Human Gene PPFIA2 (ENST00000549396.6_10) from GENCODE V47lift37
  Description: PTPRF interacting protein alpha 2, transcript variant 1 (from RefSeq NM_003625.5)
Gencode Transcript: ENST00000549396.6_10
Gencode Gene: ENSG00000139220.17_17
Transcript (Including UTRs)
   Position: hg19 chr12:81,651,754-82,153,129 Size: 501,376 Total Exon Count: 33 Strand: -
Coding Region
   Position: hg19 chr12:81,655,761-82,148,000 Size: 492,240 Coding Exon Count: 30 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr12:81,651,754-82,153,129)mRNA (may differ from genome)Protein (1257 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedReactomeUniProtKB
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: LIPA2_HUMAN
DESCRIPTION: RecName: Full=Liprin-alpha-2; AltName: Full=Protein tyrosine phosphatase receptor type f polypeptide-interacting protein alpha-2; Short=PTPRF-interacting protein alpha-2;
FUNCTION: Alters PTPRF cellular localization and induces PTPRF clustering. May regulate the disassembly of focal adhesions. May localize receptor-like tyrosine phosphatases type 2A at specific sites on the plasma membrane, possibly regulating their interaction with the extracellular environment and their association with substrates.
SUBUNIT: Forms homodimers and heterodimers with liprins-alpha and liprins-beta. Interacts with the second PTPase domain of PTPRD, PTPRF and PTPRS.
SUBCELLULAR LOCATION: Cytoplasm. Cell surface. Note=Colocalizes with PTPRF at the cell surface.
TISSUE SPECIFICITY: Expressed only in brain.
DOMAIN: The N-terminal coiled coil regions mediate homodimerization preferentially and heterodimerization type alpha/alpha. The C-terminal, non-coiled coil regions mediate heterodimerization type alpha/beta and interaction with PTPRD, PTPRF and PTPRS.
SIMILARITY: Belongs to the liprin family. Liprin-alpha subfamily.
SIMILARITY: Contains 3 SAM (sterile alpha motif) 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


-  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: 13.76 RPKM in Brain - Frontal Cortex (BA9)
Total median expression: 131.37 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 -52.80181-0.292 Picture PostScript Text
3' UTR -368.401719-0.214 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
IPR001660 - SAM
IPR013761 - SAM/pointed
IPR011510 - SAM_2
IPR021129 - SAM_type1

Pfam Domains:
PF00536 - SAM domain (Sterile alpha motif)
PF07647 - SAM domain (Sterile alpha motif)

SCOP Domains:
47769 - SAM/Pointed domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help
3TAC - X-ray MuPIT 3TAD - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on O75334
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 DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding

Biological Process:
GO:0007160 cell-matrix adhesion

Cellular Component:
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0009986 cell surface
GO:0045202 synapse
GO:0048786 presynaptic active zone
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  AB210009 - Homo sapiens mRNA for PPFIA2 variant protein, clone: fh00134.
AK126971 - Homo sapiens cDNA FLJ45024 fis, clone BRAWH3017259, highly similar to Liprin-alpha-2.
AK297372 - Homo sapiens cDNA FLJ59345 complete cds, highly similar to Liprin-alpha-2.
AK302658 - Homo sapiens cDNA FLJ59641 complete cds, highly similar to Liprin-alpha-2.
AF034799 - Homo sapiens liprin-alpha2 mRNA, complete cds.
AK299853 - Homo sapiens cDNA FLJ53184 complete cds, highly similar to Liprin-alpha-2.
AB384363 - Synthetic construct DNA, clone: pF1KSDB0024, Homo sapiens PPFIA2 gene for liprin-alpha-2, complete cds, without stop codon, in Flexi system.
BC143485 - Homo sapiens protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 2, mRNA (cDNA clone MGC:177010 IMAGE:9051993), complete cds.
AK294505 - Homo sapiens cDNA FLJ59502 complete cds, highly similar to Liprin-alpha-2.
BC104912 - Homo sapiens protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 2, mRNA (cDNA clone MGC:132572 IMAGE:8143915), complete cds.
AK307524 - Homo sapiens cDNA, FLJ97472.
AK296380 - Homo sapiens cDNA FLJ54011 complete cds, highly similar to Liprin-alpha-2.
AK123372 - Homo sapiens cDNA FLJ41378 fis, clone BRCAN2009203, highly similar to Liprin-alpha-2.
AL157453 - Homo sapiens mRNA; cDNA DKFZp761E2112 (from clone DKFZp761E2112).
JD371094 - Sequence 352118 from Patent EP1572962.
LF212354 - JP 2014500723-A/19857: Polycomb-Associated Non-Coding RNAs.
LF208883 - JP 2014500723-A/16386: Polycomb-Associated Non-Coding RNAs.
JD220737 - Sequence 201761 from Patent EP1572962.
MA447931 - JP 2018138019-A/19857: Polycomb-Associated Non-Coding RNAs.
MA444460 - JP 2018138019-A/16386: Polycomb-Associated Non-Coding RNAs.

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

Protein O75334 (Reactome details) participates in the following event(s):

R-HSA-210426 Glutamate synaptic vesicle docking and priming
R-HSA-372505 Acetylcholine synaptic vesicle docking and priming
R-HSA-374922 Noradrenalin synaptic vesicle docking and priming
R-HSA-380574 Dopamine synaptic vesicle docking and priming
R-HSA-380905 Serotonin loaded synaptic vesicle docking and priming
R-HSA-210430 release of L-Glutamate at the synapse
R-HSA-372529 Release of acetylcholine at the synapse
R-HSA-374899 Release of noradrenaline at the synapse
R-HSA-380869 Release of docked dopamine loaded synaptic vesicle
R-HSA-380901 Release of docked serotonin loaded synaptic vesicle
R-HSA-388824 PTPRF, PTPRS, PTPRD bind Liprins
R-HSA-210500 Glutamate Neurotransmitter Release Cycle
R-HSA-264642 Acetylcholine Neurotransmitter Release Cycle
R-HSA-181430 Norepinephrine Neurotransmitter Release Cycle
R-HSA-212676 Dopamine Neurotransmitter Release Cycle
R-HSA-181429 Serotonin Neurotransmitter Release Cycle
R-HSA-388844 Receptor-type tyrosine-protein phosphatases
R-HSA-112310 Neurotransmitter release cycle
R-HSA-6794362 Protein-protein interactions at synapses
R-HSA-112315 Transmission across Chemical Synapses
R-HSA-112316 Neuronal System

-  Other Names for This Gene
  Alternate Gene Symbols: B3KVT5, B3KXA0, B7Z2A6, B7Z3U9, B7Z663, B7ZKZ5, E7ERB8, E7ETG6, ENST00000549396.1, ENST00000549396.2, ENST00000549396.3, ENST00000549396.4, ENST00000549396.5, F8VP68, LIPA2_HUMAN, NM_003625, O75334, Q2M3G8, uc325ait.1, uc325ait.2
UCSC ID: ENST00000549396.6_10
RefSeq Accession: NM_003625.5
Protein: O75334 (aka LIPA2_HUMAN or LPA2_HUMAN)

-  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.