Pdlim4 (PDZ and LIM domain 4) - Rat Genome Database

Name: Pdlim4
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: Pdlim4 (PDZ and LIM domain 4) Rattus norvegicus

Analyze

Symbol:

Pdlim4

Name:

PDZ and LIM domain 4

RGD ID:

3575

Description:

Exhibits alpha-actinin binding activity. Involved in actin cytoskeleton organization; excitatory chemical synaptic transmission; and positive regulation of stress fiber assembly. Localizes to several cellular components, including dendritic spine; endosome lumen; and stress fiber. Human ortholog(s) of this gene implicated in osteoporosis. Orthologous to human PDLIM4 (PDZ and LIM domain 4); INTERACTS WITH 1,3,5-trinitro-1,3,5-triazinane; 2,3,7,8-tetrachlorodibenzodioxine; acetamide.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

H-Rev18; LIM protein RIL; PDZ and LIM domain protein 4; reversion induced LIM; reversion induced LIM gene; reversion-induced LIM protein; Ril; RIT-18

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):	PDLIM4 (PDZ and LIM domain 4)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, Panther
Mus musculus (house mouse):	Pdlim4 (PDZ and LIM domain 4)	HGNC	EggNOG, NCBI, OMA, HomoloGene, Inparanoid, Panther, OrthoDB, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Pdlim4 (PDZ and LIM domain 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	PDLIM4 (PDZ and LIM domain 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	PDLIM4 (PDZ and LIM domain 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Pdlim4 (PDZ and LIM domain 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	PDLIM4 (PDZ and LIM domain 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (African green monkey):	PDLIM4 (PDZ and LIM domain 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Pdlim4 (PDZ and LIM domain 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Mus musculus (house mouse):	Pdlim4 (PDZ and LIM domain 4)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Homo sapiens (human):	PDLIM4 (PDZ and LIM domain 4)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Danio rerio (zebrafish):	pdlim4 (PDZ and LIM domain 4)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Drosophila melanogaster (fruit fly):	CG42319	Alliance	DIOPT (OrthoFinder\|PANTHER)
Drosophila melanogaster (fruit fly):	Zasp67	Alliance	DIOPT (OrthoFinder\|PANTHER)

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	10	38,198,686 - 38,212,935 (-)	NCBI
Rnor_6.0 Ensembl	10	39,390,581 - 39,405,311 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	10	39,390,578 - 39,405,322 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	10	39,171,365 - 39,185,480 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
Celera	10	37,540,725 - 37,554,961 (-)	NCBI		Celera
Cytogenetic Map	10	q22	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Hereditary Neoplastic Syndromes (ISO)

Lung Neoplasms (ISO)

Neurodevelopmental Disorders (ISO)

osteoporosis (ISO)

polycystic ovary syndrome (ISO)

systemic primary carnitine deficiency disease (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,3,5-trinitro-1,3,5-triazinane (EXP)

17alpha-ethynylestradiol (ISO)

17beta-estradiol (ISO)

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

3-isobutyl-1-methyl-7H-xanthine (ISO)

4-\{[(5,5,8,8-tetramethyl-5,6,7,8-tetrahydronaphthalen-2-yl)carbonyl]amino\}benzoic acid (ISO)

4-hydroxyphenyl retinamide (ISO)

5-aza-2'-deoxycytidine (ISO)

8-Br-cAMP (ISO)

acetamide (EXP)

all-trans-retinoic acid (ISO)

arsenite(3-) (ISO)

benzo[a]pyrene (ISO)

bisphenol A (EXP)

cadmium atom (ISO)

carbon nanotube (ISO)

cyclosporin A (ISO)

cytarabine (ISO)

deoxynivalenol (ISO)

dexamethasone (ISO)

dibutyl phthalate (ISO)

dichloroacetic acid (ISO)

dorsomorphin (ISO)

doxorubicin (ISO)

elemental selenium (ISO)

endosulfan (EXP)

entinostat (ISO)

flavonoids (EXP)

furan (EXP)

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

paracetamol (ISO)

pirinixic acid (ISO)

potassium chromate (ISO)

SB 431542 (ISO)

selenium atom (ISO)

sodium arsenite (ISO)

Soman (EXP)

sunitinib (ISO)

tert-butyl hydroperoxide (ISO)

thimerosal (ISO)

titanium dioxide (ISO)

toluene (EXP)

Tributyltin oxide (ISO)

trichostatin A (ISO)

triclosan (ISO)

valproic acid (ISO)

vitamin E (ISO)

vorinostat (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

actin cytoskeleton organization (IBA,IDA)

actin cytoskeleton reorganization (IEA,ISO)

excitatory chemical synaptic transmission (IDA)

heart development (IBA)

muscle structure development (IBA)

positive regulation of stress fiber assembly (IDA,IMP)

Cellular Component

actin cytoskeleton (IPI)

adherens junction (IBA)

cytoplasm (ISO)

cytoskeleton (ISO)

dendritic spine (IDA)

early endosome lumen (IDA)

early endosome membrane (IEA)

filamentous actin (IBA,IEA,ISO)

lamellipodium (IEA,ISO)

nucleus (IEA,ISO)

perinuclear region of cytoplasm (IEA,ISO)

postsynaptic membrane (IDA)

recycling endosome lumen (IDA)

recycling endosome membrane (IEA)

stress fiber (IBA,IDA,IEA,ISO)

Z disc (IBA)

Molecular Function

actin binding (IBA)

actinin binding (IPI)

alpha-actinin binding (IEA,IPI,ISO)

metal ion binding (IEA)

muscle alpha-actinin binding (IBA)

protein binding (IPI,ISO)

protein homodimerization activity (IEA,ISO)

protein phosphatase binding (IEA,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.	Kiess M, etal., Oncogene 1995 Jan 5;10(1):61-8.
3.	MGD data from the GO Consortium
4.	Miyazaki K, etal., Exp Cell Res. 2012 Aug 15;318(14):1716-25. doi: 10.1016/j.yexcr.2012.05.006. Epub 2012 May 30.
5.	NCBI rat LocusLink and RefSeq merged data July 26, 2002
6.	RGD automated data pipeline
7.	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
8.	RGD automated import pipeline for gene-chemical interactions
9.	Schulz TW, etal., J Neurosci. 2004 Sep 29;24(39):8584-94.
10.	Vallenius T, etal., Exp Cell Res 2004 Feb 1;293(1):117-28.
11.	Wang H, etal., Gene 1995 Nov 20;165(2):267-71.

Additional References at PubMed

PMID:1300470	PMID:10826496	PMID:15663004	PMID:19307596	PMID:20120020	PMID:21636573	PMID:25158098

Genomics

Comparative Map Data

Pdlim4
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	10	38,198,686 - 38,212,935 (-)	NCBI
Rnor_6.0 Ensembl	10	39,390,581 - 39,405,311 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	10	39,390,578 - 39,405,322 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	10	39,171,365 - 39,185,480 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
Celera	10	37,540,725 - 37,554,961 (-)	NCBI		Celera
Cytogenetic Map	10	q22	NCBI

PDLIM4
(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	132,257,696 - 132,273,454 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	5	132,257,671 - 132,273,454 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	5	131,593,389 - 131,609,147 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	5	131,621,286 - 131,637,046 (+)	NCBI	NCBI36		hg18	NCBI36
Build 34	5	131,621,285 - 131,637,046	NCBI
Celera	5	127,723,467 - 127,739,259 (+)	NCBI
Cytogenetic Map	5	q31.1	NCBI
HuRef	5	126,785,601 - 126,801,399 (+)	NCBI		HuRef
CHM1_1	5	131,026,116 - 131,041,912 (+)	NCBI		CHM1_1

Pdlim4
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	11	53,945,754 - 53,959,858 (-)	NCBI	GRCm39		mm39
GRCm39 Ensembl	11	53,945,754 - 53,959,840 (-)	Ensembl
GRCm38	11	54,054,928 - 54,069,032 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	11	54,054,928 - 54,069,014 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	11	53,868,430 - 53,882,519 (-)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	11	53,898,355 - 53,912,391 (-)	NCBI			mm8
Celera	11	58,642,620 - 58,656,709 (-)	NCBI		Celera
Cytogenetic Map	11	B1.3	NCBI
cM Map	11	32.13	NCBI

Pdlim4
(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	3,638,264 - 3,646,600 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955408	3,638,264 - 3,647,792 (+)	NCBI	ChiLan1.0	ChiLan1.0

PDLIM4
(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	133,843,313 - 133,857,935 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	5	133,843,313 - 133,857,935 (+)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	5	127,680,339 - 127,696,172 (+)	NCBI	Mhudiblu_PPA_v0		panPan3

PDLIM4
(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	20,570,833 - 20,585,594 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
CanFam3.1	11	20,570,839 - 20,587,185 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1

Pdlim4
(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_004936647	2,891,025 - 2,905,197 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

PDLIM4
(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	134,555,666 - 134,570,350 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	2	134,555,367 - 134,570,356 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	2	139,959,492 - 139,973,907 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

PDLIM4
(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	35,087,966 - 35,102,703 (+)	NCBI
ChlSab1.1 Ensembl	23	35,088,001 - 35,105,018 (+)	Ensembl

Pdlim4
(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	39,826,435 - 39,840,280 (-)	NCBI

QTLs in Region (Rnor_6.0)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
7411611	Foco17	Food consumption QTL 17	18.7	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	10	1	42669970	Rat
10401803	Kidm50	Kidney mass QTL 50			kidney mass (VT:0002707)	both kidneys wet weight (CMO:0000085)	10	1	44902893	Rat
631554	Bp133	Blood pressure QTL 133		0.005	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	764421	66221621	Rat
2298544	Neuinf9	Neuroinflammation QTL 9	4.6		nervous system integrity trait (VT:0010566)	spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)	10	5877536	64401490	Rat
8662860	Vetf10	Vascular elastic tissue fragility QTL 10			artery integrity trait (VT:0010639)	number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)	10	6229095	75983805	Rat
61427	Cia16	Collagen induced arthritis QTL 16	3.2		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	6429075	99492409	Rat
1578761	Stresp21	Stress response QTL 21	3.3		thymus mass (VT:0004954)	thymus wet weight (CMO:0000855)	10	7521450	52521450	Rat
2303118	Mamtr7	Mammary tumor resistance QTL 7		0.003	mammary gland integrity trait (VT:0010552)	mammary tumor growth rate (CMO:0000344)	10	9841807	108540162	Rat
9590310	Scort19	Serum corticosterone level QTL 19	6.3	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	10	12639513	57639513	Rat
9590268	Scort13	Serum corticosterone level QTL 13	3.26	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	10	12639513	57639513	Rat
9589136	Insul27	Insulin level QTL 27	10.46	0.001	blood insulin amount (VT:0001560)	plasma insulin level (CMO:0000342)	10	12639513	57639513	Rat
2301967	Cm73	Cardiac mass QTL 73	4.55		heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	10	14827894	92423564	Rat
631268	Cia21	Collagen induced arthritis QTL 21	3.1		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	14827894	107857673	Rat
2316949	Gluco60	Glucose level QTL 60	3.7		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	10	14827894	110992275	Rat
1354587	Kidm21	Kidney mass QTL 21	3.3		kidney mass (VT:0002707)	right kidney wet weight (CMO:0000082)	10	15375474	62469074	Rat
631564	Apr3	Acute phase response QTL 3	3.9		blood interleukin-6 amount (VT:0008595)	plasma interleukin-6 level (CMO:0001927)	10	16468736	61468736	Rat
6893350	Bw99	Body weight QTL 99	0.87	0.16	body mass (VT:0001259)	body weight (CMO:0000012)	1	17121542	62121542	Rat
6893352	Bw100	Body weight QTL 100	0.33	0.6	body mass (VT:0001259)	body weight (CMO:0000012)	1	17121542	62121542	Rat
631532	Cm50	Cardiac mass QTL 50	6.6		heart mass (VT:0007028)	calculated heart weight (CMO:0000073)	10	18246394	53637634	Rat
1598852	Anxrr19	Anxiety related response QTL 19	5.07		body movement coordination trait (VT:0005424)	number of rearing movements in an experimental apparatus (CMO:0001752)	10	19402814	64402814	Rat
1554317	Bmd4	Bone mineral density QTL 4	9.4	0.0001	lumbar vertebra mineral mass (VT:0010511)	volumetric bone mineral density (CMO:0001553)	10	20170031	102897474	Rat
70223	Bp57	Blood pressure QTL 57	5		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	21523906	83549467	Rat
70188	BpQTLcluster1	Blood pressure QTL cluster 1	4.864		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	1	21523906	90312401	Rat
70188	BpQTLcluster1	Blood pressure QTL cluster 1	4.864		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	21523906	90312401	Rat
70188	BpQTLcluster1	Blood pressure QTL cluster 1	4.864		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	21523906	90312401	Rat
70188	BpQTLcluster1	Blood pressure QTL cluster 1	4.864		arterial blood pressure trait (VT:2000000)	pulse pressure (CMO:0000292)	1	21523906	90312401	Rat
70198	BpQTLcluster9	Blood pressure QTL cluster 9	2.94		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	21523906	90312401	Rat
1581497	Esta1	Estrogen-induced thymic atrophy QTL 1			thymus mass (VT:0004954)	thymus wet weight (CMO:0000855)	10	21707766	64648311	Rat
724556	Pur2	Proteinuria QTL 2	5.5		urine protein amount (VT:0005160)	urine protein level (CMO:0000591)	10	22901497	93886300	Rat
1331762	Rf40	Renal function QTL 40	3.873		kidney blood vessel physiology trait (VT:0100012)	absolute change in renal vascular resistance (CMO:0001900)	10	23861015	66539843	Rat
1331791	Cm31	Cardiac mass QTL 31	3.84606		heart mass (VT:0007028)	heart wet weight (CMO:0000069)	10	23861015	112626471	Rat
631267	Cia20	Collagen induced arthritis QTL 20	3.2		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	24483076	107857673	Rat
61325	Aia5	Adjuvant induced arthritis QTL 5		0.01	joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	24483076	107857673	Rat
61354	Pia10	Pristane induced arthritis QTL 10		0.01	joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	24483076	107857673	Rat
634329	Pia15	Pristane induced arthritis QTL 15	3.1		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	24884084	47487910	Rat
70224	Eae3	Experimental allergic encephalomyelitis QTL 3	4.1		nervous system integrity trait (VT:0010566)	experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)	10	27237530	64648311	Rat
1298069	Bp168	Blood pressure QTL 168	5.5		blood pressure trait (VT:0000183)	systolic blood pressure (CMO:0000004)	10	27237530	101482600	Rat
631542	Bp82	Blood pressure QTL 82	6.8		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	27237530	102427718	Rat
2300171	Bmd58	Bone mineral density QTL 58	4.9	0.0001	lumbar vertebra mineral mass (VT:0010511)	volumetric bone mineral density (CMO:0001553)	10	28789280	73789280	Rat
1600371	Mcs21	Mammary carcinoma susceptibility QTL 21	3		mammary gland integrity trait (VT:0010552)	mammary tumor growth rate (CMO:0000344)	10	30021354	54057745	Rat
2292441	Bp308	Blood pressure QTL 308			arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	30099909	75099909	Rat
10402859	Bp381	Blood pressure QTL 381		0.002	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	30099909	75099909	Rat
724527	Bp148	Blood pressure QTL 148		0.0001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	30983805	75983805	Rat
1576311	Pia26	Pristane induced arthritis QTL 26			joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	31919397	78343192	Rat
1578779	Tcas10	Tongue tumor susceptibility QTL 10	3.12		tongue integrity trait (VT:0010553)	number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)	10	33179030	78179030	Rat
631557	Bp136	Blood pressure QTL 136		0.003	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	33343192	78343192	Rat
1576319	Cia29	Collagen induced arthritis QTL 29			joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	35139424	80139424	Rat
61332	Eau3	Experimental allergic uveoretinitis QTL 3		0.004	uvea integrity trait (VT:0010551)	experimental autoimmune uveitis score (CMO:0001504)	10	35669465	46851407	Rat
6893342	Cm78	Cardiac mass QTL 78	0.1	0.88	heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	10	36185929	82675365	Rat
631552	Vetf2	Vascular elastic tissue fragility QTL 2	4.5	0.0002	aorta elastic tissue integrity trait (VT:0010556)	artery internal elastic lamina non-tumorous lesion count (CMO:0001913)	10	36185929	95845311	Rat
1354614	Hpcl1	Hepatic cholesterol level QTL 1	3.3		liver cholesterol amount (VT:0010498)	liver cholesterol level (CMO:0001597)	10	36584373	53645194	Rat
1358897	Stresp6	Stress response QTL 6	4.17	0.022	blood norepinephrine amount (VT:0005663)	plasma norepinephrine level (CMO:0001010)	10	36584373	66539843	Rat
61441	Btemp1	Thermal response to stress QTL 1	4		body temperature trait (VT:0005535)	core body temperature (CMO:0001036)	10	36584560	66015527	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	94
Count of miRNA genes:	76
Interacting mature miRNAs:	81
Transcripts:	ENSRNOT00000074616
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	3	10	11	2	6	2	1	3	72	23	36		1
Low		33	46	39	13	39	7	8	2	12	5	11	7
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_017062	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_017597029	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_017597030	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039085241	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039085242	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	CH473948	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000219	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	X76454	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000074616 ⟹ ENSRNOP00000064261

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	10	39,390,581 - 39,405,311 (-)	Ensembl

RefSeq Acc Id:

NM_017062 ⟹ NP_058758

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	10	38,198,689 - 38,212,914 (-)	NCBI
Rnor_6.0	10	39,390,581 - 39,405,311 (-)	NCBI
Rnor_5.0	10	39,171,365 - 39,185,480 (-)	NCBI
Celera	10	37,540,725 - 37,554,961 (-)	RGD

Sequence:

show sequence

AGGCGGCGGCAACGGCGGCGGCGACTCCTCCGTGTCCGCCTCCAGCTCCGGCTGCAGCTCCGGC
CCGCGATGACCCACGCGGTGACCCTGCGCGGCCCTTCACCCTGGGGCTTCCGCCTGGTGGGCGG
CCGTGACTTCAGTGCCCCCCTCACCATCTCGCGGGTTCATGCTGGGAGCAAAGCGGCCCTGGCT
GCCCTGTGCCCAGGTGACTCGATCCAAGCCATCAACGGTGAGAGCACTGAGCTCATGACACACC
TGGAGGCCCAGAACCGCATTAAAGGCTGCCACGATCACCTTACACTCTCAGTAAGCAGGCCTGA
GAACAAGAACTGGCCCAGTTCCCCTAATGACAAGGCCCAAGCGCATAGGATCCACATTGACCCT
GAGGCCCAGGATGGCAGCCCAGCCACCAGCAGGCGGTCCTCAATCTCTGGAATTAGTCTGGAGG
ACAACAGATCGGGCCTGGGATCTCCGTATGGCCAGCCACCTCGCCTTCCAGTTCCTCACAATGG
CAGCAGCAATGAGGTCACCCTGCCATCCCAGATGAGCGCTCTGCATGTGTCTCCACCCCCCAGT
GCTGACACACCCAGGATTCTCCCTCGGAACCGGGACTGCAGGGTGGACCTGGGTTCAGAGGTAT
ACAGGATGTTAAGGGAGCCAGCAGAGCCAGCAGCCTCAGAGCCCAAACAGTCTGGATCCTTCCG
CTACTTGCAAGGCATGCTAGAGGCTGGCGAAGGCGGGGATCGGCCTGGGTCTGGTGGTTCCCGG
AACCTCAAGCCAGCAGCCAGCAAGCTGGGTGCTCCACTGAGTGGCCTGCAGGGGTTACCAGAGT
GCACACGCTGTGGCCACGGGATCGTGGGAACCATCGTCAAGGCGAGGGACAAGCTCTACCATCC
CGAGTGCTTCATGTGTAGCGACTGTGGCCTGAATCTCAAGCAGCGTGGGTACTTCTTCCTAGAC
GAACGGCTGTACTGCGAGAACCATGCCAAGGCTCGAGTCAAGCCACCGGAGGGATATGACGTGG
TGGCTGTATATCCCAATGCCAAGGTGGAACTTGTCTGAGCTGGGAAATCTTGTCTTGCCTCTGC
TTCATTTAATGTCCCCCCTCCCCACCCCCGTGGCCTGTGTAAATATATGTCCTCCTGGCCTTTC
TAATAAAGTCCCTCTGCTTGTCCTCCAAAAAAAAAAAA

hide sequence

RefSeq Acc Id:

XM_017597029 ⟹ XP_017452518

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	10	38,198,686 - 38,212,932 (-)	NCBI
Rnor_6.0	10	39,390,578 - 39,405,322 (-)	NCBI

Sequence:

show sequence

GCGGGGCGGCCAGGCGGCGGCAACGGCGGCGGCGACTCCTCCGTGTCCGGCTCCAGCTCCGGCT
GCAGCTCCGGCCCGCGATGACCCACTCGGTGACCCTGCGCGGCCCTTCACCCTGGGGCTTCCGC
CTGGTGGGCGGCCGTGACTTCAGTGCCCCCCTCACCATCTCGCGGGTTCATGCTGGGAGCAAAG
CGGCCCTGGCTGCCCTGTGCCCAGGTGACTTGATCCAAGCCATCAACGGTGAGAGCACTGAGCT
CATGACACACCTGGAGGCCCAGAACCGCATTAAAGGCTGCCACGATCACCTTACACTCTCAGTA
AGCAGGCCTGAGAACAAGAACTGGCCCAGTTCCCCTGATGACAAGGCCCAAGCGCATAGGATCC
ACATTGACCCTGAGGCCCAGGCCTCACTCTTGCAGGATGGCAGCCCAGCCACCAGCAGGCGGTC
CTCAATCTCTGGAATTAGTCTGGAGGACAACAGATCGGGCCTGGGATCTCCGTATGGCCAGCCA
CCTCGCCTTCCAGTTCCTCACAATGGCAGCAGCAATGAGGTCACCCTGCCATCCCAGATGAGCG
CTCTGCATGTGTCTCCACCCCCCAGTGCTGACACACCCAGGATTCTCCCTCGGAACCGGGACTG
CAGGGTGGACCTGGGTTCAGAGGTATACAGGATGTTAAGGGAGCCAGCAGAGCCAGCAGCCTCA
GAGCCCAAACAGTCTGGATCCTTCCGCTACTTGCAAGGCATGCTAGAGGCTGGCGAAGGCGGGG
ATCGGCCTGGGTCTGGTGGTTCCCGGAACCTCAAGCCAGCAGCCAGCAAGCTGGGTGCTCCACT
GAGTGGCCTGCAGGGGTTACCAGAGTGCACACGCTGTGGCCACGGGATCGTGGGAACCATCGTC
AAGGCGAGGGACAAACTCTACCATCCCGAGTGCTTCATGTGTAGCGACTGTGGCCTGAATCTCA
AGCAGCGTGGGTACTTCTTCCTAGACGAACGGCTGTACTGCGAGAACCATGCCAAGGCTCGAGT
CAAGCCACCGGAGGGATATGACGTGGTGGCTGTATATCCCAATGCCAAGGTGGAACTTGTCTGA
GCTGGGAAATCTTGTCTTGCCTCTGCTTCATTTAATGTCCCCCCTCCCCACCCCCGTGGCCTGT
GTAAATATATGTCCTCCTGGCCTTTCTAATAAAGTCCCTCTGCTTGTCCTGGA

hide sequence

RefSeq Acc Id:

XM_017597030 ⟹ XP_017452519

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	10	38,198,686 - 38,208,448 (-)	NCBI
Rnor_6.0	10	39,390,578 - 39,401,204 (-)	NCBI

Sequence:

show sequence

ATATTTCTTGAGGCAGCCTATTTTAGGGCAAGGCAGCTTGGGCAGTGCCCACATGAAGCTTCTA
GCCAAGGAACTGCCAGCACCCGGCTTTGTCCACTCTCTATTAGAAACTGACTGAGCTGAGTCTG
AGTTGCCAAGAGCTCCCACCCCCAGCCACACTGATAGGAACAAGGTCATTAGTAATTCTTAAGC
CACAGAGAGGTGCTGGCTGCTGATACTGGGCAAGAATGAGGACTCCTTGTCTGTTCTCTATTTG
TTTCCAGGGTGCCCGGGCGCCTCAGTCCCCAGGTTCTTATTTAAATGTTGCTGAGCCTTTCCCT
ACCCCCAACCCATGGCCTTCATCAGATGACCGGAAGTGCTTGAGTCTGTTGGGTCAAATAGAGG
ATCCAGCAGAGGAAGCAGAGATGGGGTTATAACCTCGGAGTGCGGGCTGGTGGTTGGAACTGGA
TGGCTTTGAACTTGCCTAAGGAGGGGGATATACACACCTCCTCCTTTCAGTGGTTCATGCTGGG
AGCAAAGCGGCCCTGGCTGCCCTGTGCCCAGGTGACTTGATCCAAGCCATCAACGGTGAGAGCA
CTGAGCTCATGACACACCTGGAGGCCCAGAACCGCATTAAAGGCTGCCACGATCACCTTACACT
CTCAGTAAGCAGGCCTGAGAACAAGAACTGGCCCAGTTCCCCTGATGACAAGGCCCAAGCGCAT
AGGATCCACATTGACCCTGAGGCCCAGGCCTCACTCTTGCAGGATGGCAGCCCAGCCACCAGCA
GGCGGTCCTCAATCTCTGGAATTAGTCTGGAGGACAACAGATCGGGCCTGGGATCTCCGTATGG
CCAGCCACCTCGCCTTCCAGTTCCTCACAATGGCAGCAGCAATGAGGTCACCCTGCCATCCCAG
ATGAGCGCTCTGCATGTGTCTCCACCCCCCAGTGCTGACACACCCAGGATTCTCCCTCGGAACC
GGGACTGCAGGGTGGACCTGGGTTCAGAGGTATACAGGATGTTAAGGGAGCCAGCAGAGCCAGC
AGCCTCAGAGCCCAAACAGTCTGGATCCTTCCGCTACTTGCAAGGCATGCTAGAGGCTGGCGAA
GGCGGGGATCGGCCTGGGTCTGGTGGTTCCCGGAACCTCAAGCCAGCAGCCAGCAAGCTGGGTG
CTCCACTGAGTGGCCTGCAGGGGTTACCAGAGTGCACACGCTGTGGCCACGGGATCGTGGGAAC
CATCGTCAAGGCGAGGGACAAACTCTACCATCCCGAGTGCTTCATGTGTAGCGACTGTGGCCTG
AATCTCAAGCAGCGTGGGTACTTCTTCCTAGACGAACGGCTGTACTGCGAGAACCATGCCAAGG
CTCGAGTCAAGCCACCGGAGGGATATGACGTGGTGGCTGTATATCCCAATGCCAAGGTGGAACT
TGTCTGAGCTGGGAAATCTTGTCTTGCCTCTGCTTCATTTAATGTCCCCCCTCCCCACCCCCGT
GGCCTGTGTAAATATATGTCCTCCTGGCCTTTCTAATAAAGTCCCTCTGCTTGTCCTGGA

hide sequence

RefSeq Acc Id:

XM_017597031 ⟹ XP_017452520

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	10	39,390,578 - 39,400,672 (-)	NCBI

Sequence:

show sequence

TAATGGGGGACACAGGGAGTTGCTCTCAGAGTAACTGGGCCTGAGGGAGGAGTAGACTAGGTGA
TAAGCAGAGTTAAGGAGTCAGGAGATTATACCAACGTATGGGCCCATAAAGATGTCAGTGCTGT
CTGGTGCCTTTAAGTGCCCTACAGGTGTTTCTATGGGGTAGCCATAGCAATGGTGGAGCAGGCA
AAAAATGTGTGGCAGGCCTGAGAGGTTCATGCTGGGAGCAAAGCGGCCCTGGCTGCCCTGTGCC
CAGGTGACTTGATCCAAGCCATCAACGGTGAGAGCACTGAGCTCATGACACACCTGGAGGCCCA
GAACCGCATTAAAGGCTGCCACGATCACCTTACACTCTCAGTAAGCAGGCCTGAGAACAAGAAC
TGGCCCAGTTCCCCTGATGACAAGGCCCAAGCGCATAGGATCCACATTGACCCTGAGGCCCAGG
CCTCACTCTTGCAGGATGGCAGCCCAGCCACCAGCAGGCGGTCCTCAATCTCTGGAATTAGTCT
GGAGGACAACAGATCGGGCCTGGGATCTCCGTATGGCCAGCCACCTCGCCTTCCAGTTCCTCAC
AATGGCAGCAGCAATGAGGTCACCCTGCCATCCCAGATGAGCGCTCTGCATGTGTCTCCACCCC
CCAGTGCTGACACACCCAGGATTCTCCCTCGGAACCGGGACTGCAGGGTGGACCTGGGTTCAGA
GGTATACAGGATGTTAAGGGAGCCAGCAGAGCCAGCAGCCTCAGAGCCCAAACAGTCTGGATCC
TTCCGCTACTTGCAAGGCATGCTAGAGGCTGGCGAAGGCGGGGATCGGCCTGGGTCTGGTGGTT
CCCGGAACCTCAAGCCAGCAGCCAGCAAGCTGGGTGCTCCACTGAGTGGCCTGCAGGGGTTACC
AGAGTGCACACGCTGTGGCCACGGGATCGTGGGAACCATCGTCAAGGCGAGGGACAAACTCTAC
CATCCCGAGTGCTTCATGTGTAGCGACTGTGGCCTGAATCTCAAGCAGCGTGGGTACTTCTTCC
TAGACGAACGGCTGTACTGCGAGAACCATGCCAAGGCTCGAGTCAAGCCACCGGAGGGATATGA
CGTGGTGGCTGTATATCCCAATGCCAAGGTGGAACTTGTCTGAGCTGGGAAATCTTGTCTTGCC
TCTGCTTCATTTAATGTCCCCCCTCCCCACCCCCGTGGCCTGTGTAAATATATGTCCTCCTGGC
CTTTCTAATAAAGTCCCTCTGCTTGTCCTGGA

hide sequence

RefSeq Acc Id:

XM_039085241 ⟹ XP_038941169

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	10	38,198,686 - 38,212,935 (-)	NCBI

RefSeq Acc Id:

XM_039085242 ⟹ XP_038941170

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	10	38,198,686 - 38,212,932 (-)	NCBI

Protein Sequences


Protein RefSeqs	NP_058758	(Get FASTA)	NCBI Sequence Viewer
	XP_017452518	(Get FASTA)	NCBI Sequence Viewer
	XP_017452519	(Get FASTA)	NCBI Sequence Viewer
	XP_038941169	(Get FASTA)	NCBI Sequence Viewer
	XP_038941170	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	CAA53992	(Get FASTA)	NCBI Sequence Viewer
	EDM04418	(Get FASTA)	NCBI Sequence Viewer
	EDM04419	(Get FASTA)	NCBI Sequence Viewer
	EDM04420	(Get FASTA)	NCBI Sequence Viewer
	P36202	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_058758 ⟸ NM_017062

- UniProtKB:

P36202 (UniProtKB/Swiss-Prot)

- Sequence:

show sequence

MTHAVTLRGPSPWGFRLVGGRDFSAPLTISRVHAGSKAALAALCPGDSIQAINGESTELMTHLE
AQNRIKGCHDHLTLSVSRPENKNWPSSPNDKAQAHRIHIDPEAQDGSPATSRRSSISGISLEDN
RSGLGSPYGQPPRLPVPHNGSSNEVTLPSQMSALHVSPPPSADTPRILPRNRDCRVDLGSEVYR
MLREPAEPAASEPKQSGSFRYLQGMLEAGEGGDRPGSGGSRNLKPAASKLGAPLSGLQGLPECT
RCGHGIVGTIVKARDKLYHPECFMCSDCGLNLKQRGYFFLDERLYCENHAKARVKPPEGYDVVA
VYPNAKVELV

hide sequence

RefSeq Acc Id:

XP_017452518 ⟸ XM_017597029

- Peptide Label:

isoform X1

- Sequence:

show sequence

MTHSVTLRGPSPWGFRLVGGRDFSAPLTISRVHAGSKAALAALCPGDLIQAINGESTELMTHLE
AQNRIKGCHDHLTLSVSRPENKNWPSSPDDKAQAHRIHIDPEAQASLLQDGSPATSRRSSISGI
SLEDNRSGLGSPYGQPPRLPVPHNGSSNEVTLPSQMSALHVSPPPSADTPRILPRNRDCRVDLG
SEVYRMLREPAEPAASEPKQSGSFRYLQGMLEAGEGGDRPGSGGSRNLKPAASKLGAPLSGLQG
LPECTRCGHGIVGTIVKARDKLYHPECFMCSDCGLNLKQRGYFFLDERLYCENHAKARVKPPEG
YDVVAVYPNAKVELV

hide sequence

RefSeq Acc Id:

XP_017452519 ⟸ XM_017597030

- Peptide Label:

isoform X2

- Sequence:

show sequence

MTHLEAQNRIKGCHDHLTLSVSRPENKNWPSSPDDKAQAHRIHIDPEAQASLLQDGSPATSRRS
SISGISLEDNRSGLGSPYGQPPRLPVPHNGSSNEVTLPSQMSALHVSPPPSADTPRILPRNRDC
RVDLGSEVYRMLREPAEPAASEPKQSGSFRYLQGMLEAGEGGDRPGSGGSRNLKPAASKLGAPL
SGLQGLPECTRCGHGIVGTIVKARDKLYHPECFMCSDCGLNLKQRGYFFLDERLYCENHAKARV
KPPEGYDVVAVYPNAKVELV

hide sequence

RefSeq Acc Id:

XP_017452520 ⟸ XM_017597031

- Peptide Label:

isoform X2

- Sequence:

show sequence

MTHLEAQNRIKGCHDHLTLSVSRPENKNWPSSPDDKAQAHRIHIDPEAQASLLQDGSPATSRRS
SISGISLEDNRSGLGSPYGQPPRLPVPHNGSSNEVTLPSQMSALHVSPPPSADTPRILPRNRDC
RVDLGSEVYRMLREPAEPAASEPKQSGSFRYLQGMLEAGEGGDRPGSGGSRNLKPAASKLGAPL
SGLQGLPECTRCGHGIVGTIVKARDKLYHPECFMCSDCGLNLKQRGYFFLDERLYCENHAKARV
KPPEGYDVVAVYPNAKVELV

hide sequence

RefSeq Acc Id:

ENSRNOP00000064261 ⟸ ENSRNOT00000074616

RefSeq Acc Id:	XP_038941169 ⟸ XM_039085241
- Peptide Label:	isoform X3

RefSeq Acc Id:	XP_038941170 ⟸ XM_039085242
- Peptide Label:	isoform X4

Protein Domains

LIM zinc-binding PDZ

Transcriptome

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

Promoters

RGD ID:

13697184

Promoter ID:

EPDNEW_R7709

Type:

initiation region

Name:

Pdlim4_1

Description:

PDZ and LIM domain 4

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	10	39,405,284 - 39,405,344	EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)

ACI/EurMcwi (MCW)

Visual

CSV

TAB

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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)

Visual

CSV

TAB

Printer

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

ACI/N (MCW)

Visual

CSV

TAB

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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)

Visual

CSV

TAB

Printer

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

BN/SsN (MCW)

Visual

CSV

TAB

Printer

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

Buf/N (MCW)

Visual

CSV

TAB

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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)

Visual

CSV

TAB

Printer

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

F344/NCrl (RGD)

Visual

CSV

TAB

Printer

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

F344/NRrrc (MCW)

Visual

CSV

TAB

Printer

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

FHH/EurMcwi (MCW)

Visual

CSV

TAB

Printer

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

FHH/EurMcwi (RGD)

Visual

CSV

TAB

Printer

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

FHL/EurMcwi (MCW)

Visual

CSV

TAB

Printer

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

FHL/EurMcwi (RGD)

Visual

CSV

TAB

Printer

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

GH/OmrMcwi (MCW)

Visual

CSV

TAB

Printer

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

GK/Ox (RGD)

Visual

CSV

TAB

Printer

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

LE/Stm (RGD)

Visual

CSV

TAB

Printer

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

LEW/Crl (RGD)

Visual

CSV

TAB

Printer

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

LEW/NCrlBR (RGD)

Visual

CSV

TAB

Printer

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

LH/MavRrrc (RGD)

Visual

CSV

TAB

Printer

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

LL/MavRrrc (RGD)

Visual

CSV

TAB

Printer

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

LN/MavRrrc (RGD)

Visual

CSV

TAB

Printer

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

M520/N (MCW)

Visual

CSV

TAB

Printer

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

MHS/Gib (RGD)

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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:3575	AgrOrtholog
Ensembl Genes	ENSRNOG00000050794	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000064261	ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000074616	ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH	2.30.42.10	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro	DUF4749	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	PDZ	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	PDZ_sf	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Znf_LIM	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report	rno:24915	UniProtKB/Swiss-Prot
NCBI Gene	24915	ENTREZGENE
Pfam	DUF4749	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	LIM	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	PDZ	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen	Pdlim4	PhenoGen
PROSITE	LIM_DOMAIN_1	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	LIM_DOMAIN_2	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	PDZ	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART	LIM	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	PDZ	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP	SSF50156	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt	M0R4H5_RAT	UniProtKB/TrEMBL
	P36202	ENTREZGENE, UniProtKB/Swiss-Prot

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2013-08-07	Pdlim4	PDZ and LIM domain 4	Ril	reversion induced LIM gene	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2002-06-10	Ril	Reversion induced LIM gene			Symbol and Name status set to approved	70586	APPROVED

RGD Curation Notes

Note Type	Note	Reference
gene_domains	contains a LIM/double zinc finger domain	633750
gene_physical_interaction	binds alpha-actinin, binding occurs via the Ril PDZ domain	1300470
gene_protein	327-amino acids	68225

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