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

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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: Enables actin binding activity. Involved in several processes, including actin cytoskeleton organization; fibroblast migration; and maintenance of cell polarity. Located in 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
Previously 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
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81248,991,818 - 249,040,409 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1248,991,818 - 249,047,379 (-)EnsemblGRCr8
mRatBN7.21239,042,372 - 239,091,074 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1239,042,385 - 239,091,076 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1247,178,448 - 247,226,759 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01253,882,359 - 253,930,342 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01246,535,402 - 246,583,385 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01259,308,326 - 259,357,006 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1259,308,296 - 259,357,056 (-)Ensemblrn6Rnor6.0
Rnor_5.01266,752,410 - 266,800,840 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41245,350,086 - 245,399,534 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1234,889,852 - 234,937,718 (-)NCBICelera
RGSC_v3.11245,446,644 - 245,496,093 (-)NCBI
Cytogenetic Map1q54NCBI
JBrowse:




Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (EXP)
(1->4)-beta-D-glucan  (ISO)
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)
2,5-hexanedione  (EXP)
2,6-dimethoxyphenol  (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)
actinomycin D  (ISO)
adefovir pivoxil  (ISO)
aflatoxin B1  (EXP)
all-trans-retinoic acid  (EXP,ISO)
ammonium chloride  (EXP)
aristolochic acid A  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
atrazine  (ISO)
azoxystrobin  (EXP)
belinostat  (ISO)
benzo[a]pyrene  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol AF  (ISO)
Bisphenol B  (ISO)
bisphenol F  (ISO)
bleomycin A2  (EXP)
buspirone  (EXP)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
caffeine  (ISO)
cantharidin  (ISO)
chloroacetaldehyde  (ISO)
chlorpyrifos  (EXP)
cidofovir anhydrous  (ISO)
cisplatin  (ISO)
clodronic acid  (ISO)
cobalt dichloride  (ISO)
corn oil  (EXP)
coumarin  (ISO)
coumestrol  (ISO)
cyclosporin A  (ISO)
dexamethasone  (ISO)
dibutyl phthalate  (ISO)
dichlorine  (EXP)
dimethyl sulfoxide  (ISO)
dioxygen  (ISO)
diuron  (EXP)
dorsomorphin  (ISO)
doxorubicin  (ISO)
Enterolactone  (ISO)
entinostat  (ISO)
enzyme inhibitor  (ISO)
ethanol  (ISO)
ethyl methanesulfonate  (ISO)
fenofibrate  (EXP)
folpet  (ISO)
fulvestrant  (ISO)
fumonisin B1  (ISO)
furfural  (ISO)
gamma-hexachlorocyclohexane  (EXP)
gamma-linolenic acid  (ISO)
glyphosate  (EXP)
ibuprofen  (EXP,ISO)
imidacloprid  (EXP)
indometacin  (ISO)
ivermectin  (ISO)
lead diacetate  (ISO)
lipopolysaccharide  (ISO)
mercury dibromide  (ISO)
metformin  (EXP)
methylmercury chloride  (ISO)
N-nitrosodiethylamine  (EXP)
N-nitrosomorpholine  (EXP)
nefazodone  (EXP)
nimesulide  (EXP)
nitrates  (ISO)
Nutlin-3  (ISO)
oxaliplatin  (EXP)
ozone  (EXP)
panobinostat  (ISO)
paracetamol  (EXP,ISO)
paraquat  (EXP,ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (EXP)
phenformin  (EXP)
phenobarbital  (ISO)
phenylmercury acetate  (ISO)
pirinixic acid  (ISO)
prednisolone  (ISO)
progesterone  (ISO)
propiconazole  (ISO)
resveratrol  (ISO)
S-(1,2-dichlorovinyl)-L-cysteine  (ISO)
SB 431542  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
sodium chloride  (ISO)
Soman  (EXP)
sulforaphane  (ISO)
sunitinib  (ISO)
T-2 toxin  (EXP)
tamoxifen  (ISO)
tauroursodeoxycholic acid  (EXP)
temozolomide  (ISO)
tetrachloromethane  (EXP,ISO)
thiabendazole  (EXP)
thioacetamide  (EXP)
titanium dioxide  (ISO)
topotecan  (EXP)
trichostatin A  (ISO)
triphenyl phosphate  (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

Cellular Component
actin cytoskeleton  (IDA,IEA,ISO)
adherens junction  (IBA)
cytoplasm  (IDA,IEA,ISO)
cytoskeleton  (IEA,ISO)
filamentous actin  (IBA)
stress fiber  (IBA,IDA,IEA,ISO)
transcription regulator complex  (IEA,ISO)
Z disc  (IBA,IDA,IEA,ISO)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. CLP36 and RIL recruit a-actinin-1 to stress fibers and differentially regulate stress fiber dynamics in F2408 fibroblasts. 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. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
6. GOA pipeline RGD automated data pipeline
7. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
8. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
9. Tentative Sequence Identification Numbers Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
10. Cloning of a rat cDNA encoding a novel LIM domain protein with high homology to rat RIL. 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   PMID:38334094  


Genomics

Comparative Map Data
Pdlim1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81248,991,818 - 249,040,409 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1248,991,818 - 249,047,379 (-)EnsemblGRCr8
mRatBN7.21239,042,372 - 239,091,074 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1239,042,385 - 239,091,076 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1247,178,448 - 247,226,759 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01253,882,359 - 253,930,342 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01246,535,402 - 246,583,385 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01259,308,326 - 259,357,006 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1259,308,296 - 259,357,056 (-)Ensemblrn6Rnor6.0
Rnor_5.01266,752,410 - 266,800,840 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41245,350,086 - 245,399,534 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1234,889,852 - 234,937,718 (-)NCBICelera
RGSC_v3.11245,446,644 - 245,496,093 (-)NCBI
Cytogenetic Map1q54NCBI
PDLIM1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381095,237,572 - 95,291,003 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1095,237,569 - 95,291,035 (-)Ensemblhg38GRCh38
GRCh371096,997,329 - 97,050,760 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361096,987,319 - 97,040,771 (-)NCBIBuild 36Build 36hg18NCBI36
Build 341096,987,321 - 97,040,771NCBI
Celera1090,738,487 - 90,791,969 (-)NCBICelera
Cytogenetic Map10q23.33NCBI
HuRef1090,624,265 - 90,677,751 (-)NCBIHuRef
CHM1_11097,279,094 - 97,332,709 (-)NCBICHM1_1
T2T-CHM13v2.01096,116,721 - 96,170,181 (-)NCBIT2T-CHM13v2.0
Pdlim1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391940,210,683 - 40,260,060 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1940,209,617 - 40,260,286 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm381940,222,239 - 40,271,616 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1940,221,173 - 40,271,842 (-)Ensemblmm10GRCm38
MGSCv371940,296,729 - 40,346,106 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361940,275,550 - 40,324,844 (-)NCBIMGSCv36mm8
Celera1941,028,383 - 41,076,730 (-)NCBICelera
Cytogenetic Map19C3NCBI
cM Map1934.24NCBI
Pdlim1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555071,495,925 - 1,523,925 (-)Ensembl
ChiLan1.0NW_0049555071,499,223 - 1,525,924 (-)NCBIChiLan1.0ChiLan1.0
PDLIM1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v28107,141,173 - 107,194,647 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan110107,146,488 - 107,199,938 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01091,848,127 - 91,901,553 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11095,355,669 - 95,389,838 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1095,355,669 - 95,393,871 (-)EnsemblpanPan2panpan1.1
PDLIM1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1288,770,882 - 8,817,828 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl288,771,186 - 8,801,354 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha288,947,047 - 8,994,090 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0289,033,997 - 9,079,972 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl289,033,997 - 9,079,973 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1288,749,916 - 8,797,044 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0288,808,695 - 8,855,890 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0288,952,472 - 8,999,504 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Pdlim1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440721338,044,314 - 38,087,612 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366364,083,071 - 4,126,739 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049366364,083,413 - 4,126,728 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PDLIM1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl14106,735,500 - 106,794,065 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.114106,744,320 - 106,793,606 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.214116,377,059 - 116,426,077 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PDLIM1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1988,398,814 - 88,452,660 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl988,397,294 - 88,452,610 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366604849,270,732 - 49,324,931 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Pdlim1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247376,485,607 - 6,530,526 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046247376,485,607 - 6,530,511 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Pdlim1
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1239,352,546 - 39,399,052 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Pdlim1
560 total Variants
miRNA Target Status (No longer updated)

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.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1578778Pur4Proteinuria QTL 43.30.003urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)1160111531262090437Rat
1354646Kidm18Kidney mass QTL 185.7kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)1160573753266453731Rat
1357335Bw39Body weight QTL 393.3body mass (VT:0001259)body weight (CMO:0000012)1207243873252243873Rat
1354652Kidm20Kidney mass QTL 204.3kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)1186658830266453731Rat
2293674Bss39Bone structure and strength QTL 397.10.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)1210980612255980612Rat
61327Eae7Experimental allergic encephalomyelitis QTL 75.6body mass (VT:0001259)change in body weight (CMO:0002045)1226175591270518180Rat
1578775Iddm21Insulin dependent diabetes mellitus QTL 214.13blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1245782829270518180Rat
1600395Niddm69Non-insulin dependent diabetes mellitus QTL 694.140.0002blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)1205233991267096252Rat
1578763Kidm29Kidney mass QTL 293.30.0001kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1218829748263829748Rat
1354624Cm35Cardiac mass QTL355.7heart left ventricle mass (VT:0007031)calculated heart weight (CMO:0000073)1186658830266453731Rat
1600396Niddm68Non-insulin dependent diabetes mellitus QTL 684.970.0003blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1205233991267096252Rat
631837Niddm35Non-insulin dependent diabetes mellitus QTL 350.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1248619887269633915Rat
1600397Edcs4Endometrial carcinoma susceptibility QTL 42.2uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)1176288899270518180Rat
631836Stl31Serum triglyceride level QTL 314.645e-06blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)1247133834270518180Rat
1549837Hcar15Hepatocarcinoma resistance QTL 150.05liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)1162548015270518180Rat
152025235Bw194Body weight QTL 1944.86body mass (VT:0001259)1132966869252856240Rat
1600388Niddm67Non-insulin dependent diabetes mellitus QTL 675.840.000004blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1205233991267096252Rat
2293694Bss38Bone structure and strength QTL 387.050.0001femur strength trait (VT:0010010)femur stiffness (CMO:0001674)1210980612255980612Rat
1598853Memor3Memory QTL 34.5exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)1152919152268496042Rat
1578759Uae30Urinary albumin excretion QTL 303.30.003urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1160111531262090437Rat
1300108Rf8Renal function QTL 83.75renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)1237995023269633915Rat
734767Niddm57Non-insulin dependent diabetes mellitus QTL 57body mass (VT:0001259)body weight (CMO:0000012)1233480549270108840Rat
1358898Bp255Blood pressure QTL 2553.6arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1200449456256003563Rat
631215Stl8Serum triglyceride level QTL 89.270.0001blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)1234540191270518180Rat
631843Bw116Body weight QTL 1164.10.016abdominal adipose amount (VT:1000220)abdominal fat pad weight (CMO:0000088)1233480549270108840Rat
731175Uae20Urinary albumin excretion QTL 203.50.0018urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1207163993269633915Rat
2300175Bmd40Bone mineral density QTL 4015.40.0001femur mineral mass (VT:0010011)bone mineral density (CMO:0001226)1210980612255980612Rat
1354661Bw33Body weight QTL 335.2body mass (VT:0001259)body weight (CMO:0000012)1160573753266453731Rat
724538Kidm1Kidney mass QTL 13.2kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)1223134011262090599Rat
2293655Bss36Bone structure and strength QTL 3610.660.0001femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)1210980612255980612Rat
1298084Thym4Thymus enlargement QTL 410.68thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)1207243873252243873Rat
724531Uae5Urinary albumin excretion QTL 54urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)1160111426262090599Rat
2314011Gluco56Glucose level QTL 56blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1209203273254203273Rat
734769Niddm58Non-insulin dependent diabetes mellitus QTL 58body mass (VT:0001259)body weight (CMO:0000012)1225108840270108840Rat
724533Rf51Renal function QTL 515.30.0002kidney plasma flow trait (VT:0005524)renal plasma flow (CMO:0001914)1228180370266453608Rat
1354580Scort1Serum corticosterone level QTL 13.4blood corticosterone amount (VT:0005345)blood corticosterone level (CMO:0001172)1154961463266453731Rat
1358292Cm37Cardiac mass QTL 376.28e-07heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)1205674651250674651Rat
61376Bp42Blood pressure QTL 4223.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1207243873252243873Rat
634313Niddm43Non-insulin dependent diabetes mellitus QTL 43blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1208479811269633915Rat
70211Niddm24Non-insulin dependent diabetes mellitus QTL 243.79blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1224633915269633915Rat
724552Glom2Glomerulus QTL 23.30.0001kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli directly contacting the kidney surface (CMO:0001001)1232312773270518180Rat
2316896Gluco57Glucose level QTL 577.2blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1238398865255849249Rat
1358916Kidm22Kidney mass QTL 223.32kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)1212738576257738576Rat
2312564Glom18Glomerulus QTL 182.40.003kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)1194786607262083703Rat
634321Hc1Hypercalciuria QTL 12.91urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)1188241285250779312Rat
2292218Kidm35Kidney mass QTL 35kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)1208798288253798288Rat
61400Niddm1Non-insulin dependent diabetes mellitus QTL 111blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1228180243255849249Rat
631658Cm7Cardiac mass QTL 75.320.0001aorta mass (VT:0002845)aorta weight (CMO:0000076)1205674651250674651Rat
1354610Bw34Body weight QTL 344.1body mass (VT:0001259)body weight (CMO:0000012)1160573753266453731Rat
2293700Bmd27Bone mineral density QTL 276.60.0001femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)1210980612255980612Rat
2293701Bmd34Bone mineral density QTL 348.30.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)1210980612255980612Rat
7387289Uae45Urinary albumin excretion QTL 452.860.0021urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1233204160270518180Rat
1600374Mcs17Mammary carcinoma susceptibility QTL 173mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1207099883252099883Rat
1581544Rf52Renal function QTL 520.05urine total protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)1241569529269633915Rat
1600363Hc6Hypercalciuria QTL 62.7urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)1210980612255980612Rat
631536Lnnr2Liver neoplastic nodule remodeling QTL 22.90.0005liver integrity trait (VT:0010547)liver remodeling tumorous lesion number to liver total tumorous lesion number ratio (CMO:0001705)1243953669270518180Rat
738032Hcas5Hepatocarcinoma susceptibility QTL 53.12liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)1185857683270518180Rat
2302040Pia35Pristane induced arthritis QTL 353.80.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)1226175591270518180Rat
631669Iddm9Insulin dependent diabetes mellitus QTL 92.80.039blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)1233349180270518180Rat
7394701Uae46Urinary albumin excretion QTL 463.60.0056urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1210980612255980612Rat
1598821Rf55Renal function QTL 556.3renal blood flow trait (VT:2000006)ratio of change in renal blood flow to change in renal perfusion pressure (CMO:0001239)1228174566270518180Rat

Markers in Region
AI029470  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21239,042,435 - 239,042,653 (+)MAPPERmRatBN7.2
Rnor_6.01259,308,388 - 259,308,605NCBIRnor6.0
Rnor_5.01266,752,472 - 266,752,689UniSTSRnor5.0
RGSC_v3.41245,350,148 - 245,350,365UniSTSRGSC3.4
Celera1234,889,914 - 234,890,131UniSTS
RH 3.4 Map11619.02UniSTS
Cytogenetic Map1q53UniSTS
BE108553  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21239,085,522 - 239,085,690 (+)MAPPERmRatBN7.2
Rnor_6.01259,351,561 - 259,351,728NCBIRnor6.0
Rnor_5.01266,795,395 - 266,795,562UniSTSRnor5.0
RGSC_v3.41245,394,089 - 245,394,256UniSTSRGSC3.4
Celera1234,932,277 - 234,932,444UniSTS
RH 3.4 Map11618.9UniSTS
Cytogenetic Map1q53UniSTS
AU047677  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21239,086,072 - 239,086,202 (+)MAPPERmRatBN7.2
Rnor_6.01259,352,111 - 259,352,240NCBIRnor6.0
Rnor_5.01266,795,945 - 266,796,074UniSTSRnor5.0
RGSC_v3.41245,394,639 - 245,394,768UniSTSRGSC3.4
Celera1234,932,827 - 234,932,956UniSTS
Cytogenetic Map1q53UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 164 91 90 59 92 59 6 356 192 11 143 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000022000   ⟹   ENSRNOP00000022000
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1248,991,818 - 249,047,379 (-)Ensembl
mRatBN7.2 Ensembl1239,042,385 - 239,091,076 (-)Ensembl
Rnor_6.0 Ensembl1259,308,296 - 259,357,056 (-)Ensembl
RefSeq Acc Id: NM_017365   ⟹   NP_059061
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81248,991,818 - 249,040,409 (-)NCBI
mRatBN7.21239,042,374 - 239,090,968 (-)NCBI
Rnor_6.01259,308,326 - 259,357,006 (-)NCBI
Rnor_5.01266,752,410 - 266,800,840 (-)NCBI
RGSC_v3.41245,350,086 - 245,399,534 (-)RGD
Celera1234,889,852 - 234,937,718 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_059061 (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  
Ensembl Protein ENSRNOP00000022000
  ENSRNOP00000022000.1
GenBank Protein P52944 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_059061   ⟸   NM_017365
- UniProtKB: Q6IN45 (UniProtKB/Swiss-Prot),   P52944 (UniProtKB/Swiss-Prot),   A6JH56 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000022000   ⟸   ENSRNOT00000022000
Protein Domains
LIM zinc-binding   PDZ

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P52944-F1-model_v2 AlphaFold P52944 1-327 view protein structure

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 AssemblyChrPosition (strand)Source
Rnor_6.01259,357,013 - 259,357,073EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:68324 AgrOrtholog
BioCyc Gene G2FUF-55720 BioCyc
Ensembl Genes ENSRNOG00000016166 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000022000 ENTREZGENE
  ENSRNOT00000022000.5 UniProtKB/Swiss-Prot
Gene3D-CATH 2.30.42.10 UniProtKB/Swiss-Prot
  Cysteine Rich Protein UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7100446 IMAGE-MGC_LOAD
InterPro DUF4749 UniProtKB/Swiss-Prot
  PDLIM1 UniProtKB/Swiss-Prot
  PDZ UniProtKB/Swiss-Prot
  PDZ-LIM_domain 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 Pdlim1 ENTREZGENE
PANTHER PDZ AND LIM DOMAIN PROTEIN ZASP UniProtKB/Swiss-Prot
  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
RatGTEx ENSRNOG00000016166 RatGTEx
SMART LIM UniProtKB/Swiss-Prot
  PDZ UniProtKB/Swiss-Prot
  SM00735 UniProtKB/Swiss-Prot
Superfamily-SCOP Glucocorticoid receptor-like (DNA-binding domain) UniProtKB/Swiss-Prot
  SSF50156 UniProtKB/Swiss-Prot
TIGR TC205375
UniProt A6JH56 ENTREZGENE, UniProtKB/TrEMBL
  A6JH57_RAT UniProtKB/TrEMBL
  P52944 ENTREZGENE, UniProtKB/Swiss-Prot
  Q6IN45 ENTREZGENE
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