Human Gene GCC2 (ENST00000309863.11) from GENCODE V44
  Description: Homo sapiens GRIP and coiled-coil domain containing 2 (GCC2), transcript variant 1, mRNA. (from RefSeq NM_181453)
RefSeq Summary (NM_181453): The protein encoded by this gene is a peripheral membrane protein localized to the trans-Golgi network. It is sensitive to brefeldin A. This encoded protein contains a GRIP domain which is thought to be used in targeting. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2009].
Gencode Transcript: ENST00000309863.11
Gencode Gene: ENSG00000135968.22
Transcript (Including UTRs)
   Position: hg38 chr2:108,449,206-108,509,415 Size: 60,210 Total Exon Count: 23 Strand: +
Coding Region
   Position: hg38 chr2:108,449,275-108,507,630 Size: 58,356 Coding Exon Count: 23 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 09:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:108,449,206-108,509,415)mRNA (may differ from genome)Protein (1684 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCHPRDLynxMalacardsMGIneXtProt
OMIMPubMedReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: GCC2_HUMAN
DESCRIPTION: RecName: Full=GRIP and coiled-coil domain-containing protein 2; AltName: Full=185 kDa Golgi coiled-coil protein; Short=GCC185; AltName: Full=CLL-associated antigen KW-11; AltName: Full=CTCL tumor antigen se1-1; AltName: Full=Ran-binding protein 2-like 4; Short=RanBP2L4; AltName: Full=Renal carcinoma antigen NY-REN-53;
FUNCTION: Golgin which probably tethers transport vesicles to the trans-Golgi network (TGN) and regulates vesicular transport between the endosomes and the Golgi. As a RAB9A effector it is involved in recycling of the mannose 6-phosphate receptor from the late endosomes to the TGN. May also play a role in transport between the recycling endosomes and the Golgi. Required for maintenance of the Golgi structure, it is involved in the biogenesis of noncentrosomal, Golgi-associated microtubules through recruitment of CLASP1 and CLASP2.
SUBUNIT: Homodimer. Interacts (via GRIP domain) with RAB6A (preferentially in its GTP-bound form). May interact (RAB6A- dependent) with ARL1; according to PubMed:19703403, RAB6A and ARL1 are not involved in GCC2 Golgi localization as proposed by PubMed:18243103. Interacts (probably via GRIP domain) with RAB9A (preferentially in its GTP-bound form). Interacts with CLASP1 and CLASP2; recruits both proteins to membranes of the TGN. Interacts with STX16.
INTERACTION: Self; NbExp=2; IntAct=EBI-1645320, EBI-1645320; P20340:RAB6A; NbExp=4; IntAct=EBI-1645320, EBI-1052826;
SUBCELLULAR LOCATION: Cytoplasm. Golgi apparatus, trans-Golgi network membrane; Peripheral membrane protein.
TISSUE SPECIFICITY: Ubiquitous.
DOMAIN: Extended rod-like protein with coiled-coil domains.
SIMILARITY: Contains 1 GRIP domain.
SEQUENCE CAUTION: Sequence=AAG34902.1; Type=Frameshift; Positions=694, 700, 937, 940; Sequence=AAH37774.1; Type=Miscellaneous discrepancy; Note=Wrong choice of CDS; Sequence=AAI46790.1; Type=Miscellaneous discrepancy; Note=Wrong choice of CDS; Sequence=AAL99918.1; Type=Erroneous initiation; Note=Translation N-terminally shortened; Sequence=AAX88838.1; Type=Erroneous gene model prediction; Sequence=BAA20794.2; Type=Miscellaneous discrepancy; Note=Wrong choice of CDS; Sequence=EAW53882.1; Type=Erroneous gene model prediction;

-  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


-  MalaCards Disease Associations
  MalaCards Gene Search: GCC2
Diseases sorted by gene-association score: hypertrophy of breast (11)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene
  • D000082 Acetaminophen
  • C532162 2-(1H-indazol-4-yl)-6-(4-methanesulfonylpiperazin-1-ylmethyl)-4-morpholin-4-ylthieno(3,2-d)pyrimidine
  • D015123 7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide
  • D016604 Aflatoxin B1
  • D002737 Chloroprene
  • D003010 Clorgyline
  • D019327 Copper Sulfate
  • D016572 Cyclosporine
  • D011285 Pregnenolone Carbonitrile
  • D013749 Tetrachlorodibenzodioxin
          more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 9.35 RPKM in Small Intestine - Terminal Ileum
Total median expression: 279.29 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 -30.0069-0.435 Picture PostScript Text
3' UTR -421.301785-0.236 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
IPR000237 - GRIP

Pfam Domains:
PF01465 - GRIP domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help
3BBP - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q8IWJ2
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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
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0042802 identical protein binding

Biological Process:
GO:0006622 protein targeting to lysosome
GO:0015031 protein transport
GO:0031023 microtubule organizing center organization
GO:0034067 protein localization to Golgi apparatus
GO:0034453 microtubule anchoring
GO:0034499 late endosome to Golgi transport
GO:0042147 retrograde transport, endosome to Golgi
GO:0070861 regulation of protein exit from endoplasmic reticulum
GO:0071955 recycling endosome to Golgi transport
GO:0090161 Golgi ribbon formation
GO:0043001 Golgi to plasma membrane protein transport

Cellular Component:
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005794 Golgi apparatus
GO:0005802 trans-Golgi network
GO:0005829 cytosol
GO:0016020 membrane


-  Descriptions from all associated GenBank mRNAs
  AK090813 - Homo sapiens cDNA FLJ33494 fis, clone BRAMY2003898, highly similar to Homo sapiens GRIP and coiled-coil domain containing 2 (GCC2), transcript variant 1, mRNA.
AX746628 - Sequence 153 from Patent EP1308459.
BC037774 - Homo sapiens GRIP and coiled-coil domain containing 2, mRNA (cDNA clone IMAGE:5276271), partial cds.
AF432211 - Homo sapiens CLL-associated antigen KW-11 mRNA, partial cds.
AB002334 - Homo sapiens mRNA for KIAA0336 gene, partial cds.
BC146789 - Homo sapiens GRIP and coiled-coil domain containing 2, mRNA (cDNA clone MGC:166883 IMAGE:9007253), complete cds.
AK308707 - Homo sapiens cDNA, FLJ98748.
BC020645 - Homo sapiens GRIP and coiled-coil domain containing 2, mRNA (cDNA clone IMAGE:4659829), partial cds.
AB384463 - Synthetic construct DNA, clone: pF1KA0336, Homo sapiens GCC2 gene for Ran-binding protein 2-like 4, complete cds, without stop codon, in Flexi system.
KJ904629 - Synthetic construct Homo sapiens clone ccsbBroadEn_14023 GCC2 gene, encodes complete protein.
AF273042 - Homo sapiens CTCL tumor antigen se1-1 mRNA, complete cds.
JD283619 - Sequence 264643 from Patent EP1572962.
JD104719 - Sequence 85743 from Patent EP1572962.
JD392037 - Sequence 373061 from Patent EP1572962.
JD354696 - Sequence 335720 from Patent EP1572962.
JD415801 - Sequence 396825 from Patent EP1572962.
JD511935 - Sequence 492959 from Patent EP1572962.
JD209604 - Sequence 190628 from Patent EP1572962.
JD268289 - Sequence 249313 from Patent EP1572962.
JD480039 - Sequence 461063 from Patent EP1572962.
JD291656 - Sequence 272680 from Patent EP1572962.
JD467208 - Sequence 448232 from Patent EP1572962.
JD548947 - Sequence 529971 from Patent EP1572962.
JD495603 - Sequence 476627 from Patent EP1572962.
JD265265 - Sequence 246289 from Patent EP1572962.
JD174153 - Sequence 155177 from Patent EP1572962.
JD324910 - Sequence 305934 from Patent EP1572962.
JD415430 - Sequence 396454 from Patent EP1572962.
JD280306 - Sequence 261330 from Patent EP1572962.
JD224373 - Sequence 205397 from Patent EP1572962.
JD185465 - Sequence 166489 from Patent EP1572962.
JD366792 - Sequence 347816 from Patent EP1572962.
JD149548 - Sequence 130572 from Patent EP1572962.
JD117663 - Sequence 98687 from Patent EP1572962.
JD146535 - Sequence 127559 from Patent EP1572962.
JD268562 - Sequence 249586 from Patent EP1572962.
JD367735 - Sequence 348759 from Patent EP1572962.
JD537690 - Sequence 518714 from Patent EP1572962.
JD160007 - Sequence 141031 from Patent EP1572962.
JD214070 - Sequence 195094 from Patent EP1572962.
JD439942 - Sequence 420966 from Patent EP1572962.
JD279456 - Sequence 260480 from Patent EP1572962.
JD352660 - Sequence 333684 from Patent EP1572962.
JD244388 - Sequence 225412 from Patent EP1572962.
JD503810 - Sequence 484834 from Patent EP1572962.
JD503809 - Sequence 484833 from Patent EP1572962.
JD510014 - Sequence 491038 from Patent EP1572962.
JD350420 - Sequence 331444 from Patent EP1572962.

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

Protein Q8IWJ2 (Reactome details) participates in the following event(s):

R-HSA-6814674 Tethering of late endosome-derived vesicles by GARP, STX10:ST16:VTI1A and Golgins
R-HSA-6814091 ARL1 recruits TGN Golgin homodimers
R-HSA-6811431 RAB6:GTP binds the GARP and COG complexes, t-SNAREs and endosome-derived vesicles
R-HSA-6811440 Retrograde transport at the Trans-Golgi-Network
R-HSA-6811442 Intra-Golgi and retrograde Golgi-to-ER traffic
R-HSA-199991 Membrane Trafficking
R-HSA-5653656 Vesicle-mediated transport

-  Other Names for This Gene
  Alternate Gene Symbols: A6H8X8, ENST00000309863.1, ENST00000309863.10, ENST00000309863.2, ENST00000309863.3, ENST00000309863.4, ENST00000309863.5, ENST00000309863.6, ENST00000309863.7, ENST00000309863.8, ENST00000309863.9, GCC2_HUMAN, KIAA0336, NM_181453, O15045, Q4ZG46, Q8IWJ2, Q8TDH3, Q9H2G8, RANBP2L4, uc002tec.1, uc002tec.2, uc002tec.3, uc002tec.4, uc002tec.5
UCSC ID: ENST00000309863.11
RefSeq Accession: NM_181453
Protein: Q8IWJ2 (aka GCC2_HUMAN)
CCDS: CCDS33268.1

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