Pitx1 (paired-like homeodomain 1)

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Gene: Pitx1 (paired-like homeodomain 1) Rattus norvegicus

Analyze

Symbol:

Pitx1

Name:

paired-like homeodomain 1

RGD ID:

69253

Description:

Exhibits DNA-binding transcription factor activity. Involved in regulation of transcription, DNA-templated. Predicted to localize to cytoplasm; nucleus; and transcription regulator complex. Human ortholog(s) of this gene implicated in clubfoot. Orthologous to human PITX1 (paired like homeodomain 1); INTERACTS WITH 7,12-dimethyltetraphene; all-trans-retinoic acid; ammonium chloride.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

Bft; homeobox protein PITX1; paired-like homeodomain transcription factor 1; pituitary homeobox 1

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):	PITX1 (paired like homeodomain 1)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Pitx1 (paired-like homeodomain transcription factor 1)	HGNC	Treefam, EggNOG, OrthoMCL, NCBI, OMA, HomoloGene, Inparanoid, Panther, PhylomeDB, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Pitx1 (paired like homeodomain 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	PITX1 (paired like homeodomain 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	PITX1 (paired like homeodomain 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Pitx1 (paired like homeodomain 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	PITX1 (paired like homeodomain 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (African green monkey):	PITX1 (paired like homeodomain 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Pitx1 (paired like homeodomain 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	PITX1 (paired like homeodomain 1)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Mus musculus (house mouse):	Pitx1 (paired-like homeodomain transcription factor 1)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Danio rerio (zebrafish):	pitx1 (paired-like homeodomain 1)	Alliance	DIOPT (Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Drosophila melanogaster (fruit fly):	Ptx1	Alliance	DIOPT (Hieranoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Caenorhabditis elegans (roundworm):	unc-30	Alliance	DIOPT (InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)

Latest Assembly:

Rnor_6.0 - RGSC Genome Assembly v6.0

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	17	8,794,134 - 8,800,292 (+)	NCBI
Rnor_6.0 Ensembl	17	8,878,270 - 8,884,423 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	17	8,873,184 - 8,884,428 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	17	11,038,827 - 11,050,071 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	17	14,834,144 - 14,840,303 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	17	14,834,143 - 14,840,302 (+)	NCBI
Celera	17	8,876,388 - 8,882,546 (+)	NCBI		Celera
Cytogenetic Map	17	p14	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

autistic disorder (ISO)

Carpal Synostosis with Dysplastic Elbow Joints and Brachydactyly (ISO)

clubfoot (ISO)

hepatocellular carcinoma (ISO)

Hereditary Neoplastic Syndromes (ISO)

Micrognathism (ISO)

mucopolysaccharidosis Ih (ISO)

Neurodevelopmental Disorders (ISO)

Testicular Germ Cell Tumor (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

17beta-estradiol (ISO)

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

4,4'-sulfonyldiphenol (ISO)

7,12-dimethyltetraphene (EXP)

acetylsalicylic acid (ISO)

aflatoxin B1 (ISO)

all-trans-retinoic acid (EXP)

ammonium chloride (EXP)

antirheumatic drug (ISO)

arsenite(3-) (ISO)

benzo[a]pyrene (ISO)

beta-naphthoflavone (EXP)

bisphenol A (ISO)

bisphenol F (ISO)

cadmium dichloride (EXP)

cisplatin (ISO)

cytarabine (ISO)

decabromodiphenyl ether (EXP)

doxorubicin (ISO)

elemental selenium (ISO)

fenvalerate (EXP)

folic acid (ISO)

fulvestrant (ISO)

genistein (ISO)

methylmercury chloride (ISO)

N-nitrosodiethylamine (EXP)

selenium atom (ISO)

sulforaphane (ISO)

triclosan (ISO)

valproic acid (ISO)

vitamin E (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

anatomical structure morphogenesis (IBA)

branchiomeric skeletal muscle development (ISO)

cartilage development (ISO)

embryonic hindlimb morphogenesis (ISO)

hindlimb morphogenesis (ISO)

myoblast fate commitment (ISO)

negative regulation of transcription, DNA-templated (ISO)

pituitary gland development (ISO)

positive regulation of transcription by RNA polymerase II (ISO)

regulation of transcription by RNA polymerase II (IBA)

regulation of transcription, DNA-templated (IMP)

skeletal system development (ISO)

Cellular Component

cytoplasm (ISO)

nucleus (IBA,ISO,ISS)

transcription regulator complex (ISO)

Molecular Function

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

DNA-binding transcription factor activity (IMP,ISS)

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)

RNA polymerase II transcription factor binding (ISO)

sequence-specific double-stranded DNA binding (ISO)

References

References - curated


1.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2.	GOA data from the GO Consortium
3.	Kimura N, etal., Endocrinology 2001 Apr;142(4):1427-41.
4.	NCBI rat LocusLink and RefSeq merged data July 26, 2002
5.	OMIM Disease Annotation Pipeline
6.	Quentien MH, etal., J Biol Chem 2002 Nov 15;277(46):44408-16.
7.	RGD automated data pipeline
8.	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
9.	RGD automated import pipeline for gene-chemical interactions
10.	Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
11.	Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
12.	Zakaria MM, etal., Mol Endocrinol 2002 Aug;16(8):1840-52.

Additional References at PubMed

PMID:8675014	PMID:9192866	PMID:9207461	PMID:10049363	PMID:10101115	PMID:10431247	PMID:15489334	PMID:15621531	PMID:16087728	PMID:16989801	PMID:17384148	PMID:17984056
PMID:18231602	PMID:19531352	PMID:21300782	PMID:22071103	PMID:25258388	PMID:26306672	PMID:26612202	PMID:31527569

Genomics

Comparative Map Data

Pitx1
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	17	8,794,134 - 8,800,292 (+)	NCBI
Rnor_6.0 Ensembl	17	8,878,270 - 8,884,423 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	17	8,873,184 - 8,884,428 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	17	11,038,827 - 11,050,071 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	17	14,834,144 - 14,840,303 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	17	14,834,143 - 14,840,302 (+)	NCBI
Celera	17	8,876,388 - 8,882,546 (+)	NCBI		Celera
Cytogenetic Map	17	p14	NCBI

PITX1
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	5	135,027,734 - 135,034,813 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	5	135,027,734 - 135,034,228 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	5	134,363,424 - 134,369,918 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
GRCh37	5	134,363,424 - 134,369,964 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	5	134,391,323 - 134,397,863 (-)	NCBI	NCBI36		hg18	NCBI36
Build 34	5	134,391,367 - 134,397,887	NCBI
Celera	5	130,487,209 - 130,493,751 (-)	NCBI
Cytogenetic Map	5	q31.1	NCBI
HuRef	5	129,551,412 - 129,557,483 (-)	NCBI		HuRef
CHM1_1	5	133,796,087 - 133,802,610 (-)	NCBI		CHM1_1

Pitx1
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	13	55,972,857 - 55,984,002 (-)	NCBI	GRCm39		mm39
GRCm38	13	55,825,044 - 55,836,190 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	13	55,825,051 - 55,836,192 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	13	55,926,415 - 55,932,786 (-)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	13	55,834,676 - 55,841,047 (-)	NCBI			mm8
Celera	13	56,876,993 - 56,883,263 (-)	NCBI		Celera
Cytogenetic Map	13	B1	NCBI
cM Map	13	30.06	NCBI

Pitx1
(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_004955408	30,197,061 - 30,203,054 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955408	30,197,374 - 30,202,887 (-)	NCBI	ChiLan1.0	ChiLan1.0

PITX1
(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	5	136,565,285 - 136,570,346 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	5	136,565,285 - 136,570,350 (-)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	5	130,422,920 - 130,429,828 (-)	NCBI	Mhudiblu_PPA_v0		panPan3

PITX1
(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	11	23,069,716 - 23,080,941 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
CanFam3.1	11	23,069,731 - 23,075,085 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1

Pitx1
(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_004936597	2,211,087 - 2,217,065 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

PITX1
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	2	137,198,870 - 137,206,979 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	2	137,200,424 - 137,212,500 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1

PITX1
(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	23	37,807,486 - 37,820,540 (-)	NCBI
ChlSab1.1 Ensembl	23	37,807,378 - 37,813,948 (-)	Ensembl

Pitx1
(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_004624733	12,028,497 - 12,034,612 (+)	NCBI

Position Markers

U71206

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	17	8,883,663 - 8,883,771	NCBI	Rnor6.0
Rnor_5.0	17	11,049,306 - 11,049,414	UniSTS	Rnor5.0
RGSC_v3.4	17	14,839,538 - 14,839,646	UniSTS	RGSC3.4
Celera	17	8,881,781 - 8,881,889	UniSTS
Cytogenetic Map	17	p14	UniSTS

Pitx1

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	17	8,882,993 - 8,883,143	NCBI	Rnor6.0
Rnor_5.0	17	11,048,636 - 11,048,786	UniSTS	Rnor5.0
RGSC_v3.4	17	14,838,868 - 14,839,018	UniSTS	RGSC3.4
Celera	17	8,881,111 - 8,881,261	UniSTS
Cytogenetic Map	17	p14	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
9590316	Scort21	Serum corticosterone level QTL 21	4.75	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	17	1	24787908	Rat
10401807	Kidm52	Kidney mass QTL 52			kidney mass (VT:0002707)	both kidneys wet weight (CMO:0000085)	17	1	32230361	Rat
70184	BpQTLcluster14	Blood pressure QTL cluster 14	3.38		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	17	1	33303755	Rat
631207	Niddm41	Non-insulin dependent diabetes mellitus QTL 41			blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	17	1	38243814	Rat
1354658	Spl8	Serum phospholipid level QTL 8	3.8		blood VLDL phospholipid amount (VT:0010507)	blood very low density lipoprotein phospholipid level (CMO:0001571)	17	1	63676140	Rat
1354662	Rf49	Renal function QTL 49	2.9		blood creatinine amount (VT:0005328)	plasma creatinine level (CMO:0000537)	17	1	73413148	Rat
1354581	Bp247	Blood pressure QTL 247	4.5		arterial blood pressure trait (VT:2000000)	pulse pressure (CMO:0000292)	17	1	73413148	Rat
1641902	Colcr7	Colorectal carcinoma resistance QTL 7	3.35	0.0044	intestine integrity trait (VT:0010554)	benign colorectal tumor surface area measurement (CMO:0001799)	17	519770	23422380	Rat
1300123	Bp194	Blood pressure QTL 194	2.82		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	17	519770	36283402	Rat
2324619	Coatc4	Coat color QTL 4		0.001	coat/hair pigmentation trait (VT:0010463)	pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)	17	3336972	24030841	Rat
2324619	Coatc4	Coat color QTL 4		0.001	coat/hair pigmentation trait (VT:0010463)	pigmented dorsal coat/hair area to total dorsal coat/hair area ratio (CMO:0001811)	17	3336972	24030841	Rat
1354613	Kidm14	Kidney mass QTL 14	6.2		kidney mass (VT:0002707)	left kidney wet weight (CMO:0000083)	17	3336972	37790462	Rat
1354596	Bw32	Body weight QTL 32	4.5		body mass (VT:0001259)	body weight (CMO:0000012)	17	3336972	63676140	Rat
1354638	Insul1	Insulin level QTL 1	4.8		blood insulin amount (VT:0001560)	plasma insulin level (CMO:0000342)	17	3336972	73413148	Rat
1354651	Lmblg2	Limb length QTL 2	6		tibia length (VT:0004357)	tibia length (CMO:0000450)	17	3336972	73413148	Rat
1354630	Cm34	Cardiac mass QTL 34	8.7		heart left ventricle mass (VT:0007031)	heart left ventricle wet weight (CMO:0000071)	17	3336972	73413148	Rat
631499	Stl1	Serum triglyceride level QTL 1	3.6		blood triglyceride amount (VT:0002644)	blood triglyceride level (CMO:0000118)	17	3414039	28073589	Rat
2293648	Bmd31	Bone mineral density QTL 31	4.5	0.0001	femur size trait (VT:1000369)	femoral neck cortical cross-sectional area (CMO:0001702)	17	4716067	27691136	Rat
2293664	Bmd28	Bone mineral density QTL 28	5.1	0.0001	femur mineral mass (VT:0010011)	trabecular volumetric bone mineral density (CMO:0001729)	17	4716067	27691136	Rat
2303627	Vencon8	Ventilatory control QTL 8		0.001	respiration trait (VT:0001943)	tidal volume (CMO:0000222)	17	5191047	50191047	Rat
10054088	Scort28	Serum corticosterone level QTL 28	2.04	0.0102	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	17	5191047	50191047	Rat
1581553	Pur14	Proteinuria QTL 14	5.3	0.0001	total urine protein amount (VT:0000032)	urine protein excretion rate (CMO:0000759)	17	8424467	16620067	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	307
Count of miRNA genes:	175
Interacting mature miRNAs:	200
Transcripts:	ENSRNOT00000015307
Prediction methods:	Microtar, Miranda, Rnahybrid, Targetscan
Result types:	miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.

Expression

RNA-SEQ Expression

High: > 1000 TPM value Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM Below Cutoff: < 0.5 TPM

	alimentary part of gastrointestinal system	circulatory system	endocrine system	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	appendage
High
Medium											1
Low	3	6	4	4		4	1	3	15		11	9	1
Below cutoff		10	5	5	1	5	7	8	14	4	11	1	7

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_053624	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AB047298	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC061966	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH474032	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000284	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000015307 ⟹ ENSRNOP00000015307

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	17	8,878,270 - 8,884,423 (+)	Ensembl

RefSeq Acc Id:

NM_053624 ⟹ NP_446076

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	17	8,794,134 - 8,800,292 (+)	NCBI
Rnor_6.0	17	8,878,270 - 8,884,428 (+)	NCBI
Rnor_5.0	17	11,038,827 - 11,050,071 (+)	NCBI
RGSC_v3.4	17	14,834,144 - 14,840,303 (+)	RGD
Celera	17	8,876,388 - 8,882,546 (+)	RGD

Sequence:

show sequence

CTGCGGGCTCCGACCCGAGCCTTAGAAACCGGCCTCGAATCGGGACTGGGACCCGGGCCTGCCG
GGCAGCTGAGGCCGGAGCGGCGGGAGCGCGTGGCGCAGCCTCGAGCCCTGAGCCCCGTCCTGCA
GCCCCGAGAGATCGATGGAGCGCGGGCGTCGTCGCTGTGGGCGCGGGCAGCCCTGGGGGGCAGC
CGCTTAGGCGCCGCTCTCTTGTCCCCAACAGGTCGCAGCCCGGGTGGCCGGGCGCTCCCAGCTC
CGGCTCCTGGAGCGCCCTTTGCGGTCCCCACCTCCATGGACGCCTTCAAGGGAGGCATGAGCCT
GGAGAGGCTACCGGAGGGGCTGCGGCCACCGCCACCGCCGCCACACGACATGGGGCCCAGCTTC
CACCTGGCCCGCACCGCCGACCCCCGGGAGCCGCTGGAGAACTCAGCCAGCGAGTCATCCGACG
CCGATCTGCCAGACAAGGAGCGCGGTGGAGAGGCCAAGGTGCCTGAGGATGGCGGCGCGGGCAG
CGCTGGCTGCGGCAGCGCGGAAGACCCAGCCAAGAAGAAGAAACAGCGGCGTCAACGCACTCAC
TTCACAAGCCAGCAGTTGCAAGAGCTGGAGGCCACGTTCCAAAGGAACCGCTACCCGGACATGA
GCATGAGAGAGGAGATCGCGGTGTGGACCAACCTCACTGAGCCGCGAGTGCGGGTCTGGTTCAA
GAACCGGCGAGCCAAGTGGCGCAAGAGGGAGCGGAACCAGCAGTTGGACCTGTGCAAGGGCGGC
TACGTGCCGCAGTTCAGCGGCTTGGTGCAGCCCTACGAGGACGTGTACGCCGCCGCCGGCTACT
CCTACAACAACTGGGCCGCCAAGAGCTTGGCACCGGCGCCGCTGTCCACCAAGAGCTTTACCTT
CTTCAACTCCATGAGTCCGCTATCCTCTCAGTCCATGTTCTCGGCCCCCAGCTCCATCTCTTCC
ATGACCATGCCATCCAGCATGGGCCCGGGCTCCGTGCCCGGCATGCCCAACTCGGGCCTCAACA
ACATCAACAACCTCACGGGCTCCTCGCTCAACTCGGCCATGTCGCCGGGCGCCTGCCCCTACGG
CACCCCCGCCTCGCCCTACAGCGTCTACCGGGACACGTGCAACTCGAGCCTCGCCAGCCTGCGG
CTCAAGTCCAAGCAGCACTCCTCGTTTGGCTACGGCGGTCTGCAGGGTCCAGCGTCGGGCCTCA
ACGCCTGCCAGTATAACAGCTGACCGCCCCGCCGGGTCCCCGGGGCCGCCGGCCGGCAAGGCGC
AGCGGGAGCGCGCGGAGCACACGGGGCGCTCGCAGCACCTGGGACCTCACCTCTGCGCAGCCCC
TTCCTCCCCACCCTGCCTCCAGGTTGGTTTTGTGTTTGCTTTTCCGGACCCCGCTCTGCCCCCA
ATGAATAAAAAAGGGAAAAAAATCAAGCCAAGGGAGGGGGTGGGGGAGAGAAAGCAAAAAAAAT
AAAAAAATTTTAAAAAAAGGACATCGGAGAAAAATGCTGGGGGTGGGGGTGAGTTGCAATGTCC
CTGGCGATGGCGCAGGTGGTGCGTTCGAACCCTCGACCCCCAACTGTCCACTACACCAAGGGGA
TGTGGCGTGGGGGAAGCCAGCGCCAAAGTGGCTCGGAGAAGACGCCGTTCGTCCCTGCCGGAGC
GCCTCAACCCGTGAACTGAATGTAGGGAGCCTGGAGGCCCTGGGATCGTTCACCCGATCAAAAA
CCCGAGGCACCCTCTCCTAGCCTGGGCCGTCCGAGTGCATGCAGCGCGGATCACTGTTGGAGCT
TGAGCCTGGCTGGGGATGACAGCGCTGATGGGGATCCGGTGTGCCGGATTAGCCTAAGGCCCCG
GGATGCCAGAAGAGCCCAGCAGCCCTGAGCTCTGGAGCCGCACACTTCAGGCCACTGAGCCGCA
GCTGGCCGTGGCCAGTCCGCAGCAGGAGGGGAAGGGCTCAGCTCTGAGTTCCCCAGCCCCAGCT
TAGCCGCCAGCCCGGCCCTCTGCTCCACTACGGGTCCAGGAGGTGGCCCAGTGAACAGCCCCTT
CCTCACTGCTCACCCGTGCAAGAGTCGAGCCAGGAGAGCGCGGGGCCACAGCCCCAGGGCCCCC
GCCCACTTTGCACACCCGCTCTCTGGCCCGCGCCCGTTTACAGCGTCCCTGTGTATGTCGGACT
GACTGTATAGAATTATAAATCTGTCTATATCGACTTGTCCATGTACGTCTATTAAAACCATAGT
CGGAGCGTGCTAAGCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

hide sequence

RefSeq Acc Id:

XM_006253569 ⟹ XP_006253631

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	17	8,873,184 - 8,884,428 (+)	NCBI
Rnor_5.0	17	11,038,827 - 11,050,071 (+)	NCBI

Sequence:

show sequence

CCGGAGCCGACCAGCCTCAGACACAGAGCTGCCCTGGTACGGTCGCAGCCCGGGTGGCCGGGCG
CTCCCAGCTCCGGCTCCTGGAGCGCCCTTTGCGGTCCCCACCTCCATGGACGCCTTCAAGGGAG
GCATGAGCCTGGAGAGGCTACCGGAGGGGCTGCGGCCACCGCCACCGCCGCCACACGACATGGG
GCCCAGCTTCCACCTGGCCCGCACCGCCGACCCCCGGGAGCCGCTGGAGAACTCAGCCAGCGAG
TCATCCGACGCCGATCTGCCAGACAAGGAGCGCGGTGGAGAGGCCAAGGTGCCTGAGGATGGCG
GCGCGGGCAGCGCTGGCTGCGGCAGCGCGGAAGACCCAGCCAAGAAGAAGAAACAGCGGCGTCA
ACGCACTCACTTCACAAGCCAGCAGTTGCAAGAGCTGGAGGCCACGTTCCAAAGGAACCGCTAC
CCGGACATGAGCATGAGAGAGGAGATCGCGGTGTGGACCAACCTCACTGAGCCGCGAGTGCGGG
TCTGGTTCAAGAACCGGCGAGCCAAGTGGCGCAAGAGGGAGCGGAACCAGCAGTTGGACCTGTG
CAAGGGCGGCTACGTGCCGCAGTTCAGCGGCTTGGTGCAGCCCTACGAGGACGTGTACGCCGCC
GCCGGCTACTCCTACAACAACTGGGCCGCCAAGAGCTTGGCACCGGCGCCGCTGTCCACCAAGA
GCTTTACCTTCTTCAACTCCATGAGTCCGCTATCCTCTCAGTCCATGTTCTCGGCCCCCAGCTC
CATCTCTTCCATGACCATGCCATCCAGCATGGGCCCGGGCTCCGTGCCCGGCATGCCCAACTCG
GGCCTCAACAACATCAACAACCTCACGGGCTCCTCGCTCAACTCGGCCATGTCGCCGGGCGCCT
GCCCCTACGGCACCCCCGCCTCGCCCTACAGCGTCTACCGGGACACGTGCAACTCGAGCCTCGC
CAGCCTGCGGCTCAAGTCCAAGCAGCACTCCTCGTTTGGCTACGGCGGTCTGCAGGGTCCAGCG
TCGGGCCTCAACGCCTGCCAGTATAACAGCTGACCGCCCCGCCGGGTCCCCGGGGCCGCCGGCC
GGCAAGGCGCAGCGGGAGCGCGCGGAGCACACGGGGCGCTCGCAGCACCTGGGACCTCACCTCT
GCGCAGCCCCTTCCTCCCCACCCTGCCTCCAGGTTGGTTTTGTGTTTGCTTTTCCGGACCCCGC
TCTGCCCCCAATGAATAAAAAAGGGAAAAAAATCAAGCCAAGGGAGGGGGTGGGGGAGAGAAAG
CAAAAAAAATAAAAAAATTTTAAAAAAAGGACATCGGAGAAAAATGCTGGGGGTGGGGGTGAGT
TGCAATGTCCCTGGCGATGGCGCAGGTGGTGCGTTCGAACCCTCGACCCCCAACTGTCCACTAC
ACCAAGGGGATGTGGCGTGGGGGAAGCCAGCGCCAAAGTGGCTCGGAGAAGACGCCGTTCGTCC
CTGCCGGAGCGCCTCAACCCGTGAACTGAATGTAGGGAGCCTGGAGGCCCTGGGATCGTTCACC
CGATCAAAAACCCGAGGCACCCTCTCCTAGCCTGGGCCGTCCGAGTGCATGCAGCGCGGATCAC
TGTTGGAGCTTGAGCCTGGCTGGGGATGACAGCGCTGATGGGGATCCGGTGTGCCGGATTAGCC
TAAGGCCTCGGGATGCCAGAAGAGCCCAGCAGCCCTGAGCTCTGGAGCCGCACACTTCAGGCCA
CTGAGCCGCAGCTGGCCGTGGCCAGTCCGCAGCAGGAGGGGAAGGGCTCAGCTCTGAGTTCCCC
AGCCCCAGCTTAGCCGCCAGCCCGGCCCTCTGCTCCACTACGGGTCCAGGAGGTGGCCCAGTGA
ACAGCCCCTTCCTCACTGCTCACCCGTGCAAGAGTCGAGCCAGGAGAGCGCGGGGCCACAGCCC
CAGGGCCCCCGCCCACTTTGCACACCCGCTCTCTGGCCCGCGCCCGTTTACAGCGTCCCTGTGT
ATGTCGGACTGACTGTATAGAATTATAAATCTGTCTATATCGACTTGTCCATGTACGTCTATTA
AAACCATAGTCGGAGCGTGCTAAGCA

hide sequence

Protein Sequences


Protein RefSeqs	NP_446076	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAH61966	(Get FASTA)	NCBI Sequence Viewer
	BAB41202	(Get FASTA)	NCBI Sequence Viewer
	EDL93952	(Get FASTA)	NCBI Sequence Viewer
	EDL93953	(Get FASTA)	NCBI Sequence Viewer
	Q99NA7	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_446076 ⟸ NM_053624

- UniProtKB:

Q99NA7 (UniProtKB/Swiss-Prot)

- Sequence:

show sequence

MDAFKGGMSLERLPEGLRPPPPPPHDMGPSFHLARTADPREPLENSASESSDADLPDKERGGEA
KVPEDGGAGSAGCGSAEDPAKKKKQRRQRTHFTSQQLQELEATFQRNRYPDMSMREEIAVWTNL
TEPRVRVWFKNRRAKWRKRERNQQLDLCKGGYVPQFSGLVQPYEDVYAAAGYSYNNWAAKSLAP
APLSTKSFTFFNSMSPLSSQSMFSAPSSISSMTMPSSMGPGSVPGMPNSGLNNINNLTGSSLNS
AMSPGACPYGTPASPYSVYRDTCNSSLASLRLKSKQHSSFGYGGLQGPASGLNACQYNS

hide sequence

RefSeq Acc Id:

XP_006253631 ⟸ XM_006253569

- Peptide Label:

isoform X1

- Sequence:

show sequence

MDAFKGGMSLERLPEGLRPPPPPPHDMGPSFHLARTADPREPLENSASESSDADLPDKERGGEA
KVPEDGGAGSAGCGSAEDPAKKKKQRRQRTHFTSQQLQELEATFQRNRYPDMSMREEIAVWTNL
TEPRVRVWFKNRRAKWRKRERNQQLDLCKGGYVPQFSGLVQPYEDVYAAAGYSYNNWAAKSLAP
APLSTKSFTFFNSMSPLSSQSMFSAPSSISSMTMPSSMGPGSVPGMPNSGLNNINNLTGSSLNS
AMSPGACPYGTPASPYSVYRDTCNSSLASLRLKSKQHSSFGYGGLQGPASGLNACQYNS

hide sequence

RefSeq Acc Id:

ENSRNOP00000015307 ⟸ ENSRNOT00000015307

Transcriptome

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

Promoters

RGD ID:

13700290

Promoter ID:

EPDNEW_R10813

Type:

single initiation site

Name:

Pitx1_1

Description:

paired-like homeodomain 1

SO ACC ID:

SO:0000170

Source:

EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)

Experiment Methods:

Single-end sequencing.

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	17	8,878,261 - 8,878,321	EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)

ACI/EurMcwi (MCW)

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

ACI/EurMcwi (RGD)

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

ACI/N (MCW)

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

BBDP/Wor (RGD)

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

BN/SsN (MCW)

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

Buf/N (MCW)

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

COP/CrCrl (MCW & UW)

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

F344/NCrl (RGD)

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

F344/NRrrc (MCW)

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

FHH/EurMcwi (MCW)

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

FHH/EurMcwi (RGD)

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

FHL/EurMcwi (MCW)

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

FHL/EurMcwi (RGD)

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

GH/OmrMcwi (MCW)

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

GK/Ox (RGD)

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

LE/Stm (RGD)

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

LEW/Crl (RGD)

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

LEW/NCrlBR (RGD)

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

LH/MavRrrc (RGD)

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

LL/MavRrrc (RGD)

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

LN/MavRrrc (RGD)

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

M520/N (MCW)

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

MHS/Gib (RGD)

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

MNS/Gib (RGD)

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

MR/N (MCW)

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

SBH/Ygl (MCW)

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

SBH/Ygl (RGD)

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

SBN/Ygl (MCW)

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

SBN/Ygl (RGD)

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

SHR/NHsd (RGD)

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

SHRSP/Gcrc (RGD)

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

SR/JrHsd (MCW)

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

SR/JrHsd (RGD)

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

SS/Jr (RGD)

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

SS/JrHsdMcwi (MCW)

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

SS/JrHsdMcwi (RGD)

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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:69253	AgrOrtholog
Ensembl Genes	ENSRNOG00000011423	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein	ENSRNOP00000015307	ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000015307	ENTREZGENE, UniProtKB/Swiss-Prot
IMAGE_CLONE	IMAGE:5621094	IMAGE-MGC_LOAD
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:113983	UniProtKB/Swiss-Prot
MGC_CLONE	MGC:72352	IMAGE-MGC_LOAD
NCBI Gene	113983	ENTREZGENE
Pfam	Homeodomain	UniProtKB/Swiss-Prot
	OAR	UniProtKB/Swiss-Prot
PhenoGen	Pitx1	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	TC223333
UniProt	PITX1_RAT	UniProtKB/Swiss-Prot, ENTREZGENE

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2008-09-09	Pitx1	paired-like homeodomain 1	Pitx1	paired-like homeodomain transcription factor 1	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2002-06-10	Pitx1	paired-like homeodomain transcription factor 1			Name updated	70584	APPROVED

RGD Curation Notes

Note Type	Note	Reference
gene_product	belongs to family of bicoid homeodomain proteins	633538

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