Mouse Gene Cnga4 (ENSMUST00000033187.5) from GENCODE VM23 Comprehensive Transcript Set (only Basic displayed by default)
  Description: Mus musculus cyclic nucleotide gated channel alpha 4 (Cnga4), mRNA. (from RefSeq NM_001033317)
Gencode Transcript: ENSMUST00000033187.5
Gencode Gene: ENSMUSG00000030897.5
Transcript (Including UTRs)
   Position: mm10 chr7:105,404,568-105,408,742 Size: 4,175 Total Exon Count: 6 Strand: +
Coding Region
   Position: mm10 chr7:105,404,692-105,408,110 Size: 3,419 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA Structure
Protein StructureOther SpeciesGO AnnotationsmRNA DescriptionsPathwaysOther Names
Model InformationMethods
Data last updated at UCSC: 2019-09-20

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr7:105,404,568-105,408,742)mRNA (may differ from genome)Protein (575 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsMGI
PubMedReactomeSOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: CNGA4_MOUSE
DESCRIPTION: RecName: Full=Cyclic nucleotide-gated cation channel alpha-4; AltName: Full=Cyclic nucleotide-gated channel alpha-4; Short=CNG channel alpha-4; Short=CNG-4; Short=CNG4;
FUNCTION: Second messenger, cAMP, causes the opening of cation- selective cyclic nucleotide-gated (CNG) channels and depolarization of the neuron (olfactory sensory neurons, OSNs). CNGA4 is the modulatory subunit of this channel which is known to play a central role in the transduction of odorant signals and subsequent adaptation. By accelerating the calcium-mediated negative feedback in olfactory signaling it allows rapid adaptation to odor stimulation and extends its range of odor detection.
ENZYME REGULATION: Calcium-calmodulin exerts its inhibitory effect in cAMP sensitivity by binding to IQ-like motif of CNGA4 and preferably binds to the channel in the closed state. Inhibition by PIP3 of the CNG channel probably occurs via CGNA2 binding (By similarity).
SUBUNIT: Heterotetramer composed of two subunits of CNGA2, one of CNGA4 and one of CNGB1b. The complex forms the cyclic nucleotide- gated (CNG) channel of olfactory neurons (By similarity).
SUBCELLULAR LOCATION: Membrane; Multi-pass membrane protein (Potential).
SIMILARITY: Belongs to the cyclic nucleotide-gated cation channel (TC 1.A.1.5) family. CNGA4 subfamily.
SIMILARITY: Contains 1 cyclic nucleotide-binding domain.

-  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


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -31.30124-0.252 Picture PostScript Text
3' UTR -178.30632-0.282 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
IPR018490 - cNMP-bd-like
IPR018488 - cNMP-bd_CS
IPR000595 - cNMP-bd_dom
IPR005821 - Ion_trans_dom
IPR014710 - RmlC-like_jellyroll

Pfam Domains:
PF00027 - Cyclic nucleotide-binding domain
PF00520 - Ion transport protein
PF16526 - C-terminal leucine zipper domain of cyclic nucleotide-gated channels

SCOP Domains:
51206 - cAMP-binding domain-like
81324 - Voltage-gated potassium channels

ModBase Predicted Comparative 3D Structure on Q3UW12
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.
HumanRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
GenBankRGDEnsembl   
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0005216 ion channel activity
GO:0005221 intracellular cyclic nucleotide activated cation channel activity
GO:0005222 intracellular cAMP activated cation channel activity
GO:0005223 intracellular cGMP activated cation channel activity
GO:0005249 voltage-gated potassium channel activity
GO:0030552 cAMP binding
GO:0030553 cGMP binding

Biological Process:
GO:0006811 ion transport
GO:0007608 sensory perception of smell
GO:0034220 ion transmembrane transport
GO:0042391 regulation of membrane potential
GO:0050896 response to stimulus
GO:0051290 protein heterotetramerization
GO:0055085 transmembrane transport
GO:0071805 potassium ion transmembrane transport
GO:0098655 cation transmembrane transport

Cellular Component:
GO:0005886 plasma membrane
GO:0005887 integral component of plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0017071 intracellular cyclic nucleotide activated cation channel complex
GO:0043204 perikaryon


-  Descriptions from all associated GenBank mRNAs
  AK136723 - Mus musculus adult male epididymis cDNA, RIKEN full-length enriched library, clone:9230103C20 product:Cyclic-nucleotide-gated olfactory channel OCNC2 subunit homolog [Rattus norvegicus], full insert sequence.
BC107347 - Mus musculus cyclic nucleotide gated channel alpha 4, mRNA (cDNA clone MGC:130316 IMAGE:40055406), complete cds.
BC107348 - Mus musculus cyclic nucleotide gated channel alpha 4, mRNA (cDNA clone MGC:130317 IMAGE:40055413), complete cds.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
mmu04740 - Olfactory transduction

Reactome (by CSHL, EBI, and GO)

Protein Q3UW12 (Reactome details) participates in the following event(s):

R-MMU-5620914 ARF4:GTP binds VxPx-motifs of membrane proteins
R-MMU-5623519 RAB3IP and RAB8A bind to the ciliary targeting complex
R-MMU-5623513 ASAP1 stimulates GTPase activity of ARF4
R-MMU-5620921 ASAP1 recruits RAB11FIP3 and RAB11 to the ciliary targeting complex
R-MMU-5623521 RAB3IP stimulates nucleotide exchange on RAB8A
R-MMU-5623524 The exocyst complex binds to RAB3IP in the ciliary targeting complex
R-MMU-5620916 VxPx cargo-targeting to cilium
R-MMU-5620920 Cargo trafficking to the periciliary membrane
R-MMU-5617833 Cilium Assembly
R-MMU-1852241 Organelle biogenesis and maintenance

-  Other Names for This Gene
  Alternate Gene Symbols: CNGA4_MOUSE, NM_001033317, Q08EL1, Q3UW12, uc009iyc.1, uc009iyc.2
UCSC ID: uc009iyc.2
RefSeq Accession: NM_001033317
Protein: Q3UW12 (aka CNGA4_MOUSE)
CCDS: CCDS21650.1

-  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.