Human Gene PLD6 (uc002gqz.3)
  Description: Homo sapiens phospholipase D family, member 6 (PLD6), nuclear gene encoding mitochondrial protein, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr17:17,104,309-17,109,646 Size: 5,338 Total Exon Count: 2 Strand: -
Coding Region
   Position: hg19 chr17:17,106,081-17,109,600 Size: 3,520 Coding Exon Count: 2 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:17,104,309-17,109,646)mRNA (may differ from genome)Protein (252 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeTreefamUniProtKB
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PLD6_HUMAN
DESCRIPTION: RecName: Full=Mitochondrial cardiolipin hydrolase; EC=3.1.4.-; AltName: Full=Choline phosphatase 6; AltName: Full=Mitochondrial phospholipase; Short=MitoPLD; AltName: Full=Phosphatidylcholine-hydrolyzing phospholipase D6; AltName: Full=Phospholipase D6; Short=PLD 6; AltName: Full=Protein zucchini homolog;
FUNCTION: Cardiolipin hydrolase present at the mitochondrial outer membrane required both for mitochondrial fusion and piRNA metabolic process. Acts by catalyzing the hydrolysis of cardiolipin (diphosphatidylglycerol) to form phosphatidate (phosphatidic acid or PA) at the mitochondrial outer membrane surface, promoting mitochondrial fusion. The production of phosphatidate also regulates the piRNA metabolic process by promoting recruitment and/or activation of components of the meiotic nuage, also named P granule, a critical step for primary biogenesis of piRNAs. Required during spermatogenesis to repress transposable elements and prevent their mobilization via its role in the piRNA metabolic process, which mediates the repression of transposable elements during meiosis by forming complexes composed of piRNAs and Piwi proteins and govern the methylation and subsequent repression of transposons.
SUBUNIT: Homodimer.
SUBCELLULAR LOCATION: Mitochondrion outer membrane; Single-pass membrane protein.
TISSUE SPECIFICITY: Widely expressed. Expression is not limites to testis and ovary.
DOMAIN: In contrast to other members of the phospholipase D family, contains only one PLD phosphodiesterase domain, suggesting that it has a single half-catalytic and requires homodimerization to form a complete active site (PubMed:17028579).
SIMILARITY: Belongs to the phospholipase D family. MitoPLD/Zucchini subfamily.
SIMILARITY: Contains 1 PLD phosphodiesterase domain.

-  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


-  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: 8.08 RPKM in Testis
Total median expression: 53.39 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 -17.2046-0.374 Picture PostScript Text
3' UTR -598.631772-0.338 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
IPR025202 - PLD-like_dom
IPR001736 - PLipase_D/transphosphatidylase

Pfam Domains:
PF13091 - PLD-like domain

SCOP Domains:
56024 - Phospholipase D/nuclease

ModBase Predicted Comparative 3D Structure on Q8N2A8
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 orthologGenome BrowserGenome BrowserNo orthologNo ortholog
Gene Details  Gene Details  
Gene Sorter  Gene Sorter  
  EnsemblFlyBase  
  Protein SequenceProtein Sequence  
  AlignmentAlignment  

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003824 catalytic activity
GO:0004518 nuclease activity
GO:0004519 endonuclease activity
GO:0005515 protein binding
GO:0016787 hydrolase activity
GO:0035755 cardiolipin hydrolase activity
GO:0042803 protein homodimerization activity
GO:0046872 metal ion binding

Biological Process:
GO:0006629 lipid metabolic process
GO:0006654 phosphatidic acid biosynthetic process
GO:0007283 spermatogenesis
GO:0007286 spermatid development
GO:0008053 mitochondrial fusion
GO:0010636 positive regulation of mitochondrial fusion
GO:0016042 lipid catabolic process
GO:0030154 cell differentiation
GO:0030719 P granule organization
GO:0034587 piRNA metabolic process
GO:0043046 DNA methylation involved in gamete generation
GO:0051321 meiotic cell cycle
GO:0090305 nucleic acid phosphodiester bond hydrolysis

Cellular Component:
GO:0005739 mitochondrion
GO:0005741 mitochondrial outer membrane
GO:0016020 membrane
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  BC031263 - Homo sapiens phospholipase D family, member 6, mRNA (cDNA clone MGC:39730 IMAGE:5274952), complete cds.
AK098419 - Homo sapiens cDNA FLJ25553 fis, clone JTH02483.
AK090899 - Homo sapiens cDNA FLJ33580 fis, clone BRAMY2011841.
AX746668 - Sequence 193 from Patent EP1308459.
JD290941 - Sequence 271965 from Patent EP1572962.
JD130029 - Sequence 111053 from Patent EP1572962.
JD215670 - Sequence 196694 from Patent EP1572962.
JD286371 - Sequence 267395 from Patent EP1572962.
JD103668 - Sequence 84692 from Patent EP1572962.
JD382422 - Sequence 363446 from Patent EP1572962.
JD190785 - Sequence 171809 from Patent EP1572962.
JD416982 - Sequence 398006 from Patent EP1572962.
JD486420 - Sequence 467444 from Patent EP1572962.
JD223587 - Sequence 204611 from Patent EP1572962.
JD336847 - Sequence 317871 from Patent EP1572962.
JD172734 - Sequence 153758 from Patent EP1572962.
JD238947 - Sequence 219971 from Patent EP1572962.
JD356699 - Sequence 337723 from Patent EP1572962.
JD254604 - Sequence 235628 from Patent EP1572962.
JD119919 - Sequence 100943 from Patent EP1572962.
JD426709 - Sequence 407733 from Patent EP1572962.
JD255952 - Sequence 236976 from Patent EP1572962.
JD489000 - Sequence 470024 from Patent EP1572962.
JD220889 - Sequence 201913 from Patent EP1572962.
JD413832 - Sequence 394856 from Patent EP1572962.
JD413833 - Sequence 394857 from Patent EP1572962.
JD463303 - Sequence 444327 from Patent EP1572962.
JD463304 - Sequence 444328 from Patent EP1572962.
JD213396 - Sequence 194420 from Patent EP1572962.
JD407681 - Sequence 388705 from Patent EP1572962.
JD152361 - Sequence 133385 from Patent EP1572962.
JD258837 - Sequence 239861 from Patent EP1572962.
JD399338 - Sequence 380362 from Patent EP1572962.
JD353114 - Sequence 334138 from Patent EP1572962.
JD322129 - Sequence 303153 from Patent EP1572962.
JD213395 - Sequence 194419 from Patent EP1572962.
JD463302 - Sequence 444326 from Patent EP1572962.
JD213393 - Sequence 194417 from Patent EP1572962.
JD152359 - Sequence 133383 from Patent EP1572962.
JD353112 - Sequence 334136 from Patent EP1572962.
JD119299 - Sequence 100323 from Patent EP1572962.
JD325978 - Sequence 307002 from Patent EP1572962.
JD325979 - Sequence 307003 from Patent EP1572962.
JD367269 - Sequence 348293 from Patent EP1572962.
JD325980 - Sequence 307004 from Patent EP1572962.
JD367270 - Sequence 348294 from Patent EP1572962.
JD325981 - Sequence 307005 from Patent EP1572962.
JD367271 - Sequence 348295 from Patent EP1572962.
JD413668 - Sequence 394692 from Patent EP1572962.
JD427601 - Sequence 408625 from Patent EP1572962.
JD165589 - Sequence 146613 from Patent EP1572962.
JD484327 - Sequence 465351 from Patent EP1572962.
JD354995 - Sequence 336019 from Patent EP1572962.
JD237201 - Sequence 218225 from Patent EP1572962.
JD136415 - Sequence 117439 from Patent EP1572962.
JD131433 - Sequence 112457 from Patent EP1572962.
DQ582925 - Homo sapiens piRNA piR-50037, complete sequence.
JD268318 - Sequence 249342 from Patent EP1572962.
AK295282 - Homo sapiens cDNA FLJ55057 complete cds.
JD510703 - Sequence 491727 from Patent EP1572962.
JD249450 - Sequence 230474 from Patent EP1572962.
AK309336 - Homo sapiens cDNA, FLJ99377.
JD290628 - Sequence 271652 from Patent EP1572962.
JD467289 - Sequence 448313 from Patent EP1572962.
JD424312 - Sequence 405336 from Patent EP1572962.
JD443278 - Sequence 424302 from Patent EP1572962.
KJ900418 - Synthetic construct Homo sapiens clone ccsbBroadEn_09812 PLD6 gene, encodes complete protein.

-  Biochemical and Signaling Pathways
  BioCyc Knowledge Library
LIPASYN-PWY - phospholipases
PWY-3561 - choline biosynthesis III

Reactome (by CSHL, EBI, and GO)

Protein Q8N2A8 (Reactome details) participates in the following event(s):

R-HSA-1483142 PC is transphosphatidylated to PG by PLD1-4/6
R-HSA-5601887 PLD6 dimer cleaves primary piRNA transcript to pre-piRNA
R-HSA-8954398 PLD6 dimer hydrolyses cardiolipin to PA and PG
R-HSA-1483148 Synthesis of PG
R-HSA-5601884 PIWI-interacting RNA (piRNA) biogenesis
R-HSA-1483166 Synthesis of PA
R-HSA-1483206 Glycerophospholipid biosynthesis
R-HSA-211000 Gene Silencing by RNA
R-HSA-1483257 Phospholipid metabolism
R-HSA-74160 Gene expression (Transcription)
R-HSA-556833 Metabolism of lipids
R-HSA-1430728 Metabolism

-  Other Names for This Gene
  Alternate Gene Symbols: NM_178836, NP_849158, PLD6_HUMAN, Q8N2A8, Q8N5Y1
UCSC ID: uc002gqz.3
RefSeq Accession: NM_178836
Protein: Q8N2A8 (aka PLD6_HUMAN)
CCDS: CCDS11182.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_178836.3
exon count: 2CDS single in 3' UTR: no RNA size: 2591
ORF size: 759CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1631.00frame shift in genome: no % Coverage: 99.46
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.