Human Gene PGAP1 (ENST00000354764.9_7) from GENCODE V47lift37
  Description: post-GPI attachment to proteins inositol deacylase 1, transcript variant 1 (from RefSeq NM_024989.4)
Gencode Transcript: ENST00000354764.9_7
Gencode Gene: ENSG00000197121.15_9
Transcript (Including UTRs)
   Position: hg19 chr2:197,697,728-197,791,431 Size: 93,704 Total Exon Count: 27 Strand: -
Coding Region
   Position: hg19 chr2:197,705,958-197,791,340 Size: 85,383 Coding Exon Count: 27 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesGeneReviewsModel Information
Methods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:197,697,728-197,791,431)mRNA (may differ from genome)Protein (922 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PGAP1_HUMAN
DESCRIPTION: RecName: Full=GPI inositol-deacylase; EC=3.1.-.-; AltName: Full=Post-GPI attachment to proteins factor 1; Short=hPGAP1;
FUNCTION: Involved in inositol deacylation of GPI-anchored proteins. GPI inositol deacylation may important for efficient transport of GPI-anchored proteins from the endoplasmic reticulum to the Golgi (By similarity).
SUBCELLULAR LOCATION: Endoplasmic reticulum membrane; Multi-pass membrane protein (By similarity).
SIMILARITY: Belongs to the GPI inositol-deacylase family.
SEQUENCE CAUTION: Sequence=AAQ88987.1; Type=Erroneous initiation; Sequence=BC040517; Type=Frameshift; Positions=333;

-  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


-  MalaCards Disease Associations
  MalaCards Gene Search: PGAP1
Diseases sorted by gene-association score: mental retardation, autosomal recessive 42* (1019), autosomal recessive spastic paraplegia type 67* (350), autosomal recessive non-syndromic intellectual disability* (70), agnathia-otocephaly complex (11), cerebral visual impairment (10)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           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: 7.00 RPKM in Pituitary
Total median expression: 118.86 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 -33.3091-0.366 Picture PostScript Text
3' UTR -2002.508230-0.243 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
IPR012908 - PGAP1-like

Pfam Domains:
PF07819 - PGAP1-like protein

SCOP Domains:
53474 - alpha/beta-Hydrolases

ModBase Predicted Comparative 3D Structure on Q75T13
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 orthologGenome BrowserNo ortholog
Gene DetailsGene Details Gene DetailsGene Details 
Gene SorterGene Sorter Gene SorterGene Sorter 
 RGDEnsembl WormBase 
    Protein Sequence 
    Alignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004518 nuclease activity
GO:0016787 hydrolase activity
GO:0016788 hydrolase activity, acting on ester bonds
GO:0042578 phosphoric ester hydrolase activity

Biological Process:
GO:0006506 GPI anchor biosynthetic process
GO:0007605 sensory perception of sound
GO:0009880 embryonic pattern specification
GO:0009948 anterior/posterior axis specification
GO:0015031 protein transport
GO:0015798 myo-inositol transport
GO:0016255 attachment of GPI anchor to protein
GO:0021871 forebrain regionalization
GO:0060322 head development
GO:0090305 nucleic acid phosphodiester bond hydrolysis

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
  BX648642 - Homo sapiens mRNA; cDNA DKFZp686C18106 (from clone DKFZp686C18106).
AB128038 - Homo sapiens hPGAP1 mRNA for GPI inositol-deacylase PGAP1, complete cds.
BC152719 - Synthetic construct Homo sapiens clone IMAGE:100015996, MGC:184104 post-GPI attachment to proteins 1 (PGAP1) mRNA, encodes complete protein.
AB527353 - Synthetic construct DNA, clone: pF1KE0087, Homo sapiens PGAP1 gene for post-GPI attachment to proteins 1, without stop codon, in Flexi system.
BC040517 - Homo sapiens post-GPI attachment to proteins 1, mRNA (cDNA clone IMAGE:5297977), containing frame-shift errors.
AK022439 - Homo sapiens cDNA FLJ12377 fis, clone MAMMA1002524, weakly similar to HYPOTHETICAL 117.8 KD PROTEIN IN STE2-FRS2 INTERGENIC REGION.
AK302663 - Homo sapiens cDNA FLJ51154 complete cds, highly similar to Homo sapiens GPI deacylase (PGAP1), mRNA.
AK310484 - Homo sapiens cDNA, FLJ17526.
JD299581 - Sequence 280605 from Patent EP1572962.
AK001646 - Homo sapiens cDNA FLJ10784 fis, clone NT2RP4000448, highly similar to Homo sapiens mRNA; cDNA DKFZp566G0746.
AL050078 - Homo sapiens mRNA; cDNA DKFZp566G0746 (from clone DKFZp566G0746).
AK124764 - Homo sapiens cDNA FLJ42774 fis, clone BRAWH3004453.
JD315067 - Sequence 296091 from Patent EP1572962.
JD314637 - Sequence 295661 from Patent EP1572962.
JD566213 - Sequence 547237 from Patent EP1572962.
JD327340 - Sequence 308364 from Patent EP1572962.
JD214292 - Sequence 195316 from Patent EP1572962.
JD229876 - Sequence 210900 from Patent EP1572962.
JD528626 - Sequence 509650 from Patent EP1572962.
JD243683 - Sequence 224707 from Patent EP1572962.
JD120495 - Sequence 101519 from Patent EP1572962.
JD279757 - Sequence 260781 from Patent EP1572962.
JD427421 - Sequence 408445 from Patent EP1572962.
JD308319 - Sequence 289343 from Patent EP1572962.
JD435528 - Sequence 416552 from Patent EP1572962.
JD293066 - Sequence 274090 from Patent EP1572962.
JD330958 - Sequence 311982 from Patent EP1572962.
JD318506 - Sequence 299530 from Patent EP1572962.
JD078928 - Sequence 59952 from Patent EP1572962.
JD565589 - Sequence 546613 from Patent EP1572962.
JD262960 - Sequence 243984 from Patent EP1572962.
JD478677 - Sequence 459701 from Patent EP1572962.
JD543409 - Sequence 524433 from Patent EP1572962.
JD543408 - Sequence 524432 from Patent EP1572962.
JD248866 - Sequence 229890 from Patent EP1572962.
JD492868 - Sequence 473892 from Patent EP1572962.
JD513527 - Sequence 494551 from Patent EP1572962.
JD160822 - Sequence 141846 from Patent EP1572962.
JD291150 - Sequence 272174 from Patent EP1572962.
JD358543 - Sequence 339567 from Patent EP1572962.
JD113643 - Sequence 94667 from Patent EP1572962.
JD148550 - Sequence 129574 from Patent EP1572962.
JD228328 - Sequence 209352 from Patent EP1572962.
JD265875 - Sequence 246899 from Patent EP1572962.
JD328228 - Sequence 309252 from Patent EP1572962.
JD324694 - Sequence 305718 from Patent EP1572962.
JD412055 - Sequence 393079 from Patent EP1572962.
JD488938 - Sequence 469962 from Patent EP1572962.
JD067890 - Sequence 48914 from Patent EP1572962.
JD036839 - Sequence 17863 from Patent EP1572962.
JD280901 - Sequence 261925 from Patent EP1572962.
JD299584 - Sequence 280608 from Patent EP1572962.
JD191907 - Sequence 172931 from Patent EP1572962.
JD358892 - Sequence 339916 from Patent EP1572962.
JD322154 - Sequence 303178 from Patent EP1572962.
JD264741 - Sequence 245765 from Patent EP1572962.
JD119913 - Sequence 100937 from Patent EP1572962.
JD331050 - Sequence 312074 from Patent EP1572962.
JD215306 - Sequence 196330 from Patent EP1572962.
JD229328 - Sequence 210352 from Patent EP1572962.
JD252594 - Sequence 233618 from Patent EP1572962.
JD542041 - Sequence 523065 from Patent EP1572962.
JD562670 - Sequence 543694 from Patent EP1572962.
JD436462 - Sequence 417486 from Patent EP1572962.
JD147388 - Sequence 128412 from Patent EP1572962.
AK309112 - Homo sapiens cDNA, FLJ99153.
AY358624 - Homo sapiens clone DNA108738 ISPD3024 (UNQ3024) mRNA, complete cds.

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

Protein Q75T13 (Reactome details) participates in the following event(s):

R-HSA-162729 uPAR-acyl-GPI + H2O -> uPAR + long-chain fatty acid
R-HSA-162791 Attachment of GPI anchor to uPAR
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: ENST00000354764.1, ENST00000354764.2, ENST00000354764.3, ENST00000354764.4, ENST00000354764.5, ENST00000354764.6, ENST00000354764.7, ENST00000354764.8, NM_024989, PGAP1_HUMAN, Q4G0R8, Q4ZG47, Q53SM0, Q6AW92, Q6UWV4, Q75T13, Q9HA24, uc317yuc.1, uc317yuc.2, UNQ3024/PRO9822
UCSC ID: ENST00000354764.9_7
RefSeq Accession: NM_024989.4
Protein: Q75T13 (aka PGAP1_HUMAN)

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene PGAP1:
hsp (Hereditary Spastic Paraplegia Overview)

-  Gene Model Information
  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.