Pax2 (paired box 2) - Rat Genome Database

Name: Pax2
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

	Submit Data \| Help \| Video Tutorials \| News \| Publications \| Download \| REST API \| Citing RGD \| Contact
	Search RGD Grant Resources Citing RGD About Us Contact Us Genes QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data OntoMate (Literature Search) JBrowse (Genome Browser) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) RatMine GViewer (Genome Viewer) Overgo Probe Designer ACP Haplotyper Genome Scanner VCMap Aging & Age-Related Disease Cancer Cardiovascular Disease COVID-19 Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease Find Models new Genetic Models Autism Models PhenoMiner (Quantitative Phenotypes) Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes GERRC (Gene Editing Rat Resource Center) Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive Pathways Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Poster Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
	Advanced Search (OLGA)

Gene: Pax2 (paired box 2) Rattus norvegicus

Analyze

Symbol:

Pax2

Name:

paired box 2

RGD ID:

1305568

Description:

Predicted to have several functions, including C2H2 zinc finger domain binding activity; DNA-binding transcription factor activity, RNA polymerase II-specific; and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in several processes, including aging; cellular response to epidermal growth factor stimulus; and positive regulation of cell population proliferation. Localizes to lysosome and nucleus. Biomarker of nephroblastoma. Human ortholog(s) of this gene implicated in focal segmental glomerulosclerosis 7 and renal coloboma syndrome. Orthologous to human PAX2 (paired box 2); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; atrazine; bis(2-ethylhexyl) phthalate.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

LOC293992; paired box gene 2; paired box homeotic gene 2; paired box protein 2; paired box protein Pax-2; Pax-2

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):	PAX2 (paired box 2)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoMCL, Panther, Treefam
Mus musculus (house mouse):	Pax2 (paired box 2)	HGNC	EggNOG, OrthoMCL, NCBI, OMA, HomoloGene, Inparanoid, Panther, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Pax2 (paired box 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	PAX2 (paired box 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	PAX2 (paired box 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Pax2 (paired box 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	PAX2 (paired box 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (African green monkey):	LOC103216393 (paired box protein Pax-2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Pax2 (paired box 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Other homologs ²
Homo sapiens (human):	PAX5 (paired box 5)	HGNC	OrthoDB
Alliance orthologs ³
Homo sapiens (human):	PAX2 (paired box 2)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|TreeFam)
Mus musculus (house mouse):	Pax2 (paired box 2)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER)
Danio rerio (zebrafish):	pax2a (paired box 2a)	Alliance	DIOPT (Ensembl Compara\|OMA\|TreeFam)
Danio rerio (zebrafish):	pax5 (paired box 5)	Alliance	DIOPT (Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER)
Caenorhabditis elegans (roundworm):	egl-38	Alliance	DIOPT (OrthoFinder\|OrthoInspector\|PANTHER\|TreeFam)
Drosophila melanogaster (fruit fly):	sv	Alliance	DIOPT (Ensembl Compara\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|TreeFam)
Caenorhabditis elegans (roundworm):	pax-2	Alliance	DIOPT (OrthoFinder\|OrthoInspector\|PANTHER\|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	1	243,616,509 - 243,697,454 (+)	NCBI
Rnor_6.0 Ensembl	1	264,504,591 - 264,583,329 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	1	264,493,579 - 264,585,073 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	1	271,936,269 - 272,027,514 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	1	249,804,055 - 249,895,306 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	1	250,026,899 - 250,155,758 (+)	NCBI
Celera	1	239,428,164 - 239,506,765 (+)	NCBI		Celera
Cytogenetic Map	1	q54	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

CAKUT (ISO)

cystic kidney disease (ISO)

Diabetic Nephropathies (IEP)

end stage renal disease (ISO)

endometriosis (ISO)

epilepsy (ISO)

Female Urogenital Diseases (ISO)

focal segmental glomerulosclerosis (ISO)

focal segmental glomerulosclerosis 7 (ISO)

fundus dystrophy (ISO)

genetic disease (ISO)

Kidney Reperfusion Injury (IEP)

maturity-onset diabetes of the young type 5 (ISO)

nephroblastoma (IEP,ISO)

nephrotic syndrome (ISO)

renal coloboma syndrome (ISO)

visual epilepsy (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dichloroethane (ISO)

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

3,4-methylenedioxymethamphetamine (ISO)

4,4'-sulfonyldiphenol (ISO)

aflatoxin B2 (ISO)

atrazine (EXP)

benzo[a]pyrene (ISO)

benzo[b]fluoranthene (ISO)

benzo[e]pyrene (ISO)

Benzo[k]fluoranthene (ISO)

bis(2-ethylhexyl) phthalate (EXP)

bisphenol A (EXP,ISO)

bisphenol F (ISO)

C60 fullerene (EXP)

cadmium atom (ISO)

carbon nanotube (ISO)

choline (ISO)

dorsomorphin (ISO)

entinostat (ISO)

ethanol (EXP)

folic acid (ISO)

graphene oxide (ISO)

L-methionine (ISO)

lead(0) (ISO)

lead(2+) (ISO)

lipopolysaccharide (ISO)

methapyrilene (ISO)

N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal (ISO)

panobinostat (ISO)

SB 431542 (ISO)

serpentine asbestos (ISO)

sodium fluoride (ISO)

tamoxifen (ISO)

thioacetamide (EXP)

titanium dioxide (ISO)

trichloroethene (ISO)

trichostatin A (ISO)

triptonide (ISO)

valproic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

aging (IEP)

anatomical structure development (IBA)

brain morphogenesis (ISO,ISS)

branching involved in ureteric bud morphogenesis (ISO,ISS)

camera-type eye development (ISO,ISS)

cell fate determination (ISO,ISS)

cellular response to epidermal growth factor stimulus (IEP)

cellular response to glucose stimulus (ISO,ISS)

cellular response to hydrogen peroxide (ISO,ISS)

cellular response to mechanical stimulus (ISO)

cellular response to retinoic acid (ISO,ISS)

central nervous system development (ISO)

cochlea development (ISO,ISS)

cochlea morphogenesis (ISO,ISS)

glial cell differentiation (ISO,ISS)

inner ear morphogenesis (ISO,ISS)

kidney development (ISO)

mesenchymal to epithelial transition (ISO,ISS)

mesenchymal to epithelial transition involved in metanephros morphogenesis (ISO,ISS)

mesodermal cell fate specification (ISO,ISS)

mesonephric duct development (ISO)

mesonephric tubule development (ISO)

mesonephric tubule formation (ISO)

mesonephros development (ISO,ISS)

metanephric collecting duct development (ISO,ISS)

metanephric distal convoluted tubule development (ISO,ISS)

metanephric epithelium development (ISO)

metanephric mesenchymal cell differentiation (ISO,ISS)

metanephric mesenchyme development (ISO,ISS)

metanephric nephron tubule formation (ISO,ISS)

metanephros development (ISO)

negative regulation of apoptotic process (ISO,ISS)

negative regulation of apoptotic process involved in metanephric collecting duct development (ISO,ISS)

negative regulation of apoptotic process involved in metanephric nephron tubule development (ISO,ISS)

negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (ISO,ISS)

negative regulation of mesenchymal cell apoptotic process involved in metanephric nephron morphogenesis (ISO,ISS)

negative regulation of mesenchymal cell apoptotic process involved in metanephros development (ISO,ISS)

negative regulation of programmed cell death (ISO,ISS)

negative regulation of reactive oxygen species metabolic process (ISO,ISS)

negative regulation of transcription by RNA polymerase II (ISO)

negative regulation of transcription, DNA-templated (ISO,ISS)

nephric duct formation (ISO,ISS)

neural tube closure (ISO,ISS)

optic chiasma development (ISO,ISS)

optic cup morphogenesis involved in camera-type eye development (ISO,ISS)

optic nerve development (ISO,ISS)

optic nerve morphogenesis (ISO,ISS)

optic nerve structural organization (ISO,ISS)

pancreas development (ISO)

paramesonephric duct development (ISO)

positive regulation of branching involved in ureteric bud morphogenesis (ISO,ISS)

positive regulation of cell population proliferation (IMP)

positive regulation of epithelial cell proliferation (ISO)

positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis (ISO,ISS)

positive regulation of metanephric DCT cell differentiation (ISO,ISS)

positive regulation of metanephric glomerulus development (ISO,ISS)

positive regulation of optic nerve formation (ISO,ISS)

positive regulation of transcription by RNA polymerase II (ISO,ISS)

positive regulation of transcription, DNA-templated (ISO,ISS)

pronephric field specification (ISO,ISS)

pronephros development (ISO,ISS)

protein kinase B signaling (ISO,ISS)

reactive oxygen species metabolic process (ISO,ISS)

regulation of apoptotic process (ISO)

regulation of metanephric nephron tubule epithelial cell differentiation (ISO,ISS)

regulation of metanephros size (ISO,ISS)

regulation of programmed cell death (ISO)

regulation of transcription by RNA polymerase II (IBA)

response to nutrient levels (IEP)

retinal pigment epithelium development (ISO,ISS)

stem cell differentiation (ISO,ISS)

ureter development (ISO,ISS)

ureter maturation (ISO,ISS)

ureter morphogenesis (ISO)

ureteric bud development (ISO)

urogenital system development (ISO,ISS)

vestibulocochlear nerve formation (ISO,ISS)

Cellular Component

centriolar satellite (ISO,ISS)

lysosome (IDA)

microtubule organizing center (ISO,ISS)

nucleoplasm (IEA,ISO)

nucleus (IDA,ISO,ISS)

protein-containing complex (ISO,ISS)

protein-DNA complex (ISO,ISS)

Molecular Function

C2H2 zinc finger domain binding (ISO)

cis-regulatory region sequence-specific DNA binding (ISO,ISS)

DNA binding (ISO,ISS)

DNA-binding transcription factor activity (ISO)

DNA-binding transcription factor activity, RNA polymerase II-specific (IBA,ISO)

protein binding (ISO)

RNA polymerase II cis-regulatory region sequence-specific DNA binding (IBA,ISO)

sequence-specific double-stranded DNA binding (ISO)

transcription cis-regulatory region binding (ISO,ISS)

References

References - curated


1.	Abdel-Hakeem AK, etal., Am J Obstet Gynecol. 2008 Sep;199(3):252.e1-7. Epub 2008 Jul 17.
2.	Franch HA, etal., J Biol Chem. 2001 Jun 1;276(22):19126-31. Epub 2001 Mar 21.
3.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
4.	GOA data from the GO Consortium
5.	Li CM, etal., Am J Pathol. 2002 Jun;160(6):2181-90.
6.	Maeshima A, etal., J Am Soc Nephrol 2002 Dec;13(12):2850-9.
7.	Mansour H, etal., Aging Cell. 2008 Aug;7(4):526-40. Epub 2008 Jun 28.
8.	MGD data from the GO Consortium
9.	OMIM Disease Annotation Pipeline
10.	Online Mendelian Inheritance in Man, OMIM (TM).
11.	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
12.	RGD automated import pipeline for gene-chemical interactions
13.	Sharma PM, etal., Proc Natl Acad Sci U S A. 1994 Oct 11;91(21):9931-5.
14.	Sooparb S, etal., Kidney Int. 2004 Jun;65(6):2135-44.
15.	Zhang SL, etal., Kidney Int. 2004 Dec;66(6):2181-92.

Additional References at PubMed

PMID:1337742	PMID:1723950	PMID:7720589	PMID:7856737	PMID:8413205	PMID:8575306	PMID:8951055	PMID:9178767	PMID:10322633	PMID:10536059	PMID:10980123	PMID:11731455
PMID:11940591	PMID:12200151	PMID:12435636	PMID:12756174	PMID:14695376	PMID:15153556	PMID:15242798	PMID:15905411	PMID:16018995	PMID:16319112	PMID:16368682	PMID:16672320
PMID:16735463	PMID:16916509	PMID:17047028	PMID:17164400	PMID:17166926	PMID:17300925	PMID:17314325	PMID:17357786	PMID:17513325	PMID:17538188	PMID:17785448	PMID:17881463
PMID:18000879	PMID:18083586	PMID:18607644	PMID:19037705	PMID:19048125	PMID:19118900	PMID:20171952	PMID:20486844	PMID:20727173	PMID:21731775	PMID:21778682	PMID:23107969
PMID:23503776	PMID:24471428	PMID:24676634	PMID:24710423	PMID:27939388	PMID:29280536	PMID:30117015

Genomics

Comparative Map Data

Pax2
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	1	243,616,509 - 243,697,454 (+)	NCBI
Rnor_6.0 Ensembl	1	264,504,591 - 264,583,329 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	1	264,493,579 - 264,585,073 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	1	271,936,269 - 272,027,514 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	1	249,804,055 - 249,895,306 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	1	250,026,899 - 250,155,758 (+)	NCBI
Celera	1	239,428,164 - 239,506,765 (+)	NCBI		Celera
Cytogenetic Map	1	q54	NCBI

PAX2
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	10	100,735,603 - 100,829,944 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38.p13 Ensembl	10	100,735,603 - 100,829,941 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38.p13 Ensembl	10	100,735,396 - 100,829,944 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	10	100,735,396 - 100,829,944 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	10	102,495,153 - 102,589,701 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	10	102,495,458 - 102,579,688 (+)	NCBI	NCBI36		hg18	NCBI36
Build 34	10	102,495,321 - 102,579,687	NCBI
Celera	10	96,243,249 - 96,327,456 (+)	NCBI
Cytogenetic Map	10	q24.31	NCBI
HuRef	10	96,133,870 - 96,218,089 (+)	NCBI		HuRef
CHM1_1	10	102,779,745 - 102,873,990 (+)	NCBI		CHM1_1

Pax2
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	19	44,735,040 - 44,826,708 (+)	NCBI	GRCm39		mm39
GRCm39 Ensembl	19	44,744,484 - 44,826,310 (+)	Ensembl
GRCm38	19	44,746,601 - 44,838,269 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	19	44,756,045 - 44,837,871 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	19	44,831,884 - 44,910,517 (+)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	19	44,810,705 - 44,889,338 (+)	NCBI			mm8
Celera	19	45,528,146 - 45,605,640 (+)	NCBI		Celera
Cytogenetic Map	19	C3	NCBI
cM Map	19	38.09	NCBI

Pax2
(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_004955485	9,350,087 - 9,430,607 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955485	9,351,913 - 9,430,607 (-)	NCBI	ChiLan1.0	ChiLan1.0

PAX2
(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	10	100,822,676 - 100,904,065 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	10	100,822,676 - 100,904,028 (+)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	10	97,344,978 - 97,429,086 (+)	NCBI	Mhudiblu_PPA_v0		panPan3

PAX2
(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	13,442,894 - 13,519,853 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	28	13,442,893 - 13,532,094 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	28	13,606,001 - 13,692,205 (+)	NCBI
ROS_Cfam_1.0	28	13,904,432 - 13,990,703 (+)	NCBI
UMICH_Zoey_3.1	28	13,450,612 - 13,536,833 (+)	NCBI
UNSW_CanFamBas_1.0	28	13,492,258 - 13,578,015 (+)	NCBI
UU_Cfam_GSD_1.0	28	13,623,521 - 13,709,771 (+)	NCBI

Pax2
(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	33,215,941 - 33,325,282 (-)	NCBI
SpeTri2.0	NW_004936600	4,850,594 - 4,939,010 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

PAX2
(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	111,834,168 - 111,914,304 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	14	111,822,334 - 111,914,950 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	14	121,481,577 - 121,574,679 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

LOC103216393
(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	9	93,763,975 - 93,847,180 (+)	NCBI

Pax2
(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_004624831	375,851 - 453,968 (+)	NCBI

Position Markers

RH80285

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	1	264,583,201 - 264,583,418	NCBI	Rnor6.0
Rnor_5.0	1	272,025,642 - 272,025,859	UniSTS	Rnor5.0
RGSC_v3.4	1	249,895,178 - 249,895,395	UniSTS	RGSC3.4
Celera	1	239,506,637 - 239,506,854	UniSTS
Cytogenetic Map	1	q54	UniSTS

PMC19453P1

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	1	264,537,908 - 264,537,995	NCBI	Rnor6.0
Rnor_5.0	1	271,980,418 - 271,980,505	UniSTS	Rnor5.0
RGSC_v3.4	1	249,849,452 - 249,849,539	UniSTS	RGSC3.4
Celera	1	239,461,455 - 239,461,542	UniSTS
Cytogenetic Map	1	q54	UniSTS

D11Bir2

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	3	1,549,052 - 1,549,189	NCBI	Rnor6.0
Rnor_6.0	1	264,508,928 - 264,509,065	NCBI	Rnor6.0
Rnor_5.0	3	1,541,880 - 1,542,017	UniSTS	Rnor5.0
Rnor_5.0	1	271,951,604 - 271,951,741	UniSTS	Rnor5.0
RGSC_v3.4	3	2,693,184 - 2,693,321	UniSTS	RGSC3.4
RGSC_v3.4	1	249,808,393 - 249,808,530	UniSTS	RGSC3.4
Celera	3	2,044,635 - 2,044,772	UniSTS
Celera	1	239,432,502 - 239,432,639	UniSTS
Cytogenetic Map	3	p13	UniSTS
Cytogenetic Map	1	q54	UniSTS

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
2292216	Bw80	Body weight QTL 80	3.23	0.0019	body mass (VT:0001259)	body weight (CMO:0000012)	1	233490105	264802994	Rat
70211	Niddm24	Non-insulin dependent diabetes mellitus QTL 24	3.79		blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	1	236795785	281795785	Rat
631215	Stl8	Serum triglyceride level QTL 8	9.27	0.0001	blood triglyceride amount (VT:0002644)	serum triglyceride level (CMO:0000360)	1	245529606	282763074	Rat
2302040	Pia35	Pristane induced arthritis QTL 35	3.8	0.001	blood immunoglobulin amount (VT:0002460)	serum immunoglobulin G1 level (CMO:0002115)	1	236265430	281265430	Rat
2302378	Insul11	Insulin level QTL 11	3.25		blood insulin amount (VT:0001560)	serum insulin level (CMO:0000358)	1	156446196	274977688	Rat
724531	Uae5	Urinary albumin excretion QTL 5	4		urine albumin amount (VT:0002871)	urine albumin level (CMO:0000130)	1	161321152	273792054	Rat
724533	Rf51	Renal function QTL 51	5.3	0.0002	kidney plasma flow trait (VT:0005524)	renal plasma flow (CMO:0001914)	1	238830534	278228767	Rat
724538	Kidm1	Kidney mass QTL 1	3.2		kidney mass (VT:0002707)	calculated kidney weight (CMO:0000160)	1	233663100	273792054	Rat
724552	Glom2	Glomerulus QTL 2	3.3	0.0001	kidney glomerulus morphology trait (VT:0005325)	count of superficial glomeruli directly contacting the kidney surface (CMO:0001001)	1	243272341	282763074	Rat
734767	Niddm57	Non-insulin dependent diabetes mellitus QTL 57			body mass (VT:0001259)	body weight (CMO:0000012)	1	244401175	282365384	Rat
734768	Niddm59	Non-insulin dependent diabetes mellitus QTL 59			body mass (VT:0001259)	body weight (CMO:0000012)	1	235850810	280850810	Rat
734769	Niddm58	Non-insulin dependent diabetes mellitus QTL 58			body mass (VT:0001259)	body weight (CMO:0000012)	1	244992467	282365384	Rat
631669	Iddm9	Insulin dependent diabetes mellitus QTL 9	2.8	0.039	blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	1	252955158	280632620	Rat
631690	Scl5	Serum cholesterol level QTL 5	2.1		blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	1	258132568	282763074	Rat
1354580	Scort1	Serum corticosterone level QTL 1	3.4		blood corticosterone amount (VT:0005345)	blood corticosterone level (CMO:0001172)	1	167394665	278228889	Rat
1581544	Rf52	Renal function QTL 52		0.05	total urine protein amount (VT:0000032)	urine protein excretion rate to body weight ratio (CMO:0001099)	1	252948438	281795785	Rat
731175	Uae20	Urinary albumin excretion QTL 20	3.5	0.0018	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	1	241482188	281795785	Rat
738032	Hcas5	Hepatocarcinoma susceptibility QTL 5	3.12		liver integrity trait (VT:0010547)	liver tumorous lesion number (CMO:0001068)	1	191825895	279986079	Rat
631536	Lnnr2	Liver neoplastic nodule remodeling QTL 2	2.9	0.0005	liver integrity trait (VT:0010547)	liver remodeling tumorous lesion number to liver total tumorous lesion number ratio (CMO:0001705)	1	255728828	282763074	Rat
1598821	Rf55	Renal function QTL 55	6.3		renal blood flow trait (VT:2000006)	ratio of change in renal blood flow to change in renal perfusion pressure (CMO:0001239)	1	238824734	279986079	Rat
2300175	Bmd40	Bone mineral density QTL 40	15.4	0.0001	femur mineral mass (VT:0010011)	bone mineral density (CMO:0001226)	1	221901238	266901238	Rat
2293655	Bss36	Bone structure and strength QTL 36	10.66	0.0001	femur strength trait (VT:0010010)	femur ultimate force (CMO:0001675)	1	221901238	266901238	Rat
2293674	Bss39	Bone structure and strength QTL 39	7.1	0.0001	femur strength trait (VT:0010010)	femur total energy absorbed before break (CMO:0001677)	1	221901238	266901238	Rat
2293694	Bss38	Bone structure and strength QTL 38	7.05	0.0001	femur strength trait (VT:0010010)	femur stiffness (CMO:0001674)	1	221901238	266901238	Rat
2293700	Bmd27	Bone mineral density QTL 27	6.6	0.0001	femur mineral mass (VT:0010011)	trabecular volumetric bone mineral density (CMO:0001729)	1	244401175	264636028	Rat
2293701	Bmd34	Bone mineral density QTL 34	8.3	0.0001	femur strength trait (VT:0010010)	femoral neck ultimate force (CMO:0001703)	1	244401175	264636028	Rat
631836	Stl31	Serum triglyceride level QTL 31	4.64	0.00000487	blood triglyceride amount (VT:0002644)	plasma triglyceride level (CMO:0000548)	1	259295704	282763074	Rat
631837	Niddm35	Non-insulin dependent diabetes mellitus QTL 35		0.01	blood insulin amount (VT:0001560)	serum insulin level (CMO:0000358)	1	258709726	281795785	Rat
631843	Bw116	Body weight QTL 116	4.1	0.016	abdominal adipose amount (VT:1000220)	abdominal fat pad weight (CMO:0000088)	1	244401175	282365384	Rat
634313	Niddm43	Non-insulin dependent diabetes mellitus QTL 43			blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	217054291	281795785	Rat
1357399	Bw45	Body weight QTL 45	3.05		body mass (VT:0001259)	body mass index (BMI) (CMO:0000105)	1	225689973	270689973	Rat
1357404	Bw42	Body weight QTL 42	4.49	0.0001	body mass (VT:0001259)	body weight (CMO:0000012)	1	225689973	270689973	Rat
1600363	Hc6	Hypercalciuria QTL 6	2.7		urine calcium amount (VT:0002985)	urine calcium excretion rate (CMO:0000763)	1	195598053	265002735	Rat
1600388	Niddm67	Non-insulin dependent diabetes mellitus QTL 67	5.84	0.000004	blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	1	213476630	278978026	Rat
1600392	Bw123	Body weight QTL 123		0.001	body mass (VT:0001259)	body weight (CMO:0000012)	1	244087148	282763074	Rat
1600395	Niddm69	Non-insulin dependent diabetes mellitus QTL 69	4.14	0.0002	blood insulin amount (VT:0001560)	plasma insulin level (CMO:0000342)	1	213476630	278978026	Rat
1600396	Niddm68	Non-insulin dependent diabetes mellitus QTL 68	4.97	0.0003	blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	1	213476630	278978026	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	226706329	271706329	Rat
1578759	Uae30	Urinary albumin excretion QTL 30	3.3	0.003	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	1	161321256	273791893	Rat
1578763	Kidm29	Kidney mass QTL 29	3.3	0.0001	kidney mass (VT:0002707)	both kidneys wet weight (CMO:0000085)	1	196395041	282763074	Rat
1578778	Pur4	Proteinuria QTL 4	3.3	0.003	total urine protein amount (VT:0000032)	urine total protein excretion rate (CMO:0000756)	1	161321256	273791893	Rat
1300108	Rf8	Renal function QTL 8	3.75		renal blood flow trait (VT:2000006)	absolute change in renal vascular resistance (CMO:0001900)	1	249206242	281795785	Rat
1354610	Bw34	Body weight QTL 34	4.1		body mass (VT:0001259)	body weight (CMO:0000012)	1	161784169	278228889	Rat
1354624	Cm35	Cardiac mass QTL35	5.7		heart left ventricle mass (VT:0007031)	calculated heart weight (CMO:0000073)	1	192639698	278228889	Rat
1354646	Kidm18	Kidney mass QTL 18	5.7		kidney mass (VT:0002707)	calculated kidney weight (CMO:0000160)	1	161784169	278228889	Rat
1354652	Kidm20	Kidney mass QTL 20	4.3		kidney mass (VT:0002707)	calculated kidney weight (CMO:0000160)	1	192639698	278228889	Rat
1354661	Bw33	Body weight QTL 33	5.2		body mass (VT:0001259)	body weight (CMO:0000012)	1	161784169	278228889	Rat
1549910	Bw54	Body weight QTL 54		0.05	body mass (VT:0001259)	body weight (CMO:0000012)	1	236795785	281795785	Rat
2316896	Gluco57	Glucose level QTL 57	7.2		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	249607907	266793958	Rat
1549837	Hcar15	Hepatocarcinoma resistance QTL 15		0.05	liver integrity trait (VT:0010547)	liver tumorous lesion number (CMO:0001068)	1	163796316	282763074	Rat
1358191	Ept10	Estrogen-induced pituitary tumorigenesis QTL 10	3.8		pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	1	210360774	264802828	Rat
2292220	Bp306	Blood pressure QTL 306	3.47	0.00087	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	174905700	264802994	Rat
1358890	Bp259	Blood pressure QTL 259	3.06		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	230420627	282645769	Rat
1358898	Bp255	Blood pressure QTL 255	3.6		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	208517798	266948272	Rat
61327	Eae7	Experimental allergic encephalomyelitis QTL 7	5.6		body mass (VT:0001259)	change in body weight (CMO:0002045)	1	236265430	281265430	Rat
61400	Niddm1	Non-insulin dependent diabetes mellitus QTL 1	11		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	238830408	266793958	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	202571665	264802994	Rat
7394701	Uae46	Urinary albumin excretion QTL 46	3.6	0.0056	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	1	221901238	266901238	Rat
7387289	Uae45	Urinary albumin excretion QTL 45	2.86	0.0021	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	1	244148899	282763074	Rat
8655855	Arrd3	Age-related retinal degeneration QTL 3	3.07		lens clarity trait (VT:0001304)	cataract incidence/prevalence measurement (CMO:0001585)	1	202571665	264802994	Rat
10053715	Scort24	Serum corticosterone level QTL 24	2.13	0.0088	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	1	242302911	282763074	Rat
10059587	Bw173	Body weight QTL 173	3.23	0.025	body mass (VT:0001259)	body weight (CMO:0000012)	1	222492538	267492538	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	70
Count of miRNA genes:	65
Interacting mature miRNAs:	69
Transcripts:	ENSRNOT00000050076
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

	endocrine system	exocrine system	hemolymphoid system	hepatobiliary system	musculoskeletal system	nervous system	renal system	reproductive system
High
Medium						5	29	10
Low						34	6	22
Below cutoff	9	7	2	7	1	21		3

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001106361	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006231443	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_008760404	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039109033	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039109034	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039109038	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039109041	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039109046	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039109049	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC128836	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473986	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000054	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000050076 ⟹ ENSRNOP00000040130

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	1	264,504,591 - 264,583,329 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000085811 ⟹ ENSRNOP00000070907

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	1	264,507,985 - 264,538,070 (+)	Ensembl

RefSeq Acc Id:

NM_001106361 ⟹ NP_001099831

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	1	243,616,745 - 243,695,321 (+)	NCBI
Rnor_6.0	1	264,504,591 - 264,583,329 (+)	NCBI
Rnor_5.0	1	271,936,269 - 272,027,514 (+)	NCBI
RGSC_v3.4	1	249,804,055 - 249,895,306 (+)	RGD
Celera	1	239,428,164 - 239,506,765 (+)	RGD

Sequence:

show sequence

CGGCCGCGCTGCTCCCGCTCCTCTGCCTCCCCATGGATATGCACTGCAAAGCAGACCCCTTCTC
CGCGATGCACCGGCACGGGGGTGTGAACCAGCTCGGGGGGGTGTTTGTGAACGGCCGGCCCCTA
CCCGACGTGGTGAGGCAGCGCATCGTGGAGCTGGCCCACCAGGGTGTGCGGCCCTGTGACATCT
CCCGGCAGCTGCGGGTCAGCCATGGCTGTGTCAGCAAAATCCTGGGCAGGTACTACGAGACTGG
CAGCATCAAGCCCGGAGTGATTGGTGGCTCCAAGCCCAAGGTGGCAACGCCCAAAGTGGTGGAC
AAGATTGCTGAATACAAGCGACAGAACCCGACTATGTTCGCCTGGGAGATCCGGGACAGGCTGC
TAGCTGAGGGCATCTGCGACAATGATACAGTTCCCAGCGTCTCATCCATCAACAGGATCATCCG
GACCAAAGTTCAGCAGCCTTTCCACCCAACGCCGGATGGGGCAGGGACAGGAGTGACTGCCCCT
GGCCACACCATCGTTCCCAGCACGGCCTCCCCTCCTGTTTCCAGCGCCTCTAACGACCCAGTGG
GATCCTACTCCATCAACGGGATCCTGGGGATTCCTCGCTCCAACGGTGAGAAGAGGAAACGAGA
GGAAGTCGAGGTATACACTGATCCTGCCCACATTAGAGGAGGTGGAGGTTTGCATCTGGTCTGG
ACTTTAAGAGATGTGTCCGAGGGCTCTGTCCCTAATGGAGACTCCCAGAGTGGTGTGGACAGTT
TGCGGAAGCACCTGCGAGCCGACACCTTCACCCAGCAGCAGCTGGAAGCTTTGGATCGAGTCTT
TGAGCGTCCTTCCTATCCCGATGTCTTCCAAGCATCAGAGCACATCAAATCAGAACAGGGGAAT
GAATACTCTCTCCCAGCCCTGACCCCTGGGCTTGATGAAGTCAAGTCCAGTCTATCTGCATCTA
CCAACCCTGAGCTGGGCAGCAATGTGTCAGGCACACAGACGTACCCCGTCGTGACCGGTCGTGA
TATGGCGAGCACCACTCTACCTGGTTACCCCCCTCATGTGCCCCCCACTGGCCAGGGAAGCTAC
CCTACCTCCACCCTGGCAGGAATGGTGCCTGGGAGCGAGTTCTCAGGCAACCCATACAGCCATC
CCCAGTACACCGCCTACAATGAGGCTTGGAGATTCAGCAACCCCGCCTTACTAAGTTCCCCTTA
TTATTATAGTGCCGCCCCCCGGGGCTCCGCCCCTGCCGCTGCTGCCGCTGCCTATGACCGCCAC
TAGTTACCGCGGGGACCACATCAAGCTTCAGGCAGACAGCTTCGGCCTCCACATCGTCCCCGTC
TGACCGCCCACCCCAGAGGGAGGGAGGACCGAAGCGACGCGCTGCCTCTCGGCCAC

hide sequence

RefSeq Acc Id:

XM_006231443 ⟹ XP_006231505

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	1	243,616,509 - 243,697,454 (+)	NCBI
Rnor_6.0	1	264,493,579 - 264,585,073 (+)	NCBI
Rnor_5.0	1	271,936,269 - 272,027,514 (+)	NCBI

Sequence:

show sequence

TAGAGCAGATGGGCTTGTAACGAAGTCAGAGAGCAGTGTCAGGATGAACACATTAGGGATGGGG
GCTTCAGGGAATGATTGTGTGGTTCCCAAAAGTTGGAGTGAATTTTTGTAGACTTTAGAAGCTA
AGCTGAGAGCCATAAAGTCTGTGGCAGAGCCTGACAGGGTGAATAGGGGAAATCTTGGGAAAGG
AGACTCGCACGAAGTTAGAGAGGAGGCAAGGGTCAGAGCCAGTGTAGGCAGTAATTTGAAGGGG
GGCGTGTGATCGTGAAGATGAGGGGGTGGGGTAAGAGGGTTTGCTGGTGTCTAGACCCGAGGTT
TGGTCTTCGGGTGCCTCTGGGTAGCGAGGGTGTGGGTGTCGGCTTGCCGGTAGGGCTGGGGGCC
TCGGTGCGTGTGCGCGCCTGTGCGCGGCCCGGAGAGCCCGCGGCGCCTCGGCCCGTGGCTGTGC
TCGGCGGCCTGGTGTGCGAGCCAGTGCACGATCGGAGCGGAGCGCACAGCCCGCCCTGGCGGCC
GGCAGCCGCTGTTATCTGAGCCGCTCCGTCGCGGGTGGCTGCTCCCGGATCTCCCGGCTGTGGC
GGCCAAGGCGAGACCGACTGTGGGGCGGCTGAGGAGCCGGGAAGCCAAGACCCAGGCCCGGGCA
GCAGCGAGCCGAGCATGGAACAGTGTGCAGGTCGAGCAGTCCTGAAGTTGAGTTTGAGAGGCGA
CACGGCGGCGGCGGCCGCGCTGCTCCCGCTCCTCTGCCTCCCCATGGATATGCACTGCAAAGCA
GACCCCTTCTCCGCGATGCACCCAGGGCACGGGGGTGTGAACCAGCTCGGGGGGGTGTTTGTGA
ACGGCCGGCCCCTACCCGACGTGGTGAGGCAGCGCATCGTGGAGCTGGCCCACCAGGGTGTGCG
GCCCTGTGACATCTCCCGGCAGCTGCGGGTCAGCCATGGCTGTGTCAGCAAAATCCTGGGCAGG
TACTACGAGACTGGCAGCATCAAGCCCGGAGTGATTGGTGGCTCCAAGCCCAAGGTGGCAACGC
CCAAAGTGGTGGACAAGATTGCTGAATACAAGCGACAGAACCCGACTATGTTCGCCTGGGAGAT
CCGGGACAGGCTGCTAGCTGAGGGCATCTGCGACAATGATACAGTTCCCAGCGTCTCATCCATC
AACAGGATCATCCGGACCAAAGTTCAGCAGCCTTTCCACCCAACGCCGGATGGGGCAGGGACAG
GAGTGACTGCCCCTGGCCACACCATCGTTCCCAGCACGGCCTCCCCTCCTGTTTCCAGCGCCTC
TAACGACCCAGTGGGATCCTACTCCATCAACGGGATCCTGGGGATTCCTCGCTCCAACGGTGAG
AAGAGGAAACGAGAGGAAGTCGAGGTATACACTGATCCTGCCCACATTAGAGGAGGTGGAGGTT
TGCATCTGGTCTGGACTTTAAGAGATGTGTCCGAGGGCTCTGTCCCTAATGGAGACTCCCAGAG
TGGTGTGGACAGTTTGCGGAAGCACCTGCGAGCCGACACCTTCACCCAGCAGCAGCTGGAAGCT
TTGGATCGAGTCTTTGAGCGTCCTTCCTATCCCGATGTCTTCCAAGCATCAGAGCACATCAAAT
CAGAACAGGGGAATGAATACTCTCTCCCAGCCCTGACCCCTGGGCTTGATGAAGTCAAGTCCAG
TCTATCTGCATCTACCAACCCTGAGCTGGGCAGCAATGTGTCAGGCACACAGACGTACCCCGTC
GTGACCGGTCGTGATATGGCGAGCACCACTCTACCTGGTTACCCCCCTCATGTGCCCCCCACTG
GCCAGGGAAGCTACCCTACCTCCACCCTGGCAGGAATGGTGCCTGGGAGCGAGTTCTCAGGCAA
CCCATACAGCCATCCCCAGTACACCGCCTACAATGAGGCTTGGAGATTCAGCAACCCCGCCTTA
CTAATGCCGCCCCCCGGGGCTCCGCCCCTGCCGCTGCTGCCGCTGCCTATGACCGCCACTAGTT
ACCGCGGGGACCACATCAAGCTTCAGGCAGACAGCTTCGGCCTCCACATCGTCCCCGTCTGACC
GCCCACCCCAGAGGGAGGGAGGACCGAAGCGACGCGCTGCCTCTCGGCCACCGTCCCTGTCCCA
CCCCCACCTCGAGACATCCCACGCCCCCGAAGCCCTTCACGTCACCCTATCAAGGCCAGACAGG
ACAGGTGGAGCCCAGGGTGGGACCCTCAGGCCCCAGCCCCGCCCGTCGCCCCTCCCCGCCTGCC
TGGACCGCGGCGCCGCCCGGAAGCCCTCCGGCCGCTGGCCCGGGCGCCGGACACGTTTCTGTGA
CACACAATCAGCGTAGCCCACCCGGGGACAGCCCACTTTGGACGCCCGGGAGCCGGGAGGCTTC
GCTGGAGGAGCTGAGCAAGGGAAGCTAAGGAAAGGACTTTGTGCTGAAGGAGGAGCGGCTGGCG
AGGGGGGGAAATCCTGCCCCACTCCCCGAGCCTGCCAGGCTGAATCCGCCTTATGTCTGCGCCC
GGCCCCAGGCAGTGGCACTGGGACGAAAGGGTCGGACTCGAGGGACAGCTTTTGGGGCGACAGC
GTTTTCCGAGGCTGGGAACCAAGGCTAGCAGACGCCAACTGAGCTCATCCACCTGAACTGCCTC
GTTCCCCAGGGCCTGGGATCTCCTGCTGCAGTGGCTCGACTCTCGGCCCCGCCTCGCCCCTACG
TCAGCGCCTCTTCCACCTGCTGGCCTCTCACTTTTCCCTCCTGCGCTTCCTTGGCTCATCCCAC
GACACCTTGTGTTTGGTCCTAAGCACGCAGTCACGTCGGGGCCACCGCGGGAACCGTGTCCTCA
GGCTGCGGCTGTGAGCATTGATCTTTCCCATCAGTAATGTGCTGCCCCCACACCCCCGACCGGC
CCCAAACCCCCAACCTGCGGGCGCAAAGAACTTGGAGGGAACTGACGACCGAACTGCCCCGAGG
TGAAAACCCGGGACTGCCCGCCCCATTCCCCTCAACAACCCCCCTCCCCGGACCCCCCAAGCCT
TCCCTTGGGCAGATGCTGAACAGAGCCGGAAAAAAAAAGTCTACACTTATTTAATATGACAGTC
TTTGCAAAAACGAACAAAACAGAAACCCAACAGGCTGCTTTGTAGAAAGACGGTGTGTGCTGTG
AAGGCGAACCTCTCTGTGTACATATCCCCTCCCTCTCTGCCCCGCCCCGCCGGGTACCGTAGAG
TCCCTGTCCTCCCCACCACCCTGCCTGTAGATACACCCTTCTGTCCGTGCTGTGAGAGTCGCCG
CTCGCTGGGGGGGAGGGGGGACACAGCTACATGCCCACTAAAGCACAGCACGTCCTGGGGGAGG
GGGGCATTTTTTTACGTTACAAAAACAAATTATGAAAGAAATCTCTATGCAAAATGACGAACAT
GGTCCCGCGGACACCTCTCGCCTGTTTCGTTGGCTGTTTCTCTGTAATTCCGTGTTTTCGCGCT
CACCGCCCCGCATCTCTCCCTCTTCATCTCCCTTTTCTCTGCTGCTCTCGGCCCTTCTGTGTCT
CTTTCTCTGCTTCACTTGTCTCTGTCTCGGTCCCTTCTGTCCCAGGCCTCCAAGGCTACATCAA
AGGTGGCAGAGCCAATCTCGGGGCTTGGCCCCTTGTGGCCATGCCCCACGTGCCCCACCAGGCC
GCCCTGCCCCGCCCCACCCTGTAGTTGCTCTCTCGGTAGCGGCGATGCTCCCTGCATGTCTCCT
CAACCGTGGATCGTGACGACTCGAAATAACAGAAACAAAGTAAATAAAAGTGAAAAAAAAACAA
GTAAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAAAATCCTTGAACAAATCTGA
AAA

hide sequence

RefSeq Acc Id:

XM_008760404 ⟹ XP_008758626

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	1	264,493,579 - 264,583,222 (+)	NCBI

Sequence:

show sequence

TAGAGCAGATGGGCTTGTAACGAAGTCAGAGAGCAGTGTCAGGATGAACACATTAGGGATGGGG
GCTTCAGGGAATGATTGTGTGGTTCCCAAAAGTTGGAGTGAATTTTTGTAGACTTTAGAAGCTA
AGCTGAGAGCCATAAAGTCTGTGGCAGAGCCTGACAGGGTGAATAGGGGAAATCTTGGGAAAGG
AGACTCGCACGAAGTTAGAGAGGAGGCAAGGGTCAGAGCCAGTGTAGGCAGTAATTTGAAGGGG
GGCGTGTGATCGTGAAGATGAGGGGGTGGGGTAAGAGGGTTTGCTGGTGTCTAGACCCGAGGTT
TGGTCTTCGGGTGCCTCTGGGTAGCGAGGGTGTGGGTGTCGGCTTGCCGGTAGGGCTGGGGGCC
TCGGTGCGTGTGCGCGCCTGTGCGCGGCCCGGAGAGCCCGCGGCGCCTCGGCCCGTGGCTGTGC
TCGGCGGCCTGGTGTGCGAGCCAGTGCACGATCGGAGCGGAGCGCACAGCCCGCCCTGGCGGCC
GGCAGCCGCTGTTATCTGAGCCGCTCCGTCGCGGGTGGCTGCTCCCGGATCTCCCGGCTGTGGC
GGCCAAGGCGAGACCGACTGTGGGGCGGCTGAGGAGCCGGGAAGCCAAGACCCAGGCCCGGGCA
GCAGCGAGCCGAGCATGGAACAGTGTGCAGGTCGAGCAGTCCTGAAGTTGAGTTTGAGAGGCGA
CACGGCGGCGGCGGCCGCGCTGCTCCCGCTCCTCTGCCTCCCCATGGATATGCACTGCAAAGCA
GACCCCTTCTCCGCGATGCACCCAGGGCACGGGGGTGTGAACCAGCTCGGGGGGGTGTTTGTGA
ACGGCCGGCCCCTACCCGACGTGGTGAGGCAGCGCATCGTGGAGCTGGCCCACCAGGGTGTGCG
GCCCTGTGACATCTCCCGGCAGCTGCGGGTCAGCCATGGCTGTGTCAGCAAAATCCTGGGCAGG
TACTACGAGACTGGCAGCATCAAGCCCGGAGTGATTGGTGGCTCCAAGCCCAAGGTGGCAACGC
CCAAAGTGGTGGACAAGATTGCTGAATACAAGCGACAGAACCCGACTATGTTCGCCTGGGAGAT
CCGGGACAGGCTGCTAGCTGAGGGCATCTGCGACAATGATACAGTTCCCAGCGTCTCATCCATC
AACAGGATCATCCGGACCAAAGTTCAGCAGCCTTTCCACCCAACGCCGGATGGGGCAGGGACAG
GAGTGACTGCCCCTGGCCACACCATCGTTCCCAGCACGGCCTCCCCTCCTGTTTCCAGCGCCTC
TAACGACCCAGTGGGATCCTACTCCATCAACGGGATCCTGGGGATTCCTCGCTCCAACGGTGAG
AAGAGGAAACGAGAGGAAGATGTGTCCGAGGGCTCTGTCCCTAATGGAGACTCCCAGAGTGGTG
TGGACAGTTTGCGGAAGCACCTGCGAGCCGACACCTTCACCCAGCAGCAGCTGGAAGCTTTGGA
TCGAGTCTTTGAGCGTCCTTCCTATCCCGATGTCTTCCAAGCATCAGAGCACATCAAATCAGAA
CAGGGGAATGAATACTCTCTCCCAGCCCTGACCCCTGGGCTTGATGAAGTCAAGTCCAGTCTAT
CTGCATCTACCAACCCTGAGCTGGGCAGCAATGTGTCAGGCACACAGACGTACCCCGTCGTGAC
CGGTCGTGATATGGCGAGCACCACTCTACCTGGTTACCCCCCTCATGTGCCCCCCACTGGCCAG
GGAAGCTACCCTACCTCCACCCTGGCAGGAATGGTGCCTGGGAGCGAGTTCTCAGGCAACCCAT
ACAGCCATCCCCAGTACACCGCCTACAATGAGGCTTGGAGATTCAGCAACCCCGCCTTACTAAG
TGAGTACGCCACCTGGCAGGCCGGCGGCTCCCAAGGTCGCCTGCCCGCTCGCCAGCTCGGGCGC
GCAGGCTGCTTCGGGACACGGATCCCACTCAGGACCACCCCAATTCTGGGTACCCGGATGGGCC
AGGGAGACAGGCTCTTTAGAGCAGCGCTGGGTCCTGGGGATCCCTCCAGGACACCTGTGCCTCC
AGCCTCTTCCCGTCCCCGCCTCTCGGTCACTGGAAGGCTCTTGGCCAACAGTGGCCATTGGACC
CCTTGGCGGGTCCGCAGTCGGATGTCACCTGTCCTGACCCTCTCCCGCCCTATGGATGCAGCAC
TCCTCCTGGGCATCTGGCCTCGGGGCCGAGCCAGAGTCCTCCAGGCCTGATCCCGCTGGACCCG
GGGAGGGCTTTTCTTTGCTTTTCTTTCCTTTTTTGTTCTCCTGTTTGTCCTCTCACCCAGCCCA
TTCTTCTCCTGTGTTAACTTCCAGGTTCCCCTTATTATTATAGTGCCGCCCCCCGGGGCTCCGC
CCCTGCCGCTGCTGCCGCTGCCTATGACCGCCACTAGTTACCGCGGG

hide sequence

RefSeq Acc Id:

XM_039109033 ⟹ XP_038964961

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	1	243,616,645 - 243,697,454 (+)	NCBI

RefSeq Acc Id:

XM_039109034 ⟹ XP_038964962

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	1	243,616,645 - 243,697,454 (+)	NCBI

RefSeq Acc Id:

XM_039109038 ⟹ XP_038964966

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	1	243,616,645 - 243,697,454 (+)	NCBI

RefSeq Acc Id:

XM_039109041 ⟹ XP_038964969

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	1	243,616,645 - 243,697,454 (+)	NCBI

RefSeq Acc Id:

XM_039109046 ⟹ XP_038964974

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	1	243,616,509 - 243,697,454 (+)	NCBI

RefSeq Acc Id:

XM_039109049 ⟹ XP_038964977

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	1	243,616,509 - 243,697,454 (+)	NCBI

Protein Sequences


Protein RefSeqs	NP_001099831	(Get FASTA)	NCBI Sequence Viewer
	XP_006231505	(Get FASTA)	NCBI Sequence Viewer
	XP_038964961	(Get FASTA)	NCBI Sequence Viewer
	XP_038964962	(Get FASTA)	NCBI Sequence Viewer
	XP_038964966	(Get FASTA)	NCBI Sequence Viewer
	XP_038964969	(Get FASTA)	NCBI Sequence Viewer
	XP_038964974	(Get FASTA)	NCBI Sequence Viewer
	XP_038964977	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	EDL94291	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_001099831 ⟸ NM_001106361

- UniProtKB:

D4ACZ2 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MDMHCKADPFSAMHRHGGVNQLGGVFVNGRPLPDVVRQRIVELAHQGVRPCDISRQLRVSHGCV
SKILGRYYETGSIKPGVIGGSKPKVATPKVVDKIAEYKRQNPTMFAWEIRDRLLAEGICDNDTV
PSVSSINRIIRTKVQQPFHPTPDGAGTGVTAPGHTIVPSTASPPVSSASNDPVGSYSINGILGI
PRSNGEKRKREEVEVYTDPAHIRGGGGLHLVWTLRDVSEGSVPNGDSQSGVDSLRKHLRADTFT
QQQLEALDRVFERPSYPDVFQASEHIKSEQGNEYSLPALTPGLDEVKSSLSASTNPELGSNVSG
TQTYPVVTGRDMASTTLPGYPPHVPPTGQGSYPTSTLAGMVPGSEFSGNPYSHPQYTAYNEAWR
FSNPALLSSPYYYSAAPRGSAPAAAAAAYDRH

hide sequence

RefSeq Acc Id:

XP_006231505 ⟸ XM_006231443

- Peptide Label:

isoform X5

- Sequence:

show sequence

MEQCAGRAVLKLSLRGDTAAAAALLPLLCLPMDMHCKADPFSAMHPGHGGVNQLGGVFVNGRPL
PDVVRQRIVELAHQGVRPCDISRQLRVSHGCVSKILGRYYETGSIKPGVIGGSKPKVATPKVVD
KIAEYKRQNPTMFAWEIRDRLLAEGICDNDTVPSVSSINRIIRTKVQQPFHPTPDGAGTGVTAP
GHTIVPSTASPPVSSASNDPVGSYSINGILGIPRSNGEKRKREEVEVYTDPAHIRGGGGLHLVW
TLRDVSEGSVPNGDSQSGVDSLRKHLRADTFTQQQLEALDRVFERPSYPDVFQASEHIKSEQGN
EYSLPALTPGLDEVKSSLSASTNPELGSNVSGTQTYPVVTGRDMASTTLPGYPPHVPPTGQGSY
PTSTLAGMVPGSEFSGNPYSHPQYTAYNEAWRFSNPALLMPPPGAPPLPLLPLPMTATSYRGDH
IKLQADSFGLHIVPV

hide sequence

RefSeq Acc Id:

XP_008758626 ⟸ XM_008760404

- Peptide Label:

isoform X1

- Sequence:

show sequence

MEQCAGRAVLKLSLRGDTAAAAALLPLLCLPMDMHCKADPFSAMHPGHGGVNQLGGVFVNGRPL
PDVVRQRIVELAHQGVRPCDISRQLRVSHGCVSKILGRYYETGSIKPGVIGGSKPKVATPKVVD
KIAEYKRQNPTMFAWEIRDRLLAEGICDNDTVPSVSSINRIIRTKVQQPFHPTPDGAGTGVTAP
GHTIVPSTASPPVSSASNDPVGSYSINGILGIPRSNGEKRKREEDVSEGSVPNGDSQSGVDSLR
KHLRADTFTQQQLEALDRVFERPSYPDVFQASEHIKSEQGNEYSLPALTPGLDEVKSSLSASTN
PELGSNVSGTQTYPVVTGRDMASTTLPGYPPHVPPTGQGSYPTSTLAGMVPGSEFSGNPYSHPQ
YTAYNEAWRFSNPALLSEYATWQAGGSQGRLPARQLGRAGCFGTRIPLRTTPILGTRMGQGDRL
FRAALGPGDPSRTPVPPASSRPRLSVTGRLLANSGHWTPWRVRSRMSPVLTLSRPMDAALLLGI
WPRGRARVLQA

hide sequence

RefSeq Acc Id:

ENSRNOP00000070907 ⟸ ENSRNOT00000085811

RefSeq Acc Id:

ENSRNOP00000040130 ⟸ ENSRNOT00000050076

RefSeq Acc Id:	XP_038964977 ⟸ XM_039109049
- Peptide Label:	isoform X7

RefSeq Acc Id:	XP_038964974 ⟸ XM_039109046
- Peptide Label:	isoform X6

RefSeq Acc Id:	XP_038964962 ⟸ XM_039109034
- Peptide Label:	isoform X2

RefSeq Acc Id:	XP_038964969 ⟸ XM_039109041
- Peptide Label:	isoform X4

RefSeq Acc Id:	XP_038964961 ⟸ XM_039109033
- Peptide Label:	isoform X1

RefSeq Acc Id:	XP_038964966 ⟸ XM_039109038
- Peptide Label:	isoform X3

Protein Domains

Paired

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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

Damaging Variants

Assembly: RGSC_v3.4

Chromosome	Start Pos	End Pos	Reference Nucleotide	Variant Nucleotide	Variant Type	Strain
1	249807700	249807701	A	G	snv	HCR/2Mco (UMich)

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1305568	AgrOrtholog
Ensembl Genes	ENSRNOG00000014253	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000040130	ENTREZGENE, UniProtKB/TrEMBL
	ENSRNOP00000070907	UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000050076	ENTREZGENE, UniProtKB/TrEMBL
	ENSRNOT00000085811	UniProtKB/TrEMBL
Gene3D-CATH	1.10.10.10	UniProtKB/TrEMBL
InterPro	Homeodomain-like	UniProtKB/TrEMBL
	Paired_box_N	UniProtKB/TrEMBL
	PAIRED_DNA_bd_dom	UniProtKB/TrEMBL
	Pax2_C	UniProtKB/TrEMBL
	PAX_fam	UniProtKB/TrEMBL
	WH-like_DNA-bd_sf	UniProtKB/TrEMBL
KEGG Report	rno:293992	UniProtKB/TrEMBL
NCBI Gene	293992	ENTREZGENE
PANTHER	PTHR45636	UniProtKB/TrEMBL
Pfam	PAX	UniProtKB/TrEMBL
	Pax2_C	UniProtKB/TrEMBL
PharmGKB	PAX2	RGD
PhenoGen	Pax2	PhenoGen
PRINTS	PAIREDBOX	UniProtKB/TrEMBL
PROSITE	PAIRED_1	UniProtKB/TrEMBL
	PAIRED_2	UniProtKB/TrEMBL
SMART	PAX	UniProtKB/TrEMBL
Superfamily-SCOP	Homeodomain_like	UniProtKB/TrEMBL
UniProt	A0A0G2JZ47_RAT	UniProtKB/TrEMBL
	D4ACZ2	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2008-10-30	Pax2	paired box 2	Pax2	paired box gene 2	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-04-30	Pax2	paired box gene 2	Pax2_predicted	paired box gene 2 (predicted)	'predicted' is removed	2292626	APPROVED
2005-01-12	Pax2_predicted	paired box gene 2 (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

Imported Disease Annotations - CTD

Imported Disease Annotations - OMIM

Send us a Message

Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - OMIM