Rcc1l (RCC1 like) - Rat Genome Database

Name: Rcc1l
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: Rcc1l (RCC1 like) Rattus norvegicus

Analyze

Symbol:

Rcc1l

Name:

RCC1 like

RGD ID:

1307558

Description:

Predicted to have guanyl-nucleotide exchange factor activity and rRNA binding activity. Predicted to be involved in mitochondrial membrane fusion and positive regulation of mitochondrial translation. Predicted to localize to mitochondrial inner membrane. Human ortholog(s) of this gene implicated in Williams-Beuren syndrome. Orthologous to human RCC1L (RCC1 like); INTERACTS WITH 2,4-dinitrotoluene; 4-amino-2,6-dinitrotoluene; bisphenol A.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

LOC360796; Wbscr16; Williams-Beuren syndrome chromosome region 16; Williams-Beuren syndrome chromosome region 16 homolog; Williams-Beuren syndrome chromosome region 16 homolog (human)

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):	RCC1L (RCC1 like)	HGNC	Ensembl, HomoloGene, Inparanoid, NCBI, OMA, Panther, PhylomeDB
Mus musculus (house mouse):	Rcc1l (reculator of chromosome condensation 1 like)	HGNC	NCBI, OMA, HomoloGene, Inparanoid, Panther, PhylomeDB, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Rcc1l (RCC1 like)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	RCC1L (RCC1 like)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	RCC1L (RCC1 like)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Rcc1l (RCC1 like)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	RCC1L (RCC1 like)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (African green monkey):	RCC1L (RCC1 like)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Rcc1l (RCC1 like)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	RCC1L (RCC1 like)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Mus musculus (house mouse):	Rcc1l (reculator of chromosome condensation 1 like)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Caenorhabditis elegans (roundworm):	W09G3.7	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Drosophila melanogaster (fruit fly):	CG3862	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Danio rerio (zebrafish):	rcc1l	Alliance	DIOPT (PhylomeDB\|TreeFam)

Latest Assembly:

Rnor_6.0 - RGSC Genome Assembly v6.0

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	12	22,543,125 - 22,574,042 (+)	NCBI
Rnor_6.0 Ensembl	12	25,561,777 - 25,592,342 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	12	25,561,871 - 25,592,337 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	12	27,569,296 - 27,599,911 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	12	23,697,692 - 23,727,908 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	12	23,560,907 - 23,591,124 (+)	NCBI
Celera	12	24,303,024 - 24,333,330 (+)	NCBI		Celera
Cytogenetic Map	12	q12	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

pleomorphic xanthoastrocytoma (ISO)

Williams-Beuren syndrome (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(-)-demecolcine (ISO)

1,2-dimethylhydrazine (ISO)

17alpha-ethynylestradiol (ISO)

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

2,4-dinitrotoluene (EXP)

2-hydroxypropanoic acid (ISO)

4,4'-diaminodiphenylmethane (ISO)

4-amino-2,6-dinitrotoluene (EXP)

aflatoxin B1 (ISO)

AM-251 (ISO)

amiodarone (ISO)

benzo[a]pyrene (ISO)

benzo[a]pyrene diol epoxide I (ISO)

bis(2-ethylhexyl) phthalate (ISO)

bisphenol A (EXP)

copper(II) sulfate (ISO)

crocidolite asbestos (ISO)

dibutyl phthalate (ISO)

dioxygen (ISO)

flutamide (EXP)

hydrogen peroxide (ISO)

lead(0) (ISO)

lead(2+) (ISO)

paracetamol (ISO)

rac-lactic acid (ISO)

tetrachloromethane (ISO)

theophylline (ISO)

trichostatin A (ISO)

tungsten (ISO)

vincristine (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

mitochondrial membrane fusion (ISO)

positive regulation of mitochondrial translation (ISO)

regulation of catalytic activity (IEA)

Cellular Component

mitochondrial inner membrane (ISO)

mitochondrial membrane (ISO)

mitochondrion (ISO)

Molecular Function

guanyl-nucleotide exchange factor activity (ISO)

protein binding (ISO)

rRNA binding (ISO)

References

References - curated


1.	Merla G, etal., Hum Genet. 2002 May;110(5):429-38. Epub 2002 Mar 28.
2.	RGD automated import pipeline for gene-chemical interactions

Additional References at PubMed

PMID:18614015	PMID:22658674	PMID:22681889	PMID:27667664	PMID:28608466	PMID:28746876

Genomics

Comparative Map Data

Rcc1l
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	12	22,543,125 - 22,574,042 (+)	NCBI
Rnor_6.0 Ensembl	12	25,561,777 - 25,592,342 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	12	25,561,871 - 25,592,337 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	12	27,569,296 - 27,599,911 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	12	23,697,692 - 23,727,908 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	12	23,560,907 - 23,591,124 (+)	NCBI
Celera	12	24,303,024 - 24,333,330 (+)	NCBI		Celera
Cytogenetic Map	12	q12	NCBI

RCC1L
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	7	75,027,122 - 75,074,228 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	7	75,027,119 - 75,073,802 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	7	74,441,223 - 74,489,638 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
GRCh37	7	74,441,223 - 74,489,717 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	7	74,094,219 - 74,127,635 (-)	NCBI	NCBI36		hg18	NCBI36
Build 34	7	73,885,876 - 73,934,288	NCBI
Celera	7	68,097,529 - 68,130,598 (-)	NCBI
Cytogenetic Map	7	q11.23	NCBI
HuRef	7	70,110,451 - 70,155,525 (-)	NCBI		HuRef
CHM1_1	7	74,586,535 - 74,633,297 (-)	NCBI		CHM1_1
CRA_TCAGchr7v2	7	73,774,287 - 73,822,781 (-)	NCBI

Rcc1l
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	5	134,176,897 - 134,207,963 (-)	NCBI	GRCm39		mm39
GRCm38	5	134,148,058 - 134,179,124 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	5	134,148,054 - 134,176,774 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	5	134,623,928 - 134,652,637 (-)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	5	134,432,703 - 134,461,394 (-)	NCBI			mm8
Celera	5	131,150,658 - 131,179,371 (-)	NCBI		Celera
Cytogenetic Map	5	G2	NCBI

Rcc1l
(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_004955456	13,286,459 - 13,300,182 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955456	13,285,753 - 13,300,244 (-)	NCBI	ChiLan1.0	ChiLan1.0

RCC1L
(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	82,016,477 - 82,049,524 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	7	82,016,477 - 82,065,189 (+)	Ensembl	panpan1.1		panPan2

RCC1L
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	6	5,605,320 - 5,632,152 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1

Rcc1l
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
SpeTri2.0	NW_004936543	3,672,249 - 3,686,238 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

RCC1L
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	3	11,915,583 - 11,948,721 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	3	11,915,540 - 11,948,711 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	3	11,634,977 - 11,668,502 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

RCC1L
(Chlorocebus sabaeus - African green monkey)

Vervet Assembly	Chr	Position (strand)	Source	Genome Browsers
Vervet Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	28	8,215,324 - 8,250,560 (-)	NCBI
ChlSab1.1 Ensembl	28	8,215,318 - 8,250,523 (-)	Ensembl

Rcc1l
(Heterocephalus glaber - naked mole-rat)

Molerat Assembly	Chr	Position (strand)	Source	Genome Browsers
Molerat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla 1.0	NW_004624740	13,365,571 - 13,381,197 (-)	NCBI

QTLs in Region (Rnor_6.0)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
1581516	Cm56	Cardiac mass QTL 56	4.2	0.05	heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	12	1	30749723	Rat
1598855	Bp294	Blood pressure QTL 294	3.5		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	12	1	36919844	Rat
7387292	Kidm42	Kidney mass QTL 42	3.03	0.0004	kidney mass (VT:0002707)	left kidney wet weight (CMO:0000083)	12	1	38334225	Rat
9590086	Insglur6	Insulin/glucose ratio QTL 6	18.97	0.001	blood insulin amount (VT:0001560)	calculated plasma insulin level (CMO:0002170)	12	150810	45150810	Rat
9590147	Scort7	Serum corticosterone level QTL 7	13.61	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	12	150810	45150810	Rat
7411545	Bw128	Body weight QTL 128	5.2	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	12	150810	45150810	Rat
7411586	Foco5	Food consumption QTL 5	5.4	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	12	150810	45150810	Rat
7411660	Foco28	Food consumption QTL 28	10.9	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	12	150810	45150810	Rat
7411595	Foco9	Food consumption QTL 9	4	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	12	150810	45150810	Rat
8694179	Bw150	Body weight QTL 150	2.9	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	12	150810	45150810	Rat
2303575	Insul14	Insulin level QTL 14	4		blood insulin amount (VT:0001560)	blood insulin level (CMO:0000349)	12	492578	45492578	Rat
737979	Pia22	Pristane induced arthritis QTL 22	53.1		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	12	2475687	47475687	Rat
634351	Apr5	Acute phase response QTL 5	6.7		blood interleukin-6 amount (VT:0008595)	plasma interleukin-6 level (CMO:0001927)	12	2513442	47513442	Rat
2302042	Pia38	Pristane induced arthritis QTL 38	3.5	0.001	blood immunoglobulin amount (VT:0002460)	serum immunoglobulin G1 level (CMO:0002115)	12	2513442	47513442	Rat
634350	Apr4	Acute phase response QTL 4	6		orosomucoid 1 amount (VT:0010541)	plasma orosomucoid 1 level (CMO:0001467)	12	4210051	49210051	Rat
1302792	Scl21	Serum cholesterol level QTL 21	3.8	0.0011	blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	12	8954593	27911196	Rat
7411547	Bw129	Body weight QTL 129		0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	6	9223626	52716770	Rat
7411588	Foco6	Food consumption QTL 6		0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	12	9223626	52716770	Rat
7411597	Foco10	Food consumption QTL 10		0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	12	9223626	52716770	Rat
7411641	Foco19	Food consumption QTL 19	27.7	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	12	9223626	52716770	Rat
8552918	Pigfal7	Plasma insulin-like growth factor 1 level QTL 7			blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	12	9223626	52716770	Rat
8552964	Pigfal17	Plasma insulin-like growth factor 1 level QTL 17	3.5		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	12	9223626	52716770	Rat
8552912	Pigfal6	Plasma insulin-like growth factor 1 level QTL 6	5		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	12	9223630	52716770	Rat
10059594	Kidm46	Kidney mass QTL 46	3.79	0.025	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	12	9789834	52716770	Rat
2293086	Iddm30	Insulin dependent diabetes mellitus QTL 30	3.82		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	12	10175889	31975590	Rat
61331	Eau2	Experimental allergic uveoretinitis QTL 2		0.0005	uvea integrity trait (VT:0010551)	experimental autoimmune uveitis score (CMO:0001504)	12	10256890	31723732	Rat
1300157	Rf21	Renal function QTL 21	4.4		renal blood flow trait (VT:2000006)	absolute change in renal blood flow rate (CMO:0001168)	12	11764995	37522089	Rat
1331786	Kidm11	Kidney mass QTL 11	3.571		kidney mass (VT:0002707)	right kidney wet weight (CMO:0000082)	12	13127211	27285590	Rat
1331755	Bp219	Blood pressure QTL 219	3.041		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	12	13127211	31723688	Rat
1331761	Bp218	Blood pressure QTL 218	2.973		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	12	13127211	50320041	Rat
61404	Bw120	Body weight QTL 120	5.1		body mass (VT:0001259)	body mass index (BMI) (CMO:0000105)	12	14419775	52716770	Rat
1549829	Scl48	Serum cholesterol level QTL 48	5		blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	12	15021986	52716770	Rat
61416	Pia4	Pristane induced arthritis QTL 4	8.4		joint integrity trait (VT:0010548)	arthritic paw count (CMO:0001460)	12	15714609	35964508	Rat
61421	Cia12	Collagen induced arthritis QTL 12	4.6		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	12	15714609	41291738	Rat
2300186	Bmd59	Bone mineral density QTL 59	7.1	0.0001	lumbar vertebra mineral mass (VT:0010511)	volumetric bone mineral density (CMO:0001553)	12	15908900	52716770	Rat
2293699	Bss49	Bone structure and strength QTL 49	5.61	0.0001	lumbar vertebra size trait (VT:0010518)	lumbar vertebra trabecular cross-sectional area (CMO:0001692)	12	15908900	52716770	Rat
631543	Bp83	Blood pressure QTL 83	5.8		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	12	17185580	44098244	Rat
2293684	Bmd26	Bone mineral density QTL 26	4.4	0.0002	femur mineral mass (VT:0010011)	total volumetric bone mineral density (CMO:0001728)	12	17960865	38409001	Rat
1641928	Alcrsp5	Alcohol response QTL 5			response to alcohol trait (VT:0010489)	duration of loss of righting reflex (CMO:0002289)	12	18342477	52716770	Rat
2303569	Gluco44	Glucose level QTL 44	2		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	12	18342477	52716770	Rat
2302060	Pia37	Pristane induced arthritis QTL 37	6.1	0.001	blood immunoglobulin amount (VT:0002460)	serum immunoglobulin G1 level (CMO:0002115)	12	18729043	52716770	Rat
1549902	Bp269	Blood pressure QTL 269			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	12	18752593	52716770	Rat
1549912	Bp268	Blood pressure QTL 268			arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	10	18752593	52716770	Rat
2306789	Ean6	Experimental allergic neuritis QTL 6	4.9		nervous system integrity trait (VT:0010566)	experimental autoimmune neuritis severity score (CMO:0001528)	12	22650702	27190240	Rat
737822	Alc10	Alcohol consumption QTL 10	2.2		consumption behavior trait (VT:0002069)	ethanol drink intake rate (CMO:0001407)	12	22650702	45946937	Rat
5684888	Pia42	Pristane induced arthritis QTL 42			joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	12	22650702	48598906	Rat
61324	Eae5	Experimental allergic encephalomyelitis QTL 5	14		nervous system integrity trait (VT:0010566)	percentage of study population developing relapsing-remitting experimental autoimmune encephalomyelitis during a period of time (CMO:0001402)	12	22650702	52716770	Rat
1298081	Cia25	Collagen induced arthritis QTL 25	4.7		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	12	22650721	41291738	Rat
70213	Niddm27	Non-insulin dependent diabetes mellitus QTL 27	3.72		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	12	22876297	43799153	Rat
631521	Pia12	Pristane induced arthritis QTL 12	8.9		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	12	23241246	26710128	Rat
631560	Apr1	Acute phase response QTL 1	6.1		orosomucoid 1 amount (VT:0010541)	plasma orosomucoid 1 level (CMO:0001467)	12	24906590	52716770	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	103
Count of miRNA genes:	84
Interacting mature miRNAs:	93
Transcripts:	ENSRNOT00000002032
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.

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	3	35	42	30	12	30	6	8	65	35	39	9	6
Low		8	15	11	7	11	2	3	9		2	2	2
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001108332	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006249183	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039089584	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039089585	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039089586	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XR_005491647	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	CH473973	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000227	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000002032 ⟹ ENSRNOP00000002032

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	12	25,561,777 - 25,592,342 (+)	Ensembl

RefSeq Acc Id:

NM_001108332 ⟹ NP_001101802

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	12	22,543,734 - 22,574,036 (+)	NCBI
Rnor_6.0	12	25,562,029 - 25,592,332 (+)	NCBI
Rnor_5.0	12	27,569,296 - 27,599,911 (+)	NCBI
RGSC_v3.4	12	23,697,692 - 23,727,908 (+)	RGD
Celera	12	24,303,024 - 24,333,330 (+)	RGD

Sequence:

show sequence

AAAGGTGAGGCAAGATGGCGGCGCCCATAAACGGTTGAGGCGTGAAGCGAAGGATGCTGGCGGT
GGCCCGGGCTCTGCTGGAGCGGCGGCTGAGCTGGCCGGTACCGGCTCGCGAGCACTGGAGACCG
GCCGGCCGTTCACGGAGCCGGCGAGAAGCAGCTGAGGCCGAGGCGGACGCTCCGGTGTTCCAGT
ACGTGGGCGAGCGCGCGGCTCGCGCCGATCGCGTGTTCGTATGGGGCTTCAGCTTCTCCGGGGC
TCTCGGAGTGCCCAGCTTCGTGGTGCCGTCCTCGGGGCCCGGACCGCGCGCCGGCCTGAGGCCC
CGACGTAGGATCCAGCCGGTACCCTACCGTCTGGAGCTGGACCATAAGATTTCCTCTGCTGCCT
GTGGCTATGGATTCACATTGCTGTCCTCGAAAACCAAGGATGTTACGAAAGTCTGGGGCATGGG
ACTCAACAAAGATTCCCAGCTTGGATTTCACAGGAGCCGGAAGGATAAAACCAGGGGCTATGAG
TATGTCCTGGAGCCCTCGCCTGTCCCGCTGCCCCTGGACAGACCTCAGGAGACAAAGGTGTTGC
AGGTGTCCTGTGGTCGAGCACACTCCCTTGTCCTGACAGACAGAGAAGGTGTCTTCAGCATGGG
GAACAATGCCCACGGGCAGTGTGGACGGAAGGTGGTGGAGGACGAAGTATACAGTGAGAGTCAC
AAAGTGCACAGGATGCAGGACTTCGAGGGACAGGTGGTCCAGGTTGTCTGCGGTCAGGACCACA
GCCTGTTCCTCACAGACAAAGGTGAAGTCTATTCTTGTGGATGGGGTGCCGATGGACAGACAGG
CCTGGGTCACTACAACATCACCAGCACACCCAGCAAGCTGGGCGGAGACCTTGCCGGGGTGACT
GTTGTCCAGGTTGCTACCTACGGTGACTGCTGCTTGGCTTTGTCGGCCGATGGAGGTGTCTTTG
GCTGGGGAAATTCTGAGTACCTGCAGCTGGCCTCGGTCACAGACTCCACACAGGTGAATGTCCC
TCGGTGCCTGCCTTTCTCCGGAGTAGGCAAGGTGAAGCAGGTGGCTTGTGGTGGCACAGGCTGT
GCTATACTGAATGAAGAAGGACATGTTTTCGTCTGGGGCTATGGAATTCTTGGGAAAGGACCAA
ACCTCTCAGAAACGGCGCTTCCAGAAATGATCCCACCTACACTCTTTGGTTTGACAGAGTTCAA
CCCTGAAGTCAAGGTTTCCCAGATCCGATGTGGGCTTAGCCACTTTGCCGCACTCACCAACAAG
GGTGAGCTGTTTGTGTGGGGCAAGAACATCCGAGGGTGCCTTGGCATTGGACGCCTGGAAGACC
AGTACTTCCCATGGAGGGTGACGATGCCAGGTGAGCCTGTGGACGTGGCTTGTGGAGTGGATCA
CATGGTGACTCTAGCCAAGTCCTTCATCTGAACCTCTCTCTGGGCCTATCTCCTGCTGGCCCCC
GCCTGTAGCTATAAGGACAGCTATGGCTTGGCAGAAACCAGCAGAGTTTCTGAGGGTACAGGGA
GAGAGATCCAGGGCCTCTGTGGAGCAGGGTGCCTGCTCTGTGTCCTCAGTGGGAATGTTGTACG
AGGAGTTGTGGACAAGGCCCTACACCCGCTGAGGCTCCTGCCTGCTGAACTCGGCTCAGGATGG
CTACTGTTGGCTTGGCATGTTCCTGAGGAGTACCAGGGCATGAAGACCTTGGGTGCCCAGGCAG
ATTCCTTTTCCAAGTAACACATGATAGCATCTGGGGATGTGTCTAGTCTGAGACACTATTTTTA
GGGAAAGTTCACTGCTCATGACACATTTGATAATAAAGTTTAGAGACATGACAGGGCACTCAGA
AGAACCTGTAGTCTCCTGTCACAAGAGGATAAACTTGGGCCTCAGCTCAGCAAGAGAGCCAGCT
GACTTCAGTGAGGGCCTCTCTGATCAGCTGTCACCCCAGAGGTTCCCCAGAACACAGTCCAGGA
GCCCAGAATGCCTTGGCTTGAACTCTTCATGGAGTGGCCAGTGGGAGCCGTGCAGTATCCCAGC
TTTGGAACTTCCTCACTCCCTGGCTCTGAGCAGCCCAGAAGCCCCTGAAGAAAGAAGTTGAAGG
CCAAATGCTTGTGGGCTGAGGGCTGTGGAATCTTGGCTGAAGGGCCGGCCTCAGAAACTGGGAA
AATACTTGTTTTTAAAAAGCTTGTCGCTTCCTTTCAGAACAGTGTTTGGAAGGTCTTTTGGAAT
AAAGTCTATTTTCTGCCTTTTT

hide sequence

RefSeq Acc Id:

XM_006249183 ⟹ XP_006249245

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	12	22,543,125 - 22,574,042 (+)	NCBI
Rnor_6.0	12	25,561,871 - 25,592,337 (+)	NCBI
Rnor_5.0	12	27,569,296 - 27,599,911 (+)	NCBI

Sequence:

show sequence

CAAGCGCTCTACCACTGAGCTAAATCCCCAACCCCAAGCCTTTACTTTCATGTAGTAGCAATCA
TCTGCCAATAGTAAACATGGCTGCATTTCCCTTAGCGCTTCGCCTTCTGTCAGTAGTAAGCATG
GCCGTATCTACTTCCGCTAGGCCAGGGGTCAAAGGTGAGGCAAGATGGCGGCGCCCATAAACGG
TTGAGGCGTGAAGCGAAGGATGCTGGCGGTGGCCCGGGCTCTGCTGGAGCGGCGGCTGAGCTGG
CCGGTACCGGCTCGCGAGCACTGGAGACCGGCCGGCCGTTCACGGAGCCGGCGAGAAGCAGCTG
AGGCCGAGGCGGACGCTCCGGTGTTCCAGTACGTGGGCGAGCGCGCGGCTCGCGCCGATCGCGT
GTTCGTATGGGGCTTCAGCTTCTCCGGGGCTCTCGGAGTGCCCAGCTTCGTGGTGCCGTCCTCG
GGGCCCGGACCGCGCGCCGGCCTGAGGCCCCGACGTAGGATCCAGCCGGTACCCTACCGTCTGG
AGCTGGACCATAAGATTTCCTCTGCTGCCTGTGGCTATGGATTCACATTGCTGTCCTCGAAAAC
CAAGGATGTTACGAAAGTCTGGGGCATGGGACTCAACAAAGATTCCCAGCTTGGATTTCACAGG
AGCCGGAAGGATAAAACCAGGGGCTATGAGTATGTCCTGGAGCCCTCGCCTGTCCCGCTGCCCC
TGGACAGACCTCAGGAGACAAAGGTGTTGCAGGTGTCCTGTGGTCGAGCACACTCCCTTGTCCT
GACAGACAGAGAAGGTGTCTTCAGCATGGGGAACAATGCCCACGGGCAGTGTGGACGGAAGGTG
GTGGAGGACGAAGTATACAGTGAGAGTCACAAAGTGCACAGGATGCAGGACTTCGAGGGACAGG
TGGTCCAGGTTGTCTGCGGTCAGGACCACAGCCTGTTCCTCACAGACAAAGGTGAAGTCTATTC
TTGTGGATGGGGTGCCGATGGACAGACAGGCCTGGGTCACTACAACATCACCAGCACACCCAGC
AAGCTGGGCGGAGACCTTGCCGGGGTGACTGTTGTCCAGGTTGCTACCTACGGTGACTGCTGCT
TGGCTTTGTCGGCCGATGGAGGTGTCTTTGGCTGGGGAAATTCTGAGTACCTGCAGCTGGCCTC
GGTCACAGACTCCACACAGGTGAATGTCCCTCGGTGCCTGCCTTTCTCCGGAGTAGGCAAGGTG
AAGCAGGTGGCTTGTGGTGGCACAGGCTGTGCTATACTGAATGACAAGGGTGAGCTGTTTGTGT
GGGGCAAGAACATCCGAGGGTGCCTTGGCATTGGACGCCTGGAAGACCAGTACTTCCCATGGAG
GGTGACGATGCCAGGTGAGCCTGTGGACGTGGCTTGTGGAGTGGATCACATGGTGACTCTAGCC
AAGTCCTTCATCTGAACCTCTCTCTGGGCCTATCTCCTGCTGGCCCCCGCCTGTAGCTATAAGG
ACAGCTATGGCTTGGCAGAAACCAGCAGAGTTTCTGAGGGTACAGGGAGAGAGATCCAGGGCCT
CTGTGGAGCAGGGTGCCTGCTCTGTGTCCTCAGTGGGAATGTTGTACGAGGAGTTGTGGACAAG
GCCCTACACCCGCTGAGGCTCCTGCCTGCTGAACTCGGCTCAGGATGGCTACTGTTGGCTTGGC
ATGTTCCTGAGGAGTACCAGGGCATGAAGACCTTGGGTGCCCAGGCAGATTCCTTTTCCAAGTA
ACACATGATAGCATCTGGGGATGTGTCTAGTCTGAGACACTATTTTTAGGGAAAGTTCACTGCT
CATGACACATTTGATAATAAAGTTTAGAGACATGACAGGGCACTCAGAAGAACCTGTAGTCTCC
TGTCACAAGAGGATAAACTTGGGCCTCAGCTCAGCAAGAGAGCCAGCTGACTTCAGTGAGGGCC
TCTCTGATCAGCTGTCACCCCAGAGGTTCCCCAGAACACAGTCCAGGAGCCCAGAATGCCTTGG
CTTGAACTCTTCATGGAGTGGCCAGTGGGAGCCGTGCAGTATCCCAGCTTTGGAACTTCCTCAC
TCCCTGGCTCTGAGCAGCCCAGAAGCCCCTGAAGAAAGAAGTTGAAGGCCAAATGCTTGTGGGC
TGAGGGCTGTGGAATCTTGGCTGAAGGGCCGGCCTCAGAAACTGGGAAAATACTTGTTTTTAAA
AAGCTTGTCGCTTCCTTTCAGAACAGTGTTTGGAAGGTCTTTTGGAATAAAGTCTATTTTCTGC
CTTTTTAAAGA

hide sequence

RefSeq Acc Id:

XM_039089584 ⟹ XP_038945512

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	12	22,543,962 - 22,574,042 (+)	NCBI

RefSeq Acc Id:

XM_039089585 ⟹ XP_038945513

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	12	22,543,962 - 22,574,042 (+)	NCBI

RefSeq Acc Id:

XM_039089586 ⟹ XP_038945514

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	12	22,543,960 - 22,574,042 (+)	NCBI

RefSeq Acc Id:

XR_005491647

RefSeq Status:

Type:

NON-CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	12	22,543,126 - 22,574,042 (+)	NCBI

Protein Sequences


Protein RefSeqs	NP_001101802	(Get FASTA)	NCBI Sequence Viewer
	XP_006249245	(Get FASTA)	NCBI Sequence Viewer
	XP_038945512	(Get FASTA)	NCBI Sequence Viewer
	XP_038945513	(Get FASTA)	NCBI Sequence Viewer
	XP_038945514	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	EDM13446	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_001101802 ⟸ NM_001108332

- UniProtKB:

D4AE90 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MLAVARALLERRLSWPVPAREHWRPAGRSRSRREAAEAEADAPVFQYVGERAARADRVFVWGFS
FSGALGVPSFVVPSSGPGPRAGLRPRRRIQPVPYRLELDHKISSAACGYGFTLLSSKTKDVTKV
WGMGLNKDSQLGFHRSRKDKTRGYEYVLEPSPVPLPLDRPQETKVLQVSCGRAHSLVLTDREGV
FSMGNNAHGQCGRKVVEDEVYSESHKVHRMQDFEGQVVQVVCGQDHSLFLTDKGEVYSCGWGAD
GQTGLGHYNITSTPSKLGGDLAGVTVVQVATYGDCCLALSADGGVFGWGNSEYLQLASVTDSTQ
VNVPRCLPFSGVGKVKQVACGGTGCAILNEEGHVFVWGYGILGKGPNLSETALPEMIPPTLFGL
TEFNPEVKVSQIRCGLSHFAALTNKGELFVWGKNIRGCLGIGRLEDQYFPWRVTMPGEPVDVAC
GVDHMVTLAKSFI

hide sequence

RefSeq Acc Id:

XP_006249245 ⟸ XM_006249183

- Peptide Label:

isoform X1

- Sequence:

show sequence

MLAVARALLERRLSWPVPAREHWRPAGRSRSRREAAEAEADAPVFQYVGERAARADRVFVWGFS
FSGALGVPSFVVPSSGPGPRAGLRPRRRIQPVPYRLELDHKISSAACGYGFTLLSSKTKDVTKV
WGMGLNKDSQLGFHRSRKDKTRGYEYVLEPSPVPLPLDRPQETKVLQVSCGRAHSLVLTDREGV
FSMGNNAHGQCGRKVVEDEVYSESHKVHRMQDFEGQVVQVVCGQDHSLFLTDKGEVYSCGWGAD
GQTGLGHYNITSTPSKLGGDLAGVTVVQVATYGDCCLALSADGGVFGWGNSEYLQLASVTDSTQ
VNVPRCLPFSGVGKVKQVACGGTGCAILNDKGELFVWGKNIRGCLGIGRLEDQYFPWRVTMPGE
PVDVACGVDHMVTLAKSFI

hide sequence

RefSeq Acc Id:

ENSRNOP00000002032 ⟸ ENSRNOT00000002032

RefSeq Acc Id:	XP_038945514 ⟸ XM_039089586
- Peptide Label:	isoform X4

RefSeq Acc Id:	XP_038945513 ⟸ XM_039089585
- Peptide Label:	isoform X3

RefSeq Acc Id:	XP_038945512 ⟸ XM_039089584
- Peptide Label:	isoform X2

Transcriptome

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

Strain Variation

Strain Sequence Variants (Rnor 6.0)

ACI/EurMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

ACI/EurMcwi (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

ACI/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

BBDP/Wor (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

BN/SsN (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Buf/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

COP/CrCrl (MCW & UW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob) University of Wisconsin (Dr. James Shull)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Charles River Laboratories
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)

F344/NCrl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

F344/NRrrc (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

FHH/EurMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

FHH/EurMcwi (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

FHL/EurMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

FHL/EurMcwi (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

GH/OmrMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

GK/Ox (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LE/Stm (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LEW/Crl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LEW/NCrlBR (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LH/MavRrrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LL/MavRrrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LN/MavRrrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

M520/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

MHS/Gib (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

MNS/Gib (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

MR/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

SBH/Ygl (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	SBH/Ygl sequenced by MCW

SBH/Ygl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SBN/Ygl (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	SBN/Ygl sequenced by MCW

SBN/Ygl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SHR/NHsd (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SHRSP/Gcrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SR/JrHsd (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Harlan Laboratories
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

SR/JrHsd (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SS/Jr (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SS/JrHsdMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

SS/JrHsdMcwi (RGD)

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CSV

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WAG/Rij (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WKY/Gcrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WKY/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

WKY/NCrl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WKY/NHsd (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WN/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1307558	AgrOrtholog
Ensembl Genes	ENSRNOG00000001483	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000002032	ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000002032	ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH	2.130.10.30	UniProtKB/TrEMBL
InterPro	Reg_chr_condens	UniProtKB/TrEMBL
	Reg_csome_cond/b-lactamase_inh	UniProtKB/TrEMBL
KEGG Report	rno:360796	UniProtKB/TrEMBL
NCBI Gene	360796	ENTREZGENE
Pfam	RCC1	UniProtKB/TrEMBL
PhenoGen	Rcc1l	PhenoGen
PRINTS	RCCNDNSATION	UniProtKB/TrEMBL
PROSITE	RCC1_3	UniProtKB/TrEMBL
Superfamily-SCOP	RCC1/BLIP-II	UniProtKB/TrEMBL
UniProt	D4AE90	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2016-05-18	Rcc1l	RCC1 like	Wbscr16	Williams-Beuren syndrome chromosome region 16	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2013-02-04	Wbscr16	Williams-Beuren syndrome chromosome region 16	Wbscr16	Williams-Beuren syndrome chromosome region 16 homolog (human)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-04-30	Wbscr16	Williams-Beuren syndrome chromosome region 16 homolog (human)	Wbscr16_predicted	Williams-Beuren syndrome chromosome region 16 homolog (human) (predicted)	'predicted' is removed	2292626	APPROVED
2006-03-30	Wbscr16_predicted	Williams-Beuren syndrome chromosome region 16 homolog (human) (predicted)		Williams-Beuren syndrome chromosome region 16 (predicted)	Name updated	1299863	APPROVED
2005-01-12	Wbscr16_predicted	Williams-Beuren syndrome chromosome region 16 (predicted)			Symbol and Name status set to approved	70820	APPROVED

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)

Imported Disease Annotations - ClinVar