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Gene: Clrn3 (clarin 3) Rattus norvegicus

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Symbol:

Clrn3

Name:

clarin 3

RGD ID:

1305043

Description:

Predicted to be involved in sensory perception of sound. Predicted to be located in membrane. Orthologous to human CLRN3 (clarin 3); INTERACTS WITH 3-chloropropane-1,2-diol; bisphenol A; furan.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Previously known as:

clarin-3; LOC309082; RGD1305043; similar to Expressed sequence AI649392; Tmem12; transmembrane protein 12

RGD Orthologs

Alliance Orthologs

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):	CLRN3 (clarin 3)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Clrn3 (clarin 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Clrn3 (clarin 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	CLRN3 (clarin 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	CLRN3 (clarin 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Clrn3 (clarin 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	CLRN3 (clarin 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	CLRN3 (clarin 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Clrn3 (clarin 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Rattus rattus (black rat):	Clrn3 (clarin 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Other homologs ²
Homo sapiens (human):	OR2B11 (olfactory receptor family 2 subfamily B member 11)	HGNC	OMA
Alliance orthologs ³
Mus musculus (house mouse):	Clrn3 (clarin 3)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Homo sapiens (human):	CLRN3 (clarin 3)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Caenorhabditis elegans (roundworm):	Y67D8C.22	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|PANTHER)
Drosophila melanogaster (fruit fly):	CG1103	Alliance	DIOPT (Ensembl Compara\|PANTHER)
Xenopus tropicalis (tropical clawed frog):	clrn3	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Xenopus tropicalis (tropical clawed frog):	clrn3	Alliance	DIOPT (Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER)

Latest Assembly:

GRCr8 - GRCr8 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	1	199,748,863 - 199,764,486 (-)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	1	199,748,864 - 199,764,486 (-)	Ensembl				GRCr8
mRatBN7.2	1	190,319,025 - 190,334,648 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	1	190,319,026 - 190,334,648 (-)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	1	198,675,031 - 198,690,589 (-)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	1	205,833,147 - 205,848,783 (-)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	1	198,506,610 - 198,522,246 (-)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	1	207,750,627 - 207,766,250 (-)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	1	207,750,223 - 207,811,008 (-)	Ensembl			rn6	Rnor6.0
Rnor_5.0	1	214,683,449 - 214,699,072 (-)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	1	195,132,680 - 195,148,303 (-)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	1	188,034,301 - 188,049,855 (-)	NCBI		Celera
RGSC_v3.1	1	195,282,672 - 195,298,295 (-)	NCBI
Cytogenetic Map	1	q41	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Annotation Click to see Annotation Detail View

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2,4-trichloro-5-(2,5-dichlorophenyl)benzene (ISO)

1,2-dimethylhydrazine (ISO)

17beta-estradiol (ISO)

2,2',4,4',5,5'-hexachlorobiphenyl (ISO)

2,2',5,5'-tetrachlorobiphenyl (ISO)

2,4,4'-trichlorobiphenyl (ISO)

3-chloropropane-1,2-diol (EXP)

4-hydroxyphenyl retinamide (ISO)

aflatoxin B1 (ISO)

arsane (ISO)

arsenic atom (ISO)

belinostat (ISO)

benzo[a]pyrene (ISO)

bisphenol A (EXP)

Butylbenzyl phthalate (ISO)

chromium(6+) (ISO)

cobalt dichloride (ISO)

cyclosporin A (ISO)

entinostat (ISO)

fulvestrant (ISO)

furan (EXP)

nickel dichloride (EXP)

O-methyleugenol (ISO)

okadaic acid (ISO)

paracetamol (ISO)

PCB138 (ISO)

perfluorohexanesulfonic acid (ISO)

perfluorononanoic acid (ISO)

phenobarbital (ISO)

pirinixic acid (EXP)

propanal (ISO)

resveratrol (ISO)

sodium arsenite (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

sensory perception of sound (IEA)

Cellular Component

membrane (IEA)

Molecular Function

protein binding (ISO)

References

References - curated

#	Reference Title	Reference Citation
1.	GOA pipeline	RGD automated data pipeline
2.	ClinVar Automated Import and Annotation Pipeline	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions
4.	Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences.	Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.

Additional References at PubMed

PMID:15489334	PMID:19056867	PMID:23376485

Genomics

Comparative Map Data

Clrn3
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	1	199,748,863 - 199,764,486 (-)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	1	199,748,864 - 199,764,486 (-)	Ensembl				GRCr8
mRatBN7.2	1	190,319,025 - 190,334,648 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	1	190,319,026 - 190,334,648 (-)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	1	198,675,031 - 198,690,589 (-)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	1	205,833,147 - 205,848,783 (-)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	1	198,506,610 - 198,522,246 (-)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	1	207,750,627 - 207,766,250 (-)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	1	207,750,223 - 207,811,008 (-)	Ensembl			rn6	Rnor6.0
Rnor_5.0	1	214,683,449 - 214,699,072 (-)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	1	195,132,680 - 195,148,303 (-)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	1	188,034,301 - 188,049,855 (-)	NCBI		Celera
RGSC_v3.1	1	195,282,672 - 195,298,295 (-)	NCBI
Cytogenetic Map	1	q41	NCBI

CLRN3
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	10	127,877,841 - 127,892,941 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	10	127,877,841 - 127,892,947 (-)	Ensembl			hg38	GRCh38
GRCh37	10	129,676,105 - 129,691,205 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	10	129,566,104 - 129,581,201 (-)	NCBI	Build 36	Build 36	hg18	NCBI36
Celera	10	123,347,587 - 123,362,681 (-)	NCBI		Celera
Cytogenetic Map	10	q26.2	NCBI
HuRef	10	123,250,911 - 123,266,000 (-)	NCBI		HuRef
CHM1_1	10	129,958,532 - 129,973,623 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	10	128,776,372 - 128,791,469 (-)	NCBI		T2T-CHM13v2.0

Clrn3
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	7	135,113,185 - 135,130,383 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	7	135,113,195 - 135,130,383 (-)	Ensembl		GRCm39 Ensembl		GRCm39
GRCm38	7	135,511,456 - 135,528,654 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	7	135,511,466 - 135,528,654 (-)	Ensembl			mm10	GRCm38
MGSCv37	7	142,703,139 - 142,720,337 (-)	NCBI	MGSCv37	MGSCv37	mm9	NCBIm37
MGSCv36	7	135,351,069 - 135,366,985 (-)	NCBI		MGSCv36	mm8
Celera	7	135,333,741 - 135,351,380 (-)	NCBI		Celera
Cytogenetic Map	7	F3	NCBI
cM Map	7	81.27	NCBI

Clrn3
(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_004955477	5,663,488 - 5,676,459 (-)	Ensembl
ChiLan1.0	NW_004955477	5,663,188 - 5,676,430 (-)	NCBI	ChiLan1.0	ChiLan1.0

CLRN3
(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	8	139,755,788 - 139,784,556 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	10	139,760,990 - 139,789,910 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	10	124,464,925 - 124,493,994 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	10	128,714,201 - 128,729,251 (-)	NCBI	PanPan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	10	128,712,990 - 128,729,560 (-)	Ensembl			panPan2	panpan1.1

CLRN3
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	28	36,719,441 - 36,734,519 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	28	36,721,645 - 36,734,623 (-)	Ensembl			canFam3	CanFam3.1
Dog10K_Boxer_Tasha	28	36,775,045 - 36,790,108 (-)	NCBI	Dog10K_Boxer_Tasha	Dog10K_Boxer_Tasha
ROS_Cfam_1.0	28	37,351,065 - 37,366,148 (-)	NCBI	ROS_Cfam_1.0	ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	28	37,353,267 - 37,366,218 (-)	Ensembl				ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	28	36,831,220 - 36,846,275 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	28	36,826,012 - 36,841,046 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	28	37,080,684 - 37,095,782 (-)	NCBI	UU_Cfam_GSD_1.0	UU_Cfam_GSD_1.0

Clrn3
(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_024407213	10,139,776 - 10,152,939 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936486	15,408,689 - 15,421,224 (-)	Ensembl		SpeTri2.0 Ensembl
SpeTri2.0	NW_004936486	15,408,712 - 15,421,224 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

CLRN3
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	14	137,069,384 - 137,089,197 (-)	Ensembl			susScr11	Sscrofa11.1
Sscrofa11.1	14	137,063,671 - 137,089,827 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	14	148,976,961 - 148,991,675 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

CLRN3
(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	9	120,484,216 - 120,499,937 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	9	120,481,843 - 120,499,525 (-)	Ensembl		ChlSab1.1 Ensembl	chlSab2	Vervet-AGM
Vero_WHO_p1.0	NW_023666048	81,873,323 - 81,888,472 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Clrn3
(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_004624737	19,140,907 - 19,156,308 (+)	Ensembl		HetGla_female_1.0 Ensembl	hetGla2	HetGla_female_1.0 Ensembl
HetGla 1.0	NW_004624737	19,140,954 - 19,154,709 (+)	NCBI	HetGla 1.0	HetGla 1.0	hetGla2

Clrn3
(Rattus rattus - black rat)

Black Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Black Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Rrattus_CSIRO_v1	2	66,392,359 - 66,408,548 (+)	NCBI		Rrattus_CSIRO_v1

Variants

Variants in Clrn3
52 total Variants

miRNA Target Status (No longer updated)

Predicted Target Of

	Summary Value
Count of predictions:	128
Count of miRNA genes:	105
Interacting mature miRNAs:	110
Transcripts:	ENSRNOT00000031397
Prediction methods:	Miranda
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 (GRCr8)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
1578778	Pur4	Proteinuria QTL 4	3.3	0.003	urine total protein amount (VT:0000032)	urine total protein excretion rate (CMO:0000756)	1	160111531	262090437	Rat
1354646	Kidm18	Kidney mass QTL 18	5.7		kidney mass (VT:0002707)	calculated kidney weight (CMO:0000160)	1	160573753	266453731	Rat
1354652	Kidm20	Kidney mass QTL 20	4.3		kidney mass (VT:0002707)	calculated kidney weight (CMO:0000160)	1	186658830	266453731	Rat
1354653	Despr9	Despair related QTL 9		0.00019	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	1	177339686	222339686	Rat
2293673	Bss27	Bone structure and strength QTL 27	18.63	0.0001	femur morphology trait (VT:0000559)	femur midshaft cortical cross-sectional area (CMO:0001663)	1	181059071	226059071	Rat
2293677	Bss41	Bone structure and strength QTL 41	9.38	0.0001	lumbar vertebra size trait (VT:0010518)	lumbar vertebra cross-sectional area (CMO:0001689)	1	181059071	226059071	Rat
70160	Bw18	Body weight QTL 18	5.7		body mass (VT:0001259)	body weight (CMO:0000012)	1	153679879	205813246	Rat
1549830	Bss1	Bone structure and strength QTL 1	4.8		femur strength trait (VT:0010010)	femur ultimate force (CMO:0001675)	1	182039247	227039247	Rat
70163	Bw20	Body weight QTL 20	5.1		body mass (VT:0001259)	body weight (CMO:0000012)	1	183564652	228564652	Rat
1354624	Cm35	Cardiac mass QTL35	5.7		heart left ventricle mass (VT:0007031)	calculated heart weight (CMO:0000073)	1	186658830	266453731	Rat
1600397	Edcs4	Endometrial carcinoma susceptibility QTL 4	2.2		uterus morphology trait (VT:0001120)	percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)	1	176288899	270518180	Rat
631838	Niddm36	Non-insulin dependent diabetes mellitus QTL 36		0.01	insulin secretion trait (VT:0003564)	calculated pancreatic islet insulin release measurement (CMO:0001217)	1	193964073	238964073	Rat
1354636	Lmblg1	Limb length QTL 1	6.4		tibia length (VT:0004357)	tibia length (CMO:0000450)	1	160573753	210707719	Rat
1549837	Hcar15	Hepatocarcinoma resistance QTL 15		0.05	liver integrity trait (VT:0010547)	liver tumorous lesion number (CMO:0001068)	1	162548015	270518180	Rat
2293689	Bss47	Bone structure and strength QTL 47	7.25	0.0001	lumbar vertebra size trait (VT:0010518)	lumbar vertebra trabecular cross-sectional area (CMO:0001692)	1	181059071	226059071	Rat
152025235	Bw194	Body weight QTL 194	4.86		body mass (VT:0001259)		1	132966869	252856240	Rat
61341	Bp26	Blood pressure QTL 26			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	139442053	223964440	Rat
1598853	Memor3	Memory QTL 3	4.5		exploratory behavior trait (VT:0010471)	total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)	1	152919152	268496042	Rat
1354634	Kidm12	Kidney mass QTL 12	3.9		kidney mass (VT:0002707)	right kidney wet weight (CMO:0000082)	1	160573753	210707719	Rat
4889428	Stresp24	Stress response QTL 24		0.05	heart pumping trait (VT:2000009)	absolute change in electrocardiographic low frequency R-R spectral component to high frequency R-R spectral component ratio (CMO:0002162)	1	165278545	210278545	Rat
152025232	Bw192	Body weight QTL 192	3.93		body mass (VT:0001259)		1	127329268	206393015	Rat
1578759	Uae30	Urinary albumin excretion QTL 30	3.3	0.003	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	1	160111531	262090437	Rat
61343	Bp28	Blood pressure QTL 28			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	161077990	206077990	Rat
2293693	Bss22	Bone structure and strength QTL 22	33.52	0.0001	femur morphology trait (VT:0000559)	femur cross-sectional area (CMO:0001661)	1	181059071	226059071	Rat
1358902	Bw47	Body weight QTL 47	1.67		body mass (VT:0001259)	body weight (CMO:0000012)	1	99645382	221502378	Rat
2300161	Bmd43	Bone mineral density QTL 43	8.4	0.0001	femur mineral mass (VT:0010011)	volumetric bone mineral density (CMO:0001553)	1	181059071	226059071	Rat
1300145	Rf7	Renal function QTL 7	2.96		urine creatinine amount (VT:0010540)	urine creatinine level (CMO:0000125)	1	194575422	239575422	Rat
61347	Bp197	Blood pressure QTL 197	4.2		arterial blood pressure trait (VT:2000000)	blood pressure measurement (CMO:0000003)	1	168063662	213063662	Rat
8655655	Arrd2	Age-related retinal degeneration QTL 2	7.79		retinal layer morphology trait (VT:0003727)	percentage of study population developing retinopathy during a period of time (CMO:0002453)	1	193400541	238400541	Rat
61348	Bp30	Blood pressure QTL 30	2.4		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	159894717	207261263	Rat
2303622	Vencon6	Ventilatory control QTL 6		0.001	respiration trait (VT:0001943)	respiration rate (CMO:0000289)	1	163992710	208992710	Rat
631214	Bw61	Body weight QTL61	3.4	0.0001	intramuscular adipose amount (VT:0010044)	intramuscular fat area (CMO:0001162)	1	182535316	227535316	Rat
7771612	Cm80	Cardiac mass QTL 80	8.4		heart left ventricle mass (VT:0007031)	heart left ventricle weight (CMO:0000776)	1	146080545	243492863	Rat
731168	Bp154	Blood pressure QTL 154	3.4		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	103779152	223964440	Rat
631205	Bp196	Blood pressure QTL 196	4	0.0001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	98879955	208479939	Rat
2300174	Bmd42	Bone mineral density QTL 42	8.4	0.0001	lumbar vertebra mineral mass (VT:0010511)	bone mineral density (CMO:0001226)	1	181059071	226059071	Rat
737828	Hcas3	Hepatocarcinoma susceptibility QTL 3	4.9		liver integrity trait (VT:0010547)	liver tumorous lesion volume to total liver volume ratio (CMO:0001082)	1	153679879	232414077	Rat
1354661	Bw33	Body weight QTL 33	5.2		body mass (VT:0001259)	body weight (CMO:0000012)	1	160573753	266453731	Rat
1358886	Bp260	Blood pressure QTL 260	3.67		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	160574007	235238518	Rat
2293654	Bss30	Bone structure and strength QTL 30	32.65	0.0001	femur strength trait (VT:0010010)	femur midshaft polar moment of inertia (CMO:0001669)	1	181059071	226059071	Rat
724531	Uae5	Urinary albumin excretion QTL 5	4		urine albumin amount (VT:0002871)	urine albumin level (CMO:0000130)	1	160111426	262090599	Rat
2300187	Bmd41	Bone mineral density QTL 41	8.9	0.0001	femur mineral mass (VT:0010011)	volumetric bone mineral density (CMO:0001553)	1	181059071	226059071	Rat
1359018	Hrtrt20	Heart rate QTL 20	3.08		heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	1	194786607	207590403	Rat
1354580	Scort1	Serum corticosterone level QTL 1	3.4		blood corticosterone amount (VT:0005345)	blood corticosterone level (CMO:0001172)	1	154961463	266453731	Rat
70209	Niddm23	Non-insulin dependent diabetes mellitus QTL 23	2.82		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	162753891	207753891	Rat
1358294	Bw37	Body weight QTL 37	5	0.000011	body mass (VT:0001259)	body weight (CMO:0000012)	1	180739993	225739993	Rat
61378	Bp43	Blood pressure QTL 43	22.6		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	191177449	205813246	Rat
634314	Niddm44	Non-insulin dependent diabetes mellitus QTL 44			blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	51941022	208479811	Rat
724559	Pancm1	Pancreatic morphology QTL 1	7.1		islet of Langerhans morphology trait (VT:0005215)	pancreatic islet damage composite score (CMO:0001156)	1	191190115	223964326	Rat
2312420	Pur17	Proteinuria QTL 17	7.1	0.0001	urine protein amount (VT:0005160)	urine total protein excretion rate (CMO:0000756)	1	172718770	228180370	Rat
10059600	Bp378	Blood pressure QTL 378	3.08	0.05	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	186298393	231298393	Rat
1354591	Cm36	Cardiac mass QTL 36	4.1		heart left ventricle mass (VT:0007031)	calculated heart weight (CMO:0000073)	1	111949780	210707719	Rat
2312558	Glom17	Glomerulus QTL 17	3.9	0.001	kidney glomerulus morphology trait (VT:0005325)	index of glomerular damage (CMO:0001135)	1	175967553	200707874	Rat
10059597	Bp377	Blood pressure QTL 377	3.42	0.025	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	34565911	208798288	Rat
619614	Bp78	Blood pressure QTL 78		0.001	arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	1	178547286	206690557	Rat
2312564	Glom18	Glomerulus QTL 18	2.4	0.003	kidney glomerulus morphology trait (VT:0005325)	index of glomerular damage (CMO:0001135)	1	194786607	262083703	Rat
634321	Hc1	Hypercalciuria QTL 1	2.91		urine calcium amount (VT:0002985)	urine calcium excretion rate (CMO:0000763)	1	188241285	250779312	Rat
724562	Rends1	Renal damage susceptibility QTL 1		0.05	kidney glomerulus integrity trait (VT:0010546)	index of glomerular damage (CMO:0001135)	1	139442053	223964440	Rat
1300168	Bp170	Blood pressure QTL 170	2.76		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	192995199	237995199	Rat
2292222	Bp307	Blood pressure QTL 307	3.06	0.0014	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	186298393	231298393	Rat
2292220	Bp306	Blood pressure QTL 306	3.47	0.00087	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	186298393	231298393	Rat
1354615	Cm32	Cardiac mass QTL 32	5.2		heart left ventricle mass (VT:0007031)	heart left ventricle wet weight (CMO:0000071)	1	111949780	210707719	Rat
1600380	Niddm70	Non-insulin dependent diabetes mellitus QTL 70	3.1	0.0008	blood insulin amount (VT:0001560)	plasma insulin level (CMO:0000342)	1	185979875	230979875	Rat
1354610	Bw34	Body weight QTL 34	4.1		body mass (VT:0001259)	body weight (CMO:0000012)	1	160573753	266453731	Rat
1582206	Kidm33	Kidney mass QTL 33	6.9		kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	1	197807365	233480676	Rat
1354620	Kidm19	Kidney mass QTL 19	4		kidney mass (VT:0002707)	calculated kidney weight (CMO:0000160)	1	160573753	210707719	Rat
8655855	Arrd3	Age-related retinal degeneration QTL 3	3.07		lens clarity trait (VT:0001304)	cataract incidence/prevalence measurement (CMO:0001585)	1	193400541	238400541	Rat
1354618	Kidm15	Kidney mass QTL 15	5		kidney mass (VT:0002707)	left kidney wet weight (CMO:0000083)	1	165707719	210707719	Rat
6903303	Scl34	Serum cholesterol QTL 34	2.5	0.0033	blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	1	173363824	227535316	Rat
152025212	Bw190	Body weight QTL 190	5.7		body mass (VT:0001259)		1	132966869	206393015	Rat
2293083	Iddm25	Insulin dependent diabetes mellitus QTL 25	4.18		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	191260175	236260175	Rat
1354606	Bp246	Blood pressure QTL 246	3.6		arterial blood pressure trait (VT:2000000)	pulse pressure (CMO:0000292)	1	111949780	228180370	Rat
738032	Hcas5	Hepatocarcinoma susceptibility QTL 5	3.12		liver integrity trait (VT:0010547)	liver tumorous lesion number (CMO:0001068)	1	185857683	270518180	Rat
2325727	Pia41	Pristane induced arthritis QTL 41			joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	1	188241285	233241285	Rat
1354602	Bw35	Body weight QTL 35	12.2		body mass (VT:0001259)	body weight (CMO:0000012)	1	160573753	210707719	Rat
631670	Iddm10	Insulin dependent diabetes mellitus QTL 10	1.9		blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	1	183564652	205813246	Rat

Markers in Region

RH132740

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	1	190,319,118 - 190,319,335 (+)	MAPPER	mRatBN7.2
Rnor_6.0	1	207,750,721 - 207,750,937	NCBI	Rnor6.0
Rnor_5.0	1	214,683,543 - 214,683,759	UniSTS	Rnor5.0
RGSC_v3.4	1	195,132,774 - 195,132,990	UniSTS	RGSC3.4
Celera	1	188,034,395 - 188,034,611	UniSTS
RH 3.4 Map	1	1431.8	UniSTS
Cytogenetic Map	1	q41	UniSTS

Expression

RNA-SEQ Expression

Click on a value in the shaded box below the category label to view a detailed expression data table for that system.

Download All Expressed Objects for this Gene

alimentary part of gastrointestinal system	appendage	ectoderm	endocrine system	endoderm	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	mesenchyme	mesoderm	nervous system	renal system	reproductive system	respiratory system	sensory system	visual system
16	1	18	19	22	10	11	10	3	117	15	13	75	33	12	4	4

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001014026	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	BC078942	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473953	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000001	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSRNOT00000031397 ⟹ ENSRNOP00000035233

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	1	199,748,864 - 199,764,486 (-)	Ensembl
mRatBN7.2 Ensembl	1	190,319,026 - 190,334,648 (-)	Ensembl
Rnor_6.0 Ensembl	1	207,750,628 - 207,766,250 (-)	Ensembl

Ensembl Acc Id:

ENSRNOT00000080506 ⟹ ENSRNOP00000070737

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	1	207,750,223 - 207,811,008 (-)	Ensembl

RefSeq Acc Id:

NM_001014026 ⟹ NP_001014048

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	1	199,748,863 - 199,764,486 (-)	NCBI
mRatBN7.2	1	190,319,025 - 190,334,648 (-)	NCBI
Rnor_6.0	1	207,750,627 - 207,766,250 (-)	NCBI
Rnor_5.0	1	214,683,449 - 214,699,072 (-)	NCBI
RGSC_v3.4	1	195,132,680 - 195,148,303 (-)	RGD
Celera	1	188,034,301 - 188,049,855 (-)	RGD

Sequence:

show sequence

CGCACGTCTTACATTCGCAACTAAGTGCTAGACTTCCTTTCTAAACACTGGATCCCAAATGATA
AGGCCCCCAAATATTCTAAGATTGCTGTTGTCTTATCCTGGGGAGCTTTCTTCCTGAGAAAATG
CCAACCACACAGAAAACGTTGATGTTCCTGTCTGGCTTTCTCACAAGCCTGGGCTCAGTTGTTG
TCATCTGTTCTATTCTGGGGACACAGGCATGGATCACCAGCAAGATTTTCTTCACAGACACTAT
CTCCAATGGTACCATTGCTATCACCTATGGGCTTTTTCGTGGTACGAGTAGTCAAGATTTGAAC
GAAGGCCTTCAAGAGCTGGACAAAAACTTTGAAGTTTTAGGGATATTGAGCAATTCTTCCCAGA
AGTCCCTGCATGTGGTGGTCATCATACTCCTGATCCTGAGTCTGGCAGCTTCCTTGCTGAGCTC
AATGTTCACCTTCTACAACAGCATCAGCAACCCTTACCAGACGTTCCTGGGACCTATGGGAGTC
TACACCTGGAATGGACTCAGTGCATCCTTTGTGTTTCTGACCATGGTTCTGTTTGTGGGGAATG
TCGACTCCAACCATCTCTCCGAAAAGCTGTCCCAGACACTTTATCCAGATGCCATTAACAAGAA
AACAACCCACACTTATGGATACTCATTTTGGCTCATCCTGCTTGTCATCCTACTGAATATTGTC
ACCGTGGTCATCATCATTTTCTATCAGAAGGCCCGATACCATCAGAAGCAGGAGCAGAGGAAGC
CAGTGGAGTACGCTCCGAGGGATGGCATTTTATTCTGAGATCTGTCTCAAAGCACATTCGCACT
GTCTCTGCCAAGCTGGCTAGCTCCTCTGGACACGGCGTGGCAGAGCAACTGTCAGGTGCCATAA
CTCTGGAACCATGACACTGTGTGCTTCCTATAGATGGTGCTTGTACCTTTCTCCATGGACCTTT
CTCCCTGAGAAGCGTTTTCTCCCAAGATCAGGAAAATGAGTGGGAAAGGCTGTGGTCTAGAGTA
CTCTGAAAGAAAGTGGTCTATGGCCTGCAGGCCCTTCTCATTTGACCTTGCTATTCATACTATA
AAGGCCTGTGGGGATTTTTTTGCCTTTCCTGTGACTAGATAATGAATTGTGGCCCCTATGACCT
TGTCCTCTGGATTGATTAGGCATTTTGCTTCATGGTAAGTATGAAGACTTTTAGGTAGAGAAGC
ACTCTGAACCTCTTTTTCCAGTCAGAAGTTAGATGCAGAAGGATAAAGGATGAGATGATCTCTT
GTTCTGGTCCCCTGGTGGCTGTCCTGGCTCCCAGGCTTAGCTCCTTTAATGAGGGCTAGATGCT
TATAGAACTTGGGACTCGGGAAGCCCCACACAAACAGGCTAGAGGTAAAATATGGTCTCTTCCA
GTAAATTGGAAGTCAGCAAAATAACAAAGGCACCAAAATTTATTCTACGTGTTTTTTCCAGTAT
GACATTTCCTTTAAAAAATCTAATAGAGAACCCTTCAGCCTTGACTATCCTGTAGGTTGCTATG
GTGAAAACTGACAGGTCTGAAAAATGACCCCTTTCATGTGTTGATGGAGTCTTAAAGCAGTAAC
TTTGTGACAAGTGGTGGATCTTATGAACCTCAAAGATAAGTGGCCTTCAACACTCAGACTTAGA
GATGTGAGCTGGGTTCCCATGATGTCAGTGGAAGCGTGCTGGGTCCTCAACCTTGTGGTATTTA
TGTTTACTACTGGGTAGATGAGACAGACATTTAATAAGCTCTTACTTGACTCCAGTTGAAACAG
TTGCTTAGAGTTGGGGGTCATCCCTCCATTGTAGAGTACTAAAAAGCCTAGCATGTAACAGGTC
CTGGGTTCCATCTCTACCTCTGTAAAAATGAAACAACATCTAATGACAACATCGTGCTTGTGTT
TTGAAAGGATGGATTTCTATCATGCTCTACCTTGAAGATTTACTAATTCAAGGTTACTCTTACC
TACTAAATTATTAAAAGTTTACTGTACTTTAAAAAAAAAAAAAAAAAAAAAAAAAAA

hide sequence

Protein Sequences


Protein RefSeqs	NP_001014048	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAH78942	(Get FASTA)	NCBI Sequence Viewer
	EDM11792	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000035233
	ENSRNOP00000035233.3
GenBank Protein	Q6AYR5	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:

NP_001014048 ⟸ NM_001014026

- UniProtKB:

Q6AYR5 (UniProtKB/Swiss-Prot), A6HX61 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MPTTQKTLMFLSGFLTSLGSVVVICSILGTQAWITSKIFFTDTISNGTIAITYGLFRGTSSQDL
NEGLQELDKNFEVLGILSNSSQKSLHVVVIILLILSLAASLLSSMFTFYNSISNPYQTFLGPMG
VYTWNGLSASFVFLTMVLFVGNVDSNHLSEKLSQTLYPDAINKKTTHTYGYSFWLILLVILLNI
VTVVIIIFYQKARYHQKQEQRKPVEYAPRDGILF

hide sequence

Ensembl Acc Id:

ENSRNOP00000035233 ⟸ ENSRNOT00000031397

Ensembl Acc Id:

ENSRNOP00000070737 ⟸ ENSRNOT00000080506

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-Q6AYR5-F1-model_v2	AlphaFold	Q6AYR5	1-226	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:1305043	AgrOrtholog
BioCyc Gene	G2FUF-57154	BioCyc
Ensembl Genes	ENSRNOG00000028288	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000031397	ENTREZGENE
	ENSRNOT00000031397.6	UniProtKB/Swiss-Prot
Gene3D-CATH	1.20.140.150	UniProtKB/Swiss-Prot
IMAGE_CLONE	IMAGE:7109328	IMAGE-MGC_LOAD
InterPro	Clarin	UniProtKB/Swiss-Prot
KEGG Report	rno:309082	UniProtKB/Swiss-Prot
MGC_CLONE	MGC:93776	IMAGE-MGC_LOAD
NCBI Gene	309082	ENTREZGENE
PANTHER	CLARIN-3	UniProtKB/Swiss-Prot
	PTHR31548	UniProtKB/Swiss-Prot
PhenoGen	Clrn3	PhenoGen
RatGTEx	ENSRNOG00000028288	RatGTEx
UniProt	A6HX61	ENTREZGENE, UniProtKB/TrEMBL
	CLRN3_RAT	UniProtKB/Swiss-Prot, ENTREZGENE

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2008-03-04	Clrn3	clarin 3	Tmem12	transmembrane protein 12	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2006-03-30	Tmem12	transmembrane protein 12	RGD1305043	similar to Expressed sequence AI649392	Symbol and Name updated	1299863	APPROVED
2005-12-06	RGD1305043	similar to Expressed sequence AI649392	RGD1305043_predicted	similar to Expressed sequence AI649392 (predicted)	Symbol and Name updated	1559027	APPROVED
2005-01-20	RGD1305043_predicted	similar to Expressed sequence AI649392 (predicted)	LOC309082_predicted		Symbol and Name status set to approved	1331353	APPROVED
2005-01-12	LOC309082_predicted	similar to Expressed sequence AI649392 (predicted)			Symbol and Name status set to provisional	70820	PROVISIONAL

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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