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
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21239,042,372 - 239,091,074 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1239,042,385 - 239,091,076 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1247,178,448 - 247,226,759 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01253,882,359 - 253,930,342 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01246,535,402 - 246,583,385 (-)NCBIRnor_WKY
Rnor_6.01259,308,326 - 259,357,006 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1259,308,296 - 259,357,056 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01266,752,410 - 266,800,840 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41245,350,086 - 245,399,534 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11245,446,644 - 245,496,093 (-)NCBI
Celera1234,889,852 - 234,937,718 (-)NCBICelera
Cytogenetic Map1q54NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (EXP)
1,1-dichloroethene  (ISO)
1,2-dimethylhydrazine  (ISO)
1-naphthyl isothiocyanate  (EXP)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,6-dinitrotoluene  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-aza-2'-deoxycytidine  (ISO)
6-propyl-2-thiouracil  (EXP)
acetamide  (EXP)
adefovir pivoxil  (ISO)
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 F  (ISO)
bleomycin A2  (EXP)
buspirone  (EXP)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
caffeine  (ISO)
chloroacetaldehyde  (ISO)
chlorpyrifos  (EXP)
cidofovir anhydrous  (ISO)
cisplatin  (ISO)
clodronic acid  (ISO)
cobalt dichloride  (ISO)
coumarin  (ISO)
coumestrol  (ISO)
cyclosporin A  (ISO)
dexamethasone  (ISO)
dibutyl phthalate  (ISO)
dichlorine  (EXP)
dioxygen  (ISO)
diuron  (EXP)
dorsomorphin  (ISO)
doxorubicin  (ISO)
Enterolactone  (ISO)
entinostat  (ISO)
enzyme inhibitor  (ISO)
ethanol  (ISO)
ethyl methanesulfonate  (ISO)
fenofibrate  (EXP)
folpet  (ISO)
fulvestrant  (ISO)
fumonisin B1  (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)
oxaliplatin  (EXP)
ozone  (EXP)
panobinostat  (ISO)
paracetamol  (EXP,ISO)
paraquat  (EXP)
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 arsenite  (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)
topotecan  (EXP)
trichostatin A  (ISO)
Triptolide  (EXP)
troglitazone  (EXP)
trovafloxacin  (EXP)
valproic acid  (ISO)
vancomycin  (ISO)
vinclozolin  (EXP)
zinc atom  (EXP)
zinc(0)  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

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  


Genomics

Comparative Map Data
Pdlim1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21239,042,372 - 239,091,074 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1239,042,385 - 239,091,076 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1247,178,448 - 247,226,759 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01253,882,359 - 253,930,342 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01246,535,402 - 246,583,385 (-)NCBIRnor_WKY
Rnor_6.01259,308,326 - 259,357,006 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1259,308,296 - 259,357,056 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01266,752,410 - 266,800,840 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41245,350,086 - 245,399,534 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11245,446,644 - 245,496,093 (-)NCBI
Celera1234,889,852 - 234,937,718 (-)NCBICelera
Cytogenetic Map1q54NCBI
PDLIM1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381095,237,572 - 95,291,003 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl1095,237,572 - 95,291,012 (-)EnsemblGRCh38hg38GRCh38
GRCh371096,997,329 - 97,050,760 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361096,987,319 - 97,040,771 (-)NCBINCBI36Build 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 Ensembl
GRCm381940,222,239 - 40,271,616 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1940,221,173 - 40,271,842 (-)EnsemblGRCm38mm10GRCm38
MGSCv371940,296,729 - 40,346,106 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361940,275,550 - 40,324,844 (-)NCBIMGSCv36mm8
Celera1941,028,383 - 41,076,730 (-)NCBICelera
Cytogenetic Map19C3NCBI
Pdlim1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555071,495,925 - 1,523,925 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555071,499,223 - 1,525,924 (-)NCBIChiLan1.0ChiLan1.0
PDLIM1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11095,355,669 - 95,389,838 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1095,355,669 - 95,393,871 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01091,848,127 - 91,901,553 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
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 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha288,947,047 - 8,994,090 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0289,033,997 - 9,079,972 (-)NCBIROS_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_1.0
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
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 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
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 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
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_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247376,485,607 - 6,530,511 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Pdlim1
278 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:298
Count of miRNA genes:190
Interacting mature miRNAs:213
Transcripts:ENSRNOT00000022000
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
7421630Bp362Blood pressure QTL 3620.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1118608292241799120Rat
2302378Insul11Insulin level QTL 113.25blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1144267353251128347Rat
724531Uae5Urinary albumin excretion QTL 54urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)1150700142252085212Rat
1578759Uae30Urinary albumin excretion QTL 303.30.003urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1150700247252085048Rat
1578778Pur4Proteinuria QTL 43.30.003urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)1150700247252085048Rat
1354610Bw34Body weight QTL 344.1body mass (VT:0001259)body weight (CMO:0000012)1151162512256448636Rat
1354646Kidm18Kidney mass QTL 185.7kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)1151162512256448636Rat
1354661Bw33Body weight QTL 335.2body mass (VT:0001259)body weight (CMO:0000012)1151162512256448636Rat
1549837Hcar15Hepatocarcinoma resistance QTL 150.05liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)1153136852260522016Rat
1354580Scort1Serum corticosterone level QTL 13.4blood corticosterone amount (VT:0005345)blood corticosterone level (CMO:0001172)1156677124256448636Rat
2292220Bp306Blood pressure QTL 3063.470.00087arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1164310393243914901Rat
738032Hcas5Hepatocarcinoma susceptibility QTL 53.12liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)1176426412257976495Rat
1354624Cm35Cardiac mass QTL355.7heart left ventricle mass (VT:0007031)calculated heart weight (CMO:0000073)1177227632256448636Rat
1354652Kidm20Kidney mass QTL 204.3kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)1177227632256448636Rat
634321Hc1Hypercalciuria QTL 12.91urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)1178810256240830002Rat
1578763Kidm29Kidney mass QTL 293.30.0001kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1179567751260522016Rat
8655655Arrd2Age-related retinal degeneration QTL 27.79retinal layer morphology trait (VT:0003727)percentage of study population developing retinopathy during a period of time (CMO:0002453)1183970203243914901Rat
8655855Arrd3Age-related retinal degeneration QTL 33.07lens clarity trait (VT:0001304)cataract incidence/prevalence measurement (CMO:0001585)1183970203243914901Rat
1358898Bp255Blood pressure QTL 2553.6arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1191019702246062233Rat
1358191Ept10Estrogen-induced pituitary tumorigenesis QTL 103.8pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)1192825253243914732Rat
1600388Niddm67Non-insulin dependent diabetes mellitus QTL 675.840.000004blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1195804352257091168Rat
1600395Niddm69Non-insulin dependent diabetes mellitus QTL 694.140.0002blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)1195804352257091168Rat
1600396Niddm68Non-insulin dependent diabetes mellitus QTL 684.970.0003blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1195804352257091168Rat
631658Cm7Cardiac mass QTL 75.320.0001aorta mass (VT:0002845)aorta weight (CMO:0000076)1196248093241248093Rat
1358292Cm37Cardiac mass QTL 376.20.00000081heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)1196248093241248093Rat
1600374Mcs17Mammary carcinoma susceptibility QTL 173mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1197670404242670404Rat
2302375Bw83Body weight QTL 834.870.0002body mass (VT:0001259)body weight (CMO:0000012)1197697768242697768Rat
61376Bp42Blood pressure QTL 4223.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1197814409242814409Rat
1298084Thym4Thymus enlargement QTL 410.68thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)1197814409242814409Rat
1357335Bw39Body weight QTL 393.3body mass (VT:0001259)body weight (CMO:0000012)1197814409242814409Rat
634313Niddm43Non-insulin dependent diabetes mellitus QTL 43blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1199050459259647894Rat
2293694Bss38Bone structure and strength QTL 387.050.0001femur strength trait (VT:0010010)femur stiffness (CMO:0001674)1201554356246554356Rat
7394701Uae46Urinary albumin excretion QTL 463.60.0056urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1201554356246554356Rat
2300175Bmd40Bone mineral density QTL 4015.40.0001femur mineral mass (VT:0010011)bone mineral density (CMO:0001226)1201554356246554356Rat
2293655Bss36Bone structure and strength QTL 3610.660.0001femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)1201554356246554356Rat
2293674Bss39Bone structure and strength QTL 397.10.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)1201554356246554356Rat
10059587Bw173Body weight QTL 1733.230.025body mass (VT:0001259)body weight (CMO:0000012)1202069611247069611Rat
1600363Hc6Hypercalciuria QTL 62.7urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)1203995416244113296Rat
1600397Edcs4Endometrial carcinoma susceptibility QTL 42.2uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)1206081677251081677Rat
1357399Bw45Body weight QTL 453.05body mass (VT:0001259)body mass index (BMI) (CMO:0000105)1206329708251329708Rat
1357404Bw42Body weight QTL 424.490.0001body mass (VT:0001259)body weight (CMO:0000012)1206329708251329708Rat
1358916Kidm22Kidney mass QTL 223.32kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)1210702053240947965Rat
1358890Bp259Blood pressure QTL 2593.06arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1210702053260522016Rat
2292216Bw80Body weight QTL 803.230.0019body mass (VT:0001259)body weight (CMO:0000012)1213533809243914901Rat
724538Kidm1Kidney mass QTL 13.2kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)1213707201252085212Rat
734768Niddm59Non-insulin dependent diabetes mellitus QTL 59body mass (VT:0001259)body weight (CMO:0000012)1213843987258843987Rat
70211Niddm24Non-insulin dependent diabetes mellitus QTL 243.79blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1214647894259647894Rat
1549910Bw54Body weight QTL 540.05body mass (VT:0001259)body weight (CMO:0000012)1214647894259647894Rat
61327Eae7Experimental allergic encephalomyelitis QTL 75.6body mass (VT:0001259)change in body weight (CMO:0002045)1216255568260522016Rat
2302040Pia35Pristane induced arthritis QTL 353.80.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)1216255568260522016Rat
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)1218748008257976495Rat
61400Niddm1Non-insulin dependent diabetes mellitus QTL 111blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1218753689245907899Rat
724533Rf51Renal function QTL 515.30.0002kidney plasma flow trait (VT:0005524)renal plasma flow (CMO:0001914)1218753816256448513Rat
731175Uae20Urinary albumin excretion QTL 203.50.0018urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1221264111259647894Rat
10053715Scort24Serum corticosterone level QTL 242.130.0088blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1221414816260522016Rat
724552Glom2Glomerulus QTL 23.30.0001kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli directly contacting the kidney surface (CMO:0001001)1222363780260522016Rat
1600392Bw123Body weight QTL 1230.001body mass (VT:0001259)body weight (CMO:0000012)1223201027260522016Rat
2293700Bmd27Bone mineral density QTL 276.60.0001femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)1224054293243747962Rat
2293701Bmd34Bone mineral density QTL 348.30.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)1224054293243747962Rat
734767Niddm57Non-insulin dependent diabetes mellitus QTL 57body mass (VT:0001259)body weight (CMO:0000012)1224054293260122809Rat
631843Bw116Body weight QTL 1164.10.016abdominal adipose amount (VT:1000220)abdominal fat pad weight (CMO:0000088)1224054293260122809Rat
734769Niddm58Non-insulin dependent diabetes mellitus QTL 58body mass (VT:0001259)body weight (CMO:0000012)1224569538260122809Rat
631215Stl8Serum triglyceride level QTL 89.270.0001blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)1225126575260522016Rat
1300108Rf8Renal function QTL 83.75renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)1228581588259647894Rat
2316896Gluco57Glucose level QTL 577.2blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1228985440245907899Rat
1581544Rf52Renal function QTL 520.05urine total protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)1232156370259647894Rat
631669Iddm9Insulin dependent diabetes mellitus QTL 92.80.039blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)1233190394258625266Rat
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)1233948574260522016Rat
631690Scl5Serum cholesterol level QTL 52.1blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1236125214260522016Rat
631836Stl31Serum triglyceride level QTL 314.640.00000487blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)1237147813260522016Rat
631837Niddm35Non-insulin dependent diabetes mellitus QTL 350.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1238699859259647894Rat

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
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 43 50 41 19 41 8 10 28 26 36 11 8
Low 7 1 46 9 5
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000022000   ⟹   ENSRNOP00000022000
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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
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:
RefSeq Acc Id: XM_039088562   ⟹   XP_038944490
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21239,042,372 - 239,091,074 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_059061   ⟸   NM_017365
- UniProtKB: P52944 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000022000   ⟸   ENSRNOT00000022000
RefSeq Acc Id: XP_038944490   ⟸   XM_039088562
- Peptide Label: isoform X1
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 Protein ENSRNOP00000022000 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000022000 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 2.30.42.10 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7100446 IMAGE-MGC_LOAD
InterPro DUF4749 UniProtKB/Swiss-Prot
  PDLIM1 UniProtKB/Swiss-Prot
  PDZ UniProtKB/Swiss-Prot
  PDZ_sf UniProtKB/Swiss-Prot
  Zasp-like_motif UniProtKB/Swiss-Prot
  Znf_LIM UniProtKB/Swiss-Prot
KEGG Report rno:54133 UniProtKB/Swiss-Prot
MGC_CLONE MGC:91751 IMAGE-MGC_LOAD
NCBI Gene 54133 ENTREZGENE
PANTHER PTHR24214:SF5 UniProtKB/Swiss-Prot
Pfam DUF4749 UniProtKB/Swiss-Prot
  LIM UniProtKB/Swiss-Prot
  PDZ UniProtKB/Swiss-Prot
PhenoGen Pdlim1 PhenoGen
PROSITE LIM_DOMAIN_1 UniProtKB/Swiss-Prot
  LIM_DOMAIN_2 UniProtKB/Swiss-Prot
  PDZ UniProtKB/Swiss-Prot
SMART LIM UniProtKB/Swiss-Prot
  PDZ UniProtKB/Swiss-Prot
  SM00735 UniProtKB/Swiss-Prot
Superfamily-SCOP SSF50156 UniProtKB/Swiss-Prot
TIGR TC205375
UniProt P52944 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary Q6IN45 UniProtKB/Swiss-Prot


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

RGD Curation Notes
Note Type Note Reference
gene_expression decreased mRNA expression occurs in response to chemical hypoxia 68225