Pdlim3 (PDZ and LIM domain 3) - Rat Genome Database
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Gene: Pdlim3 (PDZ and LIM domain 3) Rattus norvegicus
Analyze
Symbol: Pdlim3
Name: PDZ and LIM domain 3
RGD ID: 620427
Description: Exhibits actinin binding activity. Predicted to be involved in actin filament organization; heart development; and muscle structure development. Localizes to Z disc. Orthologous to human PDLIM3 (PDZ and LIM domain 3); INTERACTS WITH 1,2-dimethylhydrazine; 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: actinin alpha 2 associated LIM protein; actinin-associated LIM protein; Actn2lp; Alp; alpha-actinin-2-associated LIM protein; PDZ and LIM domain protein 3; SK-2
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21646,352,460 - 46,383,680 (-)NCBI
Rnor_6.0 Ensembl1649,543,142 - 49,574,390 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01649,543,140 - 49,574,362 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01649,271,210 - 49,303,161 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41649,637,068 - 49,668,802 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11649,637,142 - 49,668,877 (-)NCBI
Celera1644,350,214 - 44,381,388 (-)NCBICelera
Cytogenetic Map16q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (EXP,ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2,5-hexanedione  (EXP)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-aza-2'-deoxycytidine  (ISO)
acrylamide  (EXP)
aflatoxin B1  (ISO)
ammonium chloride  (EXP)
arsane  (ISO)
arsenic atom  (ISO)
benzo[a]pyrene  (ISO)
benzo[e]pyrene  (ISO)
beta-naphthoflavone  (EXP)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
butanal  (ISO)
cadmium dichloride  (EXP)
carbon nanotube  (ISO)
choline  (ISO)
cisplatin  (ISO)
copper(II) sulfate  (ISO)
coumestrol  (ISO)
cyclosporin A  (ISO)
cylindrospermopsin  (ISO)
cytarabine  (ISO)
DDT  (EXP)
dibutyl phthalate  (ISO)
diethylstilbestrol  (EXP)
dorsomorphin  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
entinostat  (ISO)
enzyme inhibitor  (ISO)
etoposide  (ISO)
folic acid  (ISO)
L-methionine  (ISO)
losartan  (EXP)
metformin  (EXP)
methapyrilene  (ISO)
methylmercury chloride  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
N-nitrosodiethylamine  (EXP)
N-Nitrosopyrrolidine  (ISO)
nickel sulfate  (ISO)
O-methyleugenol  (ISO)
phenformin  (EXP)
phenylephrine  (EXP)
phenylmercury acetate  (ISO)
progesterone  (ISO)
raloxifene  (ISO)
rotenone  (EXP)
SB 431542  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sodium arsenite  (ISO)
sodium fluoride  (ISO)
sunitinib  (ISO)
tamoxifen  (ISO)
tert-butyl hydroperoxide  (ISO)
thalidomide  (ISO)
titanium dioxide  (ISO)
trichostatin A  (ISO)
triclosan  (ISO)
trimellitic anhydride  (ISO)
valproic acid  (ISO)
vanadyl sulfate  (ISO)
vitamin E  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
actin cytoskeleton  (ISO)
adherens junction  (IBA)
cytosol  (IEA,ISO)
filamentous actin  (IBA)
stress fiber  (IBA)
Z disc  (IBA,IDA,IEA)

Molecular Function

References

Additional References at PubMed
PMID:11238905   PMID:11329061   PMID:12477932   PMID:15489334  


Genomics

Candidate Gene Status
Pdlim3 is a candidate Gene for QTL Arunc2
Pdlim3 is a candidate Gene for QTL Arunc1
Pdlim3 is a candidate Gene for QTL Arunc4
Comparative Map Data
Pdlim3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21646,352,460 - 46,383,680 (-)NCBI
Rnor_6.0 Ensembl1649,543,142 - 49,574,390 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01649,543,140 - 49,574,362 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01649,271,210 - 49,303,161 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41649,637,068 - 49,668,802 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11649,637,142 - 49,668,877 (-)NCBI
Celera1644,350,214 - 44,381,388 (-)NCBICelera
Cytogenetic Map16q11NCBI
PDLIM3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl4185,500,660 - 185,535,507 (-)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl4185,500,660 - 185,535,612 (-)EnsemblGRCh38hg38GRCh38
GRCh384185,500,660 - 185,535,507 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh374186,421,814 - 186,456,712 (-)NCBIGRCh37GRCh37hg19GRCh37
GRCh374186,421,814 - 186,456,661 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 364186,659,899 - 186,693,650 (-)NCBINCBI36hg18NCBI36
Build 344186,798,059 - 186,831,794NCBI
Celera4183,749,238 - 183,781,710 (-)NCBI
Cytogenetic Map4q35.1NCBI
HuRef4182,175,438 - 182,209,519 (-)NCBIHuRef
CHM1_14186,398,441 - 186,430,909 (-)NCBICHM1_1
Pdlim3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39846,338,524 - 46,372,672 (+)NCBIGRCm39mm39
GRCm38845,885,487 - 45,919,635 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl845,885,461 - 45,919,548 (+)EnsemblGRCm38mm10GRCm38
MGSCv37846,970,839 - 47,004,900 (+)NCBIGRCm37mm9NCBIm37
MGSCv36847,384,302 - 47,418,363 (+)NCBImm8
Celera848,569,007 - 48,602,415 (+)NCBICelera
Cytogenetic Map8B1.1NCBI
Pdlim3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540323,546,291 - 23,579,975 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495540323,546,291 - 23,579,975 (+)NCBIChiLan1.0ChiLan1.0
PDLIM3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.14189,880,930 - 189,914,707 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl4189,880,938 - 189,914,707 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v04177,664,420 - 177,698,364 (-)NCBIMhudiblu_PPA_v0panPan3
PDLIM3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl1645,111,372 - 45,140,895 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.11645,111,358 - 45,141,444 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Pdlim3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049365543,844,896 - 3,874,168 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PDLIM3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1546,513,234 - 46,546,504 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11546,516,178 - 46,546,658 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21553,297,824 - 53,328,219 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PDLIM3
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.17131,443,131 - 131,477,575 (-)NCBI
ChlSab1.1 Ensembl7131,441,674 - 131,477,554 (-)Ensembl
Pdlim3
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462476916,341,297 - 16,374,106 (-)NCBI

Position Markers
RH143054  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01649,550,657 - 49,550,884NCBIRnor6.0
Rnor_5.01649,279,238 - 49,279,465UniSTSRnor5.0
RGSC_v3.41649,644,581 - 49,644,808UniSTSRGSC3.4
Celera1644,357,727 - 44,357,954UniSTS
RH 3.4 Map16456.3UniSTS
Cytogenetic Map16q11UniSTS
BF390733  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01649,561,734 - 49,561,891NCBIRnor6.0
Rnor_5.01649,290,315 - 49,290,472UniSTSRnor5.0
RGSC_v3.41649,655,658 - 49,655,815UniSTSRGSC3.4
Celera1644,368,804 - 44,368,961UniSTS
RH 3.4 Map16441.31UniSTS
Cytogenetic Map16q11UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1600378Arunc4Aerobic running capacity QTL 40.03exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)16109005486162972Rat
2312660Bw95Body weight QTL 950.05inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)16155018763210301Rat
2312663Slep9Serum leptin concentration QTL 90.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)16155018763210301Rat
2312666Insul16Insulin level QTL 160.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)16155018763210301Rat
2312669Stl23Serum triglyceride level QTL 230.01blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)16155018763210301Rat
61338Bp23Blood pressure QTL 234.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16501380250013802Rat
737819Hcas4Hepatocarcinoma susceptibility QTL 44.43liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)16501380250169318Rat
61405Niddm6Non-insulin dependent diabetes mellitus QTL 63.660.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)16501380252144919Rat
737826Alc11Alcohol consumption QTL 113.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16501380264012784Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor diameter (CMO:0001889)161939818770590230Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor diameter (CMO:0001889)161939818770590230Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor depth of invasion (CMO:0001888)161939818770590230Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor depth of invasion (CMO:0001888)161939818770590230Rat
70215Niddm29Non-insulin dependent diabetes mellitus QTL 293.54blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)162075555680316424Rat
2302057Pia29Pristane induced arthritis QTL 293.60.001blood autoantibody amount (VT:0003725)serum immunoglobulin M-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002111)162484654169846541Rat
8694453Bw172Body weight QTL 1728.330.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)162751998072519980Rat
6903294Stl30Serum triglyceride level QTL 302.60.0013blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)162834031573340315Rat
1298529Arunc1Aerobic running capacity QTL 14exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)163530711063909364Rat
1578768Stresp22Stress response QTL 222.8thymus mass (VT:0004954)thymus wet weight (CMO:0000855)163900002184000021Rat
2300163Bmd64Bone mineral density QTL 645.30.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)164151271086512710Rat
2293690Bss45Bone structure and strength QTL 455.130.0001lumbar vertebra morphology trait (VT:0010494)lumbar vertebra cortical cross-sectional area (CMO:0001690)164151271086512710Rat
631833Sach2Saccharin preference QTL 240.01consumption behavior trait (VT:0002069)calculated saccharin drink intake rate (CMO:0001613)164590509753253355Rat
7205510Activ5Activity QTL 53.780.00028locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)164655818890668790Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:506
Count of miRNA genes:163
Interacting mature miRNAs:192
Transcripts:ENSRNOT00000017054, ENSRNOT00000017568
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 5 4 4 8 11 4 26 11 8
Low 38 23 19 23 64 30 15
Below cutoff 14 14 14 10 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000017054   ⟹   ENSRNOP00000017054
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1649,543,142 - 49,574,390 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000017568   ⟹   ENSRNOP00000017568
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1649,543,147 - 49,574,314 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000085535   ⟹   ENSRNOP00000075153
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1649,543,144 - 49,574,321 (-)Ensembl
RefSeq Acc Id: NM_053650   ⟹   NP_446102
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21646,352,460 - 46,383,657 (-)NCBI
Rnor_6.01649,543,144 - 49,574,321 (-)NCBI
Rnor_5.01649,271,210 - 49,303,161 (-)NCBI
RGSC_v3.41649,637,068 - 49,668,802 (-)RGD
Celera1644,350,214 - 44,381,388 (-)RGD
Sequence:
RefSeq Acc Id: XM_006253119   ⟹   XP_006253181
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21646,352,460 - 46,383,680 (-)NCBI
Rnor_6.01649,543,140 - 49,574,362 (-)NCBI
Rnor_5.01649,271,210 - 49,303,161 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006253120   ⟹   XP_006253182
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21646,352,460 - 46,383,677 (-)NCBI
Rnor_6.01649,543,140 - 49,574,361 (-)NCBI
Rnor_5.01649,271,210 - 49,303,161 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_446102   ⟸   NM_053650
- Sequence:
RefSeq Acc Id: XP_006253182   ⟸   XM_006253120
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006253181   ⟸   XM_006253119
- Peptide Label: isoform X1
- UniProtKB: Q66HS7 (UniProtKB/Swiss-Prot),   A0A0G2JSM3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000075153   ⟸   ENSRNOT00000085535
RefSeq Acc Id: ENSRNOP00000017054   ⟸   ENSRNOT00000017054
RefSeq Acc Id: ENSRNOP00000017568   ⟸   ENSRNOT00000017568
Protein Domains
LIM zinc-binding   PDZ

Transcriptome

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

Promoters
RGD ID:13700111
Promoter ID:EPDNEW_R10629
Type:single initiation site
Name:Pdlim3_1
Description:PDZ and LIM domain 3
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01649,574,337 - 49,574,397EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
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
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 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
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)
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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

Database Acc Id Source(s)
AGR Gene RGD:620427 AgrOrtholog
Ensembl Genes ENSRNOG00000012658 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000017054 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000017568 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000075153 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000017054 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000017568 UniProtKB/TrEMBL
  ENSRNOT00000085535 UniProtKB/TrEMBL
Gene3D-CATH 2.30.42.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7193873 IMAGE-MGC_LOAD
InterPro DUF4749 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDZ UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDZ_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Zasp-like_motif UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_LIM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:114108 UniProtKB/Swiss-Prot
MGC_CLONE MGC:93100 IMAGE-MGC_LOAD
NCBI Gene 114108 ENTREZGENE
Pfam DUF4749 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LIM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDZ UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Pdlim3 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
  SM00735 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF50156 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2JSM3 ENTREZGENE, UniProtKB/TrEMBL
  A0A0G2K9W2_RAT UniProtKB/TrEMBL
  D3ZFR7_RAT UniProtKB/TrEMBL
  PDLI3_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary O70208 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-09-10 Pdlim3  PDZ and LIM domain 3    actinin alpha 2 associated LIM protein  Name updated 1299863 APPROVED
2002-08-07 Pdlim3  actinin alpha 2 associated LIM protein      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_disease human homolog may be a candidate gene for fascioscapulohumeral muscular dystrophy 634540
gene_domains contains an NH2-terminal PDZ domain and a COOH-terminal LIM motif  
gene_protein 39 kDa