Homo sapiens gene CHRNA3, encoding cholinergic receptor, nicotinic, alpha 3.
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SUMMARY back to top
RefSeq summary
[CHRNA3] This locus encodes a member of the nicotinic acetylcholine receptor family of proteins. Members of this family of proteins form pentameric complexes comprised of both alpha and beta subunits. This locus encodes an alpha-type subunit, as it contains characteristic adjacent cysteine residues. The encoded protein is a ligand-gated ion channel that likely plays a role in neurotransmission. Polymorphisms in this gene have been associated with an increased risk of smoking initiation and an increased susceptibility to lung cancer. Alternatively spliced transcript variants have been described. [provided by RefSeq].

RefSeq annotates 2 representative transcripts (NM included in AceView variants .a and .b), but Homo sapiens cDNA sequences in GenBank, dbEST, Trace and SRA, filtered against clone rearrangements, coaligned on the genome and clustered in a minimal non-redundant way by the manually supervised AceView program, support at least 8 spliced variants.

AceView synopsis, each blue text links to tables and details
Expression: According to AceView, this gene is well expressed, 1.1 times the average gene in this release. The sequence of this gene is defined by 135 GenBank accessions from 104 cDNA clones, some from brain (seen 19 times), neuroblastoma (18), eye (16), lung (10), thymus (9), sympathetic trunk (6), small cell carcinoma (5) and 31 other tissues. We annotate structural defects or features in 11 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 11 distinct gt-ag introns. Transcription produces 9 different mRNAs, 8 alternatively spliced variants and 1 unspliced form. There are 4 probable alternative promotors, 4 non overlapping alternative last exons and 4 validated alternative polyadenylation sites (see the diagram). The mRNAs appear to differ by truncation of the 5' end, truncation of the 3' end, presence or absence of 2 cassette exons, overlapping exons with different boundaries, splicing versus retention of one intron. 1303 bp of this gene are antisense to spliced gene CHRNA5, raising the possibility of regulated alternate expression.
Note that mRNA .cAug10 was found in vivo, although it is a predicted target of nonsense mediated mRNA decay (NMD).
Function: There are 80 articles specifically referring to this gene in PubMed. Functionally, the gene has been tested for association to diseases (OMIM: smoking as a quantitative trait locus 3; Other sources: Alzheimer Disease; Bipolar Disorder; Carcinoma, Non-Small-Cell Lung; Epilepsy, Frontal Lobe; Gait Disorders, Neurologic; Genetic Predisposition to Disease; Lung cancer susceptibility 2; Lung Neoplasms and 6 others), proposed to participate in pathway (Neuroactive ligand-receptor interaction) and processes (activation of transmembrane receptor protein tyrosine kinase activity, heart development, locomotory behavior, regulation of acetylcholine secretion, regulation of dendrite morphogenesis, regulation of excitatory postsynaptic membrane potential, regulation of membrane potential, regulation of smooth muscle contraction, response to drug, response to inorganic substance, synaptic transmission, cholinergic). Proteins are expected to have molecular functions (extracellular ligand-gated ion channel activity, receptor activity) and to localize in various compartments (endoplasmic reticulum membrane, cell junction, dendrite, neuronal cell body and 4 others). Putative protein interactors have been described (CHRNB4, UBQLN1).
Protein coding potential: 5 spliced mRNAs putatively encode good proteins, altogether 5 different isoforms (3 complete, 1 COOH complete, 1 partial), some containing domains Neurotransmitter-gated ion-channel ligand binding domain, Neurotransmitter-gated ion-channel transmembrane region [Pfam], some transmembrane domains, a coiled coil stretch [Psort2]. The remaining 4 mRNA variants (3 spliced, 1 unspliced; 2 partial) appear not to encode good proteins. Finally proteins from this gene may be modulated by phosphorylation, as detailed at PhosphoSite.

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12.
Map on chromosome 15, links to other databases and other names
Map: This gene CHRNA3 maps on chromosome 15, at 15q24 according to Entrez Gene. In AceView, it covers 28.25 kb, from 78913638 to 78885394 (NCBI 37, August 2010), on the reverse strand.
Links to: manual annotations from OMIM_612052, GAD, KEGG_04080, PhosphoSite, the SNP view, gene overviews from Entrez Gene 1136, GeneCards, expression data from ECgene, UniGene, molecular and other annotations from UCSC, or our GOLD analysis.
The previous AceView annotation is here.
Other names: The gene is also known as CHRNA3, LNCR2, PAOD2, nAChRA3 or MGC104879, LOC1136. It has been described as neuronal acetylcholine receptor subunit alpha-3, cholinergic receptor, nicotinic, alpha polypeptide 3, neuronal nicotinic acetylcholine receptor, alpha3 subunit.
Closest AceView homologs in other species ?
The closest mouse gene, according to BlastP, is the AceView gene Chrna3 (e=0.0).
The closest C.elegans genes, according to BlastP, are the AceView/WormGenes unc-63 (e=6 10-97), unc-38 (e=4 10-93), which may contain interesting functional annotation
RNA_seq discoveries back to top
Expression/conservation in primates tissues evaluated by cross-mapping to human. back to top
CHRNA3 Gene expression in 15 primates, 16 tissues, from the NHPRTR project in sFPKM BAB SkeletalMuscle WholeBlood CHP Kidney Liver Lung Spleen CMC CMM Cerebellum HUM Brain Colon Heart LymphNode Ovary Testis JMI BoneMarrow MLM OWL PTM RMC RMI Pituitary SQM Thymus MST SMY RTL 0.17 0.12 0.27 0.78 0.39 7.64 0.45 0.16 0.04 0.24 2.70 0.21 0.32 1.91 0.04 0.55 0.89 4.10 0.27 3.82 0.96 2.90 0.06 0.10 0.12 7.13 0.11 0.78 0.06 1.66 0.06 0.15 0.39 0.07 0.13 1.02 0.32 0.59 0.14 0.10 3.10 0.08 0.32 0.19 0.59 65.5 0.18 1.91 0.14 6.65 1.91 21.6 0.24 0.22 0.72 0.15 26.6 0.19 2.35 0.32 0.36 0.68 0.18 2.70 0.55 0.24 0.07 0.22 1.78 0.26 30.6 0.07 0.09 0.10 0.09 0.08 0.26 0.10 0.10 0.08 0.63 2.19 0.04 0.10 0.18 0.55 1.18 18.8 0.09 0.07 0.05 0.45 0.04 0.07 4.39 3.82 1.18 0.59 1.26 0.08 0.26 1.45 4.10 0.15 0.06 0.10 0.29 24.8 0.89 0.29 1.45 0.78 0.48 0.27 Expression quantiles None Weak 1 2 3 4 5 6 7 8 10 20 This gene All genes log2 distributions RNA-seq gene expression profile across 16 selected tissues from the Non-Human Primates Reference Transcriptome Resource (link to NHPRTR project).
- Primates: Apes (HUM: Human (Illumina BodyMap 2), CHP: Chimpanzee), Old World monkeys (PTM: Pig-Tailed Macaque, JMI Japanese Macaque, RMI Rhesus Macaque Indian, RMC Rhesus Macaque Chinese, CMM Cynomolgus Macaque Mauritian, CMC Cynomolgus Macaque Chinese, BAB Olive Baboon, SMY Sooty Mangabey); New World monkeys (MST common Marmoset, SQM Squirrel Monkey, OWL Owl Monkey); and Lemurs (MLM Mouse Lemur, RTL Ring-Tailed Lemur).
- The level for significantly expressed genes is color coded in 8 equal sized bins (light to dark green). Light gray is for weak not-accurately measured expression (2 to 8 reads above intergenic background); dark gray for no expression or no sequence conservation (0 read in gene). The plot to the right shows the distribution of measured expression values in all tissues for all genes (blue) and for this gene (green), in Magic index = log2(1000 sFPKM).
You may also examine the strand-specific genome coverage plots on the experimental AceView/Magic hub at UCSC, by tissue or by species. Tracks may be slow to load; please reload if some tracks come up yellow-greenish, and thanks to UCSC for the great work!.
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          Complete gene on genome diagram: back to top
Please choose between the zoomable GIF version., and the HTML5/SVG version.
This diagram shows in true scale the gene on the genome, the mRNAs and the cDNA clones.
Compact gene diagram back to top
Gene CHRNA3 5' 3' encoded on minus strand of chromosome 15 from 78,913,638 to 78,885,394 127456 209978 220997 248599 241346 a [NM] e-u 127456 209978 220997 248599 71 b [NM] 127456 209978 220997 248599 241346 7265 7485 c 127456 209978 248599 241346 d 209978 f 241346 2459 i 4051 g 4 h 1 2kb 0 583 bp exon 583 bp exon 1797 bp [gt-ag] intron 32 GenBank accessions 127424 RNA-seq supporting reads 35 UHR pooled cells 409 Brain 126962 Neuroblastoma 18 Other (also 155 Primates bodymap) 140 bp exon 114 bp [gt-ag] intron 39 GenBank accessions 209939 RNA-seq supporting reads 139 UHR pooled cells 915 Brain 208850 Neuroblastoma 35 Other (also 1005 Primates bodymap) 45 bp exon 1483 bp [gt-ag] intron 39 GenBank accessions 220958 RNA-seq supporting reads 154 UHR pooled cells 1072 Brain 219675 Neuroblastoma 57 Other (also 819 Primates bodymap) 110 bp exon 14759 bp [gt-ag] intron 41 GenBank accessions 248558 RNA-seq supporting reads 157 UHR pooled cells 1121 Brain 247238 Neuroblastoma 42 Other (also 948 Primates bodymap) 1012 bp exon 4520 bp [gt-ag] intron 39 GenBank accessions 241307 RNA-seq supporting reads 150 UHR pooled cells 1293 Brain 239818 Neuroblastoma 46 Other (also 1005 Primates bodymap) 1724 bp exon 43 accessions, NM_000743.4 some from eye (seen 10 times) lung (5), carcinoid (4) sympathetic trunk (4) brain (3) Validated 3' end, 11 accessions 1724 bp exon 1038 bp exon 2 accessions, some from stomach (seen once) 1038 bp exon 584 bp exon 584 bp exon 1797 bp [gt-ag] intron 32 GenBank accessions 127424 RNA-seq supporting reads 35 UHR pooled cells 409 Brain 126962 Neuroblastoma 18 Other (also 155 Primates bodymap) 140 bp exon 114 bp [gt-ag] intron 39 GenBank accessions 209939 RNA-seq supporting reads 139 UHR pooled cells 915 Brain 208850 Neuroblastoma 35 Other (also 1005 Primates bodymap) 45 bp exon 1483 bp [gt-ag] intron 39 GenBank accessions 220958 RNA-seq supporting reads 154 UHR pooled cells 1072 Brain 219675 Neuroblastoma 57 Other (also 819 Primates bodymap) 110 bp exon 14759 bp [gt-ag] intron 41 GenBank accessions 248558 RNA-seq supporting reads 157 UHR pooled cells 1121 Brain 247238 Neuroblastoma 42 Other (also 948 Primates bodymap) 1012 bp exon 8061 bp [gt-ag] intron 7 GenBank accessions 64 RNA-seq supporting reads 64 Neuroblastoma 137 bp exon 36 accessions, NM_001166694.1 some from brain (seen 13 times) neuroblastoma (13), eye (3) lung (2), small cell carcinoma (2) Validated 3' end, 2 accessions 137 bp exon 151 bp exon 1797 bp [gt-ag] intron 32 GenBank accessions 127424 RNA-seq supporting reads 35 UHR pooled cells 409 Brain 126962 Neuroblastoma 18 Other (also 155 Primates bodymap) 140 bp exon 114 bp [gt-ag] intron 39 GenBank accessions 209939 RNA-seq supporting reads 139 UHR pooled cells 915 Brain 208850 Neuroblastoma 35 Other (also 1005 Primates bodymap) 45 bp exon 1483 bp [gt-ag] intron 39 GenBank accessions 220958 RNA-seq supporting reads 154 UHR pooled cells 1072 Brain 219675 Neuroblastoma 57 Other (also 819 Primates bodymap) 110 bp exon 14759 bp [gt-ag] intron 41 GenBank accessions 248558 RNA-seq supporting reads 157 UHR pooled cells 1121 Brain 247238 Neuroblastoma 42 Other (also 948 Primates bodymap) 1012 bp exon 4520 bp [gt-ag] intron 39 GenBank accessions 241307 RNA-seq supporting reads 150 UHR pooled cells 1293 Brain 239818 Neuroblastoma 46 Other (also 1005 Primates bodymap) 193 bp exon 193 bp exon 2528 bp [gt-ag] intron 2 GenBank accessions 7263 RNA-seq supporting reads 8 UHR pooled cells 8 Brain 7247 Neuroblastoma (also 8 Primates bodymap) 98 bp exon 722 bp [gt-ag] intron 2 GenBank accessions 7483 RNA-seq supporting reads 29 UHR pooled cells 3 Brain 7451 Neuroblastoma (also 9 Primates bodymap) 19 accessions, some from brain (seen 2 times) eye (once), lung (once) neuroblastoma (once) retina (once) Validated 3' end, 2 accessions 137 bp exon 563 bp exon 1797 bp [gt-ag] intron 32 GenBank accessions 127424 RNA-seq supporting reads 35 UHR pooled cells 409 Brain 126962 Neuroblastoma 18 Other (also 155 Primates bodymap) 140 bp exon 114 bp [gt-ag] intron 39 GenBank accessions 209939 RNA-seq supporting reads 139 UHR pooled cells 915 Brain 208850 Neuroblastoma 35 Other (also 1005 Primates bodymap) 1638 bp exon 1638 bp exon 14759 bp [gt-ag] intron 41 GenBank accessions 248558 RNA-seq supporting reads 157 UHR pooled cells 1121 Brain 247238 Neuroblastoma 42 Other (also 948 Primates bodymap) 1012 bp exon 4520 bp [gt-ag] intron 39 GenBank accessions 241307 RNA-seq supporting reads 150 UHR pooled cells 1293 Brain 239818 Neuroblastoma 46 Other (also 1005 Primates bodymap) 1388 bp exon 8 accessions, some from thymus (seen 4 times) brain (once), eye (once) lung (once), neuroblastoma (once) 1388 bp exon 622 bp exon 622 bp exon 622 bp exon 114 bp [gt-ag] intron 39 GenBank accessions 209939 RNA-seq supporting reads 139 UHR pooled cells 915 Brain 208850 Neuroblastoma 35 Other (also 1005 Primates bodymap) 2 accessions, some from cerebellum (seen once) thymus (once) 32 bp exon 51 bp exon 4520 bp [gt-ag] intron 39 GenBank accessions 241307 RNA-seq supporting reads 150 UHR pooled cells 1293 Brain 239818 Neuroblastoma 46 Other (also 1005 Primates bodymap) 193 bp exon 193 bp exon 3348 bp [gt-ag] intron 2 GenBank accessions 2457 RNA-seq supporting reads 12 UHR pooled cells 11 Brain 2434 Neuroblastoma (also 15 Primates bodymap) 2 accessions Validated 3' end, 1 accession 140 bp exon 524 bp exon 524 bp exon 524 bp exon 821 bp [gt-ag] intron 1 GenBank accession 4050 RNA-seq supporting reads 16 UHR pooled cells 4 Brain 4030 Neuroblastoma (also 7 Primates bodymap) 1 accession from amygdala capped 5' end, 1 accession 67 bp exon 83 bp exon 5176 bp [gt-ag] intron 1 GenBank accession 3 RNA-seq supporting reads 3 Neuroblastoma 489 bp exon 489 bp exon 1 accession from testis capped 5' end, 1 accession 489 bp exon Alternative mRNAs are shown aligned from 5' to 3' on a virtual genome where introns have been shrunk to a minimal length. Exon size is proportional to length, intron height reflects the number of cDNAs supporting each intron, the small numbers show the support of the introns in deep sequencing (with details in mouse-over) . Introns of the same color are identical, of different colors are different. 'Good proteins' are pink, partial or not-good proteins are yellow, uORFs are green. 5' cap or3' poly A flags show completeness of the transcript.
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Sequences: click on the numbers to get the DNA back to top
mRNA variant mRNA matching the genome Best predicted protein 5' UTR 3' UTR Upstream sequence Transcription
unit
pre-mRNA		 Downstream sequence
aAug10 3614 bp 570 aa 306 bp 1595 bp 2kb possibly including promoter 26287 bp 1kb
bAug10 2028 bp 554 aa 307 bp 56 bp 2kb possibly including promoter 28242 bp 1kb
cAug10 1886 bp 528 aa 299 bp 2kb 27809 bp 1kb
dAug10 4741 bp 397 aa 2288 bp 1259 bp 2kb possibly including promoter 25931 bp 1kb
eAug10-unspliced 1038 bp 85 aa 780 bp 2kb 1038 bp 1kb
fAug10 654 bp 27 aa 2kb including Promoter 768 bp 1kb
gAug10 591 bp 96 aa 164 bp 136 bp 2kb including Promoter 1412 bp 1kb
hAug10 572 bp 114 aa 228 bp 2kb including Promoter 5748 bp 1kb
iAug10 384 bp 59 aa 204 bp 2kb 8252 bp 1kb

Gene neighbors and Navigator on chromosome 15q24 back to top
IDH3A C I R P R DNAJA4 C R P R CRABP1 D C I R P IREB2 D C I R P C P AGPHD1 D C R P PSMA4 D C I R P CHRNA5 D C I R P G C R G MORF4L1 C I R P R R D C R P ACSBG1 R C I R P WDR61 R D C I R P CHRNA3 D C I R P CHRNB4 C R P ADAMTS7 D C I R P CTSH D C I R P RASGRF1 100kb 0 IDH3A, 578 accessions 23 variants yoho, 5 accessions DNAJA4, 299 accessions 16 variants kleepey, 1 accession CRABP1, 105 accessions 3 variants IREB2, 427 accessions 18 variants justoy, 1 accession rumeru, 1 accession AGPHD1, 36 accessions 5 variants PSMA4, 520 accessions 21 variants CHRNA5, 72 accessions 5 variants LOC646934, 17 accessions 6 variants LOC646938, 5 accessions MORF4L1, 484 accessions 25 variants lorzar, 1 accession sasoru, 4 accessions, 2 variants flarjorby, 1 accession speetu, 5 accessions glarjorby, 3 accessions klyjorby, 1 accession dystoy, 1 accession duto, 1 accession skerzoybu, 1 accession deyzaw, 1 accession gato, 2 accessions dorzaw, 4 accessions farstoy, 1 accession feestoy, 2 accessions feystoy, 1 accession forstoy, 1 accession klawjorby, 1 accession wameru, 2 accessions foystoy, 1 accession slazoybu, 3 accessions gystoy, 1 accession gostoy, 1 accession garstoy, 1 accession gawstoy, 2 accessions geestoy, 1 accession gorto, 1 accession gerstoy, 1 accession gorstoy, 1 accession geystoy, 1 accession goystoy, 1 accession joto, 1 accession fazaw, 2 accessions slusorbo, 2 accessions jawstoy, 1 accession niwami, 2 accessions, 2 variants slosorbo, 1 accession rameru, 1 accession jeystoy, 1 accession joystoy, 2 accessions kastoy, 3 accessions fozaw, 1 accession slerjorby, 3 accessions kystoy, 1 accession kustoy, 1 accession kostoy, 1 accession karstoy, 2 accessions kawstoy, 1 accession slorzoybu, 1 accession keestoy, 3 accessions farzaw, 6 accessions sisi, 3 accessions sloyzoybu, 1 accession smawzoybu, 3 accessions kawto, 5 accessions smeezoybu, 1 accession sneejorby, 1 accession larstoy, 1 accession lerstoy, 1 accession leystoy, 2 accessions lorstoy, 1 accession kerto, 1 accession mastoy, 1 accession mystoy, 3 accessions spyjorby, 1 accession marstoy, 2 accessions mawstoy, 1 accession smardee, 6 accessions meystoy, 2 accessions leyzar, 7 accessions sworjorby, 1 accession nastoy, 2 accessions nystoy, 3 accessions snuzoybu, 1 accession deyjoyby, 1 accession nerstoy, 1 accession norstoy, 1 accession noystoy, 1 accession skerpley, 2 accessions parstoy, 1 accession feyjoyby, 1 accession gojoyby, 1 accession peestoy, 1 accession flojorby, 1 accession beestoy, 1 accession dozaw, 3 accessions flerjorby, 1 accession dostoy, 1 accession stertu, 1 accession darstoy, 1 accession howami, 2 accessions, 2 variants byto, 1 accession deestoy, 1 accession dorpley, 1 accession skorzoybu, 1 accession doystoy, 1 accession doto, 1 accession nawami, 2 accessions, 2 variants fastoy, 5 accessions foto, 1 accession fawto, 2 accessions fustoy, 1 accession kemuru, 2 accessions klujorby, 1 accession slysorbo, 1 accession komuru, 5 accessions doyzaw, 2 accessions kleyjorby, 1 accession geeto, 1 accession plojorby, 1 accession roypley, 1 accession jystoy, 1 accession jeeto, 1 accession worpley, 1 accession jostoy, 1 accession jeestoy, 2 accessions jorstoy, 1 accession slujorby, 1 accession slerzoybu, 1 accession shapley, 1 accession smarjorby, 1 accession romeru, 1 accession yameru, 1 accession kerstoy, 2 accessions smazoybu, 1 accession dorgler, 1 accession lystoy, 1 accession plarpley, 1 accession snarjorby, 1 accession smerzoybu, 1 accession smorzoybu, 2 accessions mustoy, 1 accession stujorby, 1 accession slersorbo, 2 accessions sterjorby, 1 accession morstoy, 1 accession moystoy, 1 accession swoyjorby, 1 accession korto, 1 accession neestoy, 3 accessions neystoy, 3 accessions pastoy, 1 accession dorjoyby, 2 accessions pystoy, 4 accessions ferjoyby, 1 accession pustoy, 1 accession postoy, 1 accession snarzoybu, 1 accession pawstoy, 1 accession nuwami, 1 accession mumeru, 1 accession CIB2, 140 accessions, 11 variants ACSBG1, 226 accessions 19 variants derzaw, 3 accessions, 2 variants WDR61, 349 accessions 22 variants swazobu, 38 accessions 2 variants CHRNA3, 119 accessions 9 variants CHRNB4, 42 accessions 12 variants ADAMTS7, 93 accessions 11 variants CTSH, 522 accessions, 21 variants RASGRF1, 110 accessions 14 variants ZOOM IN                D:disease,C:conserved,I:interactions,R:regulation,P:publications         Read more...
Annotated mRNA diagrams back to top
Bibliography:               80 articles in PubMed back to top
? Gene Summary Gene on genome mRNA:.a, .b, .c, .d, .e-u, .f, .g, .h, .i Alternative mRNAs features, proteins, introns, exons, sequences Expression Tissue Function, regulation, related genes DCI

To mine knowledge about the gene, please click the 'Gene Summary' or the 'Function, regulation, related genes ' tab at the top of the page. The 'Gene Summary' page includes all we learnt about the gene, functional annotations of neighboring genes, maps, links to other sites and the bibliography. The 'Function, regulation, related genes ' page includes Diseases (D), Pathways, GO annotations, conserved domains (C), interactions (I) reference into function, and pointers to all genes with the same functional annotation.
To compare alternative variants, their summarized annotations, predicted proteins, introns and exons, or to access any sequence, click the 'Alternative mRNAs features' tab. To see a specific mRNA variant diagram, sequence and annotation, click the variant name in the 'mRNA' tab. To examine expression data from all cDNAs clustered in this gene by AceView, click the 'Expression tissue'.

If you know more about this gene, or found errors, please share your knowledge. Thank you !