Human Gene CHRNA10 (ENST00000250699.2) from GENCODE V44
  Description: Homo sapiens cholinergic receptor nicotinic alpha 10 subunit (CHRNA10), transcript variant 1, mRNA. (from RefSeq NM_020402)
Gencode Transcript: ENST00000250699.2
Gencode Gene: ENSG00000129749.3
Transcript (Including UTRs)
   Position: hg38 chr11:3,665,587-3,671,384 Size: 5,798 Total Exon Count: 5 Strand: -
Coding Region
   Position: hg38 chr11:3,666,107-3,671,312 Size: 5,206 Coding Exon Count: 5 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr11:3,665,587-3,671,384)mRNA (may differ from genome)Protein (450 aa)
Gene SorterGenome BrowserOther Species FASTATable SchemaAlphaFoldBioGPS
EnsemblEntrez GeneExonPrimerGencodeGeneCardsHGNC
HPRDLynxMalacardsMGIneXtProtOMIM
PubMedUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: ACH10_HUMAN
DESCRIPTION: RecName: Full=Neuronal acetylcholine receptor subunit alpha-10; AltName: Full=Nicotinic acetylcholine receptor subunit alpha-10; Short=NACHR alpha-10; Flags: Precursor;
FUNCTION: Ionotropic receptor with a probable role in the modulation of auditory stimuli. Agonist binding may induce an extensive change in conformation that affects all subunits and leads to opening of an ion-conducting channel across the plasma membrane. The channel is permeable to a range of divalent cations including calcium, the influx of which may activate a potassium current which hyperpolarizes the cell membrane. In the ear, this may lead to a reduction in basilar membrane motion, altering the activity of auditory nerve fibers and reducing the range of dynamic hearing. This may protect against acoustic trauma.
SUBUNIT: Forms heterooligomeric channels in conjunction with CHRNA9. The native outer hair cell receptor may be composed of CHRNA9-CHRNA10 heterooligomers.
SUBCELLULAR LOCATION: Cell junction, synapse, postsynaptic cell membrane; Multi-pass membrane protein (Probable). Cell membrane; Multi-pass membrane protein (Probable).
TISSUE SPECIFICITY: Expressed in inner-ear tissue, tonsil, immortalized B-cells, cultured T-cells and peripheral blood lymphocytes.
MISCELLANEOUS: The heterooligomeric receptor composed of CHRNA9 and CHRNA10 has an atypical pharmacological profile, binding several non-nicotinic ligands including strychnine (a glycine receptor antagonist) and atropine (a muscarinic acetylcholine receptor antagonist).
SIMILARITY: Belongs to the ligand-gated ion channel (TC 1.A.9) family. Acetylcholine receptor (TC 1.A.9.1) subfamily. Alpha- 10/CHRNA10 sub-subfamily.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


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

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 9.06 RPKM in Muscle - Skeletal
Total median expression: 37.51 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 -22.6072-0.314 Picture PostScript Text
3' UTR -173.00520-0.333 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

ModBase Predicted Comparative 3D Structure on Q9GZZ6
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
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004888 transmembrane signaling receptor activity
GO:0005102 receptor binding
GO:0005216 ion channel activity
GO:0005230 extracellular ligand-gated ion channel activity
GO:0005262 calcium channel activity
GO:0022848 acetylcholine-gated cation-selective channel activity

Biological Process:
GO:0006811 ion transport
GO:0006816 calcium ion transport
GO:0007165 signal transduction
GO:0007204 positive regulation of cytosolic calcium ion concentration
GO:0007271 synaptic transmission, cholinergic
GO:0034220 ion transmembrane transport
GO:0042127 regulation of cell proliferation
GO:0042472 inner ear morphogenesis
GO:0050910 detection of mechanical stimulus involved in sensory perception of sound
GO:0060078 regulation of postsynaptic membrane potential
GO:0060079 excitatory postsynaptic potential
GO:0070373 negative regulation of ERK1 and ERK2 cascade
GO:0070588 calcium ion transmembrane transport

Cellular Component:
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0030054 cell junction
GO:0030424 axon
GO:0043204 perikaryon
GO:0045202 synapse
GO:0045211 postsynaptic membrane


-  Descriptions from all associated GenBank mRNAs
  AJ278118 - Homo sapiens mRNA for neuronal nicotinic acetylcholine alpha10 subunit (NACHRA10 gene).
AF199235 - Homo sapiens nicotinic acetylcholine receptor subunit alpha 10 mRNA, complete cds.
BC136250 - Homo sapiens cholinergic receptor, nicotinic, alpha 10, mRNA (cDNA clone IMAGE:9020237), partial cds.
BC143303 - Homo sapiens cDNA clone MGC:176825 IMAGE:9051808.
AJ295237 - Homo sapiens mRNA for neuronal nicotinic acetylcholine receptor subunit alpha 10 (NACHR alpha 10 gene).
BC152764 - Synthetic construct Homo sapiens clone IMAGE:100015955, MGC:184161 cholinergic receptor, nicotinic, alpha 10 (CHRNA10) mRNA, encodes complete protein.
AB528800 - Synthetic construct DNA, clone: pF1KE0266, Homo sapiens CHRNA10 gene for cholinergic receptor, nicotinic, alpha 10, without stop codon, in Flexi system.
JD408784 - Sequence 389808 from Patent EP1572962.
JD202276 - Sequence 183300 from Patent EP1572962.
JD222969 - Sequence 203993 from Patent EP1572962.
JD222968 - Sequence 203992 from Patent EP1572962.
JD096941 - Sequence 77965 from Patent EP1572962.
JD455721 - Sequence 436745 from Patent EP1572962.
JD494732 - Sequence 475756 from Patent EP1572962.
JD448755 - Sequence 429779 from Patent EP1572962.
JD343422 - Sequence 324446 from Patent EP1572962.
JD466297 - Sequence 447321 from Patent EP1572962.

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

-  Other Names for This Gene
  Alternate Gene Symbols: ACH10_HUMAN, ENST00000250699.1, NACHRA10, NM_020402, Q9GZZ6, uc001lyf.1, uc001lyf.2, uc001lyf.3
UCSC ID: ENST00000250699.2
RefSeq Accession: NM_020402
Protein: Q9GZZ6 (aka ACH10_HUMAN or ACHX_HUMAN)
CCDS: CCDS7745.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.