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    CNGA3 cyclic nucleotide gated channel subunit alpha 3 [ Homo sapiens (human) ]

    Gene ID: 1261, updated on 17-Jun-2024

    Summary

    Official Symbol
    CNGA3provided by HGNC
    Official Full Name
    cyclic nucleotide gated channel subunit alpha 3provided by HGNC
    Primary source
    HGNC:HGNC:2150
    See related
    Ensembl:ENSG00000144191 MIM:600053; AllianceGenome:HGNC:2150
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    CNG3; ACHM2; CCNC1; CCNCa; CNCG3; CCNCalpha
    Summary
    This gene encodes a member of the cyclic nucleotide-gated cation channel protein family which is required for normal vision and olfactory signal transduction. Mutations in this gene are associated with achromatopsia (rod monochromacy) and color blindness. Two alternatively spliced transcripts encoding different isoforms have been described. [provided by RefSeq, Jul 2008]
    Expression
    Low expression observed in reference dataset See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See CNGA3 in Genome Data Viewer
    Location:
    2q11.2
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (98346456..98398601)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (98804385..98856818)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (98962919..99015064)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105373501 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:98663772-98664272 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:98664273-98664773 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:98670618-98671817 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:98703358-98703858 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:98703859-98704359 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:98733463-98733964 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:98733965-98734464 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11799 Neighboring gene Sharpr-MPRA regulatory region 9320 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr2:98746447-98747273 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:98748232-98748818 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:98750133-98751332 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:98748819-98749404 Neighboring gene von Willebrand factor A domain containing 3B Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:98779443-98779989 Neighboring gene NANOG hESC enhancer GRCh37_chr2:98808643-98809198 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:98810042-98810239 Neighboring gene ATP synthase F1 subunit beta pseudogene 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:98896664-98897164 Neighboring gene NANOG hESC enhancer GRCh37_chr2:98933593-98934329 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:98950857-98951787 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:98963419-98963930 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:98993983-98994750 Neighboring gene Sharpr-MPRA regulatory region 13649 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:98998693-98999270 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr2:98999847-99000424 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:99000425-99001000 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:99004561-99004748 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16257 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:99051832-99053031 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16258 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11800 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16259 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16260 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:99079757-99080272 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16261 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16262 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16263 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:99082317-99082881 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11801 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16264 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16265 Neighboring gene inositol polyphosphate-4-phosphatase type I A Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16266 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16267 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:99136086-99136586 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:99136587-99137087 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16268 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:99170837-99171337 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:99176784-99176955 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:99190711-99190893 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:99200423-99200924 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:99209219-99209372 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16269 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:99224127-99225116 Neighboring gene cytochrome c oxidase assembly factor 5

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables cGMP binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables cGMP binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables cGMP binding IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables cadherin binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables calcium channel activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables intracellularly cAMP-activated cation channel activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables intracellularly cAMP-activated cation channel activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables intracellularly cGMP-activated cation channel activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables intracellularly cGMP-activated cation channel activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables intracellularly cGMP-activated cation channel activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables ligand-gated monoatomic ion channel activity TAS
    Traceable Author Statement
    more info
    PubMed 
    enables myosin binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein-containing complex binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables sodium channel activity IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    involved_in calcium ion transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in inorganic cation import across plasma membrane IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in monoatomic cation transmembrane transport IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in monoatomic cation transport IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in response to cAMP IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in response to magnesium ion IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in signal transduction TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in sodium ion transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in visual perception IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    located_in axon initial segment IEA
    Inferred from Electronic Annotation
    more info
     
    located_in dendrite IEA
    Inferred from Electronic Annotation
    more info
     
    located_in glial cell projection IEA
    Inferred from Electronic Annotation
    more info
     
    part_of intracellular cyclic nucleotide activated cation channel complex IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in perikaryon IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of transmembrane transporter complex IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    cyclic nucleotide-gated channel alpha-3; cyclic nucleotide-gated cation channel alpha-3
    Names
    CNG channel alpha-3
    CNG-3
    cone photoreceptor cGMP-gated channel alpha subunit
    cone photoreceptor cGMP-gated channel subunit alpha
    cone photoreceptor cGMP-gated channel subunit alpha-3
    cyclic nucleotide gated channel alpha 3

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_009097.1 RefSeqGene

      Range
      5302..57447
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001079878.2NP_001073347.1  cyclic nucleotide-gated channel alpha-3 isoform 2

      See identical proteins and their annotated locations for NP_001073347.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the coding region, compared to variant 1. The resulting protein (isoform 2) is shorter and lacks an internal segment, compared to isoform 1.
      Source sequence(s)
      AC092675, BC096299, DR002103
      Consensus CDS
      CCDS42719.1
      UniProtKB/Swiss-Prot
      Q16281
      Related
      ENSP00000410070.2, ENST00000436404.6
      Conserved Domains (4) summary
      COG0664
      Location:458628
      Crp; cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]
      cd00038
      Location:464580
      CAP_ED; effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO ...
      pfam00520
      Location:168392
      Ion_trans; Ion transport protein
      pfam16526
      Location:580650
      CLZ; C-terminal leucine zipper domain of cyclic nucleotide-gated channels
    2. NM_001298.3NP_001289.1  cyclic nucleotide-gated channel alpha-3 isoform 1

      See identical proteins and their annotated locations for NP_001289.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer protein (isoform 1).
      Source sequence(s)
      AC092675
      Consensus CDS
      CCDS2034.1
      UniProtKB/Swiss-Prot
      E9PF93, Q16281, Q4VAP7, Q53RD2, Q6ZNA7, Q9UP64
      Related
      ENSP00000272602.2, ENST00000272602.7
      Conserved Domains (3) summary
      cd00038
      Location:482598
      CAP_ED; effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO ...
      pfam00520
      Location:168410
      Ion_trans; Ion transport protein
      pfam16526
      Location:598668
      CLZ; C-terminal leucine zipper domain of cyclic nucleotide-gated channels

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      98346456..98398601
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011510554.3XP_011508856.1  cyclic nucleotide-gated cation channel alpha-3 isoform X1

      Conserved Domains (4) summary
      COG0664
      Location:531701
      Crp; cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]
      cd00038
      Location:537653
      CAP_ED; effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO ...
      pfam00520
      Location:241465
      Ion_trans; Ion transport protein
      pfam16526
      Location:653723
      CLZ; C-terminal leucine zipper domain of cyclic nucleotide-gated channels
    2. XM_047443222.1XP_047299178.1  cyclic nucleotide-gated cation channel alpha-3 isoform X1

    3. XM_006712243.3XP_006712306.1  cyclic nucleotide-gated cation channel alpha-3 isoform X2

      Conserved Domains (4) summary
      COG0664
      Location:513683
      Crp; cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]
      cd00038
      Location:519635
      CAP_ED; effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO ...
      pfam00520
      Location:223447
      Ion_trans; Ion transport protein
      pfam16526
      Location:635705
      CLZ; C-terminal leucine zipper domain of cyclic nucleotide-gated channels

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      98804385..98856818
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054340429.1XP_054196404.1  cyclic nucleotide-gated cation channel alpha-3 isoform X1

    2. XM_054340428.1XP_054196403.1  cyclic nucleotide-gated cation channel alpha-3 isoform X1

    3. XM_054340430.1XP_054196405.1  cyclic nucleotide-gated cation channel alpha-3 isoform X2