Chrna6 (cholinergic receptor nicotinic alpha 6 subunit)

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Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

RGD Manual Annotations

Gene: Chrna6 (cholinergic receptor nicotinic alpha 6 subunit) Rattus norvegicus

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Symbol:

Chrna6

Name:

cholinergic receptor nicotinic alpha 6 subunit

RGD ID:

69281

Description:

Contributes to heterocyclic compound binding activity. Predicted to be involved in several processes, including presynaptic modulation of chemical synaptic transmission; response to nicotine; and synaptic signaling. Predicted to act upstream of or within regulation of dopamine secretion. Part of protein-containing complex. Is active in postsynaptic membrane and presynaptic membrane. Orthologous to human CHRNA6 (cholinergic receptor nicotinic alpha 6 subunit); PARTICIPATES IN acetylcholine signaling pathway via nicotinic acetylcholine receptor; INTERACTS WITH ammonium chloride; bisphenol A; chlorpyrifos.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Previously known as:

cholinergic receptor, nicotinic, alpha 6; cholinergic receptor, nicotinic, alpha 6 (neuronal); cholinergic receptor, nicotinic, alpha polypeptide 6; neuronal acetylcholine receptor subunit alpha-6

RGD Orthologs

Alliance Genes

More Info

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More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	CHRNA6 (cholinergic receptor nicotinic alpha 6 subunit)	HGNC	Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, Treefam
Mus musculus (house mouse):	Chrna6 (cholinergic receptor, nicotinic, alpha polypeptide 6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Chrna6 (cholinergic receptor nicotinic alpha 6 subunit)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	CHRNA6 (cholinergic receptor nicotinic alpha 6 subunit)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	CHRNA6 (cholinergic receptor nicotinic alpha 6 subunit)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Chrna6 (cholinergic receptor nicotinic alpha 6 subunit)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	CHRNA6 (cholinergic receptor nicotinic alpha 6 subunit)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	CHRNA6 (cholinergic receptor nicotinic alpha 6 subunit)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Chrna6 (cholinergic receptor nicotinic alpha 6 subunit)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	CHRNA6 (cholinergic receptor nicotinic alpha 6 subunit)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Chrna6 (cholinergic receptor, nicotinic, alpha polypeptide 6)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	chrna6 (cholinergic receptor, nicotinic, alpha 6)	Alliance	DIOPT (Ensembl Compara\|OMA\|OrthoFinder\|PANTHER\|PhylomeDB)
Caenorhabditis elegans (roundworm):	acr-12	Alliance	DIOPT (OrthoFinder\|PANTHER\|PhylomeDB)
Caenorhabditis elegans (roundworm):	acr-2	Alliance	DIOPT (OrthoFinder\|PANTHER\|PhylomeDB)
Caenorhabditis elegans (roundworm):	acr-6	Alliance	DIOPT (OrthoFinder\|PANTHER\|PhylomeDB)
Caenorhabditis elegans (roundworm):	acr-8	Alliance	DIOPT (Ensembl Compara\|OrthoFinder\|PANTHER\|PhylomeDB)
Drosophila melanogaster (fruit fly):	nAChRalpha1	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Drosophila melanogaster (fruit fly):	nAChRalpha2	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Drosophila melanogaster (fruit fly):	nAChRbeta1	Alliance	DIOPT (Ensembl Compara\|OMA\|OrthoFinder\|PANTHER)
Drosophila melanogaster (fruit fly):	nAChRbeta2	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Drosophila melanogaster (fruit fly):	nAChRalpha3	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Drosophila melanogaster (fruit fly):	nAChRalpha4	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Caenorhabditis elegans (roundworm):	unc-38	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Caenorhabditis elegans (roundworm):	unc-63	Alliance	DIOPT (Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|SonicParanoid)
Caenorhabditis elegans (roundworm):	lev-8	Alliance	DIOPT (OrthoFinder\|PANTHER\|PhylomeDB)
Caenorhabditis elegans (roundworm):	acr-3	Alliance	DIOPT (Ensembl Compara\|OrthoFinder\|PANTHER)
Xenopus tropicalis (tropical clawed frog):	chrna6	Alliance	DIOPT (Ensembl Compara\|OMA\|OrthoFinder\|PANTHER\|PhylomeDB)

Allele / Splice:

Chrna6^em1Slot Chrna6^em2Slot

Genetic Models:

SD-Chrna6^em1Slot SD-Chrna6^em2Slot

Latest Assembly:

mRatBN7.2 - mRatBN7.2 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	16	71,400,615 - 71,407,315 (+)	NCBI		GRCr8
mRatBN7.2	16	64,697,741 - 64,704,441 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	16	64,697,741 - 64,704,441 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	16	69,989,064 - 69,996,216 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	16	73,395,406 - 73,402,558 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	16	68,633,137 - 68,639,837 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	16	68,860,018 - 68,866,718 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	16	68,860,018 - 68,866,718 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	16	68,486,608 - 68,493,308 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	16	69,012,201 - 69,018,901 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	16	69,012,406 - 69,019,107 (+)	NCBI
Celera	16	62,621,116 - 62,627,795 (+)	NCBI		Celera
Cytogenetic Map	16	q12.3	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

genetic disease (ISO)

Idiopathic Basal Ganglia Calcification 1 (ISO)

IMMUNODEFICIENCY 15 (ISO)

immunodeficiency 15B (ISO)

nicotine dependence (ISO)

Tobacco Use Disorder (ISO)

torsion dystonia 6 (ISO)

withdrawal disorder (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(S)-nicotine (ISO)

1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (ISO)

2,3,7,8-tetrachlorodibenzodioxine (ISO)

ammonium chloride (EXP)

arsenous acid (ISO)

benzo[a]pyrene (ISO)

bisphenol A (EXP)

chlorpyrifos (EXP)

diarsenic trioxide (ISO)

dibutyl phthalate (EXP)

dopamine (ISO)

epibatidine (EXP)

ethanol (ISO)

ethyl methanesulfonate (ISO)

formaldehyde (EXP,ISO)

furan (EXP)

glyphosate (ISO)

methylmercury chloride (ISO)

methylphenidate (ISO)

Muraglitazar (EXP)

N-ethyl-N-nitrosourea (EXP)

nicotine (EXP,ISO)

ozone (ISO)

paracetamol (ISO)

paraquat (EXP,ISO)

parathion-methyl (EXP)

silver atom (ISO)

silver(0) (ISO)

Tesaglitazar (EXP)

troglitazone (EXP)

valproic acid (ISO)

varenicline (EXP)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

acetylcholine receptor signaling pathway (IBA)

excitatory postsynaptic potential (IEA)

membrane depolarization (IBA,IEA,ISO)

monoatomic ion transmembrane transport (IEA)

presynaptic modulation of chemical synaptic transmission (IEA,ISO)

regulation of dopamine secretion (IEA,ISO)

response to nicotine (IBA)

synaptic transmission, cholinergic (IBA)

Cellular Component

acetylcholine-gated channel complex (IBA,IEA,ISO)

dopaminergic synapse (IEA,ISO)

neuron projection (IBA,IEA)

plasma membrane (IBA)

postsynaptic membrane (IDA,IEA,IEP,ISO)

presynapse (ISO)

presynaptic membrane (IDA,IEA,IEP,ISO)

protein-containing complex (IDA)

synapse (IBA)

Molecular Function

acetylcholine receptor activity (IBA)

acetylcholine-gated monoatomic cation-selective channel activity (IBA,IEA,ISO)

heterocyclic compound binding (IDA)

protein binding (ISO)

transmembrane signaling receptor activity (IEA)

Molecular Pathway Annotations Click to see Annotation Detail View

acetylcholine signaling pathway via nicotinic acetylcholine receptor (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.	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.
3.	Genomic organization and promoter analysis of the human nicotinic acetylcholine receptor alpha6 subunit (CHNRA6) gene: Alu and other elements direct transcriptional repression.	Ebihara M, etal., Gene 2002 Sep 18;298(1):101-8.
4.	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.
5.	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.
6.	Rat ISS GO annotations from GOA human gene data--August 2006	GOA data from the GO Consortium
7.	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.
8.	Rat ISS GO annotations from MGI mouse gene data--August 2006	MGD data from the GO Consortium
9.	Electronic Transfer of LocusLink and RefSeq Data	NCBI rat LocusLink and RefSeq merged data July 26, 2002
10.	GOA pipeline	RGD automated data pipeline
11.	ClinVar Automated Import and Annotation Pipeline	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
12.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions

Additional References at PubMed

PMID:11850448	PMID:12944511	PMID:18266937	PMID:18299323	PMID:18583454	PMID:22024738	PMID:23624852	PMID:23846688	PMID:24398291	PMID:28666811

Genomics

Comparative Map Data

Chrna6
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	16	71,400,615 - 71,407,315 (+)	NCBI		GRCr8
mRatBN7.2	16	64,697,741 - 64,704,441 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	16	64,697,741 - 64,704,441 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	16	69,989,064 - 69,996,216 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	16	73,395,406 - 73,402,558 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	16	68,633,137 - 68,639,837 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	16	68,860,018 - 68,866,718 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	16	68,860,018 - 68,866,718 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	16	68,486,608 - 68,493,308 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	16	69,012,201 - 69,018,901 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	16	69,012,406 - 69,019,107 (+)	NCBI
Celera	16	62,621,116 - 62,627,795 (+)	NCBI		Celera
Cytogenetic Map	16	q12.3	NCBI

CHRNA6
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	8	42,752,620 - 42,768,786 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	8	42,752,620 - 42,796,392 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	8	42,607,763 - 42,623,929 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	8	42,726,920 - 42,742,776 (-)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	8	42,726,936 - 42,742,776	NCBI
Celera	8	41,555,760 - 41,571,616 (-)	NCBI		Celera
Cytogenetic Map	8	p11.21	NCBI
HuRef	8	41,129,999 - 41,146,165 (-)	NCBI		HuRef
CHM1_1	8	42,654,698 - 42,670,848 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	8	43,020,720 - 43,036,889 (-)	NCBI		T2T-CHM13v2.0

Chrna6
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	8	27,893,240 - 27,903,972 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	8	27,893,240 - 27,903,972 (-)	Ensembl		GRCm39 Ensembl
GRCm38	8	27,403,212 - 27,413,944 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	8	27,403,212 - 27,413,944 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	8	28,513,684 - 28,524,416 (-)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	8	28,869,148 - 28,879,880 (-)	NCBI		MGSCv36	mm8
Celera	8	28,895,511 - 28,906,624 (-)	NCBI		Celera
Cytogenetic Map	8	A2	NCBI
cM Map	8	16.02	NCBI

Chrna6
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955536	166,212 - 172,551 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955536	166,212 - 172,551 (+)	NCBI	ChiLan1.0	ChiLan1.0

CHRNA6
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1-v2	7	61,210,352 - 61,225,975 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	8	36,926,422 - 36,942,028 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	8	42,000,748 - 42,016,913 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	8	39,444,447 - 39,460,569 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	8	39,444,447 - 39,460,569 (-)	Ensembl	panpan1.1		panPan2

CHRNA6
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	16	22,990,377 - 23,009,257 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	16	22,990,167 - 23,009,106 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	16	23,495,595 - 23,514,480 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	16	24,742,037 - 24,760,849 (+)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	16	24,742,086 - 24,760,838 (+)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	16	23,110,331 - 23,129,174 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	16	23,675,367 - 23,694,204 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	16	23,726,376 - 23,745,181 (+)	NCBI		UU_Cfam_GSD_1.0

Chrna6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024404943	45,430,209 - 46,072,980 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936785	18,147 - 27,409 (+)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936785	17,588 - 28,565 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

CHRNA6
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	17	11,725,880 - 11,739,747 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	17	11,725,880 - 11,739,949 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	17	12,640,324 - 12,654,370 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

CHRNA6
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	8	40,750,839 - 40,767,010 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	8	40,751,375 - 40,766,236 (-)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666052	1,004,827 - 1,022,056 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Chrna6
(Heterocephalus glaber - naked mole-rat)

Naked Mole-Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla 1.0	NW_004624780	462,195 - 477,568 (+)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in Chrna6
108 total Variants

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	40
Count of miRNA genes:	39
Interacting mature miRNAs:	39
Transcripts:	ENSRNOT00000016452
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.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
1600378	Arunc4	Aerobic running capacity QTL 4		0.03	exercise endurance trait (VT:0002332)	maximum distance run on treadmill (CMO:0001406)	16	380245	80345693	Rat
70205	Gcr3	Gastric cancer resistance QTL 3	2.3		stomach morphology trait (VT:0000470)	stomach tumor depth of invasion (CMO:0001888)	16	17696791	82635055	Rat
70205	Gcr3	Gastric cancer resistance QTL 3	2.3		stomach morphology trait (VT:0000470)	stomach tumor depth of invasion (CMO:0001888)	16	17696791	82635055	Rat
70205	Gcr3	Gastric cancer resistance QTL 3	2.3		stomach morphology trait (VT:0000470)	stomach tumor diameter (CMO:0001889)	16	17696791	82635055	Rat
70205	Gcr3	Gastric cancer resistance QTL 3	2.3		stomach morphology trait (VT:0000470)	stomach tumor diameter (CMO:0001889)	16	17696791	82635055	Rat
70215	Niddm29	Non-insulin dependent diabetes mellitus QTL 29	3.54		blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	16	19004435	75226532	Rat
2302057	Pia29	Pristane induced arthritis QTL 29	3.6	0.001	blood autoantibody amount (VT:0003725)	serum immunoglobulin M-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002111)	16	21735975	66735975	Rat
8694453	Bw172	Body weight QTL 172	8.33	0.001	retroperitoneal fat pad mass (VT:0010430)	retroperitoneal fat pad weight to body weight ratio (CMO:0000635)	16	24325513	69325513	Rat
6903294	Stl30	Serum triglyceride level QTL 30	2.6	0.0013	blood triglyceride amount (VT:0002644)	plasma triglyceride level (CMO:0000548)	16	25152793	70152793	Rat
1578768	Stresp22	Stress response QTL 22	2.8		thymus mass (VT:0004954)	thymus wet weight (CMO:0000855)	16	35288870	80288870	Rat
2293690	Bss45	Bone structure and strength QTL 45	5.13	0.0001	lumbar vertebra morphology trait (VT:0010494)	lumbar vertebra cortical cross-sectional area (CMO:0001690)	16	37752156	82752156	Rat
2300163	Bmd64	Bone mineral density QTL 64	5.3	0.0001	lumbar vertebra mineral mass (VT:0010511)	volumetric bone mineral density (CMO:0001553)	16	37752156	82752156	Rat
7205510	Activ5	Activity QTL 5	3.78	0.00028	locomotor behavior trait (VT:0001392)	number of entries into a discrete space in an experimental apparatus (CMO:0000960)	16	42396345	84729064	Rat
8694429	Bw164	Body weight QTL 164	5	0.001	body lean mass (VT:0010483)	lean tissue morphological measurement (CMO:0002184)	16	52726464	84729064	Rat
8694364	Abfw7	Abdominal fat weight QTL 7	12.22	0.001	visceral adipose mass (VT:0010063)	abdominal fat pad weight to body weight ratio (CMO:0000095)	16	52726464	84729064	Rat
7411648	Foco22	Food consumption QTL 22	15	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	16	52726464	84729064	Rat
631525	Pia14	Pristane induced arthritis QTL 14	4.4		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	16	55711087	83402471	Rat

Genetic Models

This gene Chrna6 is modified in the following models/strains:

SD-Chrna6^em1Slot SD-Chrna6^em2Slot

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

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_057184	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC126482	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000016	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	L08227	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENSRNOT00000016452 ⟹ ENSRNOP00000016452

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	16	64,697,741 - 64,704,441 (+)	Ensembl
Rnor_6.0 Ensembl	16	68,860,018 - 68,866,718 (+)	Ensembl

RefSeq Acc Id:

NM_057184 ⟹ NP_476532

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	16	71,400,615 - 71,407,315 (+)	NCBI
mRatBN7.2	16	64,697,741 - 64,704,441 (+)	NCBI
Rnor_6.0	16	68,860,018 - 68,866,718 (+)	NCBI
Rnor_5.0	16	68,486,608 - 68,493,308 (+)	NCBI
RGSC_v3.4	16	69,012,201 - 69,018,901 (+)	RGD
Celera	16	62,621,116 - 62,627,795 (+)	RGD

Sequence:

show sequence

GCTGCTTCAGCCAGGACACAGGGAGCAACCGTGTGGTAGCCCGTGTTTTCACTTCACAGAAGAT
CCGTGTGGACTTCAGGAGCTTCCCGAGGCTTTCGTGGTCTGATTCTTGCAGCTGACTGACAGCT
TCGGTTTCCACAGCCCTCTGTGTCGGGATCAGAATTCGTGTGCTTTTATCATGCTGAACGGCTG
GGGTCGGGGAGACCTTCGCTCCGGTTTGTGTCTGTGGATATGTGGATTCTTGGCTTTCTTTAAA
GGCAGTAGAGGCTGTGTGTCTGAAGAACAGCTCTTCCACACGCTCTTCGCCCACTACAACCGCT
TCATCCGGCCAGTGGAAAACGTTTCTGATCCCGTCACGGTGCACTTTGAGTTGGCCATCACGCA
GCTGGCCAATGTGGATGAAGTCAACCAGATTATGGAGACCAATCTGTGGCTGCGTCACGTCTGG
AAGGACTACAGATTGTGTTGGGATCCAACGGAGTACGATGGCATCGAGACGCTTCGTGTTCCAG
CAGATAACATCTGGAAGCCTGACATCGTTCTGTATAATAATGCCGTCGGTGACTTCCAGGTCGA
AGGCAAGACCAAAGCTCTTCTTAAGTACGATGGGGTGATAACCTGGACCCCGCCAGCCATCTTT
AAGAGTTCCTGTCCAATGGACATCACCTTCTTCCCATTTGATCATCAAAACTGCTCCCTGAAAT
TTGGGTCCTGGACTTACGACAAGGCTGAAATCGACCTTCTCATCATTGGCTCTAAAGTGGACAT
GAACGACTTTTGGGAAAACAGTGAGTGGGAAATTGTCGATGCCTCTGGCTACAAGCATGACATC
AAGTACAACTGCTGTGAAGAGATTTACACAGATATCACCTACTCCTTCTACATCAGGAGGCTGC
CCATGTTTTATACCATCAATCTCATCATCCCCTGCCTCTTCATTTCCTTTCTCACCGTGCTAGT
CTTTTACCTTCCTTCTGACTGTGGCGAGAAAGTGACTCTTTGCATCTCGGTTCTGCTTTCTCTG
ACTGTCTTTTTGCTGGTGATTACAGAGACCATCCCATCCACATCTCTCGTGATCCCACTAGTGG
GTGAGTATCTACTGTTCACCATGATCTTTGTCACGCTGTCCATTGTGGTGACCGTGTTTGTGTT
GAACATACACTACAGGACCCCAGCAACGCATACCATGCCCAAGTGGGTGAAGACCATGTTCCTT
CAGGTCTTCCCCTCGATTCTGATGATGAGGAGACCTCTGGACAAGACAAAGGAAATGGATGGTG
TTAAGGACCCCAAAACCCACACCAAGAGGCCGGCCAAAGTCAAGTTTACTCATCGAAAAGAACC
CAAACTTCTAAAGGAATGCCGCCACTGCCATAAGTCAAGTGAGATAGCACCTGGCAAGAGGTTA
AGCCAGCAGCCTGCACAGTGGGTAACAGAGAATTCAGAGCACCCACCTGATGTTGAAGACGTGA
TCGATAGTGTTCAATTCATAGCAGAAAACATGAAAAGCCACAATGAAACAAAGGAGGTAGAAGA
TGACTGGAAATACATGGCCATGGTGGTGGACAGAGTCTTCCTCTGGGTGTTTATAATCGTCTGT
GTGTTTGGAACTGTGGGGCTCTTTCTACAGCCACTGCTTGGGAACACAGGAGCATCTTAATTGG
GATTTTCCTCTTGCCTTCTAAATCTTTTAAATGTTGTGTTTTTTCCTCCACTACTTACCACAAG
AAAAAGTCAAGTTTGCAGTCTCCTAAACCAAG

hide sequence

Protein Sequences


Protein RefSeqs	NP_476532	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAA41674	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000016452
	ENSRNOP00000016452.6
GenBank Protein	P43143	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:	NP_476532 ⟸ NM_057184
- Peptide Label:	precursor
- UniProtKB:	P43143 (UniProtKB/Swiss-Prot), G3V7L7 (UniProtKB/TrEMBL), A6IVW8 (UniProtKB/TrEMBL)
- Sequence:	show sequence MLNGWGRGDLRSGLCLWICGFLAFFKGSRGCVSEEQLFHTLFAHYNRFIRPVENVSDPVTVHFE LAITQLANVDEVNQIMETNLWLRHVWKDYRLCWDPTEYDGIETLRVPADNIWKPDIVLYNNAVG DFQVEGKTKALLKYDGVITWTPPAIFKSSCPMDITFFPFDHQNCSLKFGSWTYDKAEIDLLIIG SKVDMNDFWENSEWEIVDASGYKHDIKYNCCEEIYTDITYSFYIRRLPMFYTINLIIPCLFISF LTVLVFYLPSDCGEKVTLCISVLLSLTVFLLVITETIPSTSLVIPLVGEYLLFTMIFVTLSIVV TVFVLNIHYRTPATHTMPKWVKTMFLQVFPSILMMRRPLDKTKEMDGVKDPKTHTKRPAKVKFT HRKEPKLLKECRHCHKSSEIAPGKRLSQQPAQWVTENSEHPPDVEDVIDSVQFIAENMKSHNET KEVEDDWKYMAMVVDRVFLWVFIIVCVFGTVGLFLQPLLGNTGAS hide sequence

RefSeq Acc Id:

ENSRNOP00000016452 ⟸ ENSRNOT00000016452

Protein Domains

Neurotransmitter-gated ion-channel ligand-binding Neurotransmitter-gated ion-channel transmembrane

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-P43143-F1-model_v2	AlphaFold	P43143	1-493	view protein structure

Transcriptome

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

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:69281	AgrOrtholog
BioCyc Gene	G2FUF-11041	BioCyc
Ensembl Genes	ENSRNOG00000012283	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000016452	ENTREZGENE
	ENSRNOT00000016452.5	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:81721	UniProtKB/Swiss-Prot
NCBI Gene	81721	ENTREZGENE
PANTHER	NEURONAL ACETYLCHOLINE RECEPTOR SUBUNIT ALPHA-6	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
PhenoGen	Chrna6	PhenoGen
PRINTS	NICOTINICR	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	NRIONCHANNEL	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE	NEUROTR_ION_CHANNEL	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx	ENSRNOG00000012283	RatGTEx
Superfamily-SCOP	SSF63712	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	SSF90112	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt	A6IVW8	ENTREZGENE, UniProtKB/TrEMBL
	ACHA6_RAT	UniProtKB/Swiss-Prot
	G3V7L7	ENTREZGENE, UniProtKB/TrEMBL
	P43143	ENTREZGENE

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2016-02-11	Chrna6	cholinergic receptor nicotinic alpha 6 subunit	Chrna6	cholinergic receptor, nicotinic, alpha 6	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2015-11-12	Chrna6	cholinergic receptor, nicotinic, alpha 6	Chrna6	cholinergic receptor, nicotinic, alpha 6 (neuronal)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2012-07-16	Chrna6	cholinergic receptor, nicotinic, alpha 6 (neuronal)	Chrna6	cholinergic receptor, nicotinic, alpha 6	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-09-29	Chrna6	cholinergic receptor, nicotinic, alpha 6	Chrna6	cholinergic receptor, nicotinic, alpha polypeptide 6	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2002-06-10	Chrna6	cholinergic receptor, nicotinic, alpha polypeptide 6			Name updated	70584	APPROVED

RGD Curation Notes

Note Type	Note	Reference

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

alimentary part of gastrointestinal system

endocrine system

hemolymphoid system

nervous system

renal system

reproductive system

Below cutoff