Chrna4 (cholinergic receptor nicotinic alpha 4 subunit) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models   new Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Gene: Chrna4 (cholinergic receptor nicotinic alpha 4 subunit) Rattus norvegicus
Analyze
Symbol: Chrna4
Name: cholinergic receptor nicotinic alpha 4 subunit
RGD ID: 2346
Description: Enables acetylcholine binding activity; acetylcholine-gated monoatomic cation-selective channel activity; and quaternary ammonium group binding activity. Contributes to heterocyclic compound binding activity. Involved in cholinergic synaptic transmission and response to acetylcholine. Located in dendrite and neuronal cell body. Part of acetylcholine-gated channel complex. Is active in cholinergic synapse; postsynaptic specialization membrane; and presynaptic membrane. Biomarker of congestive heart failure. Human ortholog(s) of this gene implicated in autosomal dominant nocturnal frontal lobe epilepsy 1 and nicotine dependence. Orthologous to human CHRNA4 (cholinergic receptor nicotinic alpha 4 subunit); PARTICIPATES IN acetylcholine signaling pathway via nicotinic acetylcholine receptor; alfentanil pharmacodynamics pathway; bupivacaine pharmacodynamics pathway; INTERACTS WITH (S)-anabasine; (S)-nicotine; 1,1-dimethyl-4-phenylpiperazinium iodide.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: cholinergic receptor, nicotinic, alpha 4; cholinergic receptor, nicotinic, alpha 4 (neuronal); cholinergic receptor, nicotinic, alpha 4 subunit; cholinergic receptor, nicotinic, alpha polypeptide 4; NARAC; neuronal acetylcholine receptor subunit alpha-4; neuronal nicotinic acetylcholine receptor alpha 4 subunit
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Chrna4em4Mcwi   Chrna4em3Mcwi   Chrna4em5Mcwi  
Genetic Models: LEW-Chrna4em4Mcwi LEW-Chrna4em5Mcwi LEW-Chrna4em3Mcwi
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83188,506,802 - 188,535,558 (-)NCBIGRCr8
mRatBN7.23168,136,246 - 168,157,839 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3168,136,266 - 168,156,957 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx3172,520,220 - 172,537,355 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.03181,479,311 - 181,496,446 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.03178,140,859 - 178,157,919 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.03176,533,182 - 176,547,965 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3176,527,516 - 176,548,208 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03180,243,234 - 180,258,017 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43170,171,214 - 170,185,998 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.13170,077,249 - 170,092,033 (-)NCBI
Celera3164,428,976 - 164,443,759 (+)NCBICelera
RH 3.4 Map31564.7RGD
RH 3.4 Map31531.39RGD
Cytogenetic Map3q43NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-lobeline  (ISO)
(S)-anabasine  (EXP)
(S)-nicotine  (EXP,ISO)
1,1-dichloroethene  (ISO)
1,1-dimethyl-4-phenylpiperazinium iodide  (EXP,ISO)
1,2-dichloroethane  (ISO)
1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine  (ISO)
13-desmethylspirolide C  (ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (ISO)
2,2',4,4'-tetrachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,4-dibromophenyl 2,4,5-tribromophenyl ether  (ISO)
3,3',5,5'-tetrabromobisphenol A  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-nonylphenol  (ISO)
4-octylphenol  (ISO)
5-fluorouracil  (ISO)
6-propyl-2-thiouracil  (EXP)
acetamiprid  (ISO)
acetylcholine  (EXP,ISO)
acrylamide  (EXP)
alcuronium  (ISO)
aldicarb  (EXP)
aldrin  (ISO)
all-trans-retinoic acid  (ISO)
aluminium hydroxide  (ISO)
Amaranth  (EXP)
ammonium chloride  (EXP)
Antimony trioxide  (ISO)
aristolochic acid A  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
atracurium  (ISO)
atropine  (EXP,ISO)
azoxystrobin  (ISO)
barium(0)  (EXP)
bendiocarb  (EXP)
bentonite  (ISO)
benzene  (ISO)
benzo[a]pyrene  (EXP,ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
Brilliant Blue  (EXP)
butan-1-ol  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
calcium atom  (EXP)
calcium(0)  (EXP)
carbachol  (EXP,ISO)
carbamazepine  (ISO)
carbaryl  (EXP)
carbon nanotube  (ISO)
chloroethene  (ISO)
chlorpyrifos  (ISO)
choline  (EXP,ISO)
cisatracurium  (ISO)
Citreoviridin  (ISO)
clothianidin  (ISO)
cocaine  (EXP)
Cuprizon  (EXP)
cytisine  (EXP,ISO)
decabromodiphenyl ether  (ISO)
decamethonium  (ISO)
deguelin  (ISO)
Desformylflustrabromine  (ISO)
diazinon  (EXP)
dichlorine  (EXP)
dichloroacetic acid  (ISO)
dichlorvos  (ISO)
dieldrin  (EXP)
diethyl maleate  (ISO)
diethylstilbestrol  (ISO)
dihydro-beta-erythroidine  (EXP,ISO)
dioxygen  (ISO)
dopamine  (EXP)
elemental selenium  (ISO)
epibatidine  (EXP,ISO)
epoxiconazole  (ISO)
EPTC  (EXP)
ethanol  (ISO)
ethylparaben  (ISO)
fenoxycarb  (EXP)
fulvestrant  (ISO)
galanthamine  (ISO)
galanthamine Trifluoroacetic acid  (ISO)
genistein  (EXP,ISO)
hexachlorophene  (ISO)
Hexamethonium  (ISO)
imidacloprid  (EXP,ISO)
indigo carmine  (EXP)
magnesium dihydroxide  (ISO)
Mecamylamine  (EXP,ISO)
mercury dichloride  (EXP)
methoxychlor  (EXP)
methyllycaconitine  (EXP,ISO)
Mivacurium  (ISO)
N-nitrosodiethylamine  (ISO)
nickel atom  (EXP)
nicotine  (EXP,ISO)
nitrofen  (EXP)
NS-398  (ISO)
ozone  (EXP)
pancuronium  (ISO)
paracetamol  (ISO)
paraoxon  (EXP)
phenobarbital  (ISO)
physostigmine  (ISO)
picoxystrobin  (ISO)
potassium dichromate  (ISO)
progesterone  (ISO)
propoxur  (EXP)
pyrazines  (ISO)
pyridines  (ISO)
pyrimidifen  (ISO)
resveratrol  (ISO)
rivastigmine  (ISO)
rocuronium  (ISO)
rotenone  (ISO)
scopolamine  (ISO)
selenium atom  (ISO)
silicon dioxide  (EXP)
sodium fluoride  (EXP,ISO)
streptozocin  (ISO)
succinylcholine  (ISO)
Sunset Yellow FCF  (EXP)
T-2 toxin  (ISO)
tacrine  (ISO)
tamoxifen  (ISO)
tartrazine  (EXP)
tetrachloroethene  (EXP,ISO)
tetrachloromethane  (EXP)
tetraphene  (ISO)
Theaflavin 3,3'-digallate  (ISO)
thifluzamide  (ISO)
toluene  (EXP,ISO)
triphenyl phosphate  (ISO)
Triptolide  (ISO)
triptonide  (ISO)
tropan-3alpha-yl 3-hydroxy-2-phenylpropanoate  (EXP,ISO)
tubocurarine  (ISO)
tunicamycin  (ISO)
urethane  (EXP)
valproic acid  (ISO)
vancomycin  (ISO)
varenicline  (EXP,ISO)
vecuronium bromide  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
acetylcholine signaling pathway via nicotinic acetylcholine receptor  (ISO)
alfentanil pharmacodynamics pathway  (ISO)
bupivacaine pharmacodynamics pathway  (ISO)
buprenorphine pharmacodynamics pathway  (ISO)
chloroprocaine pharmacodynamics pathway  (ISO)
citalopram pharmacodynamics pathway  (ISO)
cocaine pharmacodynamics pathway  (ISO)
codeine and morphine pharmacodynamics pathway  (ISO)
desipramine pharmacodynamics pathway  (ISO)
diphenoxylate pharmacodynamics pathway  (ISO)
escitalopram pharmacodynamics pathway  (ISO)
ethylmorphine pharmacodynamics pathway  (ISO)
fentanyl pharmacodynamics pathway  (ISO)
fluoxetine pharmacodynamics pathway  (ISO)
heroin pharmacodynamics pathway  (ISO)
hydrocodone pharmacodynamics pathway  (ISO)
hydromorphone pharmacodynamics pathway  (ISO)
imipramine pharmacodynamics pathway  (ISO)
levacetylmethadol pharmacodynamics pathway  (ISO)
levobupivacaine phgarmacodynamics pathway  (ISO)
levorphanol pharmacodynamics pathway  (ISO)
lidocaine pharmacodynamics pathway  (ISO)
mepivacaine pharmacodynamics pathway  (ISO)
methadone pharmacodynamics pathway  (ISO)
nalbuphine pharmacodynamics pathway  (ISO)
naloxone pharmacodynamics pathway  (ISO)
naltrexone pharmacodynamics pathway  (ISO)
nicotine pharmacodynamics pathway  (ISO)
nicotine pharmacokinetics pathway  (ISO)
oxybuprocaine pharmacodynamics pathway  (ISO)
oxycodone pharmacodynamics pathway  (ISO)
oxymorphone pharmacodynamics pathway  (ISO)
pentazocine pharmacodynamics pathway  (ISO)
prilocaine pharmacodynamics pathway  (ISO)
procaine pharmacodynamics pathway  (ISO)
remifentanil pharmacodynamics pathway  (ISO)
ropivacaine pharmacodynamics pathway  (ISO)
tramadol pharmacodynamics pathway  (ISO)

References

References - curated
# Reference Title Reference Citation
1. Mammalian nicotinic acetylcholine receptors: from structure to function. Albuquerque EX, etal., Physiol Rev. 2009 Jan;89(1):73-120. doi: 10.1152/physrev.00015.2008.
2. Regulation of neuronal type genes in congestive heart failure rats. Andersson KB, etal., Acta Physiol (Oxf). 2006 Jan;186(1):17-27.
3. Ultrastructural localization of the alpha4-subunit of the neuronal acetylcholine nicotinic receptor in the rat substantia nigra. Arroyo-Jim nez MM, etal., J Neurosci. 1999 Aug 1;19(15):6475-87.
4. Varenicline is a potent partial agonist at alpha6beta2* nicotinic acetylcholine receptors in rat and monkey striatum. Bordia T, etal., J Pharmacol Exp Ther. 2012 Aug;342(2):327-34. doi: 10.1124/jpet.112.194852. Epub 2012 May 1.
5. Alpha 4-2 beta 2 and other nicotinic acetylcholine receptor subtypes as targets of psychoactive and addictive drugs. Connolly J, etal., Br J Pharmacol 1992 Mar;105(3):657-66.
6. Properties of nicotinic receptors underlying Renshaw cell excitation by alpha-motor neurons in neonatal rat spinal cord. Dourado M and Sargent PB, J Neurophysiol 2002 Jun;87(6):3117-25.
7. Formation of oligomers containing the beta3 and beta4 subunits of the rat nicotinic receptor. Forsayeth JR and Kobrin E, J Neurosci. 1997 Mar 1;17(5):1531-8.
8. Nicotinic receptor subunit alpha5 modifies assembly, up-regulation, and response to pro-inflammatory cytokines. Gahring LC and Rogers SW, J Biol Chem. 2010 Aug 20;285(34):26049-57. doi: 10.1074/jbc.M110.105346. Epub 2010 Jun 21.
9. Subsynaptic localization of nicotinic acetylcholine receptor subunits: a comparative study in the mouse and rat striatum. Garção P, etal., Neurosci Lett. 2014 Apr 30;566:106-10. doi: 10.1016/j.neulet.2014.02.018. Epub 2014 Mar 4.
10. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
11. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
12. Members of a nicotinic acetylcholine receptor gene family are expressed in different regions of the mammalian central nervous system. Goldman D, etal., Cell 1987 Mar 27;48(6):965-73.
13. The chaperone protein 14-3-3eta interacts with the nicotinic acetylcholine receptor alpha 4 subunit. Evidence for a dynamic role in subunit stabilization. Jeanclos EM, etal., J Biol Chem. 2001 Jul 27;276(30):28281-90. Epub 2001 May 14.
14. Rat nicotinic acetylcholine receptor alpha2beta2 channels: comparison of functional properties with alpha4beta2 channels in Xenopus oocytes. Khiroug SS, etal., Neuroscience 2004;124(4):817-22.
15. High-density rat radiation hybrid maps containing over 24,000 SSLPs, genes, and ESTs provide a direct link to the rat genome sequence. Kwitek AE, etal., Genome Res. 2004 Apr;14(4):750-7
16. The calcium sensor protein visinin-like protein-1 modulates the surface expression and agonist sensitivity of the alpha 4beta 2 nicotinic acetylcholine receptor. Lin L, etal., J Biol Chem 2002 Nov 1;277(44):41872-8.
17. Quantitative analysis of the heteromeric neuronal nicotinic receptors in the rat hippocampus. Lomazzo E, etal., J Neurochem. 2010 Nov;115(3):625-34. doi: 10.1111/j.1471-4159.2010.06967.x. Epub 2010 Sep 27.
18. Nicotinic cholinergic receptors in the rat retina: simple and mixed heteromeric subtypes. Marritt AM, etal., Mol Pharmacol. 2005 Dec;68(6):1656-68. Epub 2005 Aug 29.
19. Postsynaptic alpha 4 beta 2 and alpha 7 type nicotinic acetylcholine receptors contribute to the local and endogenous acetylcholine-mediated synaptic transmissions in nigral dopaminergic neurons. Matsubayashi H, etal., Brain Res. 2004 Apr 16;1005(1-2):1-8.
20. Mutation (Ser284Leu) of neuronal nicotinic acetylcholine receptor alpha 4 subunit associated with frontal lobe epilepsy causes faster desensitization of the rat receptor expressed in oocytes. Matsushima N, etal., Epilepsy Res 2002 Feb;48(3):181-6.
21. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
22. Modulation of neuronal nicotinic acetylcholine receptors by halothane in rat cortical neurons. Mori T, etal., Mol Pharmacol. 2001 Apr;59(4):732-43.
23. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
24. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
25. Measuring nicotinic receptors with characteristics of alpha4beta2, alpha3beta2 and alpha3beta4 subtypes in rat tissues by autoradiography. Perry DC, etal., J Neurochem 2002 Aug;82(3):468-81.
26. SMPDB Annotation Import Pipeline Pipeline to import SMPDB annotations from SMPDB into RGD
27. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
28. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
29. Five ADNFLE mutations reduce the Ca2+ dependence of the mammalian alpha4beta2 acetylcholine response. Rodrigues-Pinguet N, etal., J Physiol 2003 Jul 1;550(Pt 1):11-26. Epub 2003 May 16.
30. Nicotinic acetylcholine receptor immunohistochemistry in Alzheimer's disease and dementia with Lewy bodies: differential neuronal and astroglial pathology. Teaktong T, etal., J Neurol Sci 2004 Oct 15;225(1-2):39-49.
31. Nicotinic acetylcholine receptor subtypes in rat superior cervical ganglion neurons as studied by sequential application of two alpha-subunit-specific antibodies. Voitenko LP, etal., Neurosci Lett. 2001 Apr 27;303(1):37-40.
32. The comparative pharmacology and up-regulation of rat neuronal nicotinic receptor subtype binding sites stably expressed in transfected mammalian cells. Xiao Y and Kellar KJ, J Pharmacol Exp Ther. 2004 Jul;310(1):98-107. Epub 2004 Mar 11.
Additional References at PubMed
PMID:3609304   PMID:7550350   PMID:8906617   PMID:10235262   PMID:10964949   PMID:11222635   PMID:11226318   PMID:11906696   PMID:12130686   PMID:12189247   PMID:12774304   PMID:12871652  
PMID:12944511   PMID:14623738   PMID:15296793   PMID:15469877   PMID:15528443   PMID:15569257   PMID:15741168   PMID:15955596   PMID:15963492   PMID:16014729   PMID:16033901   PMID:16332175  
PMID:16407231   PMID:17146052   PMID:17192655   PMID:17434683   PMID:17613539   PMID:17626178   PMID:17950703   PMID:17955458   PMID:18297099   PMID:18403129   PMID:18583454   PMID:18602971  
PMID:18818999   PMID:19095841   PMID:19246390   PMID:19567877   PMID:20238211   PMID:20616056   PMID:20633015   PMID:20639140   PMID:21606356   PMID:21824140   PMID:22064677   PMID:22127290  
PMID:22253754   PMID:22323734   PMID:22510484   PMID:22593584   PMID:22778816   PMID:23056257   PMID:23429044   PMID:23583932   PMID:23734673   PMID:23749479   PMID:25810076   PMID:26276394  
PMID:26858154   PMID:27721068   PMID:29114204   PMID:31901135   PMID:33092257   PMID:34052301   PMID:37495067  


Genomics

Comparative Map Data
Chrna4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83188,506,802 - 188,535,558 (-)NCBIGRCr8
mRatBN7.23168,136,246 - 168,157,839 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3168,136,266 - 168,156,957 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx3172,520,220 - 172,537,355 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.03181,479,311 - 181,496,446 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.03178,140,859 - 178,157,919 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.03176,533,182 - 176,547,965 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3176,527,516 - 176,548,208 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03180,243,234 - 180,258,017 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43170,171,214 - 170,185,998 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.13170,077,249 - 170,092,033 (-)NCBI
Celera3164,428,976 - 164,443,759 (+)NCBICelera
RH 3.4 Map31564.7RGD
RH 3.4 Map31531.39RGD
Cytogenetic Map3q43NCBI
CHRNA4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382063,343,223 - 63,361,349 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2063,343,223 - 63,378,401 (-)EnsemblGRCh38hg38GRCh38
GRCh372061,974,575 - 61,992,701 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362061,445,109 - 61,463,192 (-)NCBINCBI36Build 36hg18NCBI36
Build 342061,446,464 - 61,463,192NCBI
Celera2058,652,104 - 58,670,128 (-)NCBICelera
Cytogenetic Map20q13.33NCBI
HuRef2058,700,254 - 58,717,202 (-)NCBIHuRef
CHM1_12061,875,694 - 61,893,903 (-)NCBICHM1_1
T2T-CHM13v2.02065,149,372 - 65,167,972 (-)NCBIT2T-CHM13v2.0
Chrna4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392180,664,104 - 180,685,339 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl2180,660,173 - 180,685,339 (-)EnsemblGRCm39 Ensembl
GRCm382181,022,311 - 181,043,579 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2181,018,380 - 181,043,546 (-)EnsemblGRCm38mm10GRCm38
MGSCv372180,757,016 - 180,773,882 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv362180,951,719 - 180,968,585 (-)NCBIMGSCv36mm8
Celera2185,108,778 - 185,125,645 (-)NCBICelera
Cytogenetic Map2H4NCBI
cM Map2103.54NCBI
Chrna4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955528825,308 - 841,270 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955528825,314 - 840,994 (+)NCBIChiLan1.0ChiLan1.0
CHRNA4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22169,134,670 - 69,153,450 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12069,126,676 - 69,145,454 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02059,730,759 - 59,748,678 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12061,267,958 - 61,284,640 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2061,270,631 - 61,283,005 (-)Ensemblpanpan1.1panPan2
CHRNA4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12447,024,948 - 47,036,507 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2447,025,187 - 47,042,266 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2446,208,582 - 46,223,310 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02447,978,552 - 47,993,300 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2447,977,796 - 47,988,696 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12446,993,833 - 47,005,225 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02447,118,082 - 47,132,739 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02447,874,247 - 47,888,996 (-)NCBIUU_Cfam_GSD_1.0
Chrna4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024408640195,227,250 - 195,242,216 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493651410,680,859 - 10,695,865 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493651410,680,893 - 10,695,859 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CHRNA4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1762,423,878 - 62,435,728 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11762,424,672 - 62,436,646 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
CHRNA4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12851,790 - 862,685 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366605048,462,591 - 48,480,754 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Chrna4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474129,026,908 - 29,044,464 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474129,024,668 - 29,039,684 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Chrna4
71 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:53
Count of miRNA genes:49
Interacting mature miRNAs:50
Transcripts:ENSRNOT00000009041
Prediction methods:Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1559282Emca5Estrogen-induced mammary cancer QTL 53.9mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)343827364169034231Rat
631541Bp81Blood pressure QTL 814arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3124122556169034231Rat
1578656Vnigr2Vascular neointimal growth QTL 24.2artery morphology trait (VT:0002191)lesioned artery residual lumen area (CMO:0001417)3130656562169034231Rat
1578653Vnigr3Vascular neointimal growth QTL 33.1artery morphology trait (VT:0002191)artery neointimal hyperplastic lesion area (CMO:0001414)3130656562169034231Rat
9589106Insul23Insulin level QTL 2313.860.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)3131635904169034231Rat
2298477Eau4Experimental allergic uveoretinitis QTL 40.0011uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)3137398739169034231Rat
8552952Pigfal13Plasma insulin-like growth factor 1 level QTL 13blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)3138799500169034231Rat
1298068Bp167Blood pressure QTL 1670.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3141074471169034231Rat
2317883Alcrsp26Alcohol response QTL 261.80.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)3145526770169034231Rat
8552791Vie2Viral induced encephalitis QTL 24.1brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)3145956084169034231Rat
1300161Rf10Renal function QTL 103.57renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)3161192952169034231Rat

Markers in Region
RH94428  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23168,142,103 - 168,142,253 (+)MAPPERmRatBN7.2
Rnor_6.03176,533,221 - 176,533,370NCBIRnor6.0
Rnor_5.03180,243,273 - 180,243,422UniSTSRnor5.0
RGSC_v3.43170,171,253 - 170,171,402UniSTSRGSC3.4
Celera3164,443,571 - 164,443,720UniSTS
Cytogenetic Map3q43UniSTS
RH94555  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23168,136,281 - 168,136,371 (+)MAPPERmRatBN7.2
Rnor_6.03176,527,532 - 176,527,621NCBIRnor6.0
Rnor_5.03180,237,359 - 180,237,448UniSTSRnor5.0
RGSC_v3.43170,138,351 - 170,138,440UniSTSRGSC3.4
Celera3164,448,587 - 164,448,676UniSTS
RH 3.4 Map31564.7UniSTS
Cytogenetic Map3q43UniSTS
D2Ucl29  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23168,151,608 - 168,151,824 (+)MAPPERmRatBN7.2
Rnor_6.03176,542,726 - 176,542,941NCBIRnor6.0
Rnor_5.03180,252,778 - 180,252,993UniSTSRnor5.0
RGSC_v3.43170,180,758 - 170,180,973UniSTSRGSC3.4
Celera3164,434,000 - 164,434,215UniSTS
Cytogenetic Map3q43UniSTS


Genetic Models
This gene Chrna4 is modified in the following models/strains:
LEW-Chrna4em4Mcwi     LEW-Chrna4em5Mcwi     LEW-Chrna4em3Mcwi    


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 56 24
Low 20 13 6 7 6 18 24 15 7
Below cutoff 13 21 16 8 16 5 6 9 2 4 5

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000009041   ⟹   ENSRNOP00000009041
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3168,136,266 - 168,156,865 (-)Ensembl
Rnor_6.0 Ensembl3176,527,516 - 176,547,965 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000084339   ⟹   ENSRNOP00000073967
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3168,139,899 - 168,156,957 (-)Ensembl
Rnor_6.0 Ensembl3176,531,016 - 176,548,208 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000112623   ⟹   ENSRNOP00000087864
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3168,139,899 - 168,156,393 (-)Ensembl
RefSeq Acc Id: NM_024354   ⟹   NP_077330
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83188,517,466 - 188,534,526 (-)NCBI
mRatBN7.23168,139,899 - 168,156,957 (-)NCBI
Rnor_6.03176,533,182 - 176,547,965 (-)NCBI
Rnor_5.03180,243,234 - 180,258,017 (-)NCBI
RGSC_v3.43170,171,214 - 170,185,998 (-)RGD
Celera3164,428,976 - 164,443,759 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039104383   ⟹   XP_038960311
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83188,506,802 - 188,535,558 (-)NCBI
mRatBN7.23168,136,246 - 168,157,839 (-)NCBI
RefSeq Acc Id: XM_039104384   ⟹   XP_038960312
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83188,513,813 - 188,534,046 (-)NCBI
mRatBN7.23168,136,246 - 168,156,486 (-)NCBI
Reference Protein Sequences
RefSeq Acc Id: NP_077330   ⟸   NM_024354
- Peptide Label: precursor
- UniProtKB: A0A0G2K6W5 (UniProtKB/TrEMBL),   A6KM61 (UniProtKB/TrEMBL),   A6KM60 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000009041   ⟸   ENSRNOT00000009041
RefSeq Acc Id: ENSRNOP00000073967   ⟸   ENSRNOT00000084339
RefSeq Acc Id: XP_038960311   ⟸   XM_039104383
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038960312   ⟸   XM_039104384
- Peptide Label: isoform X2
- UniProtKB: K4DIC3 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSRNOP00000087864   ⟸   ENSRNOT00000112623
Protein Domains
Neurotransmitter-gated ion-channel ligand-binding   Neurotransmitter-gated ion-channel transmembrane

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P09483-F1-model_v2 AlphaFold P09483 1-630 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2346 AgrOrtholog
BioCyc Gene G2FUF-46306 BioCyc
Ensembl Genes ENSRNOG00000011202 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000009041.8 UniProtKB/TrEMBL
  ENSRNOT00000084339 ENTREZGENE
  ENSRNOT00000084339.3 UniProtKB/TrEMBL
  ENSRNOT00000112623.1 UniProtKB/TrEMBL
Gene3D-CATH 1.20.58.390 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  2.70.170.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Neur_chan_lig-bd UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Neur_chan_lig-bd_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Neur_channel UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Neuro-gated_channel_TM_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Neuro_actylchol_rec UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Neurotrans-gated_channel_TM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Neurotransmitter_ion_chnl_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Nicotinic_acetylcholine_rcpt UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:25590 UniProtKB/Swiss-Prot
NCBI Gene 25590 ENTREZGENE
PANTHER NEURONAL ACETYLCHOLINE RECEPTOR SUBUNIT ALPHA-4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR18945 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Neur_chan_LBD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Neur_chan_memb UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB CHRNA4 RGD
PhenoGen Chrna4 PhenoGen
PRINTS NICOTINICR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NRIONCHANNEL UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE NEUROTR_ION_CHANNEL UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000011202 RatGTEx
Superfamily-SCOP SSF63712 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF90112 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2K6W5 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6A9L0_RAT UniProtKB/TrEMBL
  A6KM60 ENTREZGENE, UniProtKB/TrEMBL
  A6KM61 ENTREZGENE, UniProtKB/TrEMBL
  A6KM62_RAT UniProtKB/TrEMBL
  ACHA4_RAT UniProtKB/Swiss-Prot
  K4DIC3 ENTREZGENE, UniProtKB/TrEMBL
  P09483 ENTREZGENE
UniProt Secondary O35769 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-11 Chrna4  cholinergic receptor nicotinic alpha 4 subunit  Chrna4  cholinergic receptor, nicotinic, alpha 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2015-11-12 Chrna4  cholinergic receptor, nicotinic, alpha 4  Chrna4  cholinergic receptor, nicotinic, alpha 4 (neuronal)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-07-16 Chrna4  cholinergic receptor, nicotinic, alpha 4 (neuronal)  Chrna4  cholinergic receptor, nicotinic, alpha 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-25 Chrna4  cholinergic receptor, nicotinic, alpha 4  Chrna4  cholinergic receptor, nicotinic, alpha polypeptide 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2001-07-23 Chrna4  Neuronal nicotinic acetylcholine receptor alpha 4 subunit      Name withdrawn 67952 WITHDRAWN
2001-07-23 Chrna4  cholinergic receptor, nicotinic, alpha polypeptide 4      Name updated to reflect Human and Mouse nomenclature 67952 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_physical_interaction interacts with visinin-like protein-1 (VILIP-1) 727641
gene_regulation surface expression and agonist sensitivity is regulated by visinin-like protein-1 (VILIP-1) 727641