Clcn1 (chloride voltage-gated channel 1)

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Gene: Clcn1 (chloride voltage-gated channel 1) Rattus norvegicus

Analyze

Symbol:

Clcn1

Name:

chloride voltage-gated channel 1

RGD ID:

2360

Description:

Enables voltage-gated chloride channel activity. Involved in chloride transport. Predicted to be located in sarcolemma. Predicted to be part of chloride channel complex. Predicted to be active in plasma membrane. Human ortholog(s) of this gene implicated in myotonia congenita. Orthologous to human CLCN1 (chloride voltage-gated channel 1); INTERACTS WITH ammonium chloride; atorvastatin calcium; bisphenol A.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Previously known as:

chloride channel 1; chloride channel 1 (skeletal muscle); chloride channel 1, skeletal muscle; chloride channel protein 1; chloride channel protein, skeletal muscle; chloride channel, voltage-sensitive 1; clC-1; SMCC

RGD Orthologs

Human

Mouse

Chinchilla

Bonobo

Dog

Squirrel

Pig

Green Monkey

Naked Mole-Rat

Alliance Genes

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	CLCN1 (chloride voltage-gated channel 1)	HGNC	Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, Panther
Mus musculus (house mouse):	Clcn1 (chloride channel, voltage-sensitive 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Clcn1 (chloride voltage-gated channel 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	CLCN1 (chloride voltage-gated channel 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	CLCN1 (chloride voltage-gated channel 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Clcn1 (chloride voltage-gated channel 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	CLCN1 (chloride voltage-gated channel 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	CLCN1 (chloride voltage-gated channel 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Clcn1 (chloride voltage-gated channel 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Other homologs ²
Homo sapiens (human):	CLCN2 (chloride voltage-gated channel 2)	HGNC	OrthoDB
Alliance orthologs ³
Homo sapiens (human):	CLCN1 (chloride voltage-gated channel 1)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Clcn1 (chloride channel, voltage-sensitive 1)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	clcn1a (chloride channel, voltage-sensitive 1a)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	clcn1b (chloride channel, voltage-sensitive 1b)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Drosophila melanogaster (fruit fly):	ClC-a	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Caenorhabditis elegans (roundworm):	clh-3	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Caenorhabditis elegans (roundworm):	clh-1	Alliance	DIOPT (OMA\|OrthoFinder\|PANTHER\|PhylomeDB)
Caenorhabditis elegans (roundworm):	clh-2	Alliance	DIOPT (OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Caenorhabditis elegans (roundworm):	clh-4	Alliance	DIOPT (OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)

Is Marker For:

Strains: WF.BBDR-(Clcn1-D4Rat228)/Wor

Candidate Gene For:

Bp116

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
mRatBN7.2	4	71,171,949 - 71,201,483 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	4	71,172,547 - 71,199,984 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	4	76,092,286 - 76,119,750 (+)	NCBI	Rnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0	4	72,005,543 - 72,033,007 (+)	NCBI	Rnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0	4	70,425,008 - 70,452,467 (+)	NCBI	Rnor_WKY
Rnor_6.0	4	71,674,218 - 71,704,318 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	4	71,675,383 - 71,702,819 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	4	136,479,719 - 136,509,472 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	4	70,052,319 - 70,081,449 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	4	70,328,448 - 70,357,579 (+)	NCBI
Celera	4	66,103,038 - 66,130,477 (+)	NCBI		Celera
RH 3.4 Map	4	433.61	RGD
Cytogenetic Map	4	q24	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

cerebral palsy (ISO)

Charcot-Marie-Tooth disease intermediate type (ISO)

congenital myopathy (ISO)

endomyocardial fibrosis (ISO)

genetic disease (ISO)

hyperkalemic periodic paralysis (ISO)

Hypokalemic Periodic Paralysis, Type 1 (ISO)

migraine (ISO)

muscular disease (ISO)

myopathy (ISO)

Myotonia (ISO)

myotonia congenita (ISO)

Myotonia Congenita, Autosomal Dominant (ISO)

Myotonia Congenita, Autosomal Recessive (ISO)

Smith-Lemli-Opitz syndrome (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

3-isobutyl-1-methyl-7H-xanthine (ISO)

ammonium chloride (EXP)

aristolochic acid A (ISO)

atorvastatin calcium (EXP)

atrazine (ISO)

benzo[a]pyrene (ISO)

bisphenol A (EXP,ISO)

calcitriol (ISO)

CGP 52608 (ISO)

clofibrate (ISO)

CPP (EXP,ISO)

dexamethasone (ISO)

disodium selenite (ISO)

fulvestrant (ISO)

genistein (EXP,ISO)

indometacin (ISO)

methoxychlor (EXP)

N-nitrosodiethylamine (EXP)

paracetamol (ISO)

phenethyl caffeate (EXP)

silicon dioxide (ISO)

testosterone (ISO)

tetrachloromethane (EXP)

trichloroethene (EXP)

vinclozolin (EXP)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

chloride transmembrane transport (IEA,ISO)

chloride transport (IBA,IDA,ISO)

muscle contraction (IEA,ISO,ISS)

neuronal action potential propagation (IEA,ISO)

regulation of monoatomic ion transmembrane transport (IEA)

Cellular Component

chloride channel complex (IEA)

membrane (IEA)

plasma membrane (ISO,ISS)

sarcolemma (IEA,ISO)

Molecular Function

protein binding (ISO)

protein homodimerization activity (IEA,ISO,ISS)

voltage-gated chloride channel activity (IBA,IDA,IEA,ISO)

References

References - curated

#	Reference Title	Reference Citation
1.	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.
2.	Rat ISS GO annotations from GOA human gene data--August 2006	GOA data from the GO Consortium
3.	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
4.	Genomic organization of the human muscle chloride channel CIC-1 and analysis of novel mutations leading to Becker-type myotonia.	Lorenz C, etal., Hum Mol Genet 1994 Jun;3(6):941-6.
5.	Rat ISS GO annotations from MGI mouse gene data--August 2006	MGD data from the GO Consortium
6.	Electronic Transfer of LocusLink and RefSeq Data	NCBI rat LocusLink and RefSeq merged data July 26, 2002
7.	OMIM Disease Annotation Pipeline	OMIM Disease Annotation Pipeline
8.	GOA pipeline	RGD automated data pipeline
9.	ClinVar Automated Import and Annotation Pipeline	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
10.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions
11.	Primary structure and functional expression of a developmentally regulated skeletal muscle chloride channel.	Steinmeyer K, etal., Nature 1991 Nov 28;354(6351):301-4.

Additional References at PubMed

PMID:2453798	PMID:7721815	PMID:15139012	PMID:19220292	PMID:19786584	PMID:22521272	PMID:26007199	PMID:26021757	PMID:26502825

Genomics

Comparative Map Data

Clcn1
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	4	71,171,949 - 71,201,483 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	4	71,172,547 - 71,199,984 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	4	76,092,286 - 76,119,750 (+)	NCBI	Rnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0	4	72,005,543 - 72,033,007 (+)	NCBI	Rnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0	4	70,425,008 - 70,452,467 (+)	NCBI	Rnor_WKY
Rnor_6.0	4	71,674,218 - 71,704,318 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	4	71,675,383 - 71,702,819 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	4	136,479,719 - 136,509,472 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	4	70,052,319 - 70,081,449 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	4	70,328,448 - 70,357,579 (+)	NCBI
Celera	4	66,103,038 - 66,130,477 (+)	NCBI		Celera
RH 3.4 Map	4	433.61	RGD
Cytogenetic Map	4	q24	NCBI

CLCN1
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	7	143,316,111 - 143,352,083 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p13 Ensembl	7	143,316,111 - 143,352,083 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	7	143,013,204 - 143,049,176 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	7	142,723,341 - 142,759,219 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	7	142,530,055 - 142,565,934	NCBI
Celera	7	137,850,084 - 137,885,958 (+)	NCBI		Celera
Cytogenetic Map	7	q34	NCBI
HuRef	7	137,350,584 - 137,386,478 (+)	NCBI		HuRef
CHM1_1	7	142,950,106 - 142,986,018 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	7	144,671,527 - 144,707,513 (+)	NCBI		T2T-CHM13v2.0
CRA_TCAGchr7v2	7	142,415,337 - 142,451,223 (+)	NCBI

Clcn1
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	6	42,263,552 - 42,292,698 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	6	42,263,619 - 42,292,690 (+)	Ensembl		GRCm39 Ensembl
GRCm38	6	42,284,851 - 42,315,764 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	6	42,286,685 - 42,315,756 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	6	42,236,684 - 42,264,655 (+)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	6	42,216,292 - 42,244,263 (+)	NCBI		MGSCv36	mm8
Celera	6	42,231,004 - 42,259,063 (+)	NCBI		Celera
Cytogenetic Map	6	B2.1	NCBI
cM Map	6	20.57	NCBI

Clcn1
(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_004955494	319,738 - 348,511 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955494	318,137 - 349,568 (-)	NCBI	ChiLan1.0	ChiLan1.0

CLCN1
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
PanPan1.1	7	147,801,440 - 147,837,654 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	7	147,801,440 - 147,836,701 (+)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	7	135,308,966 - 135,346,734 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3

CLCN1
(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	6,342,772 - 6,373,580 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	16	6,342,772 - 6,373,580 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	16	7,331,919 - 7,362,475 (-)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	16	6,196,701 - 6,227,304 (-)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	16	6,196,701 - 6,227,304 (-)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	16	6,144,363 - 6,174,910 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	16	5,996,056 - 6,026,611 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	16	6,071,349 - 6,101,933 (-)	NCBI		UU_Cfam_GSD_1.0

Clcn1
(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_024405118	12,112,783 - 12,144,385 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936527	759,047 - 790,670 (+)	Ensembl	SpeTri2.0
SpeTri2.0	NW_004936527	759,012 - 791,302 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

CLCN1
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	18	6,902,542 - 6,940,449 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	18	6,902,540 - 6,941,530 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	18	7,143,450 - 7,181,431 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

CLCN1
(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	21	112,196,136 - 112,237,836 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	21	112,197,518 - 112,236,115 (+)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666072	8,923,045 - 8,982,440 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Clcn1
(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_female_1.0 Ensembl	NW_004624800	11,418,225 - 11,446,666 (-)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624800	11,417,040 - 11,446,732 (-)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in Clcn1
123 total Variants

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	55
Count of miRNA genes:	49
Interacting mature miRNAs:	54
Transcripts:	ENSRNOT00000051265
Prediction methods:	Miranda, Rnahybrid, 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.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
619616	Bp79	Blood pressure QTL 79		0.0292	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	4	5214602	78882945	Rat
2303168	Bp330	Blood pressure QTL 330	4.25	0.017	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	4	5214602	146446691	Rat
631261	Tcas3	Tongue tumor susceptibility QTL 3	6.88		tongue integrity trait (VT:0010553)	number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)	4	10814170	91360527	Rat
2316958	Gluco58	Glucose level QTL 58	10		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	4	11320076	180699135	Rat
6909122	Insul22	Insulin level QTL 22	4.63		blood insulin amount (VT:0001560)	plasma insulin level (CMO:0000342)	4	26907285	75585128	Rat
6909128	Pancm4	Pancreatic morphology QTL 4	11.35		pancreas mass (VT:0010144)	pancreas wet weight (CMO:0000626)	4	26907285	75585128	Rat
8655906	Rf60	Renal function QTL 60	3.8		blood creatinine amount (VT:0005328)	creatinine clearance (CMO:0000765)	4	29494195	81006281	Rat
12798520	Anxrr55	Anxiety related response QTL 55	4.45	0.01	locomotor behavior trait (VT:0001392)	number of rearing movements with lid-pushing in an experimental apparatus (CMO:0002715)	4	32583980	114627242	Rat
8552782	Vie1	Viral induced encephalitis QTL 1	26.4		brain integrity trait (VT:0010579)	encephalitis incidence/prevalence measurement (CMO:0002361)	4	34430484	82490359	Rat
8552801	Bw143	Body weight QTL 143	7.3		body mass (VT:0001259)	change in body weight to body weight ratio (CMO:0002216)	4	34430484	82490359	Rat
8552809	Vie5	Viral induced encephalitis QTL 5	25.3		brain integrity trait (VT:0010579)	encephalitis incidence/prevalence measurement (CMO:0002361)	4	34430484	82490359	Rat
8655961	Kidm43	Kidney mass QTL 43	18		kidney mass (VT:0002707)	both kidneys wet weight (CMO:0000085)	4	36303261	103194984	Rat
1358352	Srcrt3	Stress Responsive Cort QTL 3	2.29		blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	4	38465774	146803430	Rat
61475	Aia2	Adjuvant induced arthritis QTL 2	5.8		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	4	39505275	73892441	Rat
1331807	Rf31	Renal function QTL 31	2.988		urine potassium amount (VT:0010539)	urine potassium level (CMO:0000128)	4	39524264	74726312	Rat
1300139	Hrtrt6	Heart rate QTL 6	2.85		heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	4	39524264	116179656	Rat
61445	Strs3	Sensitivity to stroke QTL 3	3		cerebrum integrity trait (VT:0010549)	post-insult time to onset of cerebrovascular lesion (CMO:0002343)	4	40433388	85433388	Rat
8694439	Bw168	Body weight QTL 168	9.57	0.001	retroperitoneal fat pad mass (VT:0010430)	retroperitoneal fat pad weight to body weight ratio (CMO:0000635)	4	40433414	85433414	Rat
6893678	Bw108	Body weight QTL 108	2.6	0.006	body mass (VT:0001259)	body weight (CMO:0000012)	4	43457976	88457976	Rat
1576305	Emca6	Estrogen-induced mammary cancer QTL 6	5.8		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	4	44463720	155883716	Rat
1354612	Foco1	Food consumption QTL 1	8.87		eating behavior trait (VT:0001431)	food intake rate (CMO:0000427)	4	44463908	148090542	Rat
1354660	Salc1	Saline consumption QTL 1	11.26		drinking behavior trait (VT:0001422)	saline drink intake rate (CMO:0001627)	4	44463908	148090542	Rat
2312567	Glom19	Glomerulus QTL 19	1.9	0.006	kidney glomerulus morphology trait (VT:0005325)	index of glomerular damage (CMO:0001135)	4	45456990	146803430	Rat
1298082	Stresp4	Stress response QTL 4			blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	4	50119848	146803430	Rat
4889969	Bss96	Bone structure and strength QTL 96	4.9		tibia size trait (VT:0100001)	tibia cortical bone volume (CMO:0001725)	4	56647776	78882945	Rat
4889972	Bss97	Bone structure and strength QTL 97	5.6		tibia size trait (VT:0100001)	tibia total bone volume (CMO:0001724)	4	56647776	78882945	Rat
5685009	Bmd86	Bone mineral density QTL 86	3.7		tibia mineral mass (VT:1000283)	bone mineral density (CMO:0001226)	4	56647776	78882945	Rat
5685012	Bmd87	Bone mineral density QTL 87	5.1		tibia mineral mass (VT:1000283)	bone mineral content (CMO:0001554)	4	56647776	78882945	Rat
70200	Alc18	Alcohol consumption QTL 18	9.2		drinking behavior trait (VT:0001422)	ethanol intake volume to total fluid intake volume ratio (CMO:0001591)	4	56647873	149491524	Rat
1641833	Alc21	Alcohol consumption QTL 21	8.6	0.0001	drinking behavior trait (VT:0001422)	ethanol drink intake rate (CMO:0001407)	4	56698790	126192555	Rat
631546	Bp86	Blood pressure QTL 86	3.2		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	4	57114432	91360801	Rat
634311	Sach7	Saccharin preference QTL 7			taste sensitivity trait (VT:0001986)	saccharin intake volume to total fluid intake volume ratio (CMO:0001601)	4	57114432	102114432	Rat
61336	Bp21	Blood pressure QTL 21	4.6		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	4	57114705	78881294	Rat
1358363	Sradr3	Stress Responsive Adrenal Weight QTL 3	6.19		adrenal gland mass (VT:0010420)	both adrenal glands wet weight (CMO:0000164)	4	57486946	102486946	Rat
1558651	Swd3	Spike wave discharge measurement QTL 3	4.62	0.000024	brain electrophysiology trait (VT:0010557)	brain spike-and-wave discharge frequency (CMO:0001742)	4	58432133	92991462	Rat
631671	Iddm11	Insulin dependent diabetes mellitus QTL 11	3.6	0.0012	blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	4	58635877	78886137	Rat
738009	Sach4	Saccharine consumption QTL 4	4.9	0.000016	consumption behavior trait (VT:0002069)	saccharin intake volume to total fluid intake volume ratio (CMO:0001601)	4	59948935	154902892	Rat
738016	Alc16	Alcohol consumption QTL 16	3.6	0.00015	consumption behavior trait (VT:0002069)	ethanol drink intake rate to body weight ratio (CMO:0001616)	4	59948935	154902892	Rat
738031	Alc14	Alcohol consumption QTL 14	7.6	0.00003	consumption behavior trait (VT:0002069)	ethanol drink intake rate to body weight ratio (CMO:0001616)	4	59948935	154902892	Rat
1578657	Bss12	Bone structure and strength QTL 12	8.9		femur morphology trait (VT:0000559)	femoral neck cross-sectional area (CMO:0001697)	4	60220938	105220938	Rat
1578658	Bss13	Bone structure and strength QTL 13	8		femur strength trait (VT:0010010)	femoral neck polar moment of inertia (CMO:0001670)	4	60220938	105220938	Rat
2300179	Bmd50	Bone mineral density QTL 50	5.9	0.0001	femur mineral mass (VT:0010011)	volumetric bone mineral density (CMO:0001553)	4	60928534	105928534	Rat
1549843	Bw53	Body weight QTL 53		0.0001	body mass (VT:0001259)	body weight gain (CMO:0000420)	4	61697658	103194791	Rat
1549839	Bw52	Body weight QTL 52		0.0001	body mass (VT:0001259)	body weight gain (CMO:0000420)	4	61697658	115089733	Rat
61418	Pia5	Pristane induced arthritis QTL 5	4.5		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	4	62277855	128289560	Rat
6478743	Anxrr40	Anxiety related response QTL 40		0.83076	defecation behavior trait (VT:0010462)	defecation rate (CMO:0000998)	4	62753847	107753847	Rat
6478772	Anxrr49	Anxiety related response QTL 49		0.15488	defecation behavior trait (VT:0010462)	defecation rate (CMO:0000998)	4	62753847	107753847	Rat
6478684	Anxrr30	Anxiety related response QTL 30		0.00087	defecation behavior trait (VT:0010462)	defecation rate (CMO:0000998)	4	62753847	107753847	Rat
631651	Bp124	Blood pressure QTL 124	3		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	4	62879517	107879517	Rat
7394826	Bw126	Body weight QTL 126		0.002	body mass (VT:0001259)	body weight gain (CMO:0000420)	4	62933269	87483707	Rat
8552807	Vie4	Viral induced encephalitis QTL 4	7.3		brain integrity trait (VT:0010579)	encephalitis incidence/prevalence measurement (CMO:0002361)	4	62933508	82490359	Rat
70192	BpQTLcluster5	Blood pressure QTL cluster 5	4.183		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	4	62933508	114921294	Rat
70192	BpQTLcluster5	Blood pressure QTL cluster 5	4.183		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	4	62933508	114921294	Rat
70192	BpQTLcluster5	Blood pressure QTL cluster 5	4.183		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	4	62933508	114921294	Rat
70192	BpQTLcluster5	Blood pressure QTL cluster 5	4.183		arterial blood pressure trait (VT:2000000)	percent change in mean arterial blood pressure (CMO:0002035)	4	62933508	114921294	Rat
70192	BpQTLcluster5	Blood pressure QTL cluster 5	4.183		arterial blood pressure trait (VT:2000000)	percent change in systolic blood pressure (CMO:0000747)	4	62933508	114921294	Rat
70192	BpQTLcluster5	Blood pressure QTL cluster 5	4.183		arterial blood pressure trait (VT:2000000)	absolute change in pulse pressure (CMO:0001882)	4	62933508	114921294	Rat
70192	BpQTLcluster5	Blood pressure QTL cluster 5	4.183		arterial blood pressure trait (VT:2000000)	absolute change in mean arterial blood pressure (CMO:0000533)	4	62933508	114921294	Rat
631674	Iddm14	Insulin dependent diabetes mellitus QTL 14			blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	4	64528739	157573521	Rat
2312569	Pur19	Proteinuria QTL 19	3.4	0.001	urine total protein amount (VT:0000032)	urine total protein excretion rate (CMO:0000756)	4	65882107	96130297	Rat
2317577	Eae24	Experimental allergic encephalomyelitis QTL 24			nervous system integrity trait (VT:0010566)	post-insult time to onset of experimental autoimmune encephalomyelitis (CMO:0001422)	4	66993185	72752834	Rat
2317577	Eae24	Experimental allergic encephalomyelitis QTL 24			nervous system integrity trait (VT:0010566)	percentage of study population developing experimental autoimmune encephalomyelitis during a period of time (CMO:0001047)	4	66993185	72752834	Rat
2317577	Eae24	Experimental allergic encephalomyelitis QTL 24			nervous system integrity trait (VT:0010566)	experimental autoimmune encephalomyelitis severity score (CMO:0001419)	4	66993185	72752834	Rat
61330	Eau1	Experimental allergic uveoretinitis QTL 1		0.0003	uvea integrity trait (VT:0010551)	experimental autoimmune uveitis score (CMO:0001504)	4	70362013	132642728	Rat
634344	Hcar7	Hepatocarcinoma resistance QTL 7	7.8		liver integrity trait (VT:0010547)	liver tumorous lesion area to total liver area ratio (CMO:0001075)	4	70808386	115808386	Rat
634344	Hcar7	Hepatocarcinoma resistance QTL 7	7.8		liver integrity trait (VT:0010547)	liver tumorous lesion number (CMO:0001068)	4	70808386	115808386	Rat

Markers in Region

RH94644

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	4	71,199,855 - 71,199,964 (+)	MAPPER	mRatBN7.2
Rnor_6.0	4	71,702,691 - 71,702,799	NCBI	Rnor6.0
Rnor_5.0	4	136,507,088 - 136,507,196	UniSTS	Rnor5.0
RGSC_v3.4	4	70,081,321 - 70,081,429	UniSTS	RGSC3.4
Celera	4	66,130,349 - 66,130,457	UniSTS
RH 3.4 Map	4	433.61	UniSTS
Cytogenetic Map	4	q23	UniSTS

Related Rat Strains

The following Strains have been annotated to Clcn1

WF.BBDR-(Clcn1-D4Rat228)/Wor

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							8	11			2		8
Low	2	43	10	2	13	2			74	10	36	9
Below cutoff	1		32	24	6	24				21	3	2

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_013147	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_008762873	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039107135	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039107136	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XR_005503168	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC121165	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AY112736	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AY112737	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AY112738	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AY112739	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AY112740	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473959	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000141	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	X62894	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000051265 ⟹ ENSRNOP00000043372

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	4	71,172,547 - 71,199,984 (+)	Ensembl
Rnor_6.0 Ensembl	4	71,675,383 - 71,702,819 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000104906 ⟹ ENSRNOP00000087495

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	4	71,172,547 - 71,199,984 (+)	Ensembl

RefSeq Acc Id:

NM_013147 ⟹ NP_037279

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	4	71,172,547 - 71,199,984 (+)	NCBI
Rnor_6.0	4	71,675,383 - 71,702,819 (+)	NCBI
Rnor_5.0	4	136,479,719 - 136,509,472 (+)	NCBI
RGSC_v3.4	4	70,052,319 - 70,081,449 (+)	RGD
Celera	4	66,103,038 - 66,130,477 (+)	RGD

Sequence:

show sequence

CAAAAGCAGAGGCTTAAGGAGGTACTAGGGGGAGACTAGGAGCAAGCAGGCCAAGGCCTGGCTG
GGGCTTGGGGGGAGGACACATGGAGCGGTCCCAGTCCCAGCAACATGGAGGTGAACAAAGCTGG
TGGGGCACTGCCCCCCAGTACCAGTACATGCCCTTCGAACATTGTACCAGCTATGGACTGCCCT
CAGAGAATGGGGGCCTTCAGCACCGGCCCCGAAAGGACCTGGGTCCCAGGCACAATGCCCACCC
AACACAGATATATGGCCATCACAAAGAACAATATTCATATCAGGCACAGGACAGGGGAATACCC
AAGAAGACGGACTCCAGTTCTACTGTGGACAGCTTGGATGAGGACCACTATTCTAAATGTCAAG
ACTGTGTCCATCGCCTGGGACGTGTGCTGAGAAGGAAGCTGGGGGAAGACTGGATCTTTCTTGT
GCTCCTGGGCCTACTGATGGCTCTTGTCAGCTGGTGCATGGACTATGTTAGCGCCAAGAGCCTT
CAGGCCTACAAGTGGACCTATGCCCAGATGCAGCCCAGCCTTCCTCTACAGTACTTGGCCTGGG
TCACCTTCCCACTTATCCTCATCCTCTTCAGTGCCCTCTTTTGCCAACTCATCTCTCCCCAGGC
TGTGGGCTCTGGAATCCCTGAGATGAAGACAATTCTTCGTGGTGTTGTCTTGAAGGAATACCTC
ACACTCAAGGCCTTTGTAGCCAAGGTGGTGGCCTTGACAGCCGGTCTGGGCAGTGGTATCCCTG
TGGGGAAAGAGGGTCCCTTTGTTCACATTGCCAGCATCTGTGCTGCTGTCCTCAGCAAATTCAT
GTCCATGTTCTCTGGTGTCTATGAGCAGCCATACTATTACACTGACATCCTGACAGTGGGCTGT
GCCGTGGGGGTCGGTTGCTGTTTTGGAACACCACTTGGAGGAGTGCTGTTCAGCATCGAGGTCA
CCTCTACCTACTTTGCCGTTCGGAATTACTGGCGAGGATTCTTTGCAGCCACCTTCAGTGCCTT
TGTGTTCCGCGTCCTGGCAGTGTGGAACAAGGATGCTGTCACTATTACTGCTCTGTTCAGAACT
AATTTCCGGATGGATTTCCCCTTTGACCTGAAGGAACTCCCAGCTTTTGCTGTCATTGGGATTT
GCTGCGGGTTCTTGGGAGCTGTTTTTGTTTATCTGCATCGCCAAGTCATGCTCGGTGTCCGAAA
GCACAAGGCTCTCAGCCAGTTTCTTGCTAAGCACCGCCTGCTCTATCCTGGAATCGTTACTTTT
GTCATCGCCTCACTCACCTTTCCACCAGGAATGGGTCAATTCATGGCTGGAGAGCTGATGCCCC
GTGAAGCTATCAGCACCCTCTTTGACAACAACACATGGGTAAAGCACATAGGTGATCCCAAAAG
CTTGGGCCAGTCAGCTGTGTGGATTCACCCCCAGGTCAACGTGGTCATCATCATCCTTCTCTTC
TTCGTCATGAAGTTTTGGATGTCCATTGTGGCCACGACTATGCCCATACCCTGTGGAGGCTTCA
TGCCTGTTTTTGTGCTAGGAGCTGCCTTTGGAAGGCTGGTAGGAGAGATCATGGCCATGCTGTT
CCCTGAGGGTATCTTATTTGATGATATCATCTATAAGATCTTACCAGGGGGCTATGCAGTGATT
GGAGCAGCAGCTTTGACAGGGGCTGTCTCTCACACAGTCTCCACAGCTGTGATTTGCTTCGAAT
TAACTGGTCAGATTGCTCACATCCTGCCCATGATGGTGGCTGTTATCTTGGCCAACATGGTGGC
CCAAAGTCTGCAGCCCTCCCTCTATGACAGCATCATCCAGGTCAAGAAGCTTCCCTATTTGCCA
GACCTTGGTTGGAACCAGCTCAGCAAATTTACAATTTTTGTTGAGGACATCATGGTACGTGACG
TGAAGTTTGTTTCAGCTTCTTGTACATACGGGGAACTAAGAAACCTACTCCAGACCACCACAGT
CAAGACTTTACCATTGGTTGACTCCAAAGATTCAATGATCCTGCTAGGCTCTGTGGAACGCTCA
GAACTGCAGTCCCTCCTGCAGCGCCACCTGTGTGCAGAGCGAAGGTTGAAGGCTGCCCAGGACA
TGGCTCGAAAGTTATCAGAGCTGCCCTATAATGGCCAGGCTCAGCTGGCTGGGGAGTGGCATCC
TGGTGGTCGACCTGAGTCCTTTGCCTTCGTAGATGAAGATGAAGATGAGGACGTCTCCCGGAAG
ACAGAGCTTCCACAGACTCCAACTCCTCCTCCTCCTCCCCCTCCTCCTCTGCCTCCCCAGTTTC
CTATTGCTCCATCATACCCTGAAGAGCCTAACGGGCCACTGCCCAGCCACAAACAGCCCCCTGA
AGCTTCAGACTCTGCAGATCAAAGGTCCTCCATCTTCCAGCGCCTGCTGCACTGCTTACTGGGC
AAAGCTCACTCCACAAAGAAGAAAATAACCCAGGATTCAACAGATTTAGTGGATAACATGTCAC
CTGAAGAGATTGAGGCCTGGGAGCGGGAGCAGCTGAGCCAGCCTGTGTGTTTTGATTTCTGCTG
CATTGACCAGTCTCCCTTCCAGCTGGTGGAGCAGACAACTCTGCACAAGACTCATACACTCTTC
TCACTTCTTGGCCTCCATCTTGCCTATGTGACCAGCATGGGGAAGCTCAGAGGTGTCTTGGCAC
TAGAAGAGCTACAGAAAGCTATCAAGGGCCACACCAAATCTGGAGTGCAGCTTCGCCCTCCACT
TGCCAGCTTCCGGAATACAACTTCAATTCGGAAGACCCCTGGGGGGCCACCCCCTCCTGCAGAG
AGCTGGAATGTGCCTGAGGGTGAAGATGGAGCTCCTGAAAGAGAAGTCATGGTTCCTACCATGC
CAGAGACTCCTGTCCCACCACCATCTCCAGAGGTCCCTTCCTGCCTGGCCCCAGCCAGAGTGGA
GGGTGAGCTGGAGGAACTGGAGATGGTGGGGAACCTAGGGCCTGAGGAGGACCTGGCTGACATC
TTGCATGGCCCCAGTCTGCGGTCCACTGATGAGGAAGATGAGGACGAGCTGATCCTGTGAACAA
CACCCTCCAAGCTTTCTTCATAAAAACCACAGGGCCCATGTCAGAGAGTGGGCTTGTATATGAA
ATGGGTGCCCTGAAGTTGGGGAGACCTCCATTTCATCGTTGTTCCTACCCCACTATGAAAG

hide sequence

RefSeq Acc Id:

XM_008762873 ⟹ XP_008761095

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	4	71,171,972 - 71,201,483 (+)	NCBI
Rnor_6.0	4	71,674,218 - 71,704,318 (+)	NCBI

Sequence:

show sequence

TGTTTGCTTTGTTTTTCATTTTAAAGGGGCCAGAAAAATGGCTTGATGGTTAGAAAAAACTTAC
TGCTTTGTTTAGGACCCCCAGCACCCATGTCAGGCCATACACAATTGTTAAAACTAGCTGCAGG
GCATCTTGACACCCTCCTCTGGACTCCATGGGCACCCGTACTCATGTGTACTGCACCACACGTA
AAGGCAGGTAACTAAAAATAATGACAATAAAAATTAAATTCCTTTTTGTAATTTTTTTTAATCT
TTAAAAGAAAAGGTACTTTTAATGGCGTCTTACCTTCCCACTTGGAACAATCCCATTTAACATA
GGTCAGAATCATTGCAGACCAGATATTTGGTGTGCATACCTTTCAGTCCTTGAGATGGTTACTT
GTCCATCTTCTCCTGTTTCTTGGGTTCCTACTATCACCTGCCCTGTGACTAGCTAACCTACCCT
GGTAGAACTGTCATTGGCACCACAGTCCAGTTGAGAGCTCAGTCCCTCCCTACTGATCTGAGCT
GCTGCTGGGGCTCTCACATATGTCTAGGAAATGAGAGACAATCCACACCCAGTGGTGATATGGG
TGGGGTCGAGGGGAAGGCCCCAGCGTGTTTTTAGCTGCTCTTGGCAGACTCAAGGGCCGAGAGC
TGGAGGAGAAAGCTGGGAATCTGATGCATGTGGAGAGCTGGCTGCAGAAAAGTCCAGATGAAGC
CTTAAGAGATACTGAGCTGAAACCAGCCCAACCAACAAGGAGAGATAGCAGAGAGGCGTCAGCT
GCTCTCCCAGGTGAGTTGCCTGTCTAATGTTACCAAAACACTGAGTGGCTTCGTTCAACATTCT
CTCTCCCCTCACTTACCACGAGGTCTGCGGGGACGCTCAGCTATACACACAGCCTAGAAATTTC
AGTAGGAACTTTTTCACTCTGGTCCTGCTGATACTTAGAAAGGAACTAGTGAGCCTTGTAGGAA
AGGAACAACGCTGCCGGCTGGCAGAGGGAATTCCCTGTTGGACTGTCCCATAGGTTCTCCTACC
CCCACCCCCACACTCCACTCACACCTGCTTCGACCCCAGAAGGATCAGATGTGGCAGTGGGGGG
GGGATGGGTCATGTGATGGAGAGACAGCTATAAATAGCTAGAGGTGGGCATGTTGCCCCAGACG
CCTTGGGGACAGTCAAAAGCAGAGGCTTAAGGAGGTACTAGGGGGAGACTAGGAGCAAGCAGGC
CAAGGCCTGGCTGGGGCTTGGGGGGAGGACACATGGAGCGGTCCCAGTCCCAGCAACATGGAGG
TGAACAAAGCTGGTGGGGCACTGCCCCCCAGTACCAGTACATGCCCTTCGAACATTGTACCAGC
TATGGACTGCCCTCAGAGAATGGGAGCCTTCAGCACCGGCCCCGAAAGGACCTGGGTCCCAGGC
ACAATGCCCACCCAACACAGATATATGGCCATCACAAAGAACAATATTCATATCAGGCACAGGA
CAGGGGAATACCCAAGAAGACGGACTCCAGTTCTACTGTGGACAGCTTGGATGAGGACCACTAT
TCTAAATGTCAAGACTGTGTCCATCGCCTGGGACGTGTGCTGAGAAGGAAGCTGGGGGAAGACT
GGATCTTTCTTGTGCTCCTGGGCCTACTGATGGCTCTTGTCAGCTGGTGCATGGACTATGTTAG
CGCCAAGAGCCTTCAGGCCTACAAGTGGACCTATGCCCAGATGCAGCCCAGCCTTCCTCTACAG
TACTTGGCCTGGGTCACCTTCCCACTTATCCTCATCCTCTTCAGTGCCCTCTTTTGCCAACTCA
TCTCTCCCCAGGCTGTGGGCTCTGGAATCCCTGAGATGAAGACAATTCTTCGTGGTGTTGTCTT
GAAGGAATACCTCACACTCAAGGCCTTTGTAGCCAAGGTGGTGGCCTTGACAGCCGGTCTGGGC
AGTGGTATCCCTGTGGGGAAAGAGGGTCCCTTTGTTCACATTGCCAGCATCTGTGCTGCTGTCC
TCAGCAAATTCATGTCCATGTTCTCTGGTGTCTATGAGCAGCCATACTATTACACTGACATCCT
GACAGTGGGCTGTGCCGTGGGGGTCGGTTGCTGTTTTGGAACACCACTTGGAGGAGTGCTGTTC
AGCATCGAGGTCACCTCTACCTACTTTGCCGTTCGGAATTACTGGCGAGGATTCTTTGCAGCCA
CCTTCAGTGCCTTTGTGTTCCGCGTCCTGGCAGTGTGGAACAAGGATGCTGTCACTATTACTGC
TCTGTTCAGAACTAATTTCCGGATGGATTTCCCCTTTGACCTGAAGGAACTCCCAGCTTTTGCT
GTCATTGGCCGCCTGCTCTATCCTGGAATCGTTACTTTTGTCATCGCCTCACTCACCTTTCCAC
CAGGAATGGGTCAATTCATGGCTGGAGAGCTGATGCCCCGTGAAGCTATCAGCACCCTCTTTGA
CAACAACACATGGGTAAAGCACATAGGTGATCCCAAAAGCTTGGGCCAGTCAGCTGTGTGGATT
CACCCCCAGGTCAACGTGGTCATCATCATCCTTCTCTTCTTCGTCATGAAGTTTTGGATGTCCA
TTGTGGCCACGACTATGCCCATACCCTGTGGAGGCTTCATGCCTGTTTTTGTGCTAGGAGCTGC
CTTTGGAAGGCTGGTAGGAGAGATCATGGCCATGCTGTTCCCTGAGGGTATCTTATTTGATGAT
ATCATCTATAAGATCTTACCAGGGGGCTATGCAGTGATTGGAGCAGCAGCTTTGACAGGGGCTG
TCTCTCACACAGTCTCCACAGCTGTGATTTGCTTCGAATTAACCGGTCAGATTGCTCACATCCT
GCCCATGATGGTGGCTGTTATCTTGGCCAACATGGTGGCCCAAAGTCTGCAGCCCTCCCTCTAT
GACAGCATCATCCAGGTCAAGAAGCTTCCCTATTTGCCAGACCTTGGTTGGAACCAGCTCAGCA
AATTTACAATTTTTGTTGAGGACATCATGGTACGTGACGTGAAGTTTGTTTCAGCTTCTTGTAC
ATACGGGGAACTAAGAAACCTACTCCAGACCACCACAGTCAAGACTTTACCATTGGTTGACTCC
AAAGATTCAATGATCCTGCTAGGCTCTGTGGAACGCTCAGAACTGCAGTCCCTCCTGCAGCGCC
ACCTGTGTGCAGAGCGAAGGTTGAAGGCTGCCCAGGACATGGCTCGAAAGTTATCAGAGCTGCC
CTATAATGGCCAGGCTCAGCTAGCTGGGGAGTGGCATCCTGGTGGTCGACCTGAGTCCTTTGCC
TTCGTAGATGAAGATGAAGATGAGGACGTCTCCCGGAAGACAGAGCTTCCACAGACTCCAACTC
CTCCTCCTCCTCCCCCTCCTCCTCTGCCTCCCCAGTTTCCTATTGCTCCATCATACCCTGAAGA
GCCTAACGGGCCACTGCCCAGCCACAAACAGCCCCCTGAAGCTTCAGACTCTGCAGATCAAAGG
TCCTCCATCTTCCAGCGCCTGCTGCACTGCTTACTGGGCAAAGCTCACTCCACAAAGAAGAAAA
TAACCCAGGATTCAACAGATTTAGTGGATAACATGTCACCTGAAGAGATTGAGGCCTGGGAGCA
GGAGCAGCTGAGCCAGCCTGTGTGTTTTGATTTCTGCTGCATTGACCAGTCTCCCTTCCAGCTG
GTGGAGCAGACAACTCTGCACAAGACTCATACACTCTTCTCACTTCTTGGCCTCCATCTTGCCT
ATGTGACCAGCATGGGGAAGCTCAGAGGTGTCTTGGCACTAGAAGAGCTACAGAAAGCTATCAA
GGGCCACACCAAATCTGGAGTGCAGCTTCGCCCTCCACTTGCCAGCTTCCGGAATACAACTTCA
ATTCGGAAGACCCCTGGGGGGCCACCCCCTCCTGCAGAGAGCTGGAATGTGCCTGAGGGTGAAG
ATGGAGCTCCTGAAAGAGAAGTCATGGTTCCTACCATGCCAGAGACTCCTGTCCCACCACCATC
TCCAGAGGTCCCTTCCTGCCTGGCCCCAGCCAGAGTGGAGGGTGAGCTGGAGGAACTGGAGATG
GTGGGGAACCTAGGGCCTGAGGAGGACCTGGCTGACATCTTGCATGGCCCCAGTCTGCGGTCCA
CTGATGAGGAAGATGAGGACGAGCTGATCCTGTGAACAACACCCTCCAAGCTTTCTTCATAAAA
ACCACAGGGCCCATGTCAGAGAGTGGGCTTGTATATGAAATGGGTGCCCTGAAGTTGGGGAGAC
CTCCATTTCATCATTGTTCCTACCCCACTATGAAAGGTGATGGTGATGATCTTAAGGAGAACTT
GATCTTGGGCAGGGAAGAATTTGGGTCCATCAGACCCCCCTCCCCATTTCCAGGGAGGGTTCAA
GGCCCCATGCTCAAAGGACTTCTGTGTTCCTGCTGTGCAGGTTCAGTCCCTGTCACTCTAATGC
CCCACAATTCCCAGTGTCGTTCTGTCACCATCCTGGCCCGGCATGCCTGTCTATATTTCAGTTT
CCATATGGAGTAGGTGAGTGGAGGCCCAGATTGAAAGAATCCGCAAGTGTCACATTGGAAGGGA
ATGTGGGACCACAATATTGCCATGTGGATTGACTACCCTAAAATGTGCCCCCAAGCCTGCCAGC
TGTACTTTCTACCTGTGTGCTCCCCCAAATTTGTCCTAGACCCCATCATTGCTGCCACTGTTTC
TAGGCCAAGCCCTTTATCAGGGCTGAAAAAGCCAACCTTTGTTTCCACAGAACCATGTGCAGTT
CCCTGGAAAGGAGGTTGATGATGTGTGTAGAGACAGGCGTCATGGCTCAGTACAGGTGTCAGAC
CCCTACAGCCGAGAGCTCTGTTTCTTGTCCCAGCCTCTTTGCCTAGCTCCTTGTTACACTTAAC
TAACTTAGCCCGCCAGGAGTCAGCTCTGCCTTGGGGCCACTCTTACTAGAGCTCCTCCCAAAAC
AGACAAGGCTCTGTCTCGTGCAGCTTTGGGGAATGCAGACTCCAGCCCTTTATAAACTCTGTGG
GATCCTCTGGCATAAACTGGGGCACCCTGAGCGTGGCAAGCTTTAGTTTACTCATCCTTAGAGG
GCCCCCATCTTTTTCCTTTCAAACCAGCAAGGAGCTTGATAGTCGTGCTGTACAGCATTGGCCT
GCTTAGCCTAGAAATATATGCCGGGTGTTGTAACATTCAGACACCTTGGCTCATTCATGGGTTC
TTTCTGTCCCTCACTGTATGCCTTTAGCTCTGTAGTTGAACCCTCATATATTCTCCCAGTTCTG
TCCCTTTCCCCAACTCCAGGTTTCTTCTGCCCCCCCCCCAAATAAGACACTCATAGTCAGAGGA
TGCCACCACATTCTGTTTAGTGTTGTTCAACACAGTCTCTGCCCTTCTCCAACATGGGTTCCTT
CCACCACCCCAGGCTAAGACATTGAGGCCTAGGTAGGAGGACTAGCAGGGGGCATCCAAGCCCA
TGCCCATGTGTATATAATCTATAATACTTATATATATTTATATAGAATTCTCTCTGTCATATAT
GTCATAGAATCCTTCCTGGGCCTGGGGTGAGAGTTTCACATTAAGAAAACATGCTAAGACTGAC
CATAAAAATGGGTATTTCTCAGACCTGGAAAACAGAGTGTGGGATCTATATGAACAAGGCTAAG
AACTCGTCCTTCAAGATTCCCTTCTTAACACAAGGGAAAGAAAGAAGGTGTGTGGGCTGGGGGA
GGCAATGGGAGGGAAGGAATGGAAGGTTTGGATTTTCATTTAATAAAGTCAATTGAAAATGAA

hide sequence

RefSeq Acc Id:

XM_039107135 ⟹ XP_038963063

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	4	71,171,975 - 71,201,483 (+)	NCBI

RefSeq Acc Id:

XM_039107136 ⟹ XP_038963064

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	4	71,177,427 - 71,201,483 (+)	NCBI

RefSeq Acc Id:

XR_005503168

RefSeq Status:

Type:

NON-CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	4	71,171,949 - 71,198,960 (+)	NCBI

Protein Sequences


Protein RefSeqs	NP_037279	(Get FASTA)	NCBI Sequence Viewer
	XP_008761095	(Get FASTA)	NCBI Sequence Viewer
	XP_038963063	(Get FASTA)	NCBI Sequence Viewer
	XP_038963064	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAM77485	(Get FASTA)	NCBI Sequence Viewer
	AAM77486	(Get FASTA)	NCBI Sequence Viewer
	AAM77487	(Get FASTA)	NCBI Sequence Viewer
	AAM77488	(Get FASTA)	NCBI Sequence Viewer
	AAM77489	(Get FASTA)	NCBI Sequence Viewer
	CAA44683	(Get FASTA)	NCBI Sequence Viewer
	EDM15504	(Get FASTA)	NCBI Sequence Viewer
	EDM15505	(Get FASTA)	NCBI Sequence Viewer
	EDM15506	(Get FASTA)	NCBI Sequence Viewer
	EDM15507	(Get FASTA)	NCBI Sequence Viewer
	EDM15508	(Get FASTA)	NCBI Sequence Viewer
	P35524	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_037279 ⟸ NM_013147

- UniProtKB:

P35524 (UniProtKB/Swiss-Prot)

- Sequence:

show sequence

MERSQSQQHGGEQSWWGTAPQYQYMPFEHCTSYGLPSENGGLQHRPRKDLGPRHNAHPTQIYGH
HKEQYSYQAQDRGIPKKTDSSSTVDSLDEDHYSKCQDCVHRLGRVLRRKLGEDWIFLVLLGLLM
ALVSWCMDYVSAKSLQAYKWTYAQMQPSLPLQYLAWVTFPLILILFSALFCQLISPQAVGSGIP
EMKTILRGVVLKEYLTLKAFVAKVVALTAGLGSGIPVGKEGPFVHIASICAAVLSKFMSMFSGV
YEQPYYYTDILTVGCAVGVGCCFGTPLGGVLFSIEVTSTYFAVRNYWRGFFAATFSAFVFRVLA
VWNKDAVTITALFRTNFRMDFPFDLKELPAFAVIGICCGFLGAVFVYLHRQVMLGVRKHKALSQ
FLAKHRLLYPGIVTFVIASLTFPPGMGQFMAGELMPREAISTLFDNNTWVKHIGDPKSLGQSAV
WIHPQVNVVIIILLFFVMKFWMSIVATTMPIPCGGFMPVFVLGAAFGRLVGEIMAMLFPEGILF
DDIIYKILPGGYAVIGAAALTGAVSHTVSTAVICFELTGQIAHILPMMVAVILANMVAQSLQPS
LYDSIIQVKKLPYLPDLGWNQLSKFTIFVEDIMVRDVKFVSASCTYGELRNLLQTTTVKTLPLV
DSKDSMILLGSVERSELQSLLQRHLCAERRLKAAQDMARKLSELPYNGQAQLAGEWHPGGRPES
FAFVDEDEDEDVSRKTELPQTPTPPPPPPPPLPPQFPIAPSYPEEPNGPLPSHKQPPEASDSAD
QRSSIFQRLLHCLLGKAHSTKKKITQDSTDLVDNMSPEEIEAWEREQLSQPVCFDFCCIDQSPF
QLVEQTTLHKTHTLFSLLGLHLAYVTSMGKLRGVLALEELQKAIKGHTKSGVQLRPPLASFRNT
TSIRKTPGGPPPPAESWNVPEGEDGAPEREVMVPTMPETPVPPPSPEVPSCLAPARVEGELEEL
EMVGNLGPEEDLADILHGPSLRSTDEEDEDELIL

hide sequence

RefSeq Acc Id:

XP_008761095 ⟸ XM_008762873

- Peptide Label:

isoform X2

- Sequence:

show sequence

MERSQSQQHGGEQSWWGTAPQYQYMPFEHCTSYGLPSENGSLQHRPRKDLGPRHNAHPTQIYGH
HKEQYSYQAQDRGIPKKTDSSSTVDSLDEDHYSKCQDCVHRLGRVLRRKLGEDWIFLVLLGLLM
ALVSWCMDYVSAKSLQAYKWTYAQMQPSLPLQYLAWVTFPLILILFSALFCQLISPQAVGSGIP
EMKTILRGVVLKEYLTLKAFVAKVVALTAGLGSGIPVGKEGPFVHIASICAAVLSKFMSMFSGV
YEQPYYYTDILTVGCAVGVGCCFGTPLGGVLFSIEVTSTYFAVRNYWRGFFAATFSAFVFRVLA
VWNKDAVTITALFRTNFRMDFPFDLKELPAFAVIGRLLYPGIVTFVIASLTFPPGMGQFMAGEL
MPREAISTLFDNNTWVKHIGDPKSLGQSAVWIHPQVNVVIIILLFFVMKFWMSIVATTMPIPCG
GFMPVFVLGAAFGRLVGEIMAMLFPEGILFDDIIYKILPGGYAVIGAAALTGAVSHTVSTAVIC
FELTGQIAHILPMMVAVILANMVAQSLQPSLYDSIIQVKKLPYLPDLGWNQLSKFTIFVEDIMV
RDVKFVSASCTYGELRNLLQTTTVKTLPLVDSKDSMILLGSVERSELQSLLQRHLCAERRLKAA
QDMARKLSELPYNGQAQLAGEWHPGGRPESFAFVDEDEDEDVSRKTELPQTPTPPPPPPPPLPP
QFPIAPSYPEEPNGPLPSHKQPPEASDSADQRSSIFQRLLHCLLGKAHSTKKKITQDSTDLVDN
MSPEEIEAWEQEQLSQPVCFDFCCIDQSPFQLVEQTTLHKTHTLFSLLGLHLAYVTSMGKLRGV
LALEELQKAIKGHTKSGVQLRPPLASFRNTTSIRKTPGGPPPPAESWNVPEGEDGAPEREVMVP
TMPETPVPPPSPEVPSCLAPARVEGELEELEMVGNLGPEEDLADILHGPSLRSTDEEDEDELIL

hide sequence

RefSeq Acc Id:

ENSRNOP00000043372 ⟸ ENSRNOT00000051265

RefSeq Acc Id:	XP_038963063 ⟸ XM_039107135
- Peptide Label:	isoform X1

RefSeq Acc Id:	XP_038963064 ⟸ XM_039107136
- Peptide Label:	isoform X3

RefSeq Acc Id:

ENSRNOP00000087495 ⟸ ENSRNOT00000104906

Protein Domains

CBS

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-P35524-F1-model_v2	AlphaFold	P35524	1-994	view protein structure

Transcriptome

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

Promoters

RGD ID:

13693009

Promoter ID:

EPDNEW_R3532

Type:

single initiation site

Name:

Clcn1_1

Description:

chloride voltage-gated channel 1

SO ACC ID:

SO:0000170

Source:

EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)

Experiment Methods:

Single-end sequencing.

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	4	71,675,365 - 71,675,425	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:2360	AgrOrtholog
BioCyc Gene	G2FUF-45091	BioCyc
Ensembl Genes	ENSRNOG00000016917	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000043372	ENTREZGENE
	ENSRNOP00000043372.3	UniProtKB/TrEMBL
	ENSRNOP00000087495.1	UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000051265	ENTREZGENE
	ENSRNOT00000051265.4	UniProtKB/TrEMBL
	ENSRNOT00000104906.1	UniProtKB/TrEMBL
Gene3D-CATH	3.10.580.10	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Clc chloride channel	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro	CBS_dom	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	CBS_dom_sf	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Cl-channel_core	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Cl-channel_volt-gated	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Cl_channel-1	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report	rno:25688	UniProtKB/Swiss-Prot
NCBI Gene	25688	ENTREZGENE
PANTHER	CHLORIDE CHANNEL PROTEIN 1	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	CHLORIDE CHANNEL PROTEIN 2	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam	Voltage_CLC	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen	Clcn1	PhenoGen
PRINTS	CLCHANNEL	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	CLCHANNEL1	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE	CBS	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP	SSF54631	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	SSF81340	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt	A0A8I6A8S1_RAT	UniProtKB/TrEMBL
	CLCN1_RAT	UniProtKB/Swiss-Prot
	F1LPY4_RAT	UniProtKB/TrEMBL
	P35524	ENTREZGENE

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2016-02-11	Clcn1	chloride voltage-gated channel 1	Clcn1	chloride channel, voltage-sensitive 1	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2012-07-16	Clcn1	chloride channel, voltage-sensitive 1	Clcn1	chloride channel 1, skeletal muscle	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2012-01-09	Clcn1	chloride channel 1, skeletal muscle	Clcn1	chloride channel 1	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2002-11-06	Clcn1	chloride channel 1		Chloride channel 1 (skeletal muscle)	Name updated	625702	APPROVED
2002-06-10	Clcn1	Chloride channel 1 (skeletal muscle)			Symbol and Name status set to approved	70586	APPROVED

RGD Curation Notes

Note Type	Note	Reference
gene_disease	mutation of the human homolog causes both autosomal dominant (Thomsen's disease) and autosomal recessive (Becker's disease) forms of myotonia congenita	704389

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)

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Imported Disease Annotations - CTD

Imported Disease Annotations - OMIM

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