Pdlim5 (PDZ and LIM domain 5) - Rat Genome Database
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Gene: Pdlim5 (PDZ and LIM domain 5) Rattus norvegicus
Analyze
Symbol: Pdlim5
Name: PDZ and LIM domain 5
RGD ID: 621076
Description: Exhibits cytoskeletal protein binding activity; protein N-terminus binding activity; and protein kinase C binding activity. Involved in cell growth involved in cardiac muscle cell development; regulation of dendritic spine morphogenesis; and regulation of synapse assembly. Localizes to cytosol; membrane; and postsynaptic density. Orthologous to human PDLIM5 (PDZ and LIM domain 5); INTERACTS WITH 1,2-dimethylhydrazine; 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: Enh; Enh1; enigma homolog; enigma-like PDZ and LIM domains protein; PDZ and LIM domain protein 5
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
mRatBN7.22230,952,251 - 231,120,329 (-)NCBI
Rnor_6.0 Ensembl2247,818,243 - 247,988,462 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.02247,815,214 - 247,989,198 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02266,345,722 - 266,518,817 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42240,177,301 - 240,304,192 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12240,164,042 - 240,283,654 (-)NCBI
Celera2223,009,335 - 223,173,420 (-)NCBICelera
Cytogenetic Map2q44NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-catechin  (ISO)
(-)-epigallocatechin 3-gallate  (ISO)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (EXP,ISO)
17beta-estradiol  (ISO)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2,4-dinitrotoluene  (EXP)
3-methylcholanthrene  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-amino-2,6-dinitrotoluene  (EXP)
4-hydroxyphenyl retinamide  (ISO)
5-fluorouracil  (ISO)
acrolein  (ISO)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
alpha-pinene  (ISO)
arsenous acid  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
bleomycin A2  (EXP)
Brodifacoum  (EXP)
butanal  (ISO)
chromium(6+)  (ISO)
cisplatin  (ISO)
cobalt dichloride  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
corticosterone  (EXP)
cyclosporin A  (ISO)
diarsenic trioxide  (ISO)
dibutyl phthalate  (ISO)
disulfiram  (ISO)
diuron  (EXP)
dorsomorphin  (ISO)
doxorubicin  (ISO)
enzyme inhibitor  (ISO)
ethanol  (ISO)
fenamidone  (ISO)
flavonoids  (EXP)
folic acid  (ISO)
hydrogen peroxide  (ISO)
irinotecan  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
leflunomide  (ISO)
lithium chloride  (ISO)
melphalan  (ISO)
methylmercury chloride  (ISO)
N-acetyl-L-cysteine  (ISO)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
nickel atom  (ISO)
nickel subsulfide  (EXP)
NS-398  (ISO)
ozone  (ISO)
paracetamol  (ISO)
pirinixic acid  (ISO)
potassium chromate  (ISO)
propanal  (ISO)
SB 431542  (ISO)
silicon dioxide  (ISO)
sodium arsenite  (ISO)
succimer  (ISO)
testosterone  (ISO)
tetrachloromethane  (ISO)
tetraphene  (ISO)
torcetrapib  (ISO)
trichostatin A  (ISO)
triclosan  (ISO)
troglitazone  (ISO)
urethane  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:12665800   PMID:16396499   PMID:16549780   PMID:18296710   PMID:20097676   PMID:21532576   PMID:22497889   PMID:25468996   PMID:25524223   PMID:26365342   PMID:27289039  


Genomics

Comparative Map Data
Pdlim5
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22230,952,251 - 231,120,329 (-)NCBI
Rnor_6.0 Ensembl2247,818,243 - 247,988,462 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.02247,815,214 - 247,989,198 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02266,345,722 - 266,518,817 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42240,177,301 - 240,304,192 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12240,164,042 - 240,283,654 (-)NCBI
Celera2223,009,335 - 223,173,420 (-)NCBICelera
Cytogenetic Map2q44NCBI
PDLIM5
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl494,451,857 - 94,668,227 (+)EnsemblGRCh38hg38GRCh38
GRCh38494,451,942 - 94,668,223 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37495,373,093 - 95,589,374 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36495,592,061 - 95,808,400 (+)NCBINCBI36hg18NCBI36
Build 34495,730,215 - 95,946,554NCBI
Celera492,670,285 - 92,886,273 (+)NCBI
Cytogenetic Map4q22.3NCBI
HuRef491,110,743 - 91,326,816 (+)NCBIHuRef
CHM1_1495,350,391 - 95,566,419 (+)NCBICHM1_1
Pdlim5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm393141,945,346 - 142,101,480 (-)NCBIGRCm39mm39
GRCm39 Ensembl3141,945,351 - 142,101,457 (-)Ensembl
GRCm383142,239,585 - 142,395,719 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl3142,239,590 - 142,395,696 (-)EnsemblGRCm38mm10GRCm38
MGSCv373141,903,568 - 142,058,630 (-)NCBIGRCm37mm9NCBIm37
MGSCv363142,180,044 - 142,333,004 (-)NCBImm8
Celera3148,660,401 - 148,819,753 (-)NCBICelera
Cytogenetic Map3H1NCBI
Pdlim5
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554055,109,778 - 5,315,092 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554055,109,778 - 5,312,192 (+)NCBIChiLan1.0ChiLan1.0
PDLIM5
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1497,486,566 - 97,702,060 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl497,486,566 - 97,702,060 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0486,814,136 - 87,030,605 (+)NCBIMhudiblu_PPA_v0panPan3
PDLIM5
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl3217,294,073 - 17,502,409 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.13217,294,023 - 17,505,212 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Pdlim5
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049366871,944,095 - 2,152,501 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PDLIM5
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl8125,044,028 - 125,259,948 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.18125,044,027 - 125,259,969 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.28134,331,215 - 134,558,541 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PDLIM5
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1742,702,175 - 42,912,859 (+)NCBI
ChlSab1.1 Ensembl742,819,454 - 42,908,137 (+)Ensembl
Pdlim5
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475722,332,479 - 22,597,312 (+)NCBI

Position Markers
D2Rat295  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.02247,826,701 - 247,826,948NCBIRnor6.0
Rnor_5.02266,357,209 - 266,357,456UniSTSRnor5.0
RGSC_v3.42240,185,760 - 240,186,008RGDRGSC3.4
RGSC_v3.42240,185,761 - 240,186,008UniSTSRGSC3.4
RGSC_v3.12240,172,500 - 240,172,748RGD
Celera2223,017,795 - 223,018,042UniSTS
SHRSP x BN Map298.7698UniSTS
SHRSP x BN Map298.7698RGD
Cytogenetic Map2q44UniSTS
RH129037  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.02247,881,581 - 247,881,770NCBIRnor6.0
Rnor_5.02266,412,603 - 266,412,792UniSTSRnor5.0
RGSC_v3.42240,242,672 - 240,242,861UniSTSRGSC3.4
Celera2223,073,187 - 223,073,376UniSTS
Cytogenetic Map2q44UniSTS
RH132279  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.02247,828,489 - 247,828,685NCBIRnor6.0
Rnor_5.02266,358,997 - 266,359,193UniSTSRnor5.0
RGSC_v3.42240,187,549 - 240,187,745UniSTSRGSC3.4
Celera2223,019,583 - 223,019,779UniSTS
RH 3.4 Map21580.5UniSTS
Cytogenetic Map2q44UniSTS
RH144581  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.02247,827,972 - 247,828,126NCBIRnor6.0
Rnor_5.02266,358,480 - 266,358,634UniSTSRnor5.0
RGSC_v3.42240,187,032 - 240,187,186UniSTSRGSC3.4
Celera2223,019,066 - 223,019,220UniSTS
RH 3.4 Map21580.8UniSTS
Cytogenetic Map2q44UniSTS
RH137910  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.02247,936,978 - 247,937,227NCBIRnor6.0
Rnor_5.02266,468,001 - 266,468,250UniSTSRnor5.0
RGSC_v3.42240,300,525 - 240,300,774UniSTSRGSC3.4
Celera2223,128,724 - 223,128,973UniSTS
RH 3.4 Map21537.0UniSTS
Cytogenetic Map2q44UniSTS
AI014024  
Rat AssemblyChrPosition (strand)SourceJBrowse
RH 3.4 Map21590.0UniSTS
Cytogenetic Map2q44UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2293833Kiddil8Kidney dilation QTL 82.9kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)2236318496264899009Rat
2293844Kiddil7Kidney dilation QTL 73.5kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)2236318496264899009Rat
1331767Hrtrt12Heart rate QTL 123.373heart pumping trait (VT:2000009)heart rate (CMO:0000002)2235289967257110527Rat
1298075Scl17Serum cholesterol level QTL 173.4blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)2228712271266435125Rat
631563Hcuc3Hepatic copper content QTL 33.87hepatic copper amount (VT:0003065)liver copper weight to liver dry weight ratio (CMO:0001512)2245893572266435125Rat
2317885Alcrsp28Alcohol response QTL 282.10.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2229793522266435125Rat
631514Scl8Serum cholesterol level QTL84.4blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)2231621666266435125Rat
1300126Bp175Blood pressure QTL 1753.46arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2229606682264899009Rat
1641891Alcrsp17Alcohol response QTL 17response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2155965557254121739Rat
1598813Memor9Memory QTL 92.7exploratory behavior trait (VT:0010471)average horizontal distance in proximity to the target during voluntary locomotion in an experimental apparatus (CMO:0002674)2214870793251212353Rat
1598835Anxrr18Anxiety related response QTL 182.98body movement coordination trait (VT:0005424)number of rearing movements in an experimental apparatus (CMO:0001752)2217743855262743855Rat
2298479Eau5Experimental allergic uveoretinitis QTL 50.0021uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)2217498545254132424Rat
2299161Iddm33Insulin dependent diabetes mellitus QTL 332.98blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)2221488355254121739Rat
1549836Bss2Bone structure and strength QTL 27.5femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)2228712271266435125Rat
2313073Bmd75Bone mineral density QTL 754.10.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)2231224020254132424Rat
2317752Glom23Glomerulus QTL 233.6urine protein amount (VT:0005160)urine protein level (CMO:0000591)2208594330263179188Rat
61366Iddm3Insulin dependent diabetes mellitus QTL 34.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)2204585642249585642Rat
61398Bp50Blood pressure QTL 504.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2204585642249585642Rat
8693622Alc26Alcohol consumption QTL 262.40.667drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)2237712398257579826Rat
9587428Epfw6Epididymal fat weight QTL 67.470.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)2240679103266435125Rat
7207490Bss111Bone structure and strength QTL 1116.4femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)2228712271266435125Rat
7411555Bw132Body weight QTL 1320.001body mass (VT:0001259)body weight gain (CMO:0000420)2240679103266435125Rat
7207482Bss107Bone structure and strength QTL 1077femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)2228712271266435125Rat
7207484Bss108Bone structure and strength QTL 1085.3femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)2228712271266435125Rat
8693697Alc36Alcohol consumption QTL 3620.592drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)2233013605253626471Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:11
Count of miRNA genes:11
Interacting mature miRNAs:11
Transcripts:ENSRNOT00000022387
Prediction methods:Miranda, Rnahybrid
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 48 32 19 32 8 11 72 35 34 11 8
Low 9 9 9 2 7
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_053326 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006233412 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006233416 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006233418 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006233419 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006233420 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006233421 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006233422 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006233423 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039103049 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039103050 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039103051 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039103052 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039103053 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039103054 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039103055 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039103056 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039103057 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide CH473952 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ215630 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000079 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U48247 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000022387   ⟹   ENSRNOP00000022387
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2247,818,243 - 247,988,462 (-)Ensembl
RefSeq Acc Id: NM_053326   ⟹   NP_445778
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22230,955,276 - 231,120,223 (-)NCBI
Rnor_6.02247,818,241 - 247,988,462 (-)NCBI
Rnor_5.02266,345,722 - 266,518,817 (-)NCBI
RGSC_v3.42240,177,301 - 240,304,192 (-)RGD
Celera2223,009,335 - 223,173,420 (-)RGD
Sequence:
RefSeq Acc Id: XM_006233404   ⟹   XP_006233466
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02247,815,214 - 247,989,198 (-)NCBI
Rnor_5.02266,345,722 - 266,518,817 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006233405   ⟹   XP_006233467
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02247,815,214 - 247,989,197 (-)NCBI
Rnor_5.02266,345,722 - 266,518,817 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006233406   ⟹   XP_006233468
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02247,815,214 - 247,989,196 (-)NCBI
Rnor_5.02266,345,722 - 266,518,817 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006233407   ⟹   XP_006233469
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02247,815,214 - 247,989,196 (-)NCBI
Rnor_5.02266,345,722 - 266,518,817 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006233409   ⟹   XP_006233471
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02247,815,214 - 247,989,193 (-)NCBI
Rnor_5.02266,345,722 - 266,518,817 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006233410   ⟹   XP_006233472
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02247,815,214 - 247,989,192 (-)NCBI
Rnor_5.02266,345,722 - 266,518,817 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006233411   ⟹   XP_006233473
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02247,815,214 - 247,989,190 (-)NCBI
Rnor_5.02266,345,722 - 266,518,817 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006233412   ⟹   XP_006233474
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22230,952,251 - 231,120,329 (-)NCBI
Rnor_6.02247,815,214 - 247,989,184 (-)NCBI
Rnor_5.02266,345,722 - 266,518,817 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006233413   ⟹   XP_006233475
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02247,815,214 - 247,989,195 (-)NCBI
Rnor_5.02266,345,722 - 266,518,817 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006233414   ⟹   XP_006233476
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02247,815,214 - 247,989,189 (-)NCBI
Rnor_5.02266,345,722 - 266,518,817 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006233415   ⟹   XP_006233477
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02247,815,214 - 247,989,187 (-)NCBI
Rnor_5.02266,345,722 - 266,518,817 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006233416   ⟹   XP_006233478
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22230,952,251 - 231,120,329 (-)NCBI
Rnor_6.02247,815,214 - 247,989,176 (-)NCBI
Rnor_5.02266,345,722 - 266,518,817 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006233418   ⟹   XP_006233480
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22230,952,251 - 231,120,329 (-)NCBI
Rnor_6.02247,815,214 - 247,988,960 (-)NCBI
Rnor_5.02266,345,722 - 266,518,817 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006233419   ⟹   XP_006233481
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22230,952,251 - 231,120,329 (-)NCBI
Rnor_6.02247,815,214 - 247,988,946 (-)NCBI
Rnor_5.02266,345,722 - 266,518,817 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006233420   ⟹   XP_006233482
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22231,019,247 - 231,120,329 (-)NCBI
Rnor_6.02247,881,579 - 247,988,836 (-)NCBI
Rnor_5.02266,345,722 - 266,518,817 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006233421   ⟹   XP_006233483
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22231,019,247 - 231,120,329 (-)NCBI
Rnor_6.02247,881,579 - 247,988,836 (-)NCBI
Rnor_5.02266,345,722 - 266,518,817 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006233422   ⟹   XP_006233484
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22231,019,247 - 231,120,329 (-)NCBI
Rnor_6.02247,881,579 - 247,988,836 (-)NCBI
Rnor_5.02266,345,722 - 266,518,817 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006233423   ⟹   XP_006233485
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22231,019,247 - 231,120,329 (-)NCBI
Rnor_6.02247,881,579 - 247,988,836 (-)NCBI
Rnor_5.02266,345,722 - 266,518,817 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039103049   ⟹   XP_038958977
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22230,952,251 - 231,120,329 (-)NCBI
RefSeq Acc Id: XM_039103050   ⟹   XP_038958978
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22230,952,251 - 231,120,329 (-)NCBI
RefSeq Acc Id: XM_039103051   ⟹   XP_038958979
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22230,952,251 - 231,120,329 (-)NCBI
RefSeq Acc Id: XM_039103052   ⟹   XP_038958980
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22230,952,251 - 231,120,329 (-)NCBI
RefSeq Acc Id: XM_039103053   ⟹   XP_038958981
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22230,952,251 - 231,120,329 (-)NCBI
RefSeq Acc Id: XM_039103054   ⟹   XP_038958982
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22230,952,251 - 231,120,329 (-)NCBI
RefSeq Acc Id: XM_039103055   ⟹   XP_038958983
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22230,952,251 - 231,120,329 (-)NCBI
RefSeq Acc Id: XM_039103056   ⟹   XP_038958984
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22230,952,251 - 231,120,329 (-)NCBI
RefSeq Acc Id: XM_039103057   ⟹   XP_038958985
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22231,019,247 - 231,120,329 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_445778   ⟸   NM_053326
- UniProtKB: Q62920 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006233475   ⟸   XM_006233413
- Peptide Label: isoform X9
- Sequence:
RefSeq Acc Id: XP_006233481   ⟸   XM_006233419
- Peptide Label: isoform X12
- UniProtKB: Q62920 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006233477   ⟸   XM_006233415
- Peptide Label: isoform X11
- Sequence:
RefSeq Acc Id: XP_006233473   ⟸   XM_006233411
- Peptide Label: isoform X7
- Sequence:
RefSeq Acc Id: XP_006233480   ⟸   XM_006233418
- Peptide Label: isoform X11
- Sequence:
RefSeq Acc Id: XP_006233476   ⟸   XM_006233414
- Peptide Label: isoform X10
- Sequence:
RefSeq Acc Id: XP_006233472   ⟸   XM_006233410
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: XP_006233471   ⟸   XM_006233409
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_006233478   ⟸   XM_006233416
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_006233468   ⟸   XM_006233406
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_006233467   ⟸   XM_006233405
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006233474   ⟸   XM_006233412
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006233469   ⟸   XM_006233407
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_006233466   ⟸   XM_006233404
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006233485   ⟸   XM_006233423
- Peptide Label: isoform X17
- Sequence:
RefSeq Acc Id: XP_006233484   ⟸   XM_006233422
- Peptide Label: isoform X16
- Sequence:
RefSeq Acc Id: XP_006233483   ⟸   XM_006233421
- Peptide Label: isoform X15
- Sequence:
RefSeq Acc Id: XP_006233482   ⟸   XM_006233420
- Peptide Label: isoform X14
- Sequence:
RefSeq Acc Id: ENSRNOP00000022387   ⟸   ENSRNOT00000022387
RefSeq Acc Id: XP_038958984   ⟸   XM_039103056
- Peptide Label: isoform X10
RefSeq Acc Id: XP_038958983   ⟸   XM_039103055
- Peptide Label: isoform X9
RefSeq Acc Id: XP_038958982   ⟸   XM_039103054
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038958981   ⟸   XM_039103053
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038958980   ⟸   XM_039103052
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038958978   ⟸   XM_039103050
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038958977   ⟸   XM_039103049
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038958979   ⟸   XM_039103051
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038958985   ⟸   XM_039103057
- Peptide Label: isoform X13
Protein Domains
LIM zinc-binding   PDZ

Transcriptome

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

Promoters
RGD ID:13691793
Promoter ID:EPDNEW_R2317
Type:initiation region
Name:Pdlim5_1
Description:PDZ and LIM domain 5
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_6.02247,988,478 - 247,988,538EPDNEW

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
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
2 266414737 266414738 T C snv DOB/Oda (KyushuU)
2 266423823 266423824 G A snv DOB/Oda (KyushuU)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621076 AgrOrtholog
Ensembl Genes ENSRNOG00000016419 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000022387 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000022387 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 2.30.42.10 UniProtKB/Swiss-Prot
InterPro DUF4749 UniProtKB/Swiss-Prot
  PDZ UniProtKB/Swiss-Prot
  PDZ_sf UniProtKB/Swiss-Prot
  Znf_LIM UniProtKB/Swiss-Prot
KEGG Report rno:64353 UniProtKB/Swiss-Prot
NCBI Gene 64353 ENTREZGENE
Pfam DUF4749 UniProtKB/Swiss-Prot
  LIM UniProtKB/Swiss-Prot
  PDZ UniProtKB/Swiss-Prot
PhenoGen Pdlim5 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
Superfamily-SCOP SSF50156 UniProtKB/Swiss-Prot
UniProt PDLI5_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2006-03-30 Pdlim5  PDZ and LIM domain 5  Enh  enigma homolog  Symbol and Name updated 1299863 APPROVED
2005-01-20 Enh  enigma homolog      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Enh  enigma homolog      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_domains contains three LIM domains with two zinc-finger motifs in each domain 632670
gene_drugs protein translocated from membrane fraction to cytosol on phorbol ester treatment 632670
gene_function phosphorylates protein kinase C by associating with the amino terminal region 632670