Pitx3 (paired-like homeodomain 3) - Rat Genome Database
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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 ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21245,001,106 - 245,013,881 (-)NCBI
Rnor_6.0 Ensembl1265,887,230 - 265,899,958 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01265,886,766 - 265,899,947 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01273,317,125 - 273,330,306 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41251,355,785 - 251,368,502 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11251,616,353 - 251,629,068 (-)NCBI
Celera1240,784,495 - 240,797,213 (-)NCBICelera
Cytogenetic Map1q54NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
neuronal cell body  (IDA)
nucleus  (IBA,IDA,ISO,ISS)

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 AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21245,001,106 - 245,013,881 (-)NCBI
Rnor_6.0 Ensembl1265,887,230 - 265,899,958 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01265,886,766 - 265,899,947 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01273,317,125 - 273,330,306 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41251,355,785 - 251,368,502 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11251,616,353 - 251,629,068 (-)NCBI
Celera1240,784,495 - 240,797,213 (-)NCBICelera
Cytogenetic Map1q54NCBI
PITX3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl10102,230,186 - 102,241,512 (-)EnsemblGRCh38hg38GRCh38
GRCh3810102,230,189 - 102,241,512 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh3710103,989,946 - 104,001,269 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3610103,979,936 - 103,991,221 (-)NCBINCBI36hg18NCBI36
Build 3410103,979,935 - 103,991,221NCBI
Celera1097,730,869 - 97,742,153 (-)NCBI
Cytogenetic Map10q24.32NCBI
HuRef1097,622,237 - 97,633,522 (-)NCBIHuRef
CHM1_110104,273,459 - 104,284,755 (-)NCBICHM1_1
Pitx3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391946,123,720 - 46,136,764 (-)NCBIGRCm39mm39
GRCm39 Ensembl1946,124,124 - 46,136,765 (-)Ensembl
GRCm381946,135,281 - 46,148,325 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1946,135,685 - 46,148,326 (-)EnsemblGRCm38mm10GRCm38
MGSCv371946,210,175 - 46,222,815 (-)NCBIGRCm37mm9NCBIm37
MGSCv361946,188,996 - 46,201,636 (-)NCBImm8
Celera1946,899,486 - 46,912,129 (-)NCBICelera
Cytogenetic Map19C3NCBI
cM Map1938.75NCBI
Pitx3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554858,130,244 - 8,140,292 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554858,130,244 - 8,140,292 (+)NCBIChiLan1.0ChiLan1.0
PITX3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.110102,301,528 - 102,302,943 (-)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v01098,833,330 - 98,846,292 (-)NCBIMhudiblu_PPA_v0panPan3
PITX3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl2814,761,094 - 14,762,716 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.12814,760,741 - 14,775,584 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Pitx3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049366003,607,883 - 3,619,538 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PITX3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl14113,230,965 - 113,241,360 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.114113,230,194 - 113,241,393 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.214123,084,113 - 123,095,511 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PITX3
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1995,266,257 - 95,278,333 (-)NCBI
ChlSab1.1 Ensembl995,266,582 - 95,268,139 (-)Ensembl
Pitx3
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248311,649,585 - 1,651,729 (-)NCBI

Position Markers
AF005772  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01265,887,208 - 265,887,302NCBIRnor6.0
Rnor_5.01273,317,567 - 273,317,661UniSTSRnor5.0
RGSC_v3.41251,355,763 - 251,355,857UniSTSRGSC3.4
Celera1240,784,473 - 240,784,567UniSTS
Cytogenetic Map1q54UniSTS
Pitx3  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01265,888,663 - 265,888,904NCBIRnor6.0
Rnor_5.01273,319,022 - 273,319,263UniSTSRnor5.0
RGSC_v3.41251,357,218 - 251,357,459UniSTSRGSC3.4
Celera1240,785,928 - 240,786,169UniSTS
Cytogenetic Map1q54UniSTS
RH142219  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01265,887,276 - 265,887,467NCBIRnor6.0
Rnor_5.01273,317,635 - 273,317,826UniSTSRnor5.0
RGSC_v3.41251,355,831 - 251,356,022UniSTSRGSC3.4
Celera1240,784,541 - 240,784,732UniSTS
RH 3.4 Map9495.9UniSTS
Cytogenetic Map1q54UniSTS
D1Bda64  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01265,887,871 - 265,888,560NCBIRnor6.0
Rnor_5.01273,318,230 - 273,318,919UniSTSRnor5.0
RGSC_v3.41251,356,426 - 251,357,115UniSTSRGSC3.4
Celera1240,785,136 - 240,785,825UniSTS
Cytogenetic Map1q54UniSTS
UniSTS:144187  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01265,887,878 - 265,888,089NCBIRnor6.0
Rnor_5.01273,318,237 - 273,318,448UniSTSRnor5.0
RGSC_v3.41251,356,433 - 251,356,644UniSTSRGSC3.4
Celera1240,785,143 - 240,785,354UniSTS
Cytogenetic Map1q54UniSTS
UniSTS:256827  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01265,887,832 - 265,888,542NCBIRnor6.0
Rnor_5.01273,318,191 - 273,318,901UniSTSRnor5.0
RGSC_v3.41251,356,387 - 251,357,097UniSTSRGSC3.4
Celera1240,785,097 - 240,785,807UniSTS
Cytogenetic Map1q54UniSTS
Pitx3  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01265,887,878 - 265,888,088NCBIRnor6.0
Rnor_5.01273,318,237 - 273,318,447UniSTSRnor5.0
RGSC_v3.41251,356,433 - 251,356,643UniSTSRGSC3.4
Celera1240,785,143 - 240,785,353UniSTS
Cytogenetic Map1q54UniSTS
Pitx3  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01265,887,574 - 265,888,911NCBIRnor6.0
Rnor_5.01273,317,933 - 273,319,270UniSTSRnor5.0
Celera1240,784,839 - 240,786,176UniSTS
Cytogenetic Map1q54UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70211Niddm24Non-insulin dependent diabetes mellitus QTL 243.79blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1236795785281795785Rat
631215Stl8Serum triglyceride level QTL 89.270.0001blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)1245529606282763074Rat
2302040Pia35Pristane induced arthritis QTL 353.80.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)1236265430281265430Rat
2302378Insul11Insulin level QTL 113.25blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1156446196274977688Rat
724531Uae5Urinary albumin excretion QTL 54urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)1161321152273792054Rat
724533Rf51Renal function QTL 515.30.0002kidney plasma flow trait (VT:0005524)renal plasma flow (CMO:0001914)1238830534278228767Rat
724538Kidm1Kidney mass QTL 13.2kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)1233663100273792054Rat
724552Glom2Glomerulus QTL 23.30.0001kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli directly contacting the kidney surface (CMO:0001001)1243272341282763074Rat
734767Niddm57Non-insulin dependent diabetes mellitus QTL 57body mass (VT:0001259)body weight (CMO:0000012)1244401175282365384Rat
734768Niddm59Non-insulin dependent diabetes mellitus QTL 59body mass (VT:0001259)body weight (CMO:0000012)1235850810280850810Rat
734769Niddm58Non-insulin dependent diabetes mellitus QTL 58body mass (VT:0001259)body weight (CMO:0000012)1244992467282365384Rat
631669Iddm9Insulin dependent diabetes mellitus QTL 92.80.039blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)1252955158280632620Rat
631690Scl5Serum cholesterol level QTL 52.1blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1258132568282763074Rat
1354580Scort1Serum corticosterone level QTL 13.4blood corticosterone amount (VT:0005345)blood corticosterone level (CMO:0001172)1167394665278228889Rat
1581544Rf52Renal function QTL 520.05total urine protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)1252948438281795785Rat
731175Uae20Urinary albumin excretion QTL 203.50.0018urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1241482188281795785Rat
738032Hcas5Hepatocarcinoma susceptibility QTL 53.12liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)1191825895279986079Rat
631536Lnnr2Liver neoplastic nodule remodeling QTL 22.90.0005liver integrity trait (VT:0010547)liver remodeling tumorous lesion number to liver total tumorous lesion number ratio (CMO:0001705)1255728828282763074Rat
1598821Rf55Renal function QTL 556.3renal blood flow trait (VT:2000006)ratio of change in renal blood flow to change in renal perfusion pressure (CMO:0001239)1238824734279986079Rat
2300175Bmd40Bone mineral density QTL 4015.40.0001femur mineral mass (VT:0010011)bone mineral density (CMO:0001226)1221901238266901238Rat
2293655Bss36Bone structure and strength QTL 3610.660.0001femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)1221901238266901238Rat
2293674Bss39Bone structure and strength QTL 397.10.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)1221901238266901238Rat
2293694Bss38Bone structure and strength QTL 387.050.0001femur strength trait (VT:0010010)femur stiffness (CMO:0001674)1221901238266901238Rat
631836Stl31Serum triglyceride level QTL 314.640.00000487blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)1259295704282763074Rat
631837Niddm35Non-insulin dependent diabetes mellitus QTL 350.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1258709726281795785Rat
631843Bw116Body weight QTL 1164.10.016abdominal adipose amount (VT:1000220)abdominal fat pad weight (CMO:0000088)1244401175282365384Rat
634313Niddm43Non-insulin dependent diabetes mellitus QTL 43blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1217054291281795785Rat
1357399Bw45Body weight QTL 453.05body mass (VT:0001259)body mass index (BMI) (CMO:0000105)1225689973270689973Rat
1357404Bw42Body weight QTL 424.490.0001body mass (VT:0001259)body weight (CMO:0000012)1225689973270689973Rat
1600388Niddm67Non-insulin dependent diabetes mellitus QTL 675.840.000004blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1213476630278978026Rat
1600392Bw123Body weight QTL 1230.001body mass (VT:0001259)body weight (CMO:0000012)1244087148282763074Rat
1600395Niddm69Non-insulin dependent diabetes mellitus QTL 694.140.0002blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)1213476630278978026Rat
1600396Niddm68Non-insulin dependent diabetes mellitus QTL 684.970.0003blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1213476630278978026Rat
1600397Edcs4Endometrial carcinoma susceptibility QTL 42.2uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)1226706329271706329Rat
1578759Uae30Urinary albumin excretion QTL 303.30.003urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1161321256273791893Rat
1578763Kidm29Kidney mass QTL 293.30.0001kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1196395041282763074Rat
1578778Pur4Proteinuria QTL 43.30.003total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)1161321256273791893Rat
1300108Rf8Renal function QTL 83.75renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)1249206242281795785Rat
1354610Bw34Body weight QTL 344.1body mass (VT:0001259)body weight (CMO:0000012)1161784169278228889Rat
1354624Cm35Cardiac mass QTL355.7heart left ventricle mass (VT:0007031)calculated heart weight (CMO:0000073)1192639698278228889Rat
1354646Kidm18Kidney mass QTL 185.7kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)1161784169278228889Rat
1354652Kidm20Kidney mass QTL 204.3kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)1192639698278228889Rat
1354661Bw33Body weight QTL 335.2body mass (VT:0001259)body weight (CMO:0000012)1161784169278228889Rat
1549910Bw54Body weight QTL 540.05body mass (VT:0001259)body weight (CMO:0000012)1236795785281795785Rat
2316896Gluco57Glucose level QTL 577.2blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1249607907266793958Rat
1549837Hcar15Hepatocarcinoma resistance QTL 150.05liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)1163796316282763074Rat
1358890Bp259Blood pressure QTL 2593.06arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1230420627282645769Rat
1358898Bp255Blood pressure QTL 2553.6arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1208517798266948272Rat
61327Eae7Experimental allergic encephalomyelitis QTL 75.6body mass (VT:0001259)change in body weight (CMO:0002045)1236265430281265430Rat
61400Niddm1Non-insulin dependent diabetes mellitus QTL 111blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1238830408266793958Rat
7394701Uae46Urinary albumin excretion QTL 463.60.0056urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1221901238266901238Rat
7387289Uae45Urinary albumin excretion QTL 452.860.0021urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1244148899282763074Rat
10053715Scort24Serum corticosterone level QTL 242.130.0088blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1242302911282763074Rat
10059587Bw173Body weight QTL 1733.230.025body mass (VT:0001259)body weight (CMO:0000012)1222492538267492538Rat

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

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000026013   ⟹   ENSRNOP00000026013
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1265,887,230 - 265,899,958 (-)Ensembl
RefSeq Acc Id: NM_019247   ⟹   NP_062120
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21245,001,164 - 245,013,881 (-)NCBI
Rnor_6.01265,887,230 - 265,899,947 (-)NCBI
Rnor_5.01273,317,125 - 273,330,306 (-)NCBI
RGSC_v3.41251,355,785 - 251,368,502 (-)RGD
Celera1240,784,495 - 240,797,213 (-)RGD
Sequence:
RefSeq Acc Id: XM_006231478   ⟹   XP_006231540
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21245,001,106 - 245,006,844 (-)NCBI
Rnor_6.01265,886,766 - 265,892,917 (-)NCBI
Rnor_5.01273,317,125 - 273,330,306 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_062120   ⟸   NM_019247
- UniProtKB: P81062 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006231540   ⟸   XM_006231478
- Peptide Label: isoform X1
- UniProtKB: P81062 (UniProtKB/Swiss-Prot)
- 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)
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)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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)
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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

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