Human Gene CNGA4 (uc001mco.3) Description and Page Index
  Description: Homo sapiens cyclic nucleotide gated channel alpha 4 (CNGA4), mRNA.
RefSeq Summary (NM_001037329): CNGA4 is a modulatory subunit of vertebrate cyclic nucleotide-gated membrane channels that transduce odorant signals (Munger et al., 2001 [PubMed 11739959]).[supplied by OMIM, Mar 2008]. Sequence Note: This RefSeq record was created from transcript and genomic sequence data to make the sequence consistent with the reference genome assembly. The genomic coordinates used for the transcript record were based on transcript alignments. ##Evidence-Data-START## Transcript exon combination :: AK122736.1, SRR1803612.256359.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA1968968, SAMEA2144333 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## RefSeq Select criteria :: based on conservation, expression ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr11:6,260,322-6,265,707 Size: 5,386 Total Exon Count: 6 Strand: +
Coding Region
   Position: hg19 chr11:6,260,437-6,265,639 Size: 5,203 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr11:6,260,322-6,265,707)mRNA (may differ from genome)Protein (575 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDHuman Cortex Gene ExpressionLynx
MGIneXtProtOMIMPubMedReactomeStanford SOURCE
TreefamUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: CNGA4_HUMAN
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 (By similarity).
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.
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 sensory neurons.
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.
SEQUENCE CAUTION: Sequence=AAH40277.1; Type=Erroneous initiation; Note=Translation N-terminally shortened; Sequence=AK122736; Type=Frameshift; Positions=154;

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

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 6.37 RPKM in Testis
Total median expression: 17.55 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
5' UTR -33.50115-0.291 Picture PostScript Text
3' UTR -11.7068-0.172 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 Q8IV77
FrontTopSide
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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 BrowserNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGDEnsembl   
 Protein SequenceProtein Sequence   
 AlignmentAlignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0005216 ion channel activity
GO:0005249 voltage-gated potassium channel activity
GO:0030552 cAMP 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:0055085 transmembrane transport
GO:0071805 potassium ion transmembrane transport

Cellular Component:
GO:0000139 Golgi membrane
GO:0005887 integral component of plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0030660 Golgi-associated vesicle membrane
GO:0060170 ciliary membrane


-  Descriptions from all associated GenBank mRNAs
  AK302551 - Homo sapiens cDNA FLJ51400 complete cds, highly similar to Cyclic nucleotide-gated ol factory channel subunit OCNC2.
BC040277 - Homo sapiens cyclic nucleotide gated channel alpha 4, mRNA (cDNA clone IMAGE:5167238), partial cds.
AK122736 - Homo sapiens cDNA FLJ16252 fis, clone HLUNG2014821, highly similar to CYCLIC-NUCLEOTIDE-GATED OLFACTORY CHANNEL OCNC2 SUBUNIT.
BC160170 - Synthetic construct Homo sapiens clone IMAGE:100064202, MGC:193285 cyclic nucleotide gated channel alpha 4 (CNGA4) mRNA, encodes complete protein.
KJ890943 - Synthetic construct Homo sapiens clone ccsbBroadEn_00337 CNGA4 gene, encodes complete protein.
JD079118 - Sequence 60142 from Patent EP1572962.
JD250065 - Sequence 231089 from Patent EP1572962.
JD504831 - Sequence 485855 from Patent EP1572962.
JD383332 - Sequence 364356 from Patent EP1572962.
JD495424 - Sequence 476448 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04740 - Olfactory transduction

Reactome (by CSHL, EBI, and GO)

Protein Q8IV77 (Reactome details) participates in the following event(s):

R-HSA-5620914 ARF4:GTP binds VxPx-motifs of membrane proteins
R-HSA-5620918 ASAP1 dimer binds membrane proteins
R-HSA-5623519 RAB3IP and RAB8A bind to the ciliary targeting complex
R-HSA-5623513 ASAP1 stimulates GTPase activity of ARF4
R-HSA-5620921 ASAP1 recruits RAB11FIP3 and RAB11 to the ciliary targeting complex
R-HSA-5623521 RAB3IP stimulates nucleotide exchange on RAB8A
R-HSA-5623524 The exocyst complex binds to RAB3IP in the ciliary targeting complex
R-HSA-5620916 VxPx cargo-targeting to cilium
R-HSA-5620920 Cargo trafficking to the periciliary membrane
R-HSA-5617833 Cilium Assembly
R-HSA-1852241 Organelle biogenesis and maintenance

-  Other Names for This Gene
  Alternate Gene Symbols: CNGA4_HUMAN, NM_001037329, NP_001032406, Q8IV77
UCSC ID: uc001mco.3
RefSeq Accession: NM_001037329
Protein: Q8IV77 (aka CNGA4_HUMAN)
CCDS: CCDS31408.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001037329.3
exon count: 6CDS single in 3' UTR: no RNA size: 1911
ORF size: 1728CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3288.00frame shift in genome: no % Coverage: 100.00
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
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-  Methods, Credits, and Use Restrictions
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