Pitx3 (paired-like homeodomain 3)

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Gene: Pitx3 (paired-like homeodomain 3) Rattus norvegicus

Analyze

Symbol:

Pitx3

Name:

paired-like homeodomain 3

RGD ID:

3332

Description:

Exhibits DNA-binding transcription factor activity. Involved in several processes, including cellular response to glial cell derived neurotrophic factor; positive regulation of cell proliferation in midbrain; and response to alkaloid. Localizes to neuronal cell body and nucleus. Human ortholog(s) of this gene implicated in anterior segment dysgenesis; anterior segment dysgenesis 1; cataract; cataract 11 multiple types; and cataract 9 multiple types. Orthologous to human PITX3 (paired like homeodomain 3); INTERACTS WITH 17beta-estradiol 3-benzoate; 5-azacytidine; ammonium chloride.

Type:

protein-coding

RefSeq Status:

VALIDATED

Also known as:

homeobox protein PITX3; homeobox protein PTX3; paired-like homeodomain transcription factor 3; pituitary homeobox 3

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):	PITX3 (paired like homeodomain 3)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, PhylomeDB, Treefam
Mus musculus (house mouse):	Pitx3 (paired-like homeodomain transcription factor 3)	HGNC	Treefam, EggNOG, OrthoMCL, NCBI, OMA, HomoloGene, Inparanoid, PhylomeDB, OrthoDB, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Pitx3 (paired like homeodomain 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	PITX3 (paired like homeodomain 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	PITX3 (paired like homeodomain 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Pitx3 (paired like homeodomain 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	PITX3 (paired like homeodomain 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (African green monkey):	PITX3 (paired like homeodomain 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Pitx3 (paired like homeodomain 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	PITX3 (paired like homeodomain 3)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Mus musculus (house mouse):	Pitx3 (paired-like homeodomain transcription factor 3)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Danio rerio (zebrafish):	pitx3 (paired-like homeodomain 3)	Alliance	DIOPT (OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Drosophila melanogaster (fruit fly):	Ptx1	Alliance	DIOPT (Hieranoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Caenorhabditis elegans (roundworm):	unc-30	Alliance	DIOPT (InParanoid\|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	245,001,106 - 245,013,881 (-)	NCBI
Rnor_6.0 Ensembl	1	265,887,230 - 265,899,958 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	1	265,886,766 - 265,899,947 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	1	273,317,125 - 273,330,306 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	1	251,355,785 - 251,368,502 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	1	251,616,353 - 251,629,068 (-)	NCBI
Celera	1	240,784,495 - 240,797,213 (-)	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

anterior segment dysgenesis (ISO)

anterior segment dysgenesis 1 (ISO)

Aphakia (ISO)

cataract (ISO)

cataract 11 multiple types (ISO)

cataract 9 multiple types (ISO)

microphthalmia (ISO)

Neoplasm Recurrence, Local (ISO)

Neurologic Manifestations (ISO)

Parkinson's disease (ISO,ISS)

Posterior Polar Cataract 11 with Microphthalmia and Neurodevelopmental Abnormalities (ISO)

Prostatic Neoplasms (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dimethylhydrazine (ISO)

17beta-estradiol 3-benzoate (EXP)

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

4,4'-diaminodiphenylmethane (ISO)

4,4'-sulfonyldiphenol (ISO)

5-azacytidine (EXP)

ammonium chloride (EXP)

benzo[a]pyrene (ISO)

bis(2-chloroethyl) sulfide (ISO)

bis(2-ethylhexyl) phthalate (EXP)

bisphenol A (EXP,ISO)

cocaine (ISO)

crocidolite asbestos (ISO)

diazinon (ISO)

dibutyl phthalate (EXP)

dichloroacetic acid (ISO)

folic acid (ISO)

genistein (ISO)

lipopolysaccharide (ISO)

methamphetamine (EXP)

N-methyl-4-phenylpyridinium (EXP)

pirinixic acid (ISO)

rotenone (ISO)

SCH 23390 (EXP)

sulforaphane (ISO)

tamoxifen (ISO)

tetrachloroethene (ISO)

tributylstannane (ISO)

trichloroethene (ISO)

triclosan (ISO)

urethane (ISO)

valproic acid (EXP,ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

aging (IEP)

anatomical structure morphogenesis (IBA)

cellular response to glial cell derived neurotrophic factor (IEP)

dopaminergic neuron differentiation (ISO,ISS)

lens development in camera-type eye (ISO,ISS)

lens fiber cell differentiation (ISO)

lens morphogenesis in camera-type eye (ISO,ISS)

locomotory behavior (ISO)

midbrain development (ISO,ISS)

negative regulation of gliogenesis (IDA)

negative regulation of neurogenesis (IDA)

neuron development (ISO)

positive regulation of cell proliferation in midbrain (IDA)

positive regulation of neuron apoptotic process (IDA)

positive regulation of transcription by RNA polymerase II (ISO)

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

regulation of gene expression (ISO)

regulation of transcription by RNA polymerase II (IBA)

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

response to cocaine (IEP)

response to immobilization stress (IEP)

response to methamphetamine hydrochloride (IEP)

response to morphine (IEP)

Cellular Component

neuronal cell body (IDA)

nucleus (IBA,IDA,ISO,ISS)

Molecular Function

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

DNA-binding transcription factor activity (IDA)

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

protein binding (ISO)

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

sequence-specific double-stranded DNA binding (ISO)

References

References - curated


1.	Addison PK, etal., Br J Ophthalmol. 2005 Feb;89(2):138-41.
2.	Ardayfio P, etal., Neurobiol Dis. 2008 Sep;31(3):406-12. doi: 10.1016/j.nbd.2008.05.017. Epub 2008 Jun 4.
3.	Bidinost C, etal., Invest Ophthalmol Vis Sci. 2006 Apr;47(4):1274-80.
4.	Cazorla P, etal., J Neurochem. 2000 May;74(5):1829-37.
5.	Garcia-Perez D, etal., Br J Pharmacol. 2013 Apr;168(8):1889-901. doi: 10.1111/bph.12083.
6.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
7.	GOA data from the GO Consortium
8.	Katunar MR, etal., J Neurosci Res. 2009 Mar;87(4):1014-22. doi: 10.1002/jnr.21911.
9.	Katunar MR, etal., Neurotox Res. 2010 Jul;18(1):69-81. doi: 10.1007/s12640-009-9132-z. Epub 2009 Nov 20.
10.	Krasnova IN, etal., PLoS One. 2011 Apr 25;6(4):e19179. doi: 10.1371/journal.pone.0019179.
11.	Lei Z, etal., J Neuropathol Exp Neurol. 2011 Sep;70(9):736-47.
12.	Leo D, etal., Exp Neurol. 2007 Feb;203(2):472-80. Epub 2006 Oct 27.
13.	MGD data from the GO Consortium
14.	NCBI rat LocusLink and RefSeq merged data July 26, 2002
15.	OMIM Disease Annotation Pipeline
16.	RGD automated data pipeline
17.	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
18.	RGD automated import pipeline for gene-chemical interactions
19.	Rieger DK, etal., Genomics. 2001 Feb 15;72(1):61-72.
20.	Roybon L, etal., J Neurosci. 2008 Apr 2;28(14):3644-56. doi: 10.1523/JNEUROSCI.0311-08.2008.
21.	Semina EV, etal., Nat Genet 1998 Jun;19(2):167-70.
22.	Smidt MP, etal., Proc Natl Acad Sci U S A 1997 Nov 25;94(24):13305-10.
23.	Summers KM, etal., Mol Vis. 2008;14:2010-5. Epub 2008 Nov 5.
24.	Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
25.	Wada K, etal., PLoS One. 2014 Oct 27;9(10):e111432. doi: 10.1371/journal.pone.0111432. eCollection 2014.

Additional References at PubMed

PMID:11299318	PMID:14973278	PMID:15950611	PMID:16190884	PMID:17184956	PMID:17761882	PMID:17919745	PMID:18646205	PMID:19007884	PMID:19144721	PMID:19334279	PMID:19515692
PMID:20175877	PMID:23863478	PMID:30634592

Genomics

Comparative Map Data

Pitx3
(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	245,001,106 - 245,013,881 (-)	NCBI
Rnor_6.0 Ensembl	1	265,887,230 - 265,899,958 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	1	265,886,766 - 265,899,947 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	1	273,317,125 - 273,330,306 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	1	251,355,785 - 251,368,502 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	1	251,616,353 - 251,629,068 (-)	NCBI
Celera	1	240,784,495 - 240,797,213 (-)	NCBI		Celera
Cytogenetic Map	1	q54	NCBI

PITX3
(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	102,230,186 - 102,241,512 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	10	102,230,189 - 102,241,512 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	10	103,989,946 - 104,001,269 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	10	103,979,936 - 103,991,221 (-)	NCBI	NCBI36		hg18	NCBI36
Build 34	10	103,979,935 - 103,991,221	NCBI
Celera	10	97,730,869 - 97,742,153 (-)	NCBI
Cytogenetic Map	10	q24.32	NCBI
HuRef	10	97,622,237 - 97,633,522 (-)	NCBI		HuRef
CHM1_1	10	104,273,459 - 104,284,755 (-)	NCBI		CHM1_1

Pitx3
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	19	46,123,720 - 46,136,764 (-)	NCBI	GRCm39		mm39
GRCm39 Ensembl	19	46,124,124 - 46,136,765 (-)	Ensembl
GRCm38	19	46,135,281 - 46,148,325 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	19	46,135,685 - 46,148,326 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	19	46,210,175 - 46,222,815 (-)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	19	46,188,996 - 46,201,636 (-)	NCBI			mm8
Celera	19	46,899,486 - 46,912,129 (-)	NCBI		Celera
Cytogenetic Map	19	C3	NCBI
cM Map	19	38.75	NCBI

Pitx3
(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	8,130,244 - 8,140,292 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955485	8,130,244 - 8,140,292 (+)	NCBI	ChiLan1.0	ChiLan1.0

PITX3
(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	102,301,528 - 102,302,943 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
Mhudiblu_PPA_v0	10	98,833,330 - 98,846,292 (-)	NCBI	Mhudiblu_PPA_v0		panPan3

PITX3
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1 Ensembl	28	14,761,094 - 14,762,716 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
CanFam3.1	28	14,760,741 - 14,775,584 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1

Pitx3
(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_004936600	3,607,883 - 3,619,538 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

PITX3
(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	113,230,965 - 113,241,360 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	14	113,230,194 - 113,241,393 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	14	123,084,113 - 123,095,511 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

PITX3
(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	95,266,257 - 95,278,333 (-)	NCBI
ChlSab1.1 Ensembl	9	95,266,582 - 95,268,139 (-)	Ensembl

Pitx3
(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	1,649,585 - 1,651,729 (-)	NCBI

Position Markers

AF005772

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	1	265,887,208 - 265,887,302	NCBI	Rnor6.0
Rnor_5.0	1	273,317,567 - 273,317,661	UniSTS	Rnor5.0
RGSC_v3.4	1	251,355,763 - 251,355,857	UniSTS	RGSC3.4
Celera	1	240,784,473 - 240,784,567	UniSTS
Cytogenetic Map	1	q54	UniSTS

Pitx3

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	1	265,888,663 - 265,888,904	NCBI	Rnor6.0
Rnor_5.0	1	273,319,022 - 273,319,263	UniSTS	Rnor5.0
RGSC_v3.4	1	251,357,218 - 251,357,459	UniSTS	RGSC3.4
Celera	1	240,785,928 - 240,786,169	UniSTS
Cytogenetic Map	1	q54	UniSTS

RH142219

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	1	265,887,276 - 265,887,467	NCBI	Rnor6.0
Rnor_5.0	1	273,317,635 - 273,317,826	UniSTS	Rnor5.0
RGSC_v3.4	1	251,355,831 - 251,356,022	UniSTS	RGSC3.4
Celera	1	240,784,541 - 240,784,732	UniSTS
RH 3.4 Map	9	495.9	UniSTS
Cytogenetic Map	1	q54	UniSTS

D1Bda64

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	1	265,887,871 - 265,888,560	NCBI	Rnor6.0
Rnor_5.0	1	273,318,230 - 273,318,919	UniSTS	Rnor5.0
RGSC_v3.4	1	251,356,426 - 251,357,115	UniSTS	RGSC3.4
Celera	1	240,785,136 - 240,785,825	UniSTS
Cytogenetic Map	1	q54	UniSTS

UniSTS:144187

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	1	265,887,878 - 265,888,089	NCBI	Rnor6.0
Rnor_5.0	1	273,318,237 - 273,318,448	UniSTS	Rnor5.0
RGSC_v3.4	1	251,356,433 - 251,356,644	UniSTS	RGSC3.4
Celera	1	240,785,143 - 240,785,354	UniSTS
Cytogenetic Map	1	q54	UniSTS

UniSTS:256827

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	1	265,887,832 - 265,888,542	NCBI	Rnor6.0
Rnor_5.0	1	273,318,191 - 273,318,901	UniSTS	Rnor5.0
RGSC_v3.4	1	251,356,387 - 251,357,097	UniSTS	RGSC3.4
Celera	1	240,785,097 - 240,785,807	UniSTS
Cytogenetic Map	1	q54	UniSTS

Pitx3

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	1	265,887,878 - 265,888,088	NCBI	Rnor6.0
Rnor_5.0	1	273,318,237 - 273,318,447	UniSTS	Rnor5.0
RGSC_v3.4	1	251,356,433 - 251,356,643	UniSTS	RGSC3.4
Celera	1	240,785,143 - 240,785,353	UniSTS
Cytogenetic Map	1	q54	UniSTS

Pitx3

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	1	265,887,574 - 265,888,911	NCBI	Rnor6.0
Rnor_5.0	1	273,317,933 - 273,319,270	UniSTS	Rnor5.0
Celera	1	240,784,839 - 240,786,176	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
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
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
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
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
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
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:	72
Count of miRNA genes:	59
Interacting mature miRNAs:	67
Transcripts:	ENSRNOT00000026013
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	hepatobiliary system	integumental system	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	appendage
High
Medium							1
Low		10				8	10	17	2	18		8
Below cutoff	1	18	11	10	10			30	20	16	6

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_019247	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006231478	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC119478	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AJ011005	(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:

ENSRNOT00000026013 ⟹ ENSRNOP00000026013

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	1	265,887,230 - 265,899,958 (-)	Ensembl

RefSeq Acc Id:

NM_019247 ⟹ NP_062120

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	1	245,001,164 - 245,013,881 (-)	NCBI
Rnor_6.0	1	265,887,230 - 265,899,947 (-)	NCBI
Rnor_5.0	1	273,317,125 - 273,330,306 (-)	NCBI
RGSC_v3.4	1	251,355,785 - 251,368,502 (-)	RGD
Celera	1	240,784,495 - 240,797,213 (-)	RGD

Sequence:

show sequence

GAATTCGGGCCCCCAGCCACCACCGGGAGTCTGCCTGCTGCGGGACACACTAGCCCTCCCTCCA
TGGAGTTTGGGCTGCTTGGTGAGGCAGAGGCTCGAAGCCCTGCGCTGTCATTGTCAGATGCAGG
CACTCCACACCCTCCGCTTCCAGAACATGGCTGCAAGGGGCAGGAGCACAGTGACTCGGAGAAG
GCCTCGGCCTCACTGCCGGGGGGCTCCCCTGAGGATGGCTCCCTGAAGAAGAAGCAGCGGCGGC
AGCGCACGCACTTCACCAGCCAGCAGCTGCAGGAGCTGGAGGCCACCTTCCAGAGGAATCGCTA
CCCCGACATGAGCACGCGCGAAGAGATCGCCGTGTGGACCAACCTCACTGAGGCCCGCGTGCGG
GTGTGGTTCAAGAACCGGCGCGCCAAGTGGCGGAAGCGGGAGCGCAGCCAGCAGGCGGAGCTGT
GCAAGGGCGGCTTCGCAGCCCCGCTCGGGGGCCTGGTGCCACCCTACGAGGAGGTGTACCCGGG
CTACACGTACGGCAACTGGCCGCCCAAGGCGCTCGCCCCGCCGCTCGCCGCCAAGACCTTCCCG
TTCGCCTTCAACTCGGTCAACGTGGGGCCTCTAGCTTCACAACCTGTATTCTCACCGCCCAGCT
CCATCGCTGCCTCCATGGTGCCCTCGGCGGCCGCTGCCCCGGGCACCGTCCCAGGTCCCGGAGC
CTTGCAGGGCCTGGGCGGGGCACCCCCCGGGCTGGCTCCAGCCGCCGTGTCCTCCGGGGCAGTG
TCCTGCCCTTACGCCTCGGCCGCCGCAGCCGCCGCTGCAGCCGCCTCCTCCCCTTATGTATACC
GGGACCCGTGTAACTCGAGCCTGGCTAGCCTGCGGCTCAAAGCCAAGCAGCACGCCTCTTTCAG
CTACCCCGCCGTGCCCGGGCCGCCGCCGGCCGCTAACCTTAGTCCCTGCCAGTACGCCGTGGAA
CGGCCAGTGTGAACCGCAGGTCTGTGGATCCATCCCCGAGGGCGGGGCAGTAATTCACAGCCTC
TCTGGACAGGGGTCGCCTAGACTGGCTTGCCCTTCGTCCCAGGGTCTGAAAAGGGGTGCCAGAG
CACCCGGGAAGAGGCGGCTCCGAAGAGGGCCTTTTCCCTCACAGCCCCTGAGGGGTGGTCTGAC
CCCTATACGGAGACCGCGGCCCTGGGACTAAGGCCAGGAACAGGGACCAGCTCCCCCGGGGCCA
ATTCACCCTTGGCTCACCCCGCCTTCTCCCCGAATTC

hide sequence

RefSeq Acc Id:

XM_006231478 ⟹ XP_006231540

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	1	245,001,106 - 245,006,844 (-)	NCBI
Rnor_6.0	1	265,886,766 - 265,892,917 (-)	NCBI
Rnor_5.0	1	273,317,125 - 273,330,306 (-)	NCBI

Sequence:

show sequence

TGTCTGTCTGCCTGGATGTGGGAGCGCATGTGTGGGAGAGTGTGTGTTTTTGTGCCTCTAGCTG
CAAGTCCAAGTGCTCACTGTGTCTAAGTGGAGGCCTGTGTGTGTCTGCACATGTGTCGTCTGTC
TCTGAGAGTGCACAGCTTGAACTCTGCCTGTCTCTTGCTCCGACTGCTATCCTCTTCCCGGGGC
CTCCTTCTACTGAAATAGAGGATGAAATCAAGCCACAGAGCCCTCCCTCCATGGAGTTTGGGCT
GCTTGGTGAGGCAGAGGCTCGAAGCCCTGCGCTGTCATTGTCAGATGCAGGCACTCCACACCCT
CCGCTTCCAGAACATGGCTGCAAGGGGCAGGAGCACAGTGACTCGGAGAAGGCCTCGGCCTCAC
TGCCGGGGGGCTCCCCTGAGGATGGCTCCCTGAAGAAGAAGCAGCGGCGGCAGCGCACGCACTT
CACCAGCCAGCAGCTGCAGGAGCTGGAGGCCACCTTCCAGAGGAATCGCTACCCCGACATGAGC
ACGCGCGAAGAGATCGCCGTGTGGACCAACCTCACTGAGGCCCGCGTGCGGGTGTGGTTCAAGA
ACCGGCGCGCCAAGTGGCGGAAGCGGGAGCGCAGCCAGCAGGCGGAGCTGTGCAAGGGCGGCTT
CGCAGCCCCGCTCGGGGGCCTGGTGCCACCCTACGAGGAGGTGTACCCGGGCTACACGTACGGC
AACTGGCCGCCCAAGGCGCTCGCCCCGCCGCTCGCCGCCAAGACCTTCCCGTTCGCCTTCAACT
CGGTCAACGTGGGGCCTCTGGCTTCACAACCTGTATTCTCACCGCCCAGCTCCATCGCTGCCTC
CATGGTGCCCTCGGCGGCCGCTGCCCCGGGCACCGTCCCAGGTCCCGGAGCCTTGCAGGGCCTG
GGCGGGGCACCCCCCGGGCTGGCTCCAGCCGCCGTGTCCTCCGGGGCAGTGTCCTGCCCTTACG
CCTCGGCCGCCGCAGCCGCCGCTGCAGCCGCCTCCTCCCCTTATGTATACCGGGACCCGTGTAA
CTCGAGCCTGGCTAGCCTGCGGCTCAAAGCCAAGCAGCACGCCTCTTTCAGCTACCCCGCCGTG
CCCGGGCCGCCGCCGGCCGCTAACCTTAGTCCCTGCCAGTACGCCGTGGAACGGCCAGTGTGAA
CCGCAGGTCTGTGGATCCATCCCCGAGGGCGGGGCAGTAATTCACAGCCTCTCTGGACAGGGGT
CGCCTAGACTGGCTTGCCCTCGTCCCAGGGTCTGAAAAGGGGTGCCAGAGCACCCGGGAAGAGG
CGGCTCCGAAGAGGGCCTTTTCCCTCACAGCCCCTGAGGGGTGGTCTGACCCCTATACGGAGAC
CGCGGCCCTGGGACTAAGGCCAGGAACAGGGACCAGCTCCCCCGGGGCCAATTCACCCTTGGCT
CACCCCGCCTTCTCCAGACTCCCCCTATCCCGTTTTCAAAGATCAATGAAATAAACGTGCGCGG
ACTGTCAAAGGCCTGATGATTCAGACTTGCGGTTGAGCCCTCCTTCCCCCCATCCTTCCCATTG
TCCAAAAGGACAGCTGGATGTACGGGAACGGAGTGAGCGTCCAGGCTTCTAAGGCTTCCGTCTC
ACTCCTTTTCTCCAGGATGGGGAAGCAGGGTCTCCTTGGAGTAAAGAATTTACGAAGCTTGGCG
TGACCAGCTAGTTGACAGCGATCGTCCTCTGCTGGTGCTGCGACGCCACCTGGTGGTCTCAGGG
AGGACAGCTGGTAGGCCTGGTCTCCAGCGCTTCCTTGCAGGGATCTGTTTTTGCAGTTTAGCCT
ATGACTTTAGGACTTGTTTCTCACTGTTCTTCTCAGAGGCATGGGTCTCTAACAGCAATAAACT
TCTAGTCTGTGACAGACATTTATTAAGCGCC

hide sequence

Protein Sequences


Protein RefSeqs	NP_062120	(Get FASTA)	NCBI Sequence Viewer
	XP_006231540	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	CAA09455	(Get FASTA)	NCBI Sequence Viewer
	EDL94336	(Get FASTA)	NCBI Sequence Viewer
	EDL94337	(Get FASTA)	NCBI Sequence Viewer
	EDL94338	(Get FASTA)	NCBI Sequence Viewer
	P81062	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_062120 ⟸ NM_019247

- UniProtKB:

P81062 (UniProtKB/Swiss-Prot)

- Sequence:

show sequence

MEFGLLGEAEARSPALSLSDAGTPHPPLPEHGCKGQEHSDSEKASASLPGGSPEDGSLKKKQRR
QRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERSQQAEL
CKGGFAAPLGGLVPPYEEVYPGYTYGNWPPKALAPPLAAKTFPFAFNSVNVGPLASQPVFSPPS
SIAASMVPSAAAAPGTVPGPGALQGLGGAPPGLAPAAVSSGAVSCPYASAAAAAAAAASSPYVY
RDPCNSSLASLRLKAKQHASFSYPAVPGPPPAANLSPCQYAVERPV

hide sequence

RefSeq Acc Id:	XP_006231540 ⟸ XM_006231478
- Peptide Label:	isoform X1
- UniProtKB:	P81062 (UniProtKB/Swiss-Prot)
- Sequence:	show sequence MEFGLLGEAEARSPALSLSDAGTPHPPLPEHGCKGQEHSDSEKASASLPGGSPEDGSLKKKQRR QRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERSQQAEL CKGGFAAPLGGLVPPYEEVYPGYTYGNWPPKALAPPLAAKTFPFAFNSVNVGPLASQPVFSPPS SIAASMVPSAAAAPGTVPGPGALQGLGGAPPGLAPAAVSSGAVSCPYASAAAAAAAAASSPYVY RDPCNSSLASLRLKAKQHASFSYPAVPGPPPAANLSPCQYAVERPV hide sequence

RefSeq Acc Id:

ENSRNOP00000026013 ⟸ ENSRNOT00000026013

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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CSV

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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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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

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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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

BN/SsN (MCW)

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CSV

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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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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

F344/NRrrc (MCW)

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CSV

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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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CSV

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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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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

FHL/EurMcwi (MCW)

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CSV

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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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CSV

TAB

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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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CSV

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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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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

LE/Stm (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

LEW/Crl (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

LEW/NCrlBR (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

LH/MavRrrc (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

LL/MavRrrc (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

LN/MavRrrc (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

M520/N (MCW)

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CSV

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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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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

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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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:3332	AgrOrtholog
Ensembl Genes	ENSRNOG00000019194	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein	ENSRNOP00000026013	ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000026013	ENTREZGENE, UniProtKB/Swiss-Prot
InterPro	Homeobox-like_sf	UniProtKB/Swiss-Prot
	Homeobox_CS	UniProtKB/Swiss-Prot
	Homeobox_dom	UniProtKB/Swiss-Prot
	Homeobox_Pitx/unc30	UniProtKB/Swiss-Prot
	OAR_dom	UniProtKB/Swiss-Prot
KEGG Report	rno:29609	UniProtKB/Swiss-Prot
NCBI Gene	29609	ENTREZGENE
Pfam	Homeodomain	UniProtKB/Swiss-Prot
	OAR	UniProtKB/Swiss-Prot
PhenoGen	Pitx3	PhenoGen
PIRSF	Homeobox_protein_Pitx/Unc30	UniProtKB/Swiss-Prot
PROSITE	HOMEOBOX_1	UniProtKB/Swiss-Prot
	HOMEOBOX_2	UniProtKB/Swiss-Prot
	OAR	UniProtKB/Swiss-Prot
SMART	HOX	UniProtKB/Swiss-Prot
Superfamily-SCOP	SSF46689	UniProtKB/Swiss-Prot
TIGR	TC218469
UniProt	P81062	ENTREZGENE, UniProtKB/Swiss-Prot

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2008-09-09	Pitx3	paired-like homeodomain 3	Pitx3	paired-like homeodomain transcription factor 3	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2002-06-10	Pitx3	paired-like homeodomain transcription factor 3			Name updated	70584	APPROVED

RGD Curation Notes

Note Type	Note	Reference
gene_expression	expressed specifically in neurons of the mesencephalic dopaminergic (mesDA) system	69932

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 - MGI

Imported Disease Annotations - OMIM