Human Gene CNIH3 (ENST00000272133.4_4) from GENCODE V47lift37
  Description: cornichon family AMPA receptor auxiliary protein 3, transcript variant 6 (from RefSeq NR_136287.2)
Gencode Transcript: ENST00000272133.4_4
Gencode Gene: ENSG00000143786.8_8
Transcript (Including UTRs)
   Position: hg19 chr1:224,804,019-224,928,256 Size: 124,238 Total Exon Count: 6 Strand: +
Coding Region
   Position: hg19 chr1:224,804,877-224,927,058 Size: 122,182 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:224,804,019-224,928,256)mRNA (may differ from genome)Protein (160 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIPubMedReactomeUniProtKB
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CNIH3_HUMAN
DESCRIPTION: RecName: Full=Protein cornichon homolog 3;
FUNCTION: Regulates the trafficking and gating properties of AMPA- selective glutamate receptors (AMPARs). Promotes their targeting to the cell membrane and synapses and modulates their gating properties by regulating their rates of activation, deactivation and desensitization.
SUBUNIT: Acts as an auxiliary subunit for AMPA-selective glutamate receptors (AMPARs). Found in a complex with GRIA1, GRIA2, GRIA3, GRIA4, CNIH2, CACNG2, CACNG3, CACNG4, CACNG5, CACNG7 and CACNG8 (By similarity).
SUBCELLULAR LOCATION: Cell junction, synapse, postsynaptic cell membrane; Multi-pass membrane protein (By similarity). Note=Also localizes to the cell membrane of extrasynaptic sites (dendritic shafts, spines of pyramidal cells) (By similarity).
SIMILARITY: Belongs to the cornichon family.

-  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: CNIH3
Diseases sorted by gene-association score: schizophrenia (1)

-  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: 3.58 RPKM in Brain - Frontal Cortex (BA9)
Total median expression: 38.90 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 -421.80858-0.492 Picture PostScript Text
3' UTR -378.401198-0.316 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
IPR003377 - Cornichon

Pfam Domains:
PF03311 - Cornichon protein

ModBase Predicted Comparative 3D Structure on Q8TBE1
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 orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0016247 channel regulator activity

Biological Process:
GO:0006888 ER to Golgi vesicle-mediated transport
GO:0016192 vesicle-mediated transport
GO:0035249 synaptic transmission, glutamatergic
GO:0042391 regulation of membrane potential
GO:0048208 COPII vesicle coating
GO:2000311 regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity

Cellular Component:
GO:0000139 Golgi membrane
GO:0005789 endoplasmic reticulum membrane
GO:0005886 plasma membrane
GO:0012507 ER to Golgi transport vesicle membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0030054 cell junction
GO:0032281 AMPA glutamate receptor complex
GO:0033116 endoplasmic reticulum-Golgi intermediate compartment membrane
GO:0043198 dendritic shaft
GO:0045202 synapse
GO:0045211 postsynaptic membrane


-  Descriptions from all associated GenBank mRNAs
  AK096312 - Homo sapiens cDNA FLJ38993 fis, clone NT2RI2009194, highly similar to CORNICHON-LIKE PROTEIN.
BC022780 - Homo sapiens cornichon homolog 3 (Drosophila), mRNA (cDNA clone MGC:9297 IMAGE:3894832), complete cds.
CU692706 - Synthetic construct Homo sapiens gateway clone IMAGE:100020131 5' read CNIH3 mRNA.
HQ447327 - Synthetic construct Homo sapiens clone IMAGE:100070643; CCSB002477_01 cornichon homolog 3 (Drosophila) (CNIH3) gene, encodes complete protein.
KJ895629 - Synthetic construct Homo sapiens clone ccsbBroadEn_05023 CNIH3 gene, encodes complete protein.
AF070524 - Homo sapiens clone 24453 mRNA sequence.
LF326319 - JP 2014500723-A/133822: Polycomb-Associated Non-Coding RNAs.
JC506674 - Sequence 42 from Patent EP2733220.
JC737786 - Sequence 42 from Patent WO2014075939.
JC506688 - Sequence 56 from Patent EP2733220.
JC737800 - Sequence 56 from Patent WO2014075939.
JD380305 - Sequence 361329 from Patent EP1572962.
JD144962 - Sequence 125986 from Patent EP1572962.
JD199118 - Sequence 180142 from Patent EP1572962.
JD206286 - Sequence 187310 from Patent EP1572962.
MA561896 - JP 2018138019-A/133822: Polycomb-Associated Non-Coding RNAs.
JD441899 - Sequence 422923 from Patent EP1572962.
JD329410 - Sequence 310434 from Patent EP1572962.
JD215912 - Sequence 196936 from Patent EP1572962.
JD503672 - Sequence 484696 from Patent EP1572962.
JD232336 - Sequence 213360 from Patent EP1572962.
JD193081 - Sequence 174105 from Patent EP1572962.
JD266998 - Sequence 248022 from Patent EP1572962.
JD063265 - Sequence 44289 from Patent EP1572962.
JD380526 - Sequence 361550 from Patent EP1572962.
JD096107 - Sequence 77131 from Patent EP1572962.
JD562215 - Sequence 543239 from Patent EP1572962.
JD094908 - Sequence 75932 from Patent EP1572962.
JD565978 - Sequence 547002 from Patent EP1572962.

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

Protein Q8TBE1 (Reactome details) participates in the following event(s):

R-HSA-5694442 CNIH2,3 bind GRIA1
R-HSA-5694522 Inner coat assembly and cargo binding
R-HSA-5694527 Loss of SAR1B GTPase
R-HSA-5694446 BET1:GOSR2:STX5 bind v-SNARES on tethered vesicle
R-HSA-5694417 SEC16 complex binds SAR1B:GTP:SEC23:SEC24
R-HSA-5694441 CSNK1D phosphorylates SEC23
R-HSA-5694439 COPII coat binds TRAPPCII and RAB1:GDP
R-HSA-203973 Vesicle budding
R-HSA-204008 SEC31:SEC13 and v-SNARE recruitment
R-HSA-5694418 RAB1:GTP binds USO1 and GORASP1:GOLGA2
R-HSA-5694409 Nucleotide exchange on RAB1
R-HSA-5694530 Cargo concentration in the ER
R-HSA-199977 ER to Golgi Anterograde Transport
R-HSA-204005 COPII-mediated vesicle transport
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: CNIH3_HUMAN, ENST00000272133.1, ENST00000272133.2, ENST00000272133.3, NR_136287, Q8TBE1, uc317ixm.1, uc317ixm.2
UCSC ID: ENST00000272133.4_4
RefSeq Accession: NM_152495.2
Protein: Q8TBE1 (aka CNIH3_HUMAN)

-  Gene Model Information
  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.