Mouse Gene Ptprf (ENSMUST00000049074.12) from GENCODE VM23 Comprehensive Transcript Set (only Basic displayed by default)
  Description: Mus musculus protein tyrosine phosphatase, receptor type, F (Ptprf), mRNA. (from RefSeq NM_011213)
Gencode Transcript: ENSMUST00000049074.12
Gencode Gene: ENSMUSG00000033295.14
Transcript (Including UTRs)
   Position: mm10 chr4:118,208,213-118,291,405 Size: 83,193 Total Exon Count: 33 Strand: -
Coding Region
   Position: mm10 chr4:118,209,821-118,277,439 Size: 67,619 Coding Exon Count: 31 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA Structure
Protein StructureOther SpeciesGO AnnotationsmRNA DescriptionsPathwaysOther Names
Model InformationMethods
Data last updated at UCSC: 2019-09-19

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr4:118,208,213-118,291,405)mRNA (may differ from genome)Protein (1898 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
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PubMedReactomeSOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: PTPRF_MOUSE
DESCRIPTION: RecName: Full=Receptor-type tyrosine-protein phosphatase F; EC=3.1.3.48; AltName: Full=Leukocyte common antigen related; Short=LAR; Flags: Precursor;
FUNCTION: Possible cell adhesion receptor. It possesses an intrinsic protein tyrosine phosphatase activity (PTPase) (By similarity).
CATALYTIC ACTIVITY: Protein tyrosine phosphate + H(2)O = protein tyrosine + phosphate.
SUBUNIT: Interacts with GRIP1 (By similarity). Interacts with PPFIA1, PPFIA2 and PPFIA3 (By similarity). Interacts with PTPRF (By similarity).
SUBCELLULAR LOCATION: Membrane; Single-pass membrane protein (Potential).
TISSUE SPECIFICITY: Expressed in the cell of the T lineage but not in cells of any other hemopoietic lineage.
DOMAIN: The first PTPase domain has enzymatic activity, while the second one seems to affect the substrate specificity of the first one (By similarity).
SIMILARITY: Belongs to the protein-tyrosine phosphatase family. Receptor class 2A subfamily.
SIMILARITY: Contains 8 fibronectin type-III domains.
SIMILARITY: Contains 3 Ig-like C2-type (immunoglobulin-like) domains.
SIMILARITY: Contains 2 tyrosine-protein phosphatase 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           more ... click here to view the complete list

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -177.40351-0.505 Picture PostScript Text
3' UTR -595.201608-0.370 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
IPR003961 - Fibronectin_type3
IPR007110 - Ig-like
IPR013783 - Ig-like_fold
IPR013098 - Ig_I-set
IPR003599 - Ig_sub
IPR003598 - Ig_sub2
IPR000387 - Tyr/Dual-specificity_Pase
IPR016130 - Tyr_Pase_AS
IPR000242 - Tyr_Pase_rcpt/non-rcpt

Pfam Domains:
PF00041 - Fibronectin type III domain
PF00102 - Protein-tyrosine phosphatase
PF07679 - Immunoglobulin I-set domain
PF13895 - Immunoglobulin domain
PF13927 - Immunoglobulin domain

SCOP Domains:
48726 - Immunoglobulin
49363 - Purple acid phosphatase, N-terminal domain
49265 - Fibronectin type III
49313 - Cadherin-like
52799 - (Phosphotyrosine protein) phosphatases II

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


ModBase Predicted Comparative 3D Structure on A2A8L5
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-  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.
HumanRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
GenBankRGDEnsembl   
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004721 phosphoprotein phosphatase activity
GO:0004725 protein tyrosine phosphatase activity
GO:0005001 transmembrane receptor protein tyrosine phosphatase activity
GO:0005158 insulin receptor binding
GO:0008201 heparin binding
GO:0016787 hydrolase activity
GO:0016791 phosphatase activity
GO:0030971 receptor tyrosine kinase binding
GO:0035373 chondroitin sulfate proteoglycan binding
GO:0042301 phosphate ion binding
GO:0044877 macromolecular complex binding
GO:0050839 cell adhesion molecule binding

Biological Process:
GO:0001960 negative regulation of cytokine-mediated signaling pathway
GO:0006470 protein dephosphorylation
GO:0007155 cell adhesion
GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules
GO:0007399 nervous system development
GO:0008285 negative regulation of cell proliferation
GO:0010975 regulation of neuron projection development
GO:0016311 dephosphorylation
GO:0016477 cell migration
GO:0031102 neuron projection regeneration
GO:0031345 negative regulation of cell projection organization
GO:0035335 peptidyl-tyrosine dephosphorylation
GO:0042059 negative regulation of epidermal growth factor receptor signaling pathway
GO:0043065 positive regulation of apoptotic process
GO:0043525 positive regulation of neuron apoptotic process
GO:0046627 negative regulation of insulin receptor signaling pathway
GO:0048679 regulation of axon regeneration
GO:0050775 positive regulation of dendrite morphogenesis
GO:0050803 regulation of synapse structure or activity
GO:0051387 negative regulation of neurotrophin TRK receptor signaling pathway
GO:1900121 negative regulation of receptor binding

Cellular Component:
GO:0005768 endosome
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0030426 growth cone
GO:0043005 neuron projection
GO:0043025 neuronal cell body
GO:0043231 intracellular membrane-bounded organelle
GO:0060076 excitatory synapse


-  Descriptions from all associated GenBank mRNAs
  BC057166 - Mus musculus protein tyrosine phosphatase, receptor type, F, mRNA (cDNA clone IMAGE:4949338), partial cds.
AF300943 - Mus musculus tyrosine phosphatase LAR (Ptprf) mRNA, complete cds.
BC172929 - Synthetic construct Mus musculus clone IMAGE:9094505 protein tyrosine phosphatase, receptor type, F (Ptprf) gene, partial cds.
BC039767 - Mus musculus protein tyrosine phosphatase, receptor type, F, mRNA (cDNA clone IMAGE:4161424).
BC052322 - Mus musculus protein tyrosine phosphatase, receptor type, F, mRNA (cDNA clone IMAGE:5004354).
AK161629 - Mus musculus 8 days embryo whole body cDNA, RIKEN full-length enriched library, clone:5730410O11 product:protein tyrosine phosphatase, receptor type, F, full insert sequence.
AK135889 - Mus musculus in vitro fertilized eggs cDNA, RIKEN full-length enriched library, clone:7420433I19 product:unknown EST, full insert sequence.
AK133085 - Mus musculus adult male testis cDNA, RIKEN full-length enriched library, clone:4930569M20 product:protein tyrosine phosphatase, receptor type, F, full insert sequence.
Z37988 - M.musculus LAR mRNA encoding protein tyrosine phosphatase.
BC172930 - Synthetic construct Mus musculus clone IMAGE:9094506 protein tyrosine phosphatase, receptor type, F (Ptprf) gene, partial cds.
Z23061 - M.musculus protein-tyrosine-phosphatase mRNA, partial CDS.
Z23049 - M.musculus protein-tyrosine-phosphatase mRNA, partial CDS.
BC172928 - Synthetic construct Mus musculus clone IMAGE:9094504 protein tyrosine phosphatase, receptor type, F (Ptprf) gene, partial cds.
BC172927 - Synthetic construct Mus musculus clone IMAGE:9094503 protein tyrosine phosphatase, receptor type, F (Ptprf) gene, partial cds.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
mmu04514 - Cell adhesion molecules (CAMs)
mmu04520 - Adherens junction
mmu04910 - Insulin signaling pathway

Reactome (by CSHL, EBI, and GO)

Protein A2A8L5 (Reactome details) participates in the following event(s):

R-MMU-388824 PTPRF, PTPRS, PTPRD bind Liprins
R-MMU-6798258 PRTPRF, PTPRS, PTPRD bind LRRC4B
R-MMU-8855648 SALM3 binds LAR-RPTP
R-MMU-388844 Receptor-type tyrosine-protein phosphatases
R-MMU-8849932 Synaptic adhesion-like molecules
R-MMU-6794362 Protein-protein interactions at synapses
R-MMU-112316 Neuronal System

-  Other Names for This Gene
  Alternate Gene Symbols: A2A8L5, Lar, NM_011213, PTPRF_MOUSE, Q6PG86, Q9EQ17, uc008ujq.1, uc008ujq.2
UCSC ID: uc008ujq.2
RefSeq Accession: NM_011213
Protein: A2A8L5 (aka PTPRF_MOUSE)
CCDS: CCDS18546.1

-  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.