Human Gene PIGZ (uc003fxh.3) Description and Page Index
  Description: Homo sapiens phosphatidylinositol glycan anchor biosynthesis, class Z (PIGZ), mRNA.
RefSeq Summary (NM_025163): The glycosylphosphatidylinositol (GPI) anchor is a glycolipid found on many blood cells that serves to anchor proteins to the cell surface. This gene encodes a protein that is localized to the endoplasmic reticulum, and is involved in GPI anchor biosynthesis. As shown for the yeast homolog, which is a member of a family of dolichol-phosphate-mannose (Dol-P-Man)-dependent mannosyltransferases, this protein can also add a side-branching fourth mannose to GPI precursors during the assembly of GPI anchors. [provided by RefSeq, Jul 2008]. ##Evidence-Data-START## Transcript exon combination :: AK022830.1, SRR1660805.108837.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA1968540, SAMEA1968832 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000412723.6/ ENSP00000413405.1 RefSeq Select criteria :: based on conservation, expression ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr3:196,673,214-196,695,704 Size: 22,491 Total Exon Count: 3 Strand: -
Coding Region
   Position: hg19 chr3:196,674,028-196,678,902 Size: 4,875 Coding Exon Count: 2 

Page IndexSequence and LinksUniProtKB CommentsCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr3:196,673,214-196,695,704)mRNA (may differ from genome)Protein (579 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeStanford SOURCEUniProtKB

-  Comments and Description Text from UniProtKB
  ID: PIGZ_HUMAN
DESCRIPTION: RecName: Full=GPI mannosyltransferase 4; EC=2.4.1.-; AltName: Full=GPI mannosyltransferase IV; Short=GPI-MT-IV; AltName: Full=Phosphatidylinositol-glycan biosynthesis class Z protein; Short=PIG-Z; AltName: Full=SMP3 homolog; Short=hSMP3;
FUNCTION: Mannosyltransferase involved in glycosylphosphatidylinositol-anchor biosynthesis. Transfers a fourth mannose to some trimannosyl-GPIs during GPI precursor assembly. The presence of a fourth mannose in GPI is facultative and only scarcely detected, suggesting that it only exists in some tissues.
PATHWAY: Glycolipid biosynthesis; glycosylphosphatidylinositol- anchor biosynthesis.
SUBCELLULAR LOCATION: Endoplasmic reticulum membrane; Multi-pass membrane protein.
TISSUE SPECIFICITY: Widely expressed at low level, with highest level in brain and colon.
SIMILARITY: Belongs to the glycosyltransferase 22 family. PIGZ subfamily.
CAUTION: It is uncertain whether Met-1 or Met-32 is the initiator.

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 24.02 RPKM in Colon - Transverse
Total median expression: 251.21 RPKM



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

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -78.40147-0.533 Picture PostScript Text
3' UTR -259.90814-0.319 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
IPR005599 - GPI_mannosylTrfase

Pfam Domains:
PF03901 - Alg9-like mannosyltransferase family

ModBase Predicted Comparative 3D Structure on Q86VD9
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 orthologGenome BrowserNo orthologGenome Browser
Gene Details  Gene Details Gene Details
Gene Sorter  Gene Sorter Gene Sorter
   FlyBase SGD
   Protein Sequence Protein Sequence
   Alignment Alignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000026 alpha-1,2-mannosyltransferase activity
GO:0000030 mannosyltransferase activity
GO:0016740 transferase activity
GO:0016757 transferase activity, transferring glycosyl groups

Biological Process:
GO:0006506 GPI anchor biosynthetic process
GO:0016254 preassembly of GPI anchor in ER membrane
GO:0097502 mannosylation

Cellular Component:
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0016020 membrane
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  BC018804 - Homo sapiens phosphatidylinositol glycan anchor biosynthesis, class Z, mRNA (cDNA clone IMAGE:4859591).
BC044640 - Homo sapiens phosphatidylinositol glycan anchor biosynthesis, class Z, mRNA (cDNA clone MGC:52163 IMAGE:4871581), complete cds.
AK022830 - Homo sapiens cDNA FLJ12768 fis, clone NT2RP2001576, weakly similar to HYPOTHETICAL 62.2 KD PROTEIN C4G8.12C IN CHROMOSOME I.
JD277397 - Sequence 258421 from Patent EP1572962.
JD318034 - Sequence 299058 from Patent EP1572962.
JD051413 - Sequence 32437 from Patent EP1572962.
JD234701 - Sequence 215725 from Patent EP1572962.
JD494199 - Sequence 475223 from Patent EP1572962.
AK296867 - Homo sapiens cDNA FLJ53840 complete cds, highly similar to GPI mannosyltransferase 4 (EC 2.4.1.-).
JD053169 - Sequence 34193 from Patent EP1572962.
JD495361 - Sequence 476385 from Patent EP1572962.
JD264946 - Sequence 245970 from Patent EP1572962.
JD268132 - Sequence 249156 from Patent EP1572962.
JD549521 - Sequence 530545 from Patent EP1572962.
JD427999 - Sequence 409023 from Patent EP1572962.
JD422699 - Sequence 403723 from Patent EP1572962.
JD367879 - Sequence 348903 from Patent EP1572962.
JD386701 - Sequence 367725 from Patent EP1572962.
JD324911 - Sequence 305935 from Patent EP1572962.
JD174154 - Sequence 155178 from Patent EP1572962.
JD087977 - Sequence 69001 from Patent EP1572962.
JD377442 - Sequence 358466 from Patent EP1572962.
JD087976 - Sequence 69000 from Patent EP1572962.
JD140933 - Sequence 121957 from Patent EP1572962.
JD486542 - Sequence 467566 from Patent EP1572962.
JD367769 - Sequence 348793 from Patent EP1572962.
JD561577 - Sequence 542601 from Patent EP1572962.
KJ903294 - Synthetic construct Homo sapiens clone ccsbBroadEn_12688 PIGZ gene, encodes complete protein.
CU692228 - Synthetic construct Homo sapiens gateway clone IMAGE:100022504 5' read PIGZ mRNA.
JD226598 - Sequence 207622 from Patent EP1572962.
JD405940 - Sequence 386964 from Patent EP1572962.
JD100745 - Sequence 81769 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa00563 - Glycosylphosphatidylinositol(GPI)-anchor biosynthesis

Reactome (by CSHL, EBI, and GO)

Protein Q86VD9 (Reactome details) participates in the following event(s):

R-HSA-162797 mannose (a1-2) mannose (a1-6) (ethanolamineP) mannose (a1-4) glucosaminyl-acyl-PI -> mannose (a1) mannose (a1-2) mannose (a1-6) (ethanolamineP) mannose (a1-4) glucosaminyl-acyl-PI
R-HSA-162710 Synthesis of glycosylphosphatidylinositol (GPI)
R-HSA-163125 Post-translational modification: synthesis of GPI-anchored proteins
R-HSA-597592 Post-translational protein modification
R-HSA-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: NM_025163, NP_079439, PIGZ_HUMAN, Q86VD9, Q9H9G6, SMP3
UCSC ID: uc003fxh.3
RefSeq Accession: NM_025163
Protein: Q86VD9 (aka PIGZ_HUMAN)
CCDS: CCDS3324.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_025163.2
exon count: 3CDS single in 3' UTR: no RNA size: 2721
ORF size: 1740CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3169.00frame shift in genome: no % Coverage: 99.27
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
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-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.