Human Gene PDLIM5 (uc003hth.4) Description and Page Index
  Description: Homo sapiens PDZ and LIM domain 5 (PDLIM5), transcript variant 2, mRNA.
RefSeq Summary (NM_001011513): This gene encodes a member of a family of proteins that possess a 100-amino acid PDZ domain at the N terminus and one to three LIM domains at the C-terminus. This family member functions as a scaffold protein that tethers protein kinases to the Z-disk in striated muscles. It is thought to function in cardiomyocyte expansion and in restraining postsynaptic growth of excitatory synapses. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Jan 2012].
Transcript (Including UTRs)
   Position: hg19 chr4:95,373,008-95,589,378 Size: 216,371 Total Exon Count: 13 Strand: +
Coding Region
   Position: hg19 chr4:95,376,440-95,585,218 Size: 208,779 Coding Exon Count: 12 

Page IndexSequence and LinksGenetic AssociationsMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-15

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr4:95,373,008-95,589,378)mRNA (may differ from genome)Protein (487 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCLynxMGIOMIM
PubMedReactomeStanford SOURCEUniProtKBWikipedia

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): PDLIM5
CDC HuGE Published Literature: PDLIM5
Positive Disease Associations: Cholesterol , Cholesterol, LDL , Parietal Lobe , prostate cancer , Prostatic Neoplasms , schizophrenia
Related Studies:
  1. Cholesterol
    Sekar Kathiresan et al. BMC medical genetics 2007, A genome-wide association study for blood lipid phenotypes in the Framingham Heart Study., BMC medical genetics. [PubMed 17903299]
    Using a 100K genome-wide scan, we have generated a set of putative associations for common sequence variants and lipid phenotypes. Validation of selected hypotheses in additional samples did not identify any new loci underlying variability in blood lipids. Lack of replication may be due to inadequate statistical power to detect modest quantitative trait locus effects (i.e., <1% of trait variance explained) or reduced genomic coverage of the 100K array. GWAS in FHS using a denser genome-wide genotyping platform and a better-powered replication strategy may identify novel loci underlying blood lipids.
  2. Cholesterol, LDL
    Sekar Kathiresan et al. BMC medical genetics 2007, A genome-wide association study for blood lipid phenotypes in the Framingham Heart Study., BMC medical genetics. [PubMed 17903299]
    Using a 100K genome-wide scan, we have generated a set of putative associations for common sequence variants and lipid phenotypes. Validation of selected hypotheses in additional samples did not identify any new loci underlying variability in blood lipids. Lack of replication may be due to inadequate statistical power to detect modest quantitative trait locus effects (i.e., <1% of trait variance explained) or reduced genomic coverage of the 100K array. GWAS in FHS using a denser genome-wide genotyping platform and a better-powered replication strategy may identify novel loci underlying blood lipids.
  3. Parietal Lobe
    Sudha Seshadri et al. BMC medical genetics 2007, Genetic correlates of brain aging on MRI and cognitive test measures: a genome-wide association and linkage analysis in the Framingham Study., BMC medical genetics. [PubMed 17903297]
    Our results suggest that genes associated with clinical neurological disease also have detectable effects on subclinical phenotypes. These hypothesis generating data illustrate the use of an unbiased approach to discover novel pathways that may be involved in brain aging, and could be used to replicate observations made in other studies.
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: PDLIM5
Diseases sorted by gene-association score: nail-patella syndrome (12), nephrogenic adenofibroma (11), bipolar disorder (10), schizophrenia (3), left ventricular noncompaction (1)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene
  • D013749 Tetrachlorodibenzodioxin
  • D000082 Acetaminophen
  • D001564 Benzo(a)pyrene
  • C016403 2,4-dinitrotoluene
  • C023514 2,6-dinitrotoluene
  • C548651 2-(1'H-indolo-3'-carbonyl)thiazole-4-carboxylic acid methyl ester
  • C035207 4-amino-2,6-dinitrotoluene
  • D015123 7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide
  • D015127 9,10-Dimethyl-1,2-benzanthracene
  • D000111 Acetylcysteine
          more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 54.03 RPKM in Heart - Left Ventricle
Total median expression: 613.38 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -80.00181-0.442 Picture PostScript Text
3' UTR -1096.634160-0.264 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  Pfam Domains:
PF00412 - LIM domain
PF00595 - PDZ domain (Also known as DHR or GLGF)
PF15936 - Domain of unknown function (DUF4749)

SCOP Domains:
50156 - PDZ domain-like
57716 - Glucocorticoid receptor-like (DNA-binding domain)

ModBase Predicted Comparative 3D Structure on Q96HC4-4
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
      
      
      

-  Descriptions from all associated GenBank mRNAs
  BC017902 - Homo sapiens PDZ and LIM domain 5, mRNA (cDNA clone IMAGE:4271274), complete cds.
BC008741 - Homo sapiens PDZ and LIM domain 5, mRNA (cDNA clone MGC:2010 IMAGE:3345715), complete cds.
AK291898 - Homo sapiens cDNA FLJ77159 complete cds, highly similar to Homo sapiens PDZ and LIM domain 5 (PDLIM5), transcript variant 5, mRNA.
AK291624 - Homo sapiens cDNA FLJ76869 complete cds, highly similar to Homo sapiens PDZ and LIM domain 5 (PDLIM5), mRNA.
AK304125 - Homo sapiens cDNA FLJ61541 complete cds, highly similar to Homo sapiens PDZ and LIM domain 5 (PDLIM5), transcript variant 2, mRNA.
AK296980 - Homo sapiens cDNA FLJ54018 complete cds, highly similar to PDZ and LIM domain protein 5.
AL832686 - Homo sapiens mRNA; cDNA DKFZp313C0434 (from clone DKFZp313C0434).
AL832157 - Homo sapiens mRNA; cDNA DKFZp686G1014 (from clone DKFZp686G1014).
AF061258 - Homo sapiens LIM protein mRNA, complete cds.
AL833151 - Homo sapiens mRNA; cDNA DKFZp313J2240 (from clone DKFZp313J2240).
AL833438 - Homo sapiens mRNA; cDNA DKFZp313E0842 (from clone DKFZp313E0842).
BC026029 - Homo sapiens PDZ and LIM domain 5, mRNA (cDNA clone IMAGE:5428538).
AM393485 - Synthetic construct Homo sapiens clone IMAGE:100002229 for hypothetical protein (PDLIM5 gene).
AM393621 - Synthetic construct Homo sapiens clone IMAGE:100002228 for hypothetical protein (PDLIM5 gene).
AM393306 - Synthetic construct Homo sapiens clone IMAGE:100002397 for hypothetical protein (PDLIM5 gene).
AM393394 - Synthetic construct Homo sapiens clone IMAGE:100002199 for hypothetical protein (PDLIM5 gene).
AM393813 - Synthetic construct Homo sapiens clone IMAGE:100002302 for hypothetical protein (PDLIM5 gene).
DQ890686 - Synthetic construct clone IMAGE:100003316; FLH165110.01X; RZPDo839G01158D PDZ and LIM domain 5 (PDLIM5) gene, encodes complete protein.
DQ893868 - Synthetic construct Homo sapiens clone IMAGE:100008328; FLH165106.01L; RZPDo839G01157D PDZ and LIM domain 5 (PDLIM5) gene, encodes complete protein.
AB587372 - Synthetic construct DNA, clone: pF1KB4614, Homo sapiens PDLIM5 gene for PDZ and LIM domain 5, without stop codon, in Flexi system.
CU679071 - Synthetic construct Homo sapiens gateway clone IMAGE:100020402 5' read PDLIM5 mRNA.
CU676108 - Synthetic construct Homo sapiens gateway clone IMAGE:100022131 5' read PDLIM5 mRNA.
KJ898255 - Synthetic construct Homo sapiens clone ccsbBroadEn_07649 PDLIM5 gene, encodes complete protein.
KJ898254 - Synthetic construct Homo sapiens clone ccsbBroadEn_07648 PDLIM5 gene, encodes complete protein.
BT007328 - Homo sapiens LIM protein (similar to rat protein kinase C-binding enigma) mRNA, complete cds.
AY598328 - Homo sapiens L9 mRNA, complete cds.
AB209531 - Homo sapiens mRNA for Enigma homolog protein.
AY345240 - Homo sapiens PDZ and LIM domain 5 (PDLIM5) mRNA, complete cds.
AL833439 - Homo sapiens mRNA; cDNA DKFZp313G1842 (from clone DKFZp313G1842).
AF116705 - Homo sapiens PRO2489 mRNA, complete cds.
DQ582995 - Homo sapiens piRNA piR-50107, complete sequence.
JD051374 - Sequence 32398 from Patent EP1572962.
AK027217 - Homo sapiens cDNA: FLJ23564 fis, clone LNG10773.
JD530560 - Sequence 511584 from Patent EP1572962.
JD346124 - Sequence 327148 from Patent EP1572962.
JD509043 - Sequence 490067 from Patent EP1572962.
JD188896 - Sequence 169920 from Patent EP1572962.
JD381250 - Sequence 362274 from Patent EP1572962.
JD344247 - Sequence 325271 from Patent EP1572962.
JD410074 - Sequence 391098 from Patent EP1572962.
JD404836 - Sequence 385860 from Patent EP1572962.
JD454054 - Sequence 435078 from Patent EP1572962.
JD375910 - Sequence 356934 from Patent EP1572962.
JD473995 - Sequence 455019 from Patent EP1572962.
JD084403 - Sequence 65427 from Patent EP1572962.
JD430337 - Sequence 411361 from Patent EP1572962.
JD557462 - Sequence 538486 from Patent EP1572962.
JD529456 - Sequence 510480 from Patent EP1572962.
JD169741 - Sequence 150765 from Patent EP1572962.
JD169742 - Sequence 150766 from Patent EP1572962.
JD306389 - Sequence 287413 from Patent EP1572962.
JD055254 - Sequence 36278 from Patent EP1572962.
JD125743 - Sequence 106767 from Patent EP1572962.
JD125744 - Sequence 106768 from Patent EP1572962.
JD447014 - Sequence 428038 from Patent EP1572962.
JD177492 - Sequence 158516 from Patent EP1572962.
JD177493 - Sequence 158517 from Patent EP1572962.
JD334177 - Sequence 315201 from Patent EP1572962.
JD036709 - Sequence 17733 from Patent EP1572962.
JD226297 - Sequence 207321 from Patent EP1572962.
JD542806 - Sequence 523830 from Patent EP1572962.
JD212779 - Sequence 193803 from Patent EP1572962.
JD198174 - Sequence 179198 from Patent EP1572962.
JD488029 - Sequence 469053 from Patent EP1572962.
JD228210 - Sequence 209234 from Patent EP1572962.
JD524495 - Sequence 505519 from Patent EP1572962.
JD413480 - Sequence 394504 from Patent EP1572962.
JD247071 - Sequence 228095 from Patent EP1572962.
JD247072 - Sequence 228096 from Patent EP1572962.
JD257753 - Sequence 238777 from Patent EP1572962.
JD323787 - Sequence 304811 from Patent EP1572962.
JD167616 - Sequence 148640 from Patent EP1572962.
JD481190 - Sequence 462214 from Patent EP1572962.
JD481191 - Sequence 462215 from Patent EP1572962.
JD481192 - Sequence 462216 from Patent EP1572962.
JD179281 - Sequence 160305 from Patent EP1572962.
JD208889 - Sequence 189913 from Patent EP1572962.
JD350774 - Sequence 331798 from Patent EP1572962.
JD417587 - Sequence 398611 from Patent EP1572962.
JD417586 - Sequence 398610 from Patent EP1572962.
JD289575 - Sequence 270599 from Patent EP1572962.
JD411818 - Sequence 392842 from Patent EP1572962.
JD410067 - Sequence 391091 from Patent EP1572962.
JD544136 - Sequence 525160 from Patent EP1572962.
JD484990 - Sequence 466014 from Patent EP1572962.
JD144147 - Sequence 125171 from Patent EP1572962.
JD537423 - Sequence 518447 from Patent EP1572962.
JD194918 - Sequence 175942 from Patent EP1572962.
JD243319 - Sequence 224343 from Patent EP1572962.
JD421434 - Sequence 402458 from Patent EP1572962.
JD315105 - Sequence 296129 from Patent EP1572962.
JD091588 - Sequence 72612 from Patent EP1572962.
JD261664 - Sequence 242688 from Patent EP1572962.
JD430139 - Sequence 411163 from Patent EP1572962.
JD557308 - Sequence 538332 from Patent EP1572962.
JD529122 - Sequence 510146 from Patent EP1572962.
JD169202 - Sequence 150226 from Patent EP1572962.
JD041232 - Sequence 22256 from Patent EP1572962.
JD320990 - Sequence 302014 from Patent EP1572962.
JD388032 - Sequence 369056 from Patent EP1572962.
JD388033 - Sequence 369057 from Patent EP1572962.
JD118197 - Sequence 99221 from Patent EP1572962.
AK129886 - Homo sapiens cDNA FLJ26376 fis, clone HRT06353.
AL049969 - Homo sapiens mRNA; cDNA DKFZp564A072 (from clone DKFZp564A072).

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q96HC4 (Reactome details) participates in the following event(s):

R-HSA-6794354 NMDA receptor complex:DLG2,DLG3,DLG4:SPAR binds PDLIM5
R-HSA-6794361 Neurexins and neuroligins
R-HSA-6794362 Protein-protein interactions at synapses
R-HSA-112316 Neuronal System

-  Other Names for This Gene
  Alternate Gene Symbols: ENH, L9, NM_001011513, NP_001011513, Q96HC4-4, uc003hth.3
UCSC ID: uc003hth.4
RefSeq Accession: NM_001011513
Protein: Q96HC4-4 CCDS: CCDS47102.1, CCDS58917.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001011513.3
exon count: 13CDS single in 3' UTR: no RNA size: 5805
ORF size: 1464CDS single in intron: no Alignment % ID: 99.98
txCdsPredict score: 3128.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: yes # AT/AC introns 0
selenocysteine: no end bleed into intron: 4192# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.