Human Gene CHRNA1 (uc002uje.2) Description and Page Index
  Description: Homo sapiens cholinergic receptor, nicotinic, alpha 1 (muscle) (CHRNA1), transcript variant 2, mRNA.
RefSeq Summary (NM_000079): The muscle acetylcholine receptor consiststs of 5 subunits of 4 different types: 2 alpha subunits and 1 each of the beta, gamma, and delta subunits. This gene encodes an alpha subunit that plays a role in acetlycholine binding/channel gating. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Nov 2012].
Transcript (Including UTRs)
   Position: hg19 chr2:175,612,323-175,629,200 Size: 16,878 Total Exon Count: 9 Strand: -
Coding Region
   Position: hg19 chr2:175,612,852-175,629,122 Size: 16,271 Coding Exon Count: 9 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesGeneReviewsModel Information
Methods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:175,612,323-175,629,200)mRNA (may differ from genome)Protein (457 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCLynxMGIOMIMPubMed
Stanford SOURCETreefamUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: Q53SH4_HUMAN
DESCRIPTION: SubName: Full=Cholinergic receptor, nicotinic, alpha 1 (Muscle), isoform CRA_a; SubName: Full=Putative uncharacterized protein CHRNA1; SubName: Full=cDNA FLJ77888, highly similar to Human muscle acetylcholine receptor alpha-subunit; SubName: Full=cDNA, FLJ96344, Homo sapiens cholinergic receptor, nicotinic, alpha polypeptide 1(muscle) (CHRNA1), mRNA;
SIMILARITY: Belongs to the ligand-gated ion channel (TC 1.A.9) family.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): CHRNA1
CDC HuGE Published Literature: CHRNA1
Positive Disease Associations: autoimmune myasthenia gravis
Related Studies:
  1. autoimmune myasthenia gravis
    Heckmann JM et al. 1996, Human muscle acetylcholine receptor alpha-subunit gene (CHRNA1) association with autoimmune myasthenia gravis in black mixed-ancestry and Caucasian subjects., Journal of autoimmunity. 1996 Apr;9(2):175-80. [PubMed 8738961]
    Our results suggest that the CHRNA1 locus harbours a minor susceptibility gene for developing MG, though we cannot rule out linkage disequilibrium with another major gene locus on chromosome 2.

-  MalaCards Disease Associations
  MalaCards Gene Search: CHRNA1
Diseases sorted by gene-association score: myasthenic syndrome, congenital, 1a, slow-channel* (1231), myasthenic syndrome, congenital, 1b, fast-channel* (1231), multiple pterygium syndrome, lethal type* (912), slow-channel congenital myasthenic syndrome* (419), postsynaptic congenital myasthenic syndromes* (111), chrna1-related multiple pterygium syndrome, lethal type* (100), chrna1-related congenital myasthenic syndrome* (100), myasthenia gravis (32), escobar syndrome (17), congenital myasthenic syndrome (11), fetal akinesia deformation sequence (6), neuromuscular junction disease (6), oligohydramnios (6), deafness, autosomal recessive 25 (5)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 23.39 RPKM in Muscle - Skeletal
Total median expression: 28.50 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -19.4078-0.249 Picture PostScript Text
3' UTR -131.10529-0.248 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
IPR006202 - Neur_chan_lig-bd
IPR006201 - Neur_channel
IPR006029 - Neurotrans-gated_channel_TM
IPR018000 - Neurotransmitter_ion_chnl_CS
IPR002394 - Nicotinic_acetylcholine_rcpt

Pfam Domains:
PF02931 - Neurotransmitter-gated ion-channel ligand binding domain
PF02932 - Neurotransmitter-gated ion-channel transmembrane region

SCOP Domains:
63712 - Nicotinic receptor ligand binding domain-like
90112 - Neurotransmitter-gated ion-channel transmembrane pore

ModBase Predicted Comparative 3D Structure on Q53SH4
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.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserGenome BrowserNo orthologNo orthologNo ortholog
 Gene Details    
 Gene Sorter    
 RGDEnsembl   
 Protein SequenceProtein Sequence   
 AlignmentAlignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004888 transmembrane signaling receptor activity
GO:0005216 ion channel activity
GO:0005230 extracellular ligand-gated ion channel activity
GO:0022848 acetylcholine-gated cation-selective channel activity

Biological Process:
GO:0006811 ion transport
GO:0007165 signal transduction
GO:0034220 ion transmembrane transport
GO:0060078 regulation of postsynaptic membrane potential
GO:0060079 excitatory postsynaptic potential

Cellular Component:
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0030054 cell junction
GO:0045202 synapse
GO:0045211 postsynaptic membrane


-  Descriptions from all associated GenBank mRNAs
  BC043196 - Homo sapiens cholinergic receptor, nicotinic, alpha 1 (muscle), mRNA (cDNA clone IMAGE:5288924), with apparent retained intron.
AK299445 - Homo sapiens cDNA FLJ58615 complete cds, highly similar to Acetylcholine receptor protein subunit alpha precursor.
S77094 - nicotinic acetylcholine receptor alpha subunit|AChR alpha subunit [human, thymic carcinoma, myasthenia gravis-associated thymoma patient 1494/88, mRNA Partial, 1676 nt].
Y00762 - Human mRNA for muscle acetylcholine receptor alpha-subunit.
JD500866 - Sequence 481890 from Patent EP1572962.
JD244924 - Sequence 225948 from Patent EP1572962.
AK291338 - Homo sapiens cDNA FLJ77888 complete cds, highly similar to Human mRNA for muscle acetylcholine receptor alpha-subunit.
JD411470 - Sequence 392494 from Patent EP1572962.
JD419373 - Sequence 400397 from Patent EP1572962.
JD503043 - Sequence 484067 from Patent EP1572962.
AK315312 - Homo sapiens cDNA, FLJ96344, Homo sapiens cholinergic receptor, nicotinic, alpha polypeptide 1(muscle) (CHRNA1), mRNA.
BC006314 - Homo sapiens cholinergic receptor, nicotinic, alpha 1 (muscle), mRNA (cDNA clone IMAGE:4124038), with apparent retained intron.
KJ901339 - Synthetic construct Homo sapiens clone ccsbBroadEn_10733 CHRNA1 gene, encodes complete protein.
KR710048 - Synthetic construct Homo sapiens clone CCSBHm_00009235 CHRNA1 (CHRNA1) mRNA, encodes complete protein.
KR710049 - Synthetic construct Homo sapiens clone CCSBHm_00009237 CHRNA1 (CHRNA1) mRNA, encodes complete protein.
KR710050 - Synthetic construct Homo sapiens clone CCSBHm_00009238 CHRNA1 (CHRNA1) mRNA, encodes complete protein.
KR710051 - Synthetic construct Homo sapiens clone CCSBHm_00009239 CHRNA1 (CHRNA1) mRNA, encodes complete protein.
DQ323657 - Homo sapiens clone 66 muscle nicotinic acetylcholine receptor mRNA, partial cds.
DQ323658 - Homo sapiens clone 67 muscle nicotinic acetylcholine receptor mRNA, partial cds.
JD050179 - Sequence 31203 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04080 - Neuroactive ligand-receptor interaction

BioCarta from NCI Cancer Genome Anatomy Project
h_botulinPathway - Blockade of Neurotransmitter Relase by Botulinum Toxin
h_agrPathway - Agrin in Postsynaptic Differentiation
h_no1Pathway - Actions of Nitric Oxide in the Heart

-  Other Names for This Gene
  Alternate Gene Symbols: hCG_1811440, NM_000079, NP_000070, Q53SH4, Q53SH4_HUMAN
UCSC ID: uc002uje.2
RefSeq Accession: NM_000079
Protein: Q53SH4 CCDS: CCDS2261.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene CHRNA1:
cms (Congenital Myasthenic Syndromes)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_000079.3
exon count: 9CDS single in 3' UTR: no RNA size: 2019
ORF size: 1374CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2948.00frame shift in genome: no % Coverage: 98.12
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
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.