Chrna4 (cholinergic receptor nicotinic alpha 4 subunit) - Rat Genome Database
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Gene: Chrna4 (cholinergic receptor nicotinic alpha 4 subunit) Rattus norvegicus
Analyze
Symbol: Chrna4
Name: cholinergic receptor nicotinic alpha 4 subunit
RGD ID: 2346
Description: Exhibits acetylcholine binding activity and acetylcholine-gated cation-selective channel activity. Predicted to contribute to acetylcholine receptor activity. Involved in cholinergic synaptic transmission and regulation of acetylcholine-gated cation channel activity. Localizes to several cellular components, including cholinergic synapse; integral component of plasma membrane; and neuronal cell body. 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; 17alpha-ethynylestradiol.
Type: protein-coding
RefSeq Status: VALIDATED
Also 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: Rnor_6.0 - RGSC Genome Assembly v6.0
NCBI Annotation Information: Annotation category: partial on reference assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
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 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.13170,077,249 - 170,092,033 (-)NCBI
Celera3164,428,976 - 164,443,759 (+)NCBICelera
Cytogenetic Map3q43NCBI
RH 3.4 Map31531.39RGD
RH 3.4 Map31564.7RGD
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  (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)
arsane  (ISO)
arsenic atom  (ISO)
atracurium  (ISO)
atropine  (EXP,ISO)
barium(0)  (EXP)
bendiocarb  (EXP)
bentonite  (ISO)
benzo[a]pyrene  (EXP,ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
Brilliant Blue  (EXP)
butan-1-ol  (ISO)
calcium atom  (EXP)
calcium(0)  (EXP)
carbachol  (EXP,ISO)
carbamazepine  (ISO)
carbaryl  (EXP)
carbon nanotube  (ISO)
chloroethene  (ISO)
choline  (EXP,ISO)
cisatracurium  (ISO)
Citreoviridin  (ISO)
clothianidin  (ISO)
cocaine  (EXP)
cytisine  (ISO)
decabromodiphenyl ether  (ISO)
decamethonium  (ISO)
diazinon  (EXP)
dichlorine  (EXP)
dichloroacetic acid  (ISO)
dichlorvos  (ISO)
dieldrin  (EXP)
diethylstilbestrol  (ISO)
dihydro-beta-erythroidine  (EXP,ISO)
dioxygen  (ISO)
elemental selenium  (ISO)
epibatidine  (EXP,ISO)
EPTC  (EXP)
ethanol  (ISO)
fenoxycarb  (EXP)
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)
potassium dichromate  (ISO)
progesterone  (ISO)
propoxur  (EXP)
pyrazines  (ISO)
pyridines  (ISO)
resveratrol  (ISO)
rivastigmine  (ISO)
rocuronium  (ISO)
scopolamine  (ISO)
selenium atom  (ISO)
sodium fluoride  (EXP)
succinylcholine  (ISO)
Sunset Yellow FCF  (EXP)
T-2 toxin  (ISO)
tacrine  (ISO)
tamoxifen  (ISO)
tartrazine  (EXP)
tetrachloroethene  (EXP,ISO)
tetrachloromethane  (EXP)
tetraphene  (ISO)
toluene  (EXP,ISO)
triphenyl phosphate  (ISO)
tropan-3alpha-yl 3-hydroxy-2-phenylpropanoate  (EXP,ISO)
tubocurarine  (ISO)
urethane  (EXP)
valproic acid  (ISO)
vancomycin  (ISO)
varenicline  (EXP,ISO)
vecuronium bromide  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

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
1. Albuquerque EX, etal., Physiol Rev. 2009 Jan;89(1):73-120. doi: 10.1152/physrev.00015.2008.
2. Andersson KB, etal., Acta Physiol (Oxf). 2006 Jan;186(1):17-27.
3. Arroyo-Jim nez MM, etal., J Neurosci. 1999 Aug 1;19(15):6475-87.
4. Bordia T, etal., J Pharmacol Exp Ther. 2012 Aug;342(2):327-34. doi: 10.1124/jpet.112.194852. Epub 2012 May 1.
5. Connolly J, etal., Br J Pharmacol 1992 Mar;105(3):657-66.
6. Dourado M and Sargent PB, J Neurophysiol 2002 Jun;87(6):3117-25.
7. Forsayeth JR and Kobrin E, J Neurosci. 1997 Mar 1;17(5):1531-8.
8. 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. Garção P, etal., Neurosci Lett. 2014 Apr 30;566:106-10. doi: 10.1016/j.neulet.2014.02.018. Epub 2014 Mar 4.
10. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
11. GOA data from the GO Consortium
12. Goldman D, etal., Cell 1987 Mar 27;48(6):965-73.
13. Jeanclos EM, etal., J Biol Chem. 2001 Jul 27;276(30):28281-90. Epub 2001 May 14.
14. Khiroug SS, etal., Neuroscience 2004;124(4):817-22.
15. Kwitek AE, etal., Genome Res. 2004 Apr;14(4):750-7
16. Lin L, etal., J Biol Chem 2002 Nov 1;277(44):41872-8.
17. 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. Marritt AM, etal., Mol Pharmacol. 2005 Dec;68(6):1656-68. Epub 2005 Aug 29.
19. Matsubayashi H, etal., Brain Res. 2004 Apr 16;1005(1-2):1-8.
20. Matsushima N, etal., Epilepsy Res 2002 Feb;48(3):181-6.
21. MGD data from the GO Consortium
22. Mori T, etal., Mol Pharmacol. 2001 Apr;59(4):732-43.
23. NCBI rat LocusLink and RefSeq merged data July 26, 2002
24. OMIM Disease Annotation Pipeline
25. Perry DC, etal., J Neurochem 2002 Aug;82(3):468-81.
26. Pipeline to import SMPDB annotations from SMPDB into RGD
27. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
28. RGD automated import pipeline for gene-chemical interactions
29. Rodrigues-Pinguet N, etal., J Physiol 2003 Jul 1;550(Pt 1):11-26. Epub 2003 May 16.
30. Teaktong T, etal., J Neurol Sci 2004 Oct 15;225(1-2):39-49.
31. Voitenko LP, etal., Neurosci Lett. 2001 Apr 27;303(1):37-40.
32. 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  


Genomics

Comparative Map Data
Chrna4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
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 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.13170,077,249 - 170,092,033 (-)NCBI
Celera3164,428,976 - 164,443,759 (+)NCBICelera
Cytogenetic Map3q43NCBI
RH 3.4 Map31531.39RGD
RH 3.4 Map31564.7RGD
CHRNA4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2063,343,223 - 63,378,401 (-)EnsemblGRCh38hg38GRCh38
GRCh382063,343,223 - 63,375,471 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh372061,974,662 - 62,009,487 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362061,445,109 - 61,463,192 (-)NCBINCBI36hg18NCBI36
Build 342061,446,464 - 61,463,192NCBI
Celera2058,652,104 - 58,670,128 (-)NCBI
Cytogenetic Map20q13.33NCBI
HuRef2058,700,254 - 58,717,202 (-)NCBIHuRef
CHM1_12061,875,694 - 61,893,903 (-)NCBICHM1_1
Chrna4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392180,664,104 - 180,685,365 (-)NCBIGRCm39mm39
GRCm382181,022,311 - 181,043,579 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2181,018,380 - 181,043,546 (-)EnsemblGRCm38mm10GRCm38
MGSCv372180,757,016 - 180,773,882 (-)NCBIGRCm37mm9NCBIm37
MGSCv362180,951,719 - 180,968,585 (-)NCBImm8
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
PanPan1.12061,267,958 - 61,284,640 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2061,270,631 - 61,283,005 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02059,730,759 - 59,748,678 (-)NCBIMhudiblu_PPA_v0panPan3
CHRNA4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl2447,025,187 - 47,042,266 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.12447,024,948 - 47,036,507 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Chrna4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_00493651410,680,893 - 10,695,859 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CHRNA4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1762,420,546 - 62,436,165 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11762,424,672 - 62,436,646 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
CHRNA4
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12851,790 - 862,685 (+)NCBI
Chrna4
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474129,024,668 - 29,039,684 (-)NCBI

Position Markers
RH94428  
Rat AssemblyChrPosition (strand)SourceJBrowse
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
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
Cytogenetic Map3q43UniSTS
RH 3.4 Map31564.7UniSTS
D2Ucl29  
Rat AssemblyChrPosition (strand)SourceJBrowse
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


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1578656Vnigr2Vascular neointimal growth QTL 24.2artery morphology trait (VT:0002191)lesioned artery residual lumen area (CMO:0001417)3138374177177699992Rat
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)345406058177699992Rat
1298068Bp167Blood pressure QTL 1670.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3150368003177699992Rat
1578653Vnigr3Vascular neointimal growth QTL 33.1artery morphology trait (VT:0002191)artery neointimal hyperplastic lesion area (CMO:0001414)3138374177177699992Rat
2317883Alcrsp26Alcohol response QTL 261.80.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)3153918022177699992Rat
631541Bp81Blood pressure QTL 814arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3129787213177699992Rat
2298477Eau4Experimental allergic uveoretinitis QTL 40.0011uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)3146232777177699992Rat
1300161Rf10Renal function QTL 103.57renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)3170428815177699992Rat
9589106Insul23Insulin level QTL 2313.860.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)3139578365177699992Rat
8552791Vie2Viral induced encephalitis QTL 24.1brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)3153412455177699992Rat
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)3148034701177699992Rat


Genetic Models
This gene Chrna4 is modified in the following models/strains
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.


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
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl3176,527,516 - 176,547,965 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000084339   ⟹   ENSRNOP00000073967
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl3176,531,016 - 176,548,208 (-)Ensembl
RefSeq Acc Id: NM_024354   ⟹   NP_077330
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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:
Reference Sequences
RefSeq Acc Id: NP_077330   ⟸   NM_024354
- Peptide Label: precursor
- Sequence:
RefSeq Acc Id: ENSRNOP00000009041   ⟸   ENSRNOT00000009041
RefSeq Acc Id: ENSRNOP00000073967   ⟸   ENSRNOT00000084339
Protein Domains
Neur_chan_LBD   Neur_chan_memb

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2346 AgrOrtholog
Ensembl Genes ENSRNOG00000011202 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000009041 UniProtKB/TrEMBL
  ENSRNOP00000073967 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000009041 UniProtKB/TrEMBL
  ENSRNOT00000084339 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 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
  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 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
Superfamily-SCOP SSF63712 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF90112 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGRFAMs LIC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniGene Rn.9697 ENTREZGENE
UniProt A0A0G2K6W5_RAT UniProtKB/TrEMBL
  ACHA4_RAT UniProtKB/Swiss-Prot
  K4DIC3_RAT 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