Human Gene PDLIM5 (uc011cdx.2)
  Description: Homo sapiens PDZ and LIM domain 5 (PDLIM5), transcript variant 7, mRNA.
RefSeq Summary (NM_001256427): 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: 15 Strand: +
Coding Region
   Position: hg19 chr4:95,376,440-95,587,177 Size: 210,738 Coding Exon Count: 14 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsMalaCards
CTDGene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein Structure
Other SpeciesGO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr4:95,373,008-95,589,378)mRNA (may differ from genome)Protein (483 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
H-INVHGNCLynxMalacardsMGIOMIM
PubMedUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: B7Z8X5_HUMAN
DESCRIPTION: SubName: Full=cDNA FLJ61541, highly similar to Homo sapiens PDZ and LIM domain 5 (PDLIM5), transcript variant 2, mRNA;
SIMILARITY: Contains 1 PDZ (DHR) domain.
SIMILARITY: Contains 3 LIM zinc-binding domains.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  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 -535.762201-0.243 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
  InterPro Domains: Graphical view of domain structure
IPR001478 - PDZ
IPR001781 - Znf_LIM

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 B7Z8X5
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     
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0046872 metal ion binding

Cellular Component:
GO:0005737 cytoplasm


-  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.
AK129886 - Homo sapiens cDNA FLJ26376 fis, clone HRT06353.
AL049969 - Homo sapiens mRNA; cDNA DKFZp564A072 (from clone DKFZp564A072).

-  Other Names for This Gene
  Alternate Gene Symbols: B7Z8X5, B7Z8X5_HUMAN, NM_001256427, NP_001243356, uc011cdx.1
UCSC ID: uc011cdx.2
RefSeq Accession: NM_001256427
Protein: B7Z8X5 CCDS: CCDS47102.1, CCDS58917.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001256427.1
exon count: 15CDS single in 3' UTR: no RNA size: 3834
ORF size: 1452CDS single in intron: no Alignment % ID: 99.97
txCdsPredict score: 3104.00frame 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: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# 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.