Human Gene PLD5 (uc001hzl.4)
  Description: Homo sapiens phospholipase D family, member 5 (PLD5), transcript variant 2, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr1:242,251,689-242,612,784 Size: 361,096 Total Exon Count: 10 Strand: -
Coding Region
   Position: hg19 chr1:242,253,156-242,612,658 Size: 359,503 Coding Exon Count: 10 

Page IndexSequence and LinksPrimersGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA Descriptions
Other NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:242,251,689-242,612,784)mRNA (may differ from genome)Protein (474 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsH-INV
HGNCLynxMGIPubMedTreefamUniProtKB
WikipediaBioGrid CRISPR DB

-  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): PLD5
CDC HuGE Published Literature: PLD5
Positive Disease Associations: Socioeconomic Factors , Urinalysis
Related Studies:
  1. Socioeconomic Factors
    , , . [PubMed 0]
  2. Urinalysis
    Shih-Jen Hwang et al. BMC medical genetics 2007, A genome-wide association for kidney function and endocrine-related traits in the NHLBI's Framingham Heart Study., BMC medical genetics. [PubMed 17903292]
    Kidney function traits and TSH are associated with SNPs on the Affymetrix GeneChip Human Mapping 100K SNP set. These data will serve as a valuable resource for replication as more SNPs associated with kidney function and endocrine traits are identified.

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  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: 4.52 RPKM in Brain - Cerebellar Hemisphere
Total median expression: 27.56 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 -44.50126-0.353 Picture PostScript Text
3' UTR -353.851467-0.241 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:
PF13091 - PLD-like domain
PF13918 - PLD-like domain

SCOP Domains:
56024 - Phospholipase D/nuclease

ModBase Predicted Comparative 3D Structure on Q8N7P1-4
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
  KJ903987 - Synthetic construct Homo sapiens clone ccsbBroadEn_13381 PLD5 gene, encodes complete protein.
AK091691 - Homo sapiens cDNA FLJ34372 fis, clone FEBRA2017223, weakly similar to Mus musculus schwannoma-associated protein (SAM9) mRNA.
AX747130 - Sequence 655 from Patent EP1308459.
AY461578 - Homo sapiens PLDc protein mRNA, complete cds.
AK098092 - Homo sapiens cDNA FLJ40773 fis, clone TRACH2004845, weakly similar to PROTEIN K4.
BC101373 - Homo sapiens phospholipase D family, member 5, mRNA (cDNA clone MGC:120565 IMAGE:40025860), complete cds.
BC101374 - Homo sapiens phospholipase D family, member 5, mRNA (cDNA clone MGC:120566 IMAGE:40025861), complete cds.
BC101375 - Homo sapiens phospholipase D family, member 5, mRNA (cDNA clone MGC:120567 IMAGE:40025862), complete cds.
AK295421 - Homo sapiens cDNA FLJ57051 complete cds, highly similar to Mus musculus phospholipase D family, member 5 (Pld5), mRNA.
AY391836 - Homo sapiens HSD-37-like mRNA, complete sequence.
AK307857 - Homo sapiens cDNA, FLJ97805.
JD375083 - Sequence 356107 from Patent EP1572962.
JD299713 - Sequence 280737 from Patent EP1572962.
JD304999 - Sequence 286023 from Patent EP1572962.
JD039648 - Sequence 20672 from Patent EP1572962.
JD506929 - Sequence 487953 from Patent EP1572962.
JD496493 - Sequence 477517 from Patent EP1572962.
JD465692 - Sequence 446716 from Patent EP1572962.
JD186051 - Sequence 167075 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: NM_001195811, NP_001182741, Q8N7P1-4
UCSC ID: uc001hzl.4
RefSeq Accession: NM_001195811
Protein: Q8N7P1-4, splice isoform of Q8N7P1 CCDS: CCDS55692.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001195811.1
exon count: 10CDS single in 3' UTR: no RNA size: 3018
ORF size: 1425CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2996.50frame 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.