Human Gene COG6 (uc001uxh.2)
  Description: Homo sapiens component of oligomeric golgi complex 6 (COG6), transcript variant 1, mRNA.
RefSeq Summary (NM_020751): This gene encodes a subunit of the conserved oligomeric Golgi complex that is required for maintaining normal structure and activity of the Golgi apparatus. The encoded protein is organized with conserved oligomeric Golgi complex components 5, 7 and 8 into a sub-complex referred to as lobe B. Alternative splicing results in multiple transcript variants.[provided by RefSeq, Feb 2009].
Transcript (Including UTRs)
   Position: hg19 chr13:40,229,764-40,326,765 Size: 97,002 Total Exon Count: 19 Strand: +
Coding Region
   Position: hg19 chr13:40,229,864-40,325,230 Size: 95,367 Coding Exon Count: 19 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsMalaCards
CTDGene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein Structure
Other SpeciesGO AnnotationsmRNA DescriptionsPathwaysOther NamesGeneReviews
Model InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr13:40,229,764-40,326,765)mRNA (may differ from genome)Protein (657 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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MGIneXtProtOMIMPubMedReactomeTreefam
UniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: COG6_HUMAN
DESCRIPTION: RecName: Full=Conserved oligomeric Golgi complex subunit 6; Short=COG complex subunit 6; AltName: Full=Component of oligomeric Golgi complex 6;
FUNCTION: Required for normal Golgi function (By similarity).
SUBUNIT: Component of the conserved oligomeric Golgi complex which is composed of eight different subunits and is required for normal Golgi morphology and localization (By similarity).
SUBCELLULAR LOCATION: Golgi apparatus membrane; Peripheral membrane protein (By similarity).
DISEASE: Defects in COG6 are the cause of congenital disorder of glycosylation type 2L (CDG2L) [MIM:614576]. CDG2L is 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. Clinical features of CDG2L include neonatal intractable focal seizures, vomiting, loss of consciousness, intracranial bleeding due to vitamin K deficiency, and death in infancy.
SIMILARITY: Belongs to the COG6 family.
SEQUENCE CAUTION: Sequence=AAD29633.1; Type=Erroneous translation; Note=Wrong choice of CDS;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): COG6
CDC HuGE Published Literature: COG6
Positive Disease Associations: Alanine Transaminase , Blood Pressure , Colitis, Ulcerative , Cornea , Iron , psoriasis
Related Studies:
  1. Alanine Transaminase
    Emelia J Benjamin et al. BMC medical genetics 2007, Genome-wide association with select biomarker traits in the Framingham Heart Study., BMC medical genetics. [PubMed 17903293]
    The Framingham GWAS represents a resource to describe potentially novel genetic influences on systemic biomarker variability. The newly described associations will need to be replicated in other studies.
  2. Alanine Transaminase
    Emelia J Benjamin et al. BMC medical genetics 2007, Genome-wide association with select biomarker traits in the Framingham Heart Study., BMC medical genetics. [PubMed 17903293]
    The Framingham GWAS represents a resource to describe potentially novel genetic influences on systemic biomarker variability. The newly described associations will need to be replicated in other studies.
  3. Alanine Transaminase
    Emelia J Benjamin et al. BMC medical genetics 2007, Genome-wide association with select biomarker traits in the Framingham Heart Study., BMC medical genetics. [PubMed 17903293]
    The Framingham GWAS represents a resource to describe potentially novel genetic influences on systemic biomarker variability. The newly described associations will need to be replicated in other studies.
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: COG6
Diseases sorted by gene-association score: congenital disorder of glycosylation, type iil* (1550), shaheen syndrome* (869), hypohidrosis (33), congenital disorder of glycosylation, type iih (13), corneal dystrophy, posterior amorphous (7), intellectual disability (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 7.18 RPKM in Pituitary
Total median expression: 145.97 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -54.80100-0.548 Picture PostScript Text
3' UTR -338.501535-0.221 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR010490 - COG_su6

Pfam Domains:
PF06419 - Conserved oligomeric complex COG6

ModBase Predicted Comparative 3D Structure on Q9Y2V7
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-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserGenome BrowserGenome BrowserGenome BrowserNo ortholog
Gene DetailsGene Details Gene DetailsGene Details 
Gene SorterGene Sorter Gene SorterGene Sorter 
 RGDEnsemblFlyBaseWormBase 
 Protein SequenceProtein SequenceProtein SequenceProtein Sequence 
 AlignmentAlignmentAlignmentAlignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding

Biological Process:
GO:0006888 ER to Golgi vesicle-mediated transport
GO:0006891 intra-Golgi vesicle-mediated transport
GO:0015031 protein transport
GO:0070085 glycosylation

Cellular Component:
GO:0000139 Golgi membrane
GO:0005794 Golgi apparatus
GO:0016020 membrane
GO:0017119 Golgi transport complex
GO:0032588 trans-Golgi network membrane


-  Descriptions from all associated GenBank mRNAs
  KJ899345 - Synthetic construct Homo sapiens clone ccsbBroadEn_08739 COG6 gene, encodes complete protein.
AK294443 - Homo sapiens cDNA FLJ56431 complete cds, highly similar to Conserved oligomeric Golgi complex component 6.
BC051723 - Homo sapiens component of oligomeric golgi complex 6, mRNA (cDNA clone MGC:48438 IMAGE:5263056), complete cds.
CR627406 - Homo sapiens mRNA; cDNA DKFZp313D191 (from clone DKFZp313D191).
HM005354 - Homo sapiens clone HTL-T-41 testicular tissue protein Li 41 mRNA, complete cds.
AB032960 - Homo sapiens mRNA for KIAA1134 protein, partial cds.
AF116827 - Homo sapiens clone HAW1052 unknown mRNA.
AK026638 - Homo sapiens cDNA: FLJ22985 fis, clone KAT11645, highly similar to AF116827 Homo sapiens clone HAW1052 unknown mRNA.
JD200419 - Sequence 181443 from Patent EP1572962.
JD545882 - Sequence 526906 from Patent EP1572962.
JD336624 - Sequence 317648 from Patent EP1572962.
JD041661 - Sequence 22685 from Patent EP1572962.
AK310953 - Homo sapiens cDNA, FLJ17995.
BC027469 - Homo sapiens component of oligomeric golgi complex 6, mRNA (cDNA clone IMAGE:4480105), with apparent retained intron.
JD350088 - Sequence 331112 from Patent EP1572962.
JD566420 - Sequence 547444 from Patent EP1572962.
JD508256 - Sequence 489280 from Patent EP1572962.
JD357650 - Sequence 338674 from Patent EP1572962.
JD549504 - Sequence 530528 from Patent EP1572962.
JD103692 - Sequence 84716 from Patent EP1572962.
JD304337 - Sequence 285361 from Patent EP1572962.
JD355481 - Sequence 336505 from Patent EP1572962.
JD544829 - Sequence 525853 from Patent EP1572962.
JD126299 - Sequence 107323 from Patent EP1572962.
JD552396 - Sequence 533420 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9Y2V7 (Reactome details) participates in the following event(s):

R-HSA-6809006 Vesicle is tethered through binding GOLGA2:GORASP1, GOLGB1 and the COG complex
R-HSA-6811433 The COG tethering complex interacts with numerous SNAREs at the Golgi membrane
R-HSA-8847544 The COG complex and CUX1 and GOLGA5 dimers contribute to intra-Golgi vesicle tethering
R-HSA-8849748 The COG complex binds RABs at the Golgi membrane
R-HSA-6811431 RAB6:GTP binds the GARP and COG complexes, t-SNAREs and endosome-derived vesicles
R-HSA-6809011 cis-Golgi t-SNAREs bind YKT6 on tethered vesicle
R-HSA-6807878 COPI-mediated anterograde transport
R-HSA-6811438 Intra-Golgi traffic
R-HSA-6811440 Retrograde transport at the Trans-Golgi-Network
R-HSA-199977 ER to Golgi Anterograde Transport
R-HSA-6811442 Intra-Golgi and retrograde Golgi-to-ER traffic
R-HSA-199991 Membrane Trafficking
R-HSA-948021 Transport to the Golgi and subsequent modification
R-HSA-5653656 Vesicle-mediated transport
R-HSA-446203 Asparagine N-linked glycosylation
R-HSA-597592 Post-translational protein modification
R-HSA-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: COG6_HUMAN, KIAA1134, NM_020751, NP_065802, Q5T0U1, Q6AI19, Q86V49, Q9ULT5, Q9Y2V7
UCSC ID: uc001uxh.2
RefSeq Accession: NM_020751
Protein: Q9Y2V7 (aka COG6_HUMAN)
CCDS: CCDS9370.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene COG6:
cdg (Congenital Disorders of N-Linked Glycosylation and Multiple Pathway Overview)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_020751.2
exon count: 19CDS single in 3' UTR: no RNA size: 3627
ORF size: 1974CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 4246.00frame shift in genome: no % Coverage: 99.50
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.