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

Gene ID: 1261, updated on 23-Nov-2023

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
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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 IMP
Inferred from Mutant Phenotype
more info
PubMed 
enables cadherin binding IEA
Inferred from Electronic Annotation
more info
 
enables intracellular cAMP-activated cation channel activity IBA
Inferred from Biological aspect of Ancestor
more info
 
enables intracellular cGMP-activated cation channel activity IBA
Inferred from Biological aspect of Ancestor
more info
 
enables intracellular 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
 
Process Evidence Code Pubs
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 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
 
part_of transmembrane transporter complex IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
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
cyclic nucleotide gated channel alpha 3

NCBI Reference Sequences (RefSeq)

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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 cation 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 cation 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