Human Gene PTPRM (ENST00000580170.6_7) from GENCODE V47lift37
  Description: protein tyrosine phosphatase receptor type M, transcript variant 8 (from RefSeq NM_001378147.1)
Gencode Transcript: ENST00000580170.6_7
Gencode Gene: ENSG00000173482.17_13
Transcript (Including UTRs)
   Position: hg19 chr18:7,567,314-8,406,854 Size: 839,541 Total Exon Count: 33 Strand: +
Coding Region
   Position: hg19 chr18:7,567,817-8,406,160 Size: 838,344 Coding Exon Count: 33 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr18:7,567,314-8,406,854)mRNA (may differ from genome)Protein (1465 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedUniProtKBWikipedia
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PTPRM_HUMAN
DESCRIPTION: RecName: Full=Receptor-type tyrosine-protein phosphatase mu; Short=Protein-tyrosine phosphatase mu; Short=R-PTP-mu; EC=3.1.3.48; Flags: Precursor;
FUNCTION: Involved in cell-cell adhesion through homophilic interactions. May play a key role in signal transduction and growth control.
CATALYTIC ACTIVITY: Protein tyrosine phosphate + H(2)O = protein tyrosine + phosphate.
SUBCELLULAR LOCATION: Membrane; Single-pass type I membrane protein.
SIMILARITY: Belongs to the protein-tyrosine phosphatase family. Receptor class 2B subfamily.
SIMILARITY: Contains 4 fibronectin type-III domains.
SIMILARITY: Contains 1 Ig-like C2-type (immunoglobulin-like) domain.
SIMILARITY: Contains 1 MAM domain.
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

+  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: 30.68 RPKM in Adipose - Subcutaneous
Total median expression: 574.22 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 -268.60503-0.534 Picture PostScript Text
3' UTR -166.00694-0.239 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
IPR008985 - ConA-like_lec_gl_sf
IPR003961 - Fibronectin_type3
IPR007110 - Ig-like
IPR013783 - Ig-like_fold
IPR003599 - Ig_sub
IPR013151 - Immunoglobulin
IPR000998 - MAM_dom
IPR000387 - Tyr/Dual-specificity_Pase
IPR016130 - Tyr_Pase_AS
IPR000242 - Tyr_Pase_rcpt/non-rcpt

Pfam Domains:
PF00041 - Fibronectin type III domain
PF00047 - Immunoglobulin domain
PF00102 - Protein-tyrosine phosphatase
PF00629 - MAM domain, meprin/A5/mu

SCOP Domains:
48726 - Immunoglobulin
49265 - Fibronectin type III
49899 - Concanavalin A-like lectins/glucanases
52799 - (Phosphotyrosine protein) phosphatases II

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1RPM - X-ray MuPIT 2C9A - X-ray MuPIT 2V5Y - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P28827
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:0004721 phosphoprotein phosphatase activity
GO:0004725 protein tyrosine phosphatase activity
GO:0005001 transmembrane receptor protein tyrosine phosphatase activity
GO:0005515 protein binding
GO:0016787 hydrolase activity
GO:0016791 phosphatase activity
GO:0042802 identical protein binding
GO:0045296 cadherin binding

Biological Process:
GO:0001937 negative regulation of endothelial cell proliferation
GO:0006470 protein dephosphorylation
GO:0007155 cell adhesion
GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules
GO:0007165 signal transduction
GO:0010596 negative regulation of endothelial cell migration
GO:0010842 retina layer formation
GO:0016311 dephosphorylation
GO:0016525 negative regulation of angiogenesis
GO:0031175 neuron projection development
GO:0031290 retinal ganglion cell axon guidance
GO:0035335 peptidyl-tyrosine dephosphorylation
GO:0042493 response to drug

Cellular Component:
GO:0005737 cytoplasm
GO:0005886 plasma membrane
GO:0005887 integral component of plasma membrane
GO:0005911 cell-cell junction
GO:0005913 cell-cell adherens junction
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0030027 lamellipodium
GO:0048471 perinuclear region of cytoplasm


-  Descriptions from all associated GenBank mRNAs
  BC151842 - Homo sapiens protein tyrosine phosphatase, receptor type, M, mRNA (cDNA clone MGC:166994 IMAGE:8860327), complete cds.
AK303652 - Homo sapiens cDNA FLJ58084 complete cds, highly similar to Receptor-type tyrosine-protein phosphatase mu precursor (EC 3.1.3.48).
X58288 - H.sapiens hR-PTPu gene for protein tyrosine phosphatase.
KJ901684 - Synthetic construct Homo sapiens clone ccsbBroadEn_11078 PTPRM gene, encodes complete protein.
AK294492 - Homo sapiens cDNA FLJ55898 complete cds, highly similar to Receptor-type tyrosine-protein phosphatase mu precursor (EC 3.1.3.48).
BC040543 - Homo sapiens protein tyrosine phosphatase, receptor type, M, mRNA (cDNA clone IMAGE:5271160), complete cds.
JD539449 - Sequence 520473 from Patent EP1572962.
JD486852 - Sequence 467876 from Patent EP1572962.
JD326682 - Sequence 307706 from Patent EP1572962.
JD201583 - Sequence 182607 from Patent EP1572962.
JD082470 - Sequence 63494 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: A7MBN1, D3DUH8, ENST00000580170.1, ENST00000580170.2, ENST00000580170.3, ENST00000580170.4, ENST00000580170.5, J3QL11, NM_001378147, P28827, PTPRL1, PTPRM_HUMAN, uc326ilt.1, uc326ilt.2
UCSC ID: ENST00000580170.6_7
RefSeq Accession: NM_001105244.2
Protein: P28827 (aka PTPRM_HUMAN or PTPM_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.