A FEZF1 ZNF2 ZBTB7B YY1 SLC30A9 SMG1P7 DDX19B COG4 CLEC18A PDXDC2P-NPIPB14P SF3B3 NFAT5 NONOP1 FUK PDXDC2P
GH16H070287 1.4 ENCODE dbSUPER 21.3 +234.1 234107 4 PKNOX1 FOXA2 ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 ZNF766 FOS PDPR DDX19A DDX19B SMG1P7 LOC400541 NFAT5 SF3B3 NONOP1 PDXDC2P-NPIPB14P COG4
GH16H070414 1.9 FANTOM5 Ensembl ENCODE dbSUPER 14 +104.3 104310 10 HDGF PKNOX1 ATF1 ARNT ARID4B TCF12 ZNF121 ZNF766 GATA2 ATF7 FUK COG4 RPS27P26 RNU6-23P LOC100506083 AARS DDX19B SMG1P7 PDXDC2P-NPIPB14P WWP2
GH16H070250 1.1 ENCODE 22.2 +272.0 272032 2 HDGF PKNOX1 MLX ARNT ZFP64 ARID4B SIN3A DMAP1 ZNF2 YY1 EXOSC6 COG4 NPIPB14P DDX19B HYDIN SF3B3 PDPR NONOP1 LOC100506083 PDXDC2P-NPIPB14P
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around COG4 on UCSC Golden Path with GeneCards custom track

Promoters for COG4 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000087577 -435 2401 PKNOX1 ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF766 ZNF207 ZHX2

Genomic Location for COG4 Gene

Chromosome:
16
Start:
70,480,568 bp from pter
End:
70,523,565 bp from pter
Size:
42,998 bases
Orientation:
Minus strand

Genomic View for COG4 Gene

Genes around COG4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
COG4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for COG4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for COG4 Gene

Proteins for COG4 Gene

  • Protein details for COG4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9H9E3-COG4_HUMAN
    Recommended name:
    Conserved oligomeric Golgi complex subunit 4
    Protein Accession:
    Q9H9E3
    Secondary Accessions:
    • B4DMN8
    • C9JS23
    • Q96D40
    • Q9BRF0
    • Q9BVZ2
    • Q9H5Y4
    • Q9Y3W3

    Protein attributes for COG4 Gene

    Size:
    785 amino acids
    Molecular mass:
    89083 Da
    Quaternary structure:
    • Monomer. Component of the conserved oligomeric Golgi (COG) complex which is composed of eight different subunits and is required for normal Golgi morphology and localization. Mediates interaction of SCFD1 with the COG complex. Interacts with STX5.
    SequenceCaution:
    • Sequence=BAB15483.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for COG4 Gene

    Alternative splice isoforms for COG4 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for COG4 Gene

Post-translational modifications for COG4 Gene

  • Ubiquitination at posLast=7373
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for COG4 Gene

Domains & Families for COG4 Gene

Gene Families for COG4 Gene

Protein Domains for COG4 Gene

InterPro:
ProtoNet:

Graphical View of Domain Structure for InterPro Entry

Q9H9E3

UniProtKB/Swiss-Prot:

COG4_HUMAN :
  • Belongs to the COG4 family.
Family:
  • Belongs to the COG4 family.
genes like me logo Genes that share domains with COG4: view

Function for COG4 Gene

Molecular function for COG4 Gene

UniProtKB/Swiss-Prot Function:
Required for normal Golgi function. Plays a role in SNARE-pin assembly and Golgi-to-ER retrograde transport via its interaction with SCFD1.

Gene Ontology (GO) - Molecular Function for COG4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 15047703
genes like me logo Genes that share ontologies with COG4: view
genes like me logo Genes that share phenotypes with COG4: view

Human Phenotype Ontology for COG4 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

CRISPR Products

miRNA for COG4 Gene

miRTarBase miRNAs that target COG4

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for COG4
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Animal Models , Transcription Factor Targets and HOMER Transcription for COG4 Gene

Localization for COG4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for COG4 Gene

Golgi apparatus membrane; Peripheral membrane protein; Cytoplasmic side.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for COG4 gene
Compartment Confidence
golgi apparatus 5
nucleus 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Golgi apparatus (2)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for COG4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000139 Golgi membrane TAS --
GO:0005794 Golgi apparatus IEA --
GO:0016020 membrane IEA --
GO:0017119 Golgi transport complex IDA 15047703
GO:0032588 trans-Golgi network membrane TAS --
genes like me logo Genes that share ontologies with COG4: view

Pathways & Interactions for COG4 Gene

genes like me logo Genes that share pathways with COG4: view

Gene Ontology (GO) - Biological Process for COG4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000301 retrograde transport, vesicle recycling within Golgi IBA --
GO:0006810 transport IEA --
GO:0006888 ER to Golgi vesicle-mediated transport TAS --
GO:0006890 retrograde vesicle-mediated transport, Golgi to ER IMP 19536132
GO:0007030 Golgi organization IMP 19536132
genes like me logo Genes that share ontologies with COG4: view

No data available for SIGNOR curated interactions for COG4 Gene

Drugs & Compounds for COG4 Gene

No Compound Related Data Available

Transcripts for COG4 Gene

Unigene Clusters for COG4 Gene

Component of oligomeric golgi complex 4:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for COG4
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

Alternative Splicing Database (ASD) splice patterns (SP) for COG4 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10a · 10b ^ 11a · 11b ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17a · 17b ^ 18 ^ 19 ^ 20 ^ 21a · 21b · 21c
SP1: - -
SP2: - - -
SP3: - - - -
SP4: - - -
SP5:
SP6: -
SP7:

Relevant External Links for COG4 Gene

GeneLoc Exon Structure for
COG4
ECgene alternative splicing isoforms for
COG4

Expression for COG4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for COG4 Gene

Protein differential expression in normal tissues from HIPED for COG4 Gene

This gene is overexpressed in Bone (60.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for COG4 Gene



Protein tissue co-expression partners for COG4 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of COG4 Gene:

COG4

SOURCE GeneReport for Unigene cluster for COG4 Gene:

Hs.208680

Evidence on tissue expression from TISSUES for COG4 Gene

  • Nervous system(4.9)
  • Intestine(4.3)
  • Skin(4.3)
  • Blood(4.2)
  • Muscle(4.2)
  • Lung(2.4)

Phenotype-based relationships between genes and organs from Gene ORGANizer for COG4 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • digestive
  • immune
  • nervous
  • respiratory
  • skeletal muscle
Organs:
Head and neck:
  • brain
  • head
Thorax:
  • chest wall
Abdomen:
  • abdominal wall
  • biliary tract
  • liver
genes like me logo Genes that share expression patterns with COG4: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for COG4 Gene

Orthologs for COG4 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for COG4 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia COG4 33 34
  • 99.12 (n)
oppossum
(Monodelphis domestica)
Mammalia COG4 34
  • 93 (a)
OneToOne
dog
(Canis familiaris)
Mammalia COG4 33 34
  • 92.98 (n)
cow
(Bos Taurus)
Mammalia COG4 33 34
  • 91.93 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia COG4 34
  • 91 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Cog4 33
  • 90.32 (n)
mouse
(Mus musculus)
Mammalia Cog4 33 16 34
  • 89.68 (n)
chicken
(Gallus gallus)
Aves COG4 33 34
  • 80.17 (n)
lizard
(Anolis carolinensis)
Reptilia COG4 34
  • 79 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100145689 33
  • 75.8 (n)
zebrafish
(Danio rerio)
Actinopterygii cog4 33 34
  • 69.67 (n)
Dr.214 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.10077 33
fruit fly
(Drosophila melanogaster)
Insecta CG7456 35 33 34
  • 50.93 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP008875 33
  • 50.3 (n)
worm
(Caenorhabditis elegans)
Secernentea cogc-4 33 34
  • 47.04 (n)
Y51H7C.6a 35
  • 32 (a)
Y51H7C.6b 35
  • 32 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes COG4 34 36
  • 18 (a)
OneToOne
thale cress
(Arabidopsis thaliana)
eudicotyledons AT4G01400 33
  • 46.35 (n)
rice
(Oryza sativa)
Liliopsida Os02g0456000 33
  • 43.2 (n)
Os.15610 33
Species where no ortholog for COG4 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for COG4 Gene

ENSEMBL:
Gene Tree for COG4 (if available)
TreeFam:
Gene Tree for COG4 (if available)

Paralogs for COG4 Gene

No data available for Paralogs for COG4 Gene

Variants for COG4 Gene

Sequence variations from dbSNP and Humsavar for COG4 Gene

SNP ID Clin Chr 16 pos Sequence Context AA Info Type
VAR_063767 Congenital disorder of glycosylation 2J (CDG2J) [MIM:613489]
rs267606740 Pathogenic 70,481,397(-) TTGCC(C/T)GGCTC nc-transcript-variant, downstream-variant-500B, reference, missense
rs387907202 Pathogenic 70,512,280(-) TGCAT(G/T)AGGAG nc-transcript-variant, reference, stop-gained
rs387907203 Pathogenic 70,481,062(-) GGTGC(G/T)GGCCC nc-transcript-variant, downstream-variant-500B, reference, missense
rs376663459 Likely pathogenic 70,514,350(+) CTGTC(A/G)GCTGA nc-transcript-variant, reference, stop-gained

Structural Variations from Database of Genomic Variants (DGV) for COG4 Gene

Variant ID Type Subtype PubMed ID
esv1193820 CNV deletion 17803354
esv2008425 CNV deletion 18987734
esv2047908 CNV deletion 18987734
esv2425317 CNV deletion 19546169
esv2439753 CNV deletion 19546169
esv2673546 CNV deletion 23128226
esv2675941 CNV deletion 23128226
esv2676236 CNV deletion 23128226
esv2714671 CNV deletion 23290073
esv2714672 CNV deletion 23290073
esv3553626 CNV deletion 23714750
esv3892881 CNV gain 25118596
esv3892883 CNV gain 25118596
esv4553 CNV loss 18987735
esv8463 CNV loss 19470904
nsv1070772 CNV deletion 25765185
nsv1113819 CNV deletion 24896259
nsv1123063 CNV deletion 24896259
nsv7285 OTHER inversion 18451855
nsv833272 CNV loss 17160897
nsv958048 CNV deletion 24416366

Variation tolerance for COG4 Gene

Residual Variation Intolerance Score: 32.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.38; 42.16% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for COG4 Gene

Human Gene Mutation Database (HGMD)
COG4
SNPedia medical, phenotypic, and genealogical associations of SNPs for
COG4

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for COG4 Gene

Disorders for COG4 Gene

MalaCards: The human disease database

(2) MalaCards diseases for COG4 Gene - From: HGMD, OMIM, ClinVar, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
congenital disorder of glycosylation, type iij
  • cog4-cdg
congenital disorder of glycosylation, type ii
  • congenital disorder of glycosylation, type iie
- elite association - COSMIC cancer census association via MalaCards
Search COG4 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

COG4_HUMAN
  • Congenital disorder of glycosylation 2J (CDG2J) [MIM:613489]: A multisystem disorder caused by a defect in glycoprotein biosynthesis and characterized by under-glycosylated serum glycoproteins. Congenital disorders of glycosylation result in a wide variety of clinical features, such as defects in the nervous system development, psychomotor retardation, dysmorphic features, hypotonia, coagulation disorders, and immunodeficiency. The broad spectrum of features reflects the critical role of N-glycoproteins during embryonic development, differentiation, and maintenance of cell functions. {ECO:0000269 PubMed:19494034, ECO:0000269 PubMed:19651599}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for COG4

Genetic Association Database (GAD)
COG4
Human Genome Epidemiology (HuGE) Navigator
COG4
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
COG4
genes like me logo Genes that share disorders with COG4: view

No data available for Genatlas for COG4 Gene

Publications for COG4 Gene

  1. Structural basis for a human glycosylation disorder caused by mutation of the COG4 gene. (PMID: 19651599) Richardson BC … Hughson FM (Proceedings of the National Academy of Sciences of the United States of America 2009) 3 4 60
  2. Direct interaction between the COG complex and the SM protein, Sly1, is required for Golgi SNARE pairing. (PMID: 19536132) Laufman O … Lev S (The EMBO journal 2009) 3 4 60
  3. Golgi function and dysfunction in the first COG4-deficient CDG type II patient. (PMID: 19494034) Reynders E … Matthijs G (Human molecular genetics 2009) 3 4 60
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 60
  5. An unappreciated role for RNA surveillance. (PMID: 14759258) Hillman RT … Brenner SE (Genome biology 2004) 3 4 60

Products for COG4 Gene

Sources for COG4 Gene

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