Chrna5 (cholinergic receptor nicotinic alpha 5 subunit) - Rat Genome Database

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Gene: Chrna5 (cholinergic receptor nicotinic alpha 5 subunit) Rattus norvegicus
Analyze
Symbol: Chrna5
Name: cholinergic receptor nicotinic alpha 5 subunit
RGD ID: 2347
Description: Enables acetylcholine binding activity and acetylcholine-gated cation-selective channel activity. Involved in several processes, including behavioral response to nicotine; cellular response to nicotine; and detection of mechanical stimulus involved in sensory perception of pain. Located in dendrite; neuronal cell body; and plasma membrane. Part of acetylcholine-gated channel complex. Human ortholog(s) of this gene implicated in chronic obstructive pulmonary disease; cocaine abuse; esophagus squamous cell carcinoma; nicotine dependence; and respiratory system cancer (multiple). Orthologous to human CHRNA5 (cholinergic receptor nicotinic alpha 5 subunit); PARTICIPATES IN acetylcholine signaling pathway via nicotinic acetylcholine receptor; INTERACTS WITH 1-naphthyl isothiocyanate; ammonium chloride; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: Acetylcholine receptor alpha 5; cetylcholine receptor alpha 5; cholinergic receptor, nicotinic, alpha 5; cholinergic receptor, nicotinic, alpha 5 (neuronal); cholinergic receptor, nicotinic, alpha polypeptide 5; neuronal acetylcholine receptor subunit alpha-5
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Chrna5em1Mcwi   Chrna5em2Mcwi   Chrna5em18Pas   Chrna5em20(D398N)Pas  
Genetic Models: LE-Chrna5em18Pas LE-Chrna5em20(D398N)Pas LEW-Chrna5em1Mcwi LEW-Chrna5em2Mcwi
Candidate Gene For: Bp273
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2855,369,794 - 55,398,526 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl855,369,794 - 55,398,146 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx860,911,231 - 60,939,461 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0859,190,233 - 59,218,459 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0857,054,472 - 57,082,703 (+)NCBIRnor_WKY
Rnor_6.0859,561,817 - 59,590,172 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl859,561,721 - 59,590,172 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0858,143,974 - 58,172,330 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4858,538,002 - 58,566,388 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1858,557,055 - 58,585,442 (+)NCBI
Celera854,856,809 - 54,885,137 (+)NCBICelera
RH 3.4 Map8615.2RGD
Cytogenetic Map8q24NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
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. Nicotinic acetylcholine receptor region on chromosome 15q25 and lung cancer risk among African Americans: a case-control study. Amos CI, etal., J Natl Cancer Inst. 2010 Aug 4;102(15):1199-205. doi: 10.1093/jnci/djq232. Epub 2010 Jun 16.
3. Profound alteration in reward processing due to a human polymorphism in CHRNA5: a role in alcohol dependence and feeding behavior. Besson M, etal., Neuropsychopharmacology. 2019 Oct;44(11):1906-1916. doi: 10.1038/s41386-019-0462-0. Epub 2019 Jul 9.
4. Alpha 3, alpha 5, and beta 4: three members of the rat neuronal nicotinic acetylcholine receptor-related gene family form a gene cluster. Boulter J, etal., J Biol Chem 1990 Mar 15;265(8):4472-82.
5. Nicotinic cholinergic receptors in esophagus: Early alteration during carcinogenesis and prognostic value. Chianello Nicolau M, etal., World J Gastroenterol. 2016 Aug 21;22(31):7146-56. doi: 10.3748/wjg.v22.i31.7146.
6. Molecular biology and electrophysiology of neuronal nicotinic receptors of rat chromaffin cells. Di Angelantonio S, etal., Eur J Neurosci 2003 Jun;17(11):2313-22.
7. Multiple isoforms and differential allelic expression of CHRNA5 in lung tissue and lung adenocarcinoma. Falvella FS, etal., Carcinogenesis. 2013 Jun;34(6):1281-5. doi: 10.1093/carcin/bgt062. Epub 2013 Feb 19.
8. Transcription deregulation at the 15q25 locus in association with lung adenocarcinoma risk. Falvella FS, etal., Clin Cancer Res. 2009 Mar 1;15(5):1837-42. doi: 10.1158/1078-0432.CCR-08-2107. Epub 2009 Feb 17.
9. A Human Polymorphism in CHRNA5 Is Linked to Relapse to Nicotine Seeking in Transgenic Rats. Forget B, etal., Curr Biol. 2018 Oct 22;28(20):3244-3253.e7. doi: 10.1016/j.cub.2018.08.044. Epub 2018 Oct 4.
10. Alterations in nicotinic receptor alpha5 subunit gene differentially impact early and later stages of cocaine addiction: a translational study in transgenic rats and patients. Forget B, etal., Prog Neurobiol. 2021 Feb;197:101898. doi: 10.1016/j.pneurobio.2020.101898. Epub 2020 Aug 22.
11. Habenular α5 nicotinic receptor subunit signalling controls nicotine intake. Fowler CD, etal., Nature. 2011 Mar 31;471(7340):597-601. doi: 10.1038/nature09797. Epub 2011 Jan 30.
12. 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.
13. 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.
14. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
15. Fine mapping of chromosome 15q25.1 lung cancer susceptibility in African-Americans. Hansen HM, etal., Hum Mol Genet. 2010 Sep 15;19(18):3652-61. doi: 10.1093/hmg/ddq268. Epub 2010 Jun 29.
16. Chr15q25 genetic variant (rs16969968) independently confers risk of lung cancer, COPD and smoking intensity in a prospective study of high-risk smokers. Hopkins RJ, etal., Thorax. 2021 Mar;76(3):272-280. doi: 10.1136/thoraxjnl-2020-214839. Epub 2021 Jan 8.
17. ASCL1 regulates the expression of the CHRNA5/A3/B4 lung cancer susceptibility locus. Improgo MR, etal., Mol Cancer Res. 2010 Feb;8(2):194-203. doi: 10.1158/1541-7786.MCR-09-0185. Epub 2010 Feb 2.
18. Role of a genetic variant on the 15q25.1 lung cancer susceptibility locus in smoking-associated nasopharyngeal carcinoma. Ji X, etal., PLoS One. 2014 Oct 20;9(10):e109036. doi: 10.1371/journal.pone.0109036. eCollection 2014.
19. 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
20. 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.
21. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
22. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
23. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
24. Nicotinic acetylcholine receptor alpha 7 regulates cAMP signal within lipid rafts. Oshikawa J, etal., Am J Physiol Cell Physiol. 2003 Sep;285(3):C567-74. Epub 2003 May 14.
25. CHRNA3 rs1051730 and CHRNA5 rs16969968 polymorphisms are associated with heavy smoking, lung cancer, and chronic obstructive pulmonary disease in a mexican population. Pérez-Morales R, etal., Ann Hum Genet. 2018 Nov;82(6):415-424. doi: 10.1111/ahg.12264. Epub 2018 Jul 11.
26. GOA pipeline RGD automated data pipeline
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. The CHRNA5-CHRNA3-CHRNB4 nicotinic receptor subunit gene cluster affects risk for nicotine dependence in African-Americans and in European-Americans. Saccone NL, etal., Cancer Res. 2009 Sep 1;69(17):6848-56. doi: 10.1158/0008-5472.CAN-09-0786. Epub 2009 Aug 25.
30. CHRNA5 gene D398N polymorphism in Japanese lung adenocarcinoma. Sasaki H, etal., J Surg Res. 2010 Jul;162(1):75-8. doi: 10.1016/j.jss.2009.01.008. Epub 2009 Feb 7.
31. CHRNA5 polymorphism and susceptibility to lung cancer in a Chinese population. Shen B, etal., Braz J Med Biol Res. 2013 Jan;46(1):79-84. doi: 10.1590/1414-431x20122451. Epub 2013 Jan 11.
32. Knock down of the alpha 5 nicotinic acetylcholine receptor in spinal nerve-ligated rats alleviates mechanical allodynia. Vincler MA and Eisenach JC, Pharmacol Biochem Behav. 2005 Jan;80(1):135-43. doi: 10.1016/j.pbb.2004.10.011. Epub 2004 Nov 18.
33. 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.
34. Integrating expression-related SNPs into genome-wide gene- and pathway-based analyses identified novel lung cancer susceptibility genes. Wang Y, etal., Int J Cancer. 2018 Apr 15;142(8):1602-1610. doi: 10.1002/ijc.31182. Epub 2017 Dec 12.
35. Genetic variants of CHRNA5-A3 and CHRNB3-A6 predict survival of patients with advanced non-small cell lung cancer. Wang Y, etal., Oncotarget. 2016 May 3;7(18):26436-43. doi: 10.18632/oncotarget.8510.
36. Association of CHRNA5-A3-B4 variation with esophageal squamous cell carcinoma risk and smoking behaviors in a Chinese population. Wang Y, etal., PLoS One. 2013 Jul 2;8(7):e67664. doi: 10.1371/journal.pone.0067664. Print 2013.
37. Expression of alpha5 nicotinic acetylcholine receptor subunit mRNA during hippocampal and cortical development. Winzer-Serhan UH and Leslie FM, J Comp Neurol. 2005 Jan 3;481(1):19-30. doi: 10.1002/cne.20357.
38. Functionally significant nicotine acetylcholine receptor subunit α5 promoter haplotypes are associated with susceptibility to lung cancer in Chinese. Zheng X, etal., Cancer. 2011 Oct 15;117(20):4714-23. doi: 10.1002/cncr.26017. Epub 2011 Mar 29.
Additional References at PubMed
PMID:1542648   PMID:9495872   PMID:14741388   PMID:17192625   PMID:17434683   PMID:18227835   PMID:19693710   PMID:22380605   PMID:26842251   PMID:29299690  


Genomics

Comparative Map Data
Chrna5
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2855,369,794 - 55,398,526 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl855,369,794 - 55,398,146 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx860,911,231 - 60,939,461 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0859,190,233 - 59,218,459 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0857,054,472 - 57,082,703 (+)NCBIRnor_WKY
Rnor_6.0859,561,817 - 59,590,172 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl859,561,721 - 59,590,172 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0858,143,974 - 58,172,330 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4858,538,002 - 58,566,388 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1858,557,055 - 58,585,442 (+)NCBI
Celera854,856,809 - 54,885,137 (+)NCBICelera
RH 3.4 Map8615.2RGD
Cytogenetic Map8q24NCBI
CHRNA5
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381578,565,520 - 78,595,269 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl1578,565,520 - 78,595,269 (+)EnsemblGRCh38hg38GRCh38
GRCh371578,857,862 - 78,887,611 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361576,644,961 - 76,673,515 (+)NCBINCBI36Build 36hg18NCBI36
Build 341576,644,960 - 76,673,513NCBI
Celera1555,794,174 - 55,823,924 (+)NCBICelera
Cytogenetic Map15q25.1NCBI
HuRef1555,614,929 - 55,644,700 (+)NCBIHuRef
CHM1_11578,976,380 - 79,006,179 (+)NCBICHM1_1
T2T-CHM13v2.01576,428,193 - 76,457,938 (+)NCBIT2T-CHM13v2.0
Chrna5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39954,888,112 - 54,918,704 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl954,888,164 - 54,915,063 (+)EnsemblGRCm39 Ensembl
GRCm38954,980,827 - 55,011,420 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl954,980,880 - 55,007,779 (+)EnsemblGRCm38mm10GRCm38
MGSCv37954,828,687 - 54,855,586 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36954,784,760 - 54,804,712 (+)NCBIMGSCv36mm8
Celera952,224,119 - 52,251,187 (+)NCBICelera
Cytogenetic Map9BNCBI
cM Map929.84NCBI
Chrna5
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955450946,898 - 974,457 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955450945,400 - 974,129 (+)NCBIChiLan1.0ChiLan1.0
CHRNA5
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11576,457,459 - 76,486,376 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1576,455,165 - 76,486,376 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01557,493,730 - 57,530,463 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
CHRNA5
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11338,343,966 - 38,355,534 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1338,346,104 - 38,355,468 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1338,303,745 - 38,339,919 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01338,817,161 - 38,853,192 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1338,819,299 - 38,851,688 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11338,508,310 - 38,544,251 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01338,617,724 - 38,654,019 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01339,092,761 - 39,127,369 (-)NCBIUU_Cfam_GSD_1.0
Chrna5
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024408640118,602,432 - 118,644,746 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647136,452,965 - 36,492,618 (-)EnsemblSpeTri2.0
SpeTri2.0NW_00493647136,451,070 - 36,492,774 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CHRNA5
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl747,383,792 - 47,425,841 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1747,382,860 - 47,425,871 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2752,760,970 - 52,784,694 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CHRNA5
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1264,747,734 - 4,779,231 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl264,749,766 - 4,776,822 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666048137,018,864 - 137,048,250 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Chrna5
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248942,357,193 - 2,400,699 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Chrna5
383 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:170
Count of miRNA genes:118
Interacting mature miRNAs:142
Transcripts:ENSRNOT00000065771
Prediction methods:Miranda, Targetscan
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
2316950Scl66Serum cholesterol level QTL 664.1blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)830848259105647037Rat
737824Hcar10Hepatocarcinoma resistance QTL 102.9liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)84071306682925667Rat
1298065Scl16Serum cholesterol level QTL 163.8blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)83085640475856404Rat
1298079Activ2Activity QTL 29.50.000001voluntary movement trait (VT:0003491)rearing measurement (CMO:0001515)84186687686866876Rat
631650Stl6Serum triglyceride level QTL 640.0019blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)810378157112202585Rat
631664Hcar3Hepatocarcinoma resistance QTL 32.90.0005liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)85423764499103503Rat
4889938Bss89Bone structure and strength QTL 893.8tibia size trait (VT:0100001)tibia cortical bone volume (CMO:0001725)85009524982460899Rat
5684973Bss100Bone structure and strength QTL 1004.7tibia area (VT:1000281)tibia area measurement (CMO:0001382)85009524982460899Rat
731182Uae24Urinary albumin excretion QTL 246.4urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)81933115293965294Rat
631271Lecl1Lens clarity QTL 10.001lens clarity trait (VT:0001304)age of onset/diagnosis of cataract (CMO:0001584)81898416884531599Rat
8662823Vetf5Vascular elastic tissue fragility QTL 51.9artery integrity trait (VT:0010639)patent ductus arteriosus score (CMO:0002566)82824291299525068Rat
1300146Rf17Renal function QTL 172.9renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)82824291273242912Rat
1300150Cm3Cardiac mass QTL 33.97heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)85423781455523877Rat
1331744Bp217Blood pressure QTL 2173.398arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)83084815458482492Rat
10402857Bp380Blood pressure QTL 3800.95arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)85396876598968765Rat
1331769Rf39Renal function QTL 393.871urine output (VT:0003620)timed urine volume (CMO:0000260)84186687675097878Rat
1331838Niddm61Non-insulin dependent diabetes mellitus QTL 613.530.0004blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)83646953599083736Rat
1300177Cm2Cardiac mass QTL 23.65heart mass (VT:0007028)heart weight (CMO:0000017)854259986100382532Rat
1549908Neudeg1Neurodegradation QTL 15.50nervous system integrity trait (VT:0010566)logarithm of the ratio of the lesioned side motor neuron count to contralateral side motor neuron count (CMO:0001986)83018886794457446Rat
1558646Swd5Spike wave discharge measurement QTL 53.450.00036brain electrophysiology trait (VT:0010557)brain spike-and-wave discharge frequency (CMO:0001742)81490675159906751Rat
1554321Bmd3Bone mineral density QTL 37.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)840952565123900184Rat
1358896Bp262Blood pressure QTL 2622.89arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)82720571599103503Rat
1358906Bp253Blood pressure QTL 25340.0004arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)84071306693965294Rat
1359033Bp273Blood pressure QTL 273arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)83084815461290444Rat
1582254Kidm31Kidney mass QTL 313kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)85423764485365202Rat
1581557Eae16Experimental allergic encephalomyelitis QTL 163.8nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)88462195110921472Rat
1578755Pur5Proteinuria QTL 53.30.0001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)830848154101699754Rat
1578765Klgr1Kidney lesion grade QTL 13.30.0001kidney morphology trait (VT:0002135)organ lesion measurement (CMO:0000677)830848154101699754Rat
1578769Uae31Urinary albumin excretion QTL 313.30.001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)830848154101699754Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)846531639119088624Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)846531639119088624Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)846531639119088624Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)846531639119088624Rat
631216Stl9Serum triglyceride level QTL 94.710.0001blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)84186701070386132Rat
70161Bp62Blood pressure QTL 622.90.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)84269268490165460Rat
724514Uae15Urinary albumin excretion QTL 152.9urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)82950266570386295Rat
2303564Gluco43Glucose level QTL 433blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)82613018771130187Rat
2303570Gluco48Glucose level QTL 482blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)84980583194805831Rat
2301402Bp316Blood pressure QTL 3160.005arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)85396876598968765Rat
12879878Bw183Body weight QTL 1830.001body mass (VT:0001259)body weight (CMO:0000012)84329616998968765Rat
1582243Bw66Body weight QTL 663.40.0048body mass (VT:0001259)body weight (CMO:0000012)85423764485365202Rat
1331837Bw23Body weight QTL 234.190.00007body mass (VT:0001259)body weight (CMO:0000012)84653172299083736Rat
1358892Kidm26Kidney mass QTL 263.69kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)82720571599103503Rat
1582222Epfw2Epididymal fat weight QTL 23.20.0005epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)83173772976737729Rat
61358Bp39Blood pressure QTL 392arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)83555193880551938Rat
61464Niddm11Non-insulin dependent diabetes mellitus QTL 113.10.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)83558203280582032Rat
12879879Cm99Cardiac mass QTL 990.001heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)84329616998968765Rat
1358907Cm40Cardiac mass QTL 401.89heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)82720571599103503Rat
61353Bp35Blood pressure QTL 350.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)83084815461290444Rat
61353Bp35Blood pressure QTL 350.001arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)83084815461290444Rat
61353Bp35Blood pressure QTL 350.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)83084815461290444Rat
61353Bp35Blood pressure QTL 350.001arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)83084815461290444Rat
1358912Bw51Body weight QTL 512.95body mass (VT:0001259)body weight (CMO:0000012)851351728107062046Rat
2313046Bss78Bone structure and strength QTL 783.50.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)83084815482460899Rat
2293697Bmd39Bone mineral density QTL 39femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)85404374498968765Rat
2313067Bss77Bone structure and strength QTL 773.10.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)83084815482460899Rat
2313088Bss75Bone structure and strength QTL 753.10.0001body length (VT:0001256)body length, nose to rump (CMO:0000079)83084815482460899Rat
12879882Am8Aortic mass QTL 80.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)84329616998968765Rat
12879880Cm100Cardiac mass QTL 1000.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)84329616998968765Rat
12879881Cm101Cardiac mass QTL 1010.001heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)84329616998968765Rat
12879883Kidm65Kidney mass QTL 650.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)84329616998968765Rat
631842Inf1Infertility severity QTL 14.10.001seminal gland mass (VT:0010524)seminal vesicle wet weight (CMO:0001603)82266233067662330Rat
11556286Cm81Cardiac mass QTL 810.01heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)83084815461290444Rat
61373Mcs4Mammary carcinoma susceptibility QTL 41.1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)81629044461290444Rat
2303572Insul13Insulin level QTL 132blood insulin amount (VT:0001560)blood insulin level (CMO:0000349)82613018771130187Rat
2313057Bss76Bone structure and strength QTL 7630.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)83084815482460899Rat
2313086Bss60Bone structure and strength QTL 604.10.0001tibia length (VT:0004357)tibia length (CMO:0000450)85009524982460899Rat

Markers in Region
Chrna5  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2855,397,469 - 55,397,573 (+)MAPPERmRatBN7.2
Rnor_6.0859,589,496 - 59,589,599NCBIRnor6.0
Rnor_5.0858,171,654 - 58,171,757UniSTSRnor5.0
RGSC_v3.4858,565,712 - 58,565,815UniSTSRGSC3.4
Celera854,884,461 - 54,884,564UniSTS
RH 3.4 Map8615.2UniSTS
Cytogenetic Map8q24UniSTS


Genetic Models
This gene Chrna5 is modified in the following models/strains

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

alimentary part of gastrointestinal system 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 2 1
Low 3 13 26 10 16 10 1 1 68 9 33 11 1
Below cutoff 24 27 27 3 27 7 10 4 24 7 7

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000065771   ⟹   ENSRNOP00000062227
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl855,369,794 - 55,398,146 (+)Ensembl
Rnor_6.0 Ensembl859,561,817 - 59,590,017 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000088304   ⟹   ENSRNOP00000072632
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl859,561,817 - 59,590,172 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000093107   ⟹   ENSRNOP00000075937
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl859,561,721 - 59,589,144 (+)Ensembl
RefSeq Acc Id: NM_017078   ⟹   NP_058774
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2855,369,794 - 55,398,146 (+)NCBI
Rnor_6.0859,561,817 - 59,590,172 (+)NCBI
Rnor_5.0858,143,974 - 58,172,330 (+)NCBI
RGSC_v3.4858,538,002 - 58,566,388 (+)RGD
Celera854,856,809 - 54,885,137 (+)RGD
Sequence:
RefSeq Acc Id: XM_039080868   ⟹   XP_038936796
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2855,387,103 - 55,398,526 (+)NCBI
RefSeq Acc Id: XM_039080869   ⟹   XP_038936797
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2855,382,938 - 55,398,526 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_058774   ⟸   NM_017078
- Peptide Label: precursor
- UniProtKB: A0A8J8XM73 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000062227   ⟸   ENSRNOT00000065771
RefSeq Acc Id: ENSRNOP00000075937   ⟸   ENSRNOT00000093107
RefSeq Acc Id: ENSRNOP00000072632   ⟸   ENSRNOT00000088304
RefSeq Acc Id: XP_038936797   ⟸   XM_039080869
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038936796   ⟸   XM_039080868
- Peptide Label: isoform X1
Protein Domains
Neur_chan_LBD   Neur_chan_memb

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P20420-F1-model_v2 AlphaFold P20420 1-452 view protein structure

Transcriptome

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

Promoters
RGD ID:13695994
Promoter ID:EPDNEW_R6514
Type:single initiation site
Name:Chrna5_1
Description:cholinergic receptor nicotinic alpha 5 subunit
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0859,561,887 - 59,561,947EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2347 AgrOrtholog
BioCyc Gene G2FUF-30386 BioCyc
Ensembl Genes ENSRNOG00000013610 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000062227 ENTREZGENE
  ENSRNOP00000062227.3 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000065771 ENTREZGENE
  ENSRNOT00000065771.4 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
NCBI Gene 25102 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 CHRNA5 RGD
PhenoGen Chrna5 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
UniProt A0A8J8XM73 ENTREZGENE, UniProtKB/TrEMBL
  ACHA5_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  Q6PW50_RAT UniProtKB/TrEMBL
UniProt Secondary G3V9X4 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-11 Chrna5  cholinergic receptor nicotinic alpha 5 subunit  Chrna5  cholinergic receptor, nicotinic, alpha 5  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2015-11-12 Chrna5  cholinergic receptor, nicotinic, alpha 5  Chrna5  cholinergic receptor, nicotinic, alpha 5 (neuronal)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-07-16 Chrna5  cholinergic receptor, nicotinic, alpha 5 (neuronal)  Chrna5  cholinergic receptor, nicotinic, alpha 5  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-29 Chrna5  cholinergic receptor, nicotinic, alpha 5  Chrna5  cholinergic receptor, nicotinic, alpha polypeptide 5  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2001-07-23 Chrna5  Acetylcholine receptor alpha 5      Name withdrawn 67952 WITHDRAWN
2001-07-23 Chrna5  cholinergic receptor, nicotinic, alpha polypeptide 5      Name updated to reflect Human and Mouse nomenclature 67952 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_cellular_localization expressed in small numbers of nuclei in central nervous system 724746
gene_expression expressed on chromaffin cells of adrenal medulla 1298760
gene_function neuronal nicotinic acetylcholine receptor activated by acetylcholine 1298760
gene_protein 424 amino acid protein 724746
gene_regulation activation by acetylcholine mediates release of catecholamines into bloodstream 1298760