Human Gene COG4 (uc002ezc.3) Description and Page Index
  Description: Homo sapiens component of oligomeric golgi complex 4 (COG4), transcript variant 1, mRNA.
RefSeq Summary (NM_015386): 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]. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: SRR1660809.118636.1, SRR1803616.277363.1 [ECO:0000332] RNAseq introns :: mixed/partial sample support SAMEA1965299, SAMEA1966682 [ECO:0000350] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000323786.10/ ENSP00000315775.5 RefSeq Select criteria :: based on manual assertion, conservation, expression, longest protein ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr16:70,514,472-70,557,457 Size: 42,986 Total Exon Count: 19 Strand: -
Coding Region
   Position: hg19 chr16:70,514,913-70,557,446 Size: 42,534 Coding Exon Count: 19 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
mRNA DescriptionsOther NamesGeneReviewsModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr16:70,514,472-70,557,457)mRNA (may differ from genome)Protein (789 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
OMIMPubMedStanford SOURCETreefamUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: J3KNI1_HUMAN
DESCRIPTION: SubName: Full=Conserved oligomeric Golgi complex subunit 4;
CAUTION: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered as preliminary data.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): COG4
CDC HuGE Published Literature: COG4

-  MalaCards Disease Associations
  MalaCards Gene Search: COG4
Diseases sorted by gene-association score: congenital disorder of glycosylation, type iij* (1569), congenital disorder of glycosylation, type ii (7)
* = 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
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 39.16 RPKM in Testis
Total median expression: 901.08 RPKM



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

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
3' UTR -172.70441-0.392 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
IPR013167 - COG_su4

Pfam Domains:
PF08318 - COG4 transport protein

ModBase Predicted Comparative 3D Structure on J3KNI1
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  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 orthologNo orthologGenome BrowserGenome BrowserGenome BrowserGenome Browser
Gene Details  Gene DetailsGene DetailsGene Details
Gene Sorter  Gene SorterGene SorterGene Sorter
  EnsemblFlyBaseWormBaseSGD
  Protein SequenceProtein SequenceProtein SequenceProtein Sequence
  AlignmentAlignmentAlignmentAlignment

-  Descriptions from all associated GenBank mRNAs
  AL050101 - Homo sapiens mRNA; cDNA DKFZp586E1519 (from clone DKFZp586E1519).
AK297557 - Homo sapiens cDNA FLJ56623 complete cds, highly similar to Conserved oligomeric Golgi complex component 4.
BC027726 - Homo sapiens component of oligomeric golgi complex 4, mRNA (cDNA clone IMAGE:4844771), partial cds.
BC072438 - Homo sapiens component of oligomeric golgi complex 4, mRNA (cDNA clone MGC:90212 IMAGE:6011802), complete cds.
BX648010 - Homo sapiens mRNA; cDNA DKFZp686I0659 (from clone DKFZp686I0659).
AK096557 - Homo sapiens cDNA FLJ39238 fis, clone OCBBF2007946.
AK026435 - Homo sapiens cDNA: FLJ22782 fis, clone KAIA1981.
BC013347 - Homo sapiens component of oligomeric golgi complex 4, mRNA (cDNA clone IMAGE:3952952), partial cds.
BC006306 - Homo sapiens component of oligomeric golgi complex 4, mRNA (cDNA clone IMAGE:4106997), partial cds.
AB088369 - Homo sapiens mRNA for Cog4S, complete cds.
AK022874 - Homo sapiens cDNA FLJ12812 fis, clone NT2RP2002498, highly similar to Homo sapiens component of oligomeric golgi complex 4 (COG4), mRNA.
AK293235 - Homo sapiens cDNA FLJ53466 complete cds, highly similar to Conserved oligomeric Golgi complex component 4.
KJ902378 - Synthetic construct Homo sapiens clone ccsbBroadEn_11772 COG4 gene, encodes complete protein.
KJ902379 - Synthetic construct Homo sapiens clone ccsbBroadEn_11773 COG4 gene, encodes complete protein.
BC000796 - Homo sapiens, clone IMAGE:3451845, mRNA, partial cds.
JD342627 - Sequence 323651 from Patent EP1572962.
JD224293 - Sequence 205317 from Patent EP1572962.
JD058766 - Sequence 39790 from Patent EP1572962.
JD073221 - Sequence 54245 from Patent EP1572962.
JD343978 - Sequence 325002 from Patent EP1572962.
JD189626 - Sequence 170650 from Patent EP1572962.
JD408605 - Sequence 389629 from Patent EP1572962.
JD267947 - Sequence 248971 from Patent EP1572962.
JD119525 - Sequence 100549 from Patent EP1572962.
JD130130 - Sequence 111154 from Patent EP1572962.
JD554963 - Sequence 535987 from Patent EP1572962.
CU680568 - Synthetic construct Homo sapiens gateway clone IMAGE:100017393 5' read COG4 mRNA.
BC128144 - Homo sapiens component of oligomeric golgi complex 4, mRNA (cDNA clone IMAGE:40112536), partial cds.
BC128145 - Homo sapiens component of oligomeric golgi complex 4, mRNA (cDNA clone IMAGE:40112540), partial cds.

-  Other Names for This Gene
  Alternate Gene Symbols: J3KNI1, J3KNI1_HUMAN, NM_015386, NP_056201
UCSC ID: uc002ezc.3
RefSeq Accession: NM_015386
Protein: J3KNI1 CCDS: CCDS10892.2

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene COG4:
cdg (Congenital Disorders of N-Linked Glycosylation and Multiple Pathway Overview)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_015386.2
exon count: 19CDS single in 3' UTR: no RNA size: 2838
ORF size: 2370CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 4825.00frame shift in genome: no % Coverage: 99.44
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
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