Pdlim1 (PDZ and LIM domain 1) - Rat Genome Database

Name: Pdlim1
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: Pdlim1 (PDZ and LIM domain 1) Rattus norvegicus

Analyze

Symbol:

Pdlim1

Name:

PDZ and LIM domain 1

RGD ID:

68324

Description:

Exhibits actin binding activity. Involved in several processes, including actin cytoskeleton organization; fibroblast migration; and maintenance of cell polarity. Localizes to Z disc and stress fiber. Orthologous to human PDLIM1 (PDZ and LIM domain 1); INTERACTS WITH (+)-schisandrin B; 1-naphthyl isothiocyanate; 2,3,7,8-tetrachlorodibenzodioxine.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

C-terminal LIM domain protein 1; CLP36; elfin; LIM domain protein CLP-36; LIM protein; PDZ and LIM domain 1 (elfin); PDZ and LIM domain protein 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):	PDLIM1 (PDZ and LIM domain 1)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Pdlim1 (PDZ and LIM domain 1 (elfin))	HGNC	Treefam, EggNOG, OrthoMCL, NCBI, OMA, HomoloGene, Inparanoid, Panther, PhylomeDB, OrthoDB, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Pdlim1 (PDZ and LIM domain 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	PDLIM1 (PDZ and LIM domain 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	PDLIM1 (PDZ and LIM domain 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Pdlim1 (PDZ and LIM domain 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	PDLIM1 (PDZ and LIM domain 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (African green monkey):	PDLIM1 (PDZ and LIM domain 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Pdlim1 (PDZ and LIM domain 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	PDLIM1 (PDZ and LIM domain 1)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Mus musculus (house mouse):	Pdlim1 (PDZ and LIM domain 1 (elfin))	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Danio rerio (zebrafish):	pdlim1 (PDZ and LIM domain 1 (elfin))	Alliance	DIOPT (PhylomeDB\|TreeFam)
Caenorhabditis elegans (roundworm):	alp-1	Alliance	DIOPT (Ensembl Compara\|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	1	239,042,372 - 239,091,074 (-)	NCBI
Rnor_6.0 Ensembl	1	259,308,296 - 259,357,056 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	1	259,308,326 - 259,357,006 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	1	266,752,410 - 266,800,840 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	1	245,350,086 - 245,399,534 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	1	245,446,644 - 245,496,093 (-)	NCBI
Celera	1	234,889,852 - 234,937,718 (-)	NCBI		Celera
Cytogenetic Map	1	q54	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(+)-schisandrin B (EXP)

1,1-dichloroethene (ISO)

1,2-dimethylhydrazine (ISO)

1-naphthyl isothiocyanate (EXP)

17alpha-ethynylestradiol (ISO)

17beta-estradiol (ISO)

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

2,6-dinitrotoluene (EXP)

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

4,4'-sulfonyldiphenol (ISO)

4-hydroxyphenyl retinamide (ISO)

5-aza-2'-deoxycytidine (ISO)

6-propyl-2-thiouracil (EXP)

acetamide (EXP)

adefovir pivoxil (ISO)

all-trans-retinoic acid (EXP,ISO)

ammonium chloride (EXP)

arsane (ISO)

arsenic atom (ISO)

atrazine (ISO)

belinostat (ISO)

benzo[a]pyrene (ISO)

bis(2-ethylhexyl) phthalate (ISO)

bisphenol A (EXP,ISO)

bisphenol F (ISO)

bleomycin A2 (EXP)

buspirone (EXP)

cadmium atom (ISO)

cadmium dichloride (ISO)

chloroacetaldehyde (ISO)

cidofovir anhydrous (ISO)

cisplatin (ISO)

clodronic acid (ISO)

cobalt dichloride (ISO)

coumestrol (ISO)

cyclosporin A (ISO)

dexamethasone (ISO)

dibutyl phthalate (ISO)

dichlorine (EXP)

dioxygen (ISO)

diuron (EXP)

dorsomorphin (ISO)

doxorubicin (ISO)

Enterolactone (ISO)

entinostat (ISO)

enzyme inhibitor (ISO)

ethanol (ISO)

ethyl methanesulfonate (ISO)

fenofibrate (EXP)

folpet (ISO)

fumonisin B1 (ISO)

gamma-hexachlorocyclohexane (EXP)

gamma-linolenic acid (ISO)

ibuprofen (EXP,ISO)

indometacin (ISO)

lead diacetate (ISO)

mercury dibromide (ISO)

metformin (EXP)

methylmercury chloride (ISO)

N-nitrosodiethylamine (EXP)

N-nitrosomorpholine (EXP)

nefazodone (EXP)

nimesulide (EXP)

oxaliplatin (EXP)

ozone (EXP)

panobinostat (ISO)

paracetamol (ISO)

perfluorooctanoic acid (EXP)

phenformin (EXP)

phenobarbital (ISO)

phenylmercury acetate (ISO)

pirinixic acid (ISO)

prednisolone (ISO)

progesterone (ISO)

propiconazole (ISO)

resveratrol (ISO)

SB 431542 (ISO)

sodium arsenite (ISO)

Soman (EXP)

sulforaphane (ISO)

sunitinib (ISO)

T-2 toxin (EXP)

tamoxifen (ISO)

tauroursodeoxycholic acid (EXP)

tetrachloromethane (EXP,ISO)

thioacetamide (EXP)

topotecan (EXP)

trichostatin A (ISO)

Triptolide (EXP)

troglitazone (EXP)

trovafloxacin (EXP)

valproic acid (ISO)

vancomycin (ISO)

vinclozolin (EXP)

zinc atom (EXP)

zinc(0) (EXP)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

actin cytoskeleton organization (IBA,IMP)

establishment or maintenance of actin cytoskeleton polarity (IMP)

fibroblast migration (IMP)

heart development (IBA)

maintenance of cell polarity (IMP)

muscle structure development (IBA)

positive regulation of transcription, DNA-templated (IEA)

regulation of transcription by RNA polymerase II (ISO)

response to hypoxia (IEP)

stress fiber assembly (IMP)

Cellular Component

actin cytoskeleton (IDA)

adherens junction (IBA)

cytoplasm (IDA,ISO)

cytoskeleton (ISO)

filamentous actin (IBA)

stress fiber (IBA,IDA,ISO)

transcription regulator complex (ISO)

Z disc (IBA,IDA,ISO)

Molecular Function

actin binding (IBA,IDA)

metal ion binding (IEA)

muscle alpha-actinin binding (IBA)

protein binding (IPI,ISO)

transcription coactivator activity (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.	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 gene-chemical interactions
8.	Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
9.	Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
10.	Wang H, etal., Gene 1995 Nov 20;165(2):267-71.

Additional References at PubMed

PMID:10861853	PMID:11110697	PMID:12464179	PMID:15489334	PMID:17964547	PMID:19780892	PMID:20381583	PMID:20599268	PMID:21423176	PMID:25468996

Genomics

Comparative Map Data

Pdlim1
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	1	239,042,372 - 239,091,074 (-)	NCBI
Rnor_6.0 Ensembl	1	259,308,296 - 259,357,056 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	1	259,308,326 - 259,357,006 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	1	266,752,410 - 266,800,840 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	1	245,350,086 - 245,399,534 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	1	245,446,644 - 245,496,093 (-)	NCBI
Celera	1	234,889,852 - 234,937,718 (-)	NCBI		Celera
Cytogenetic Map	1	q54	NCBI

PDLIM1
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	10	95,237,572 - 95,291,012 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	10	95,237,569 - 95,291,006 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	10	96,997,329 - 97,050,760 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	10	96,987,319 - 97,040,771 (-)	NCBI	NCBI36		hg18	NCBI36
Build 34	10	96,987,321 - 97,040,771	NCBI
Celera	10	90,738,487 - 90,791,969 (-)	NCBI
Cytogenetic Map	10	q23.33	NCBI
HuRef	10	90,624,265 - 90,677,751 (-)	NCBI		HuRef
CHM1_1	10	97,279,094 - 97,332,709 (-)	NCBI		CHM1_1

Pdlim1
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	19	40,210,683 - 40,260,060 (-)	NCBI	GRCm39		mm39
GRCm39 Ensembl	19	40,209,617 - 40,260,286 (-)	Ensembl
GRCm38	19	40,222,239 - 40,271,616 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	19	40,221,173 - 40,271,842 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	19	40,296,729 - 40,346,106 (-)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	19	40,275,550 - 40,324,844 (-)	NCBI			mm8
Celera	19	41,028,383 - 41,076,730 (-)	NCBI		Celera
Cytogenetic Map	19	C3	NCBI

Pdlim1
(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_004955507	1,495,925 - 1,523,925 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955507	1,499,223 - 1,525,924 (-)	NCBI	ChiLan1.0	ChiLan1.0

PDLIM1
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
PanPan1.1	10	95,355,669 - 95,389,838 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	10	95,355,669 - 95,393,871 (-)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	10	91,848,127 - 91,901,553 (-)	NCBI	Mhudiblu_PPA_v0		panPan3

PDLIM1
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1 Ensembl	28	8,771,186 - 8,801,354 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
CanFam3.1	28	8,770,882 - 8,817,828 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1

Pdlim1
(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_004936636	4,083,413 - 4,126,728 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

PDLIM1
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	14	106,735,492 - 106,794,777 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	14	106,744,320 - 106,793,606 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	14	116,377,059 - 116,426,077 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

PDLIM1
(Chlorocebus sabaeus - African green monkey)

Vervet Assembly	Chr	Position (strand)	Source	Genome Browsers
Vervet Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	9	88,398,814 - 88,452,660 (-)	NCBI
ChlSab1.1 Ensembl	9	88,397,294 - 88,452,610 (-)	Ensembl

Pdlim1
(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_004624737	6,485,607 - 6,530,511 (-)	NCBI

Position Markers

AI029470

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	1	259,308,388 - 259,308,605	NCBI	Rnor6.0
Rnor_5.0	1	266,752,472 - 266,752,689	UniSTS	Rnor5.0
RGSC_v3.4	1	245,350,148 - 245,350,365	UniSTS	RGSC3.4
Celera	1	234,889,914 - 234,890,131	UniSTS
RH 3.4 Map	1	1619.02	UniSTS
Cytogenetic Map	1	q53	UniSTS

BE108553

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	1	259,351,561 - 259,351,728	NCBI	Rnor6.0
Rnor_5.0	1	266,795,395 - 266,795,562	UniSTS	Rnor5.0
RGSC_v3.4	1	245,394,089 - 245,394,256	UniSTS	RGSC3.4
Celera	1	234,932,277 - 234,932,444	UniSTS
RH 3.4 Map	1	1618.9	UniSTS
Cytogenetic Map	1	q53	UniSTS

AU047677

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	1	259,352,111 - 259,352,240	NCBI	Rnor6.0
Rnor_5.0	1	266,795,945 - 266,796,074	UniSTS	Rnor5.0
RGSC_v3.4	1	245,394,639 - 245,394,768	UniSTS	RGSC3.4
Celera	1	234,932,827 - 234,932,956	UniSTS
Cytogenetic Map	1	q53	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
7794788	Mcs32	Mammary carcinoma susceptibility QTL 32	2.61		mammary gland integrity trait (VT:0010552)	mammary tumor incidence/prevalence measurement (CMO:0000946)	1	122614824	262664716	Rat
7421630	Bp362	Blood pressure QTL 362		0.001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	125875758	262433692	Rat
2302378	Insul11	Insulin level QTL 11	3.25		blood insulin amount (VT:0001560)	serum insulin level (CMO:0000358)	1	156446196	274977688	Rat
724531	Uae5	Urinary albumin excretion QTL 5	4		urine albumin amount (VT:0002871)	urine albumin level (CMO:0000130)	1	161321152	273792054	Rat
1578759	Uae30	Urinary albumin excretion QTL 30	3.3	0.003	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	1	161321256	273791893	Rat
1578778	Pur4	Proteinuria QTL 4	3.3	0.003	total urine protein amount (VT:0000032)	urine total protein excretion rate (CMO:0000756)	1	161321256	273791893	Rat
1354646	Kidm18	Kidney mass QTL 18	5.7		kidney mass (VT:0002707)	calculated kidney weight (CMO:0000160)	1	161784169	278228889	Rat
1354661	Bw33	Body weight QTL 33	5.2		body mass (VT:0001259)	body weight (CMO:0000012)	1	161784169	278228889	Rat
1354610	Bw34	Body weight QTL 34	4.1		body mass (VT:0001259)	body weight (CMO:0000012)	1	161784169	278228889	Rat
1549837	Hcar15	Hepatocarcinoma resistance QTL 15		0.05	liver integrity trait (VT:0010547)	liver tumorous lesion number (CMO:0001068)	1	163796316	282763074	Rat
1354580	Scort1	Serum corticosterone level QTL 1	3.4		blood corticosterone amount (VT:0005345)	blood corticosterone level (CMO:0001172)	1	167394665	278228889	Rat
2292220	Bp306	Blood pressure QTL 306	3.47	0.00087	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	174905700	264802994	Rat
738032	Hcas5	Hepatocarcinoma susceptibility QTL 5	3.12		liver integrity trait (VT:0010547)	liver tumorous lesion number (CMO:0001068)	1	191825895	279986079	Rat
1354652	Kidm20	Kidney mass QTL 20	4.3		kidney mass (VT:0002707)	calculated kidney weight (CMO:0000160)	1	192639698	278228889	Rat
1354624	Cm35	Cardiac mass QTL35	5.7		heart left ventricle mass (VT:0007031)	calculated heart weight (CMO:0000073)	1	192639698	278228889	Rat
634321	Hc1	Hypercalciuria QTL 1	2.91		urine calcium amount (VT:0002985)	urine calcium excretion rate (CMO:0000763)	1	193968438	261264776	Rat
1600363	Hc6	Hypercalciuria QTL 6	2.7		urine calcium amount (VT:0002985)	urine calcium excretion rate (CMO:0000763)	1	195598053	265002735	Rat
1578763	Kidm29	Kidney mass QTL 29	3.3	0.0001	kidney mass (VT:0002707)	both kidneys wet weight (CMO:0000085)	1	196395041	282763074	Rat
8655855	Arrd3	Age-related retinal degeneration QTL 3	3.07		lens clarity trait (VT:0001304)	cataract incidence/prevalence measurement (CMO:0001585)	1	202571665	264802994	Rat
8655655	Arrd2	Age-related retinal degeneration QTL 2	7.79		retinal layer morphology trait (VT:0003727)	percentage of study population developing retinopathy during a period of time (CMO:0002453)	1	202571665	264802994	Rat
1358898	Bp255	Blood pressure QTL 255	3.6		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	208517798	266948272	Rat
1358191	Ept10	Estrogen-induced pituitary tumorigenesis QTL 10	3.8		pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	1	210360774	264802828	Rat
1600388	Niddm67	Non-insulin dependent diabetes mellitus QTL 67	5.84	0.000004	blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	1	213476630	278978026	Rat
1600395	Niddm69	Non-insulin dependent diabetes mellitus QTL 69	4.14	0.0002	blood insulin amount (VT:0001560)	plasma insulin level (CMO:0000342)	1	213476630	278978026	Rat
1600396	Niddm68	Non-insulin dependent diabetes mellitus QTL 68	4.97	0.0003	blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	1	213476630	278978026	Rat
1600374	Mcs17	Mammary carcinoma susceptibility QTL 17	3		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	1	215684498	260684498	Rat
2302375	Bw83	Body weight QTL 83	4.87	0.0002	body mass (VT:0001259)	body weight (CMO:0000012)	1	215711860	260711860	Rat
1298084	Thym4	Thymus enlargement QTL 4	10.68		thymus mass (VT:0004954)	thymus weight to body weight ratio (CMO:0000612)	1	215828102	260828102	Rat
1357335	Bw39	Body weight QTL 39	3.3		body mass (VT:0001259)	body weight (CMO:0000012)	1	215828102	260828102	Rat
61376	Bp42	Blood pressure QTL 42	23.4		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	215828102	260828102	Rat
631658	Cm7	Cardiac mass QTL 7	5.32	0.0001	aorta mass (VT:0002845)	aorta weight (CMO:0000076)	1	216324817	261324817	Rat
1358292	Cm37	Cardiac mass QTL 37	6.2	0.00000081	heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	1	216324817	261324817	Rat
634313	Niddm43	Non-insulin dependent diabetes mellitus QTL 43			blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	217054291	281795785	Rat
2300175	Bmd40	Bone mineral density QTL 40	15.4	0.0001	femur mineral mass (VT:0010011)	bone mineral density (CMO:0001226)	1	221901238	266901238	Rat
2293655	Bss36	Bone structure and strength QTL 36	10.66	0.0001	femur strength trait (VT:0010010)	femur ultimate force (CMO:0001675)	1	221901238	266901238	Rat
2293674	Bss39	Bone structure and strength QTL 39	7.1	0.0001	femur strength trait (VT:0010010)	femur total energy absorbed before break (CMO:0001677)	1	221901238	266901238	Rat
2293694	Bss38	Bone structure and strength QTL 38	7.05	0.0001	femur strength trait (VT:0010010)	femur stiffness (CMO:0001674)	1	221901238	266901238	Rat
7394701	Uae46	Urinary albumin excretion QTL 46	3.6	0.0056	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	1	221901238	266901238	Rat
10059587	Bw173	Body weight QTL 173	3.23	0.025	body mass (VT:0001259)	body weight (CMO:0000012)	1	222492538	267492538	Rat
1357399	Bw45	Body weight QTL 45	3.05		body mass (VT:0001259)	body mass index (BMI) (CMO:0000105)	1	225689973	270689973	Rat
1357404	Bw42	Body weight QTL 42	4.49	0.0001	body mass (VT:0001259)	body weight (CMO:0000012)	1	225689973	270689973	Rat
1600397	Edcs4	Endometrial carcinoma susceptibility QTL 4	2.2		uterus morphology trait (VT:0001120)	percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)	1	226706329	271706329	Rat
1358916	Kidm22	Kidney mass QTL 22	3.32		kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	1	230420627	262031693	Rat
1358890	Bp259	Blood pressure QTL 259	3.06		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	230420627	282645769	Rat
2292216	Bw80	Body weight QTL 80	3.23	0.0019	body mass (VT:0001259)	body weight (CMO:0000012)	1	233490105	264802994	Rat
724538	Kidm1	Kidney mass QTL 1	3.2		kidney mass (VT:0002707)	calculated kidney weight (CMO:0000160)	1	233663100	273792054	Rat
734768	Niddm59	Non-insulin dependent diabetes mellitus QTL 59			body mass (VT:0001259)	body weight (CMO:0000012)	1	235850810	280850810	Rat
2302040	Pia35	Pristane induced arthritis QTL 35	3.8	0.001	blood immunoglobulin amount (VT:0002460)	serum immunoglobulin G1 level (CMO:0002115)	1	236265430	281265430	Rat
61327	Eae7	Experimental allergic encephalomyelitis QTL 7	5.6		body mass (VT:0001259)	change in body weight (CMO:0002045)	1	236265430	281265430	Rat
70211	Niddm24	Non-insulin dependent diabetes mellitus QTL 24	3.79		blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	1	236795785	281795785	Rat
1549910	Bw54	Body weight QTL 54		0.05	body mass (VT:0001259)	body weight (CMO:0000012)	1	236795785	281795785	Rat
1598821	Rf55	Renal function QTL 55	6.3		renal blood flow trait (VT:2000006)	ratio of change in renal blood flow to change in renal perfusion pressure (CMO:0001239)	1	238824734	279986079	Rat
61400	Niddm1	Non-insulin dependent diabetes mellitus QTL 1	11		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	238830408	266793958	Rat
724533	Rf51	Renal function QTL 51	5.3	0.0002	kidney plasma flow trait (VT:0005524)	renal plasma flow (CMO:0001914)	1	238830534	278228767	Rat
731175	Uae20	Urinary albumin excretion QTL 20	3.5	0.0018	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	1	241482188	281795785	Rat
10053715	Scort24	Serum corticosterone level QTL 24	2.13	0.0088	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	1	242302911	282763074	Rat
724552	Glom2	Glomerulus QTL 2	3.3	0.0001	kidney glomerulus morphology trait (VT:0005325)	count of superficial glomeruli directly contacting the kidney surface (CMO:0001001)	1	243272341	282763074	Rat
1600392	Bw123	Body weight QTL 123		0.001	body mass (VT:0001259)	body weight (CMO:0000012)	1	244087148	282763074	Rat
7387289	Uae45	Urinary albumin excretion QTL 45	2.86	0.0021	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	1	244148899	282763074	Rat
2293700	Bmd27	Bone mineral density QTL 27	6.6	0.0001	femur mineral mass (VT:0010011)	trabecular volumetric bone mineral density (CMO:0001729)	1	244401175	264636028	Rat
2293701	Bmd34	Bone mineral density QTL 34	8.3	0.0001	femur strength trait (VT:0010010)	femoral neck ultimate force (CMO:0001703)	1	244401175	264636028	Rat
631843	Bw116	Body weight QTL 116	4.1	0.016	abdominal adipose amount (VT:1000220)	abdominal fat pad weight (CMO:0000088)	1	244401175	282365384	Rat
734767	Niddm57	Non-insulin dependent diabetes mellitus QTL 57			body mass (VT:0001259)	body weight (CMO:0000012)	1	244401175	282365384	Rat
734769	Niddm58	Non-insulin dependent diabetes mellitus QTL 58			body mass (VT:0001259)	body weight (CMO:0000012)	1	244992467	282365384	Rat
631215	Stl8	Serum triglyceride level QTL 8	9.27	0.0001	blood triglyceride amount (VT:0002644)	serum triglyceride level (CMO:0000360)	1	245529606	282763074	Rat
1300108	Rf8	Renal function QTL 8	3.75		renal blood flow trait (VT:2000006)	absolute change in renal vascular resistance (CMO:0001900)	1	249206242	281795785	Rat
2316896	Gluco57	Glucose level QTL 57	7.2		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	249607907	266793958	Rat
1581544	Rf52	Renal function QTL 52		0.05	total urine protein amount (VT:0000032)	urine protein excretion rate to body weight ratio (CMO:0001099)	1	252948438	281795785	Rat
631669	Iddm9	Insulin dependent diabetes mellitus QTL 9	2.8	0.039	blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	1	252955158	280632620	Rat
631536	Lnnr2	Liver neoplastic nodule remodeling QTL 2	2.9	0.0005	liver integrity trait (VT:0010547)	liver remodeling tumorous lesion number to liver total tumorous lesion number ratio (CMO:0001705)	1	255728828	282763074	Rat
631690	Scl5	Serum cholesterol level QTL 5	2.1		blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	1	258132568	282763074	Rat
631837	Niddm35	Non-insulin dependent diabetes mellitus QTL 35		0.01	blood insulin amount (VT:0001560)	serum insulin level (CMO:0000358)	1	258709726	281795785	Rat
631836	Stl31	Serum triglyceride level QTL 31	4.64	0.00000487	blood triglyceride amount (VT:0002644)	plasma triglyceride level (CMO:0000548)	1	259295704	282763074	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	298
Count of miRNA genes:	190
Interacting mature miRNAs:	213
Transcripts:	ENSRNOT00000022000
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	43	50	41	19	41	8	10	28	26	36	11	8
Low			7					1	46	9	5
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_017365	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039088562	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC128172	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC072465	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473986	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ214797	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ227333	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000054	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	U23769	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000022000 ⟹ ENSRNOP00000022000

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	1	259,308,296 - 259,357,056 (-)	Ensembl

RefSeq Acc Id:

NM_017365 ⟹ NP_059061

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	1	239,042,374 - 239,090,968 (-)	NCBI
Rnor_6.0	1	259,308,326 - 259,357,006 (-)	NCBI
Rnor_5.0	1	266,752,410 - 266,800,840 (-)	NCBI
RGSC_v3.4	1	245,350,086 - 245,399,534 (-)	RGD
Celera	1	234,889,852 - 234,937,718 (-)	RGD

Sequence:

show sequence

CCGGGATCCCTGCGCGCCGTGGTGTTCTGTGCCTTGCCGGTCTGTTCCCTCCGATTGTGCCTAG
CAATGACCACCCAGCAGATTGTTCTCCAGGGCCCGGGACCCTGGGGTTTCCGACTCGTGGGCGG
CAAGGACTTTGAGCAACCTCTCGCCATTTCCCGGGTCACTCCCGGGAGCAAGGCTGCTATAGCT
AACTTATGCATAGGAGATTTGATCACAGCCATTGATGGGGAAGATACCAGCAGTATGACACACT
TGGAAGCTCAGAACAAAATCAAGGGCTGCGTAGACAACATGACGCTCACAGTATCCAGGTCTGA
GCAGAAGATTTGGTCTCCTCTAGTGACCGAGGAGGGGAAACGTCACCCCTACAAGATGAATTTA
GCGTCGGAACCCCAAGAAGTCCTGCACATCGGAAGTGCCCACAACCGTAGTGCTATGCCATTTA
CCGCCTCACCTGCTCCTGGCACCCGGGTCATCACAAACCAGTACAACAGCCCTACCGGCCTCTA
CTCATCTGAAAACATCTCTAACTTCAACAATGCAGTGGAGTCAAAGACCTCAGCCAGTGGGGAG
GAGGCGAACAGCAGGCCCTCGGCTCAGCCTCATCCCTCCGGCGGCCTTATCATCGACAAGGAAT
CCGAAGTTTACAAGATGCTTCAGGAGAAGCAAGAGTTAAACGAGCCCCCCAAACAGTCCACATC
ATTCCTGGTTCTGCAGGAGATCCTGGAGTCGGATGGGAAAGGGGACCCCAACAAGCCATCAGGA
TTTAGAAGTGTTAAAGCTCCAGTCACCAAAGTGGCTGCATCTGTTGGAAATGCTCAGAAGCTGC
CCATCTGTGACAAATGTGGAACCGGCATTGTTGGTGTGTTTGTGAAGCTGAGGGACCATCATCC
CCACCCTGAATGTTATGTGTGCACCGACTGTGGCATCAACCTGAAACAGAAGGGCCATTTCTTT
GTAGGGGATCAGATTTATTGTGAAAAGCATGCCCGGGAGAGGGTCACACCACCTGAGGGCTATG
ATGTGGTCACAGTGTTCCCCAAGTGATCGAGAGGACCTGCCCTGTCTGCTGCCCTCCAGCCTGC
CTGCTGCACCTGGTTGTCAGAATGTTCTGGTTCTCTCCTCCCTGACAGTCCTGTGCTTAGTGTT
AGTCCTGCTCAGTAAACATTGAGTTTCTCCTGTACTGACTGACCCTGACTGGCAGTGTGACACC
TGCTTTTACATTACCGGGAGGTGGTTTTGTCCCTGTCCCCTCACCCACACCACAATGCACCTTC
TTCCCTTGGAGTCTTCCCTGCTGAAAATGGACATTGGTCACATTGGAATTAAGCCAAATGTTTT
ATCTCTGATGTTACTTTGTTTTACTTAATAAATTTAGACTTTAAAGC

hide sequence

RefSeq Acc Id:

XM_039088562 ⟹ XP_038944490

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	1	239,042,372 - 239,091,074 (-)	NCBI

Protein Sequences


Protein RefSeqs	NP_059061	(Get FASTA)	NCBI Sequence Viewer
	XP_038944490	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAA92046	(Get FASTA)	NCBI Sequence Viewer
	AAH72465	(Get FASTA)	NCBI Sequence Viewer
	EDL94180	(Get FASTA)	NCBI Sequence Viewer
	EDL94181	(Get FASTA)	NCBI Sequence Viewer
	P52944	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_059061 ⟸ NM_017365

- UniProtKB:

P52944 (UniProtKB/Swiss-Prot)

- Sequence:

show sequence

MTTQQIVLQGPGPWGFRLVGGKDFEQPLAISRVTPGSKAAIANLCIGDLITAIDGEDTSSMTHL
EAQNKIKGCVDNMTLTVSRSEQKIWSPLVTEEGKRHPYKMNLASEPQEVLHIGSAHNRSAMPFT
ASPAPGTRVITNQYNSPTGLYSSENISNFNNAVESKTSASGEEANSRPSAQPHPSGGLIIDKES
EVYKMLQEKQELNEPPKQSTSFLVLQEILESDGKGDPNKPSGFRSVKAPVTKVAASVGNAQKLP
ICDKCGTGIVGVFVKLRDHHPHPECYVCTDCGINLKQKGHFFVGDQIYCEKHARERVTPPEGYD
VVTVFPK

hide sequence

RefSeq Acc Id:

ENSRNOP00000022000 ⟸ ENSRNOT00000022000

RefSeq Acc Id:	XP_038944490 ⟸ XM_039088562
- Peptide Label:	isoform X1

Protein Domains

LIM zinc-binding PDZ

Transcriptome

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

Promoters

RGD ID:

13690896

Promoter ID:

EPDNEW_R1421

Type:

initiation region

Name:

Pdlim1_1

Description:

PDZ and LIM domain 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	1	259,357,013 - 259,357,073	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:68324	AgrOrtholog
Ensembl Genes	ENSRNOG00000016166	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein	ENSRNOP00000022000	ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000022000	ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH	2.30.42.10	UniProtKB/Swiss-Prot
IMAGE_CLONE	IMAGE:7100446	IMAGE-MGC_LOAD
InterPro	DUF4749	UniProtKB/Swiss-Prot
	PDLIM1	UniProtKB/Swiss-Prot
	PDZ	UniProtKB/Swiss-Prot
	PDZ_sf	UniProtKB/Swiss-Prot
	Zasp-like_motif	UniProtKB/Swiss-Prot
	Znf_LIM	UniProtKB/Swiss-Prot
KEGG Report	rno:54133	UniProtKB/Swiss-Prot
MGC_CLONE	MGC:91751	IMAGE-MGC_LOAD
NCBI Gene	54133	ENTREZGENE
PANTHER	PTHR24214:SF5	UniProtKB/Swiss-Prot
Pfam	DUF4749	UniProtKB/Swiss-Prot
	LIM	UniProtKB/Swiss-Prot
	PDZ	UniProtKB/Swiss-Prot
PhenoGen	Pdlim1	PhenoGen
PROSITE	LIM_DOMAIN_1	UniProtKB/Swiss-Prot
	LIM_DOMAIN_2	UniProtKB/Swiss-Prot
	PDZ	UniProtKB/Swiss-Prot
SMART	LIM	UniProtKB/Swiss-Prot
	PDZ	UniProtKB/Swiss-Prot
	SM00735	UniProtKB/Swiss-Prot
Superfamily-SCOP	SSF50156	UniProtKB/Swiss-Prot
TIGR	TC205375
UniProt	P52944	ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary	Q6IN45	UniProtKB/Swiss-Prot

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2009-02-26	Pdlim1	PDZ and LIM domain 1	Pdlim1	PDZ and LIM domain 1 (elfin)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2004-09-10	Pdlim1	PDZ and LIM domain 1 (elfin)		PDZ and LIM domain 1	Name updated	1299863	APPROVED
2002-06-10	Pdlim1	PDZ and LIM domain 1			Name updated	70584	APPROVED

RGD Curation Notes

Note Type	Note	Reference
gene_expression	decreased mRNA expression occurs in response to chemical hypoxia	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)