Human Gene PTPN4 (ENST00000263708.7_4) from GENCODE V47lift37

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Description: protein tyrosine phosphatase non-receptor type 4 (from RefSeq NM_002830.4)
Gencode Transcript: ENST00000263708.7_4
Gencode Gene: ENSG00000088179.9_10
Transcript (Including UTRs)
Position: hg19 chr2:120,517,498-120,742,475 Size: 224,978 Total Exon Count: 27 Strand: +
Coding Region
Position: hg19 chr2:120,567,430-120,734,646 Size: 167,217 Coding Exon Count: 26

Page Index	Sequence and Links	UniProtKB Comments	Primers	CTD	Gene Alleles
RNA-Seq Expression	Microarray Expression	RNA Structure	Protein Structure	Other Species	GO Annotations
mRNA Descriptions	Pathways	Other Names	Model Information	Methods

Data last updated at UCSC: 2024-08-22 23:36:26

Sequence and Links to Tools and Databases

Genomic Sequence (chr2:120,517,498-120,742,475)			mRNA (may differ from genome)		Protein (926 aa)
Gene Sorter	Genome Browser	Other Species FASTA	VisiGene	Gene interactions	Table Schema
AlphaFold	BioGPS	Ensembl	Entrez Gene	ExonPrimer	GeneCards
HGNC	MGI	OMIM	PubMed	Reactome	UniProtKB
Wikipedia	BioGrid CRISPR DB

Comments and Description Text from UniProtKB


	ID: PTN4_HUMAN DESCRIPTION: RecName: Full=Tyrosine-protein phosphatase non-receptor type 4; EC=3.1.3.48; AltName: Full=Protein-tyrosine phosphatase MEG1; Short=MEG; Short=PTPase-MEG1; FUNCTION: May act at junctions between the membrane and the cytoskeleton. CATALYTIC ACTIVITY: Protein tyrosine phosphate + H(2)O = protein tyrosine + phosphate. INTERACTION: P46108:CRK; NbExp=3; IntAct=EBI-710431, EBI-886; Q92993:KAT5; NbExp=2; IntAct=EBI-710431, EBI-399080; P16333:NCK1; NbExp=3; IntAct=EBI-710431, EBI-389883; SUBCELLULAR LOCATION: Cell membrane; Peripheral membrane protein; Cytoplasmic side (By similarity). Cytoplasm, cytoskeleton (By similarity). SIMILARITY: Belongs to the protein-tyrosine phosphatase family. Non-receptor class subfamily. SIMILARITY: Contains 1 FERM domain. SIMILARITY: Contains 1 PDZ (DHR) domain. SIMILARITY: Contains 1 tyrosine-protein phosphatase domain.

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 C006253 pirinixic acid D001564 Benzo(a)pyrene D002737 Chloroprene D020849 Raloxifene D013629 Tamoxifen C045651 epigallocatechin gallate C027373 potassium chromate(VI) C004648 testosterone enanthate

Common Gene Haplotype Alleles


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RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)


	Highest median expression: 8.60 RPKM in Brain - Cerebellum Total median expression: 101.71 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

Region	Fold Energy	Bases	Energy/Base	Display As
5' UTR	-243.70	480	-0.508	Picture	PostScript	Text
3' UTR	-1800.60	7829	-0.230	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
IPR019749 - Band_41_domain
IPR019750 - Band_41_fam
IPR014847 - FERM-adjacent
IPR014352 - FERM/acyl-CoA-bd_prot_3-hlx
IPR019748 - FERM_central
IPR019747 - FERM_CS
IPR000299 - FERM_domain
IPR018979 - FERM_N
IPR018980 - FERM_PH-like_C
IPR001478 - PDZ
IPR011993 - PH_like_dom
IPR000387 - Tyr/Dual-specificity_Pase
IPR016130 - Tyr_Pase_AS
IPR012151 - Tyr_Pase_non-rcpt_typ-3/4
IPR000242 - Tyr_Pase_rcpt/non-rcpt

Pfam Domains:
PF00102 - Protein-tyrosine phosphatase
PF00373 - FERM central domain
PF00595 - PDZ domain
PF08736 - FERM adjacent (FA)
PF09379 - FERM N-terminal domain
PF09380 - FERM C-terminal PH-like domain

SCOP Domains:
47031 - Second domain of FERM
50156 - PDZ domain-like
50729 - PH domain-like
52799 - (Phosphotyrosine protein) phosphatases II
54236 - Ubiquitin-like

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

2CS5 - NMR MuPIT

2I75 - X-ray MuPIT

2VPH - X-ray MuPIT

3NFK - X-ray MuPIT

3NFL - X-ray MuPIT

ModBase Predicted Comparative 3D Structure on P29074


Front	Top	Side

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.

Mouse	Rat	Zebrafish	D. melanogaster	C. elegans	S. cerevisiae
No ortholog	No ortholog	No ortholog	No ortholog	Genome Browser	No ortholog
Gene Details	Gene Details		Gene Details	Gene Details
Gene Sorter	Gene Sorter		Gene Sorter	Gene Sorter
	RGD	Ensembl		WormBase
				Protein Sequence
				Alignment

Gene Ontology (GO) Annotations with Structured Vocabulary


	Molecular Function: GO:0004721 phosphoprotein phosphatase activity GO:0004725 protein tyrosine phosphatase activity GO:0004726 non-membrane spanning protein tyrosine phosphatase activity GO:0005515 protein binding GO:0008092 cytoskeletal protein binding GO:0016787 hydrolase activity GO:0016791 phosphatase activity Biological Process: GO:0006470 protein dephosphorylation GO:0016311 dephosphorylation GO:0035335 peptidyl-tyrosine dephosphorylation GO:0071345 cellular response to cytokine stimulus Cellular Component: GO:0005654 nucleoplasm GO:0005737 cytoplasm GO:0005856 cytoskeleton GO:0005886 plasma membrane GO:0009898 cytoplasmic side of plasma membrane GO:0016020 membrane

Descriptions from all associated GenBank mRNAs


	M68941 - Human protein-tyrosine phosphatase mRNA, complete cds. LF383637 - JP 2014500723-A/191140: Polycomb-Associated Non-Coding RNAs. AK314836 - Homo sapiens cDNA, FLJ95723, highly similar to Homo sapiens protein tyrosine phosphatase, non-receptor type 4 (megakaryocyte) (PTPN4), mRNA. BC010674 - Homo sapiens protein tyrosine phosphatase, non-receptor type 4 (megakaryocyte), mRNA (cDNA clone MGC:9204 IMAGE:3853914), complete cds. KJ891947 - Synthetic construct Homo sapiens clone ccsbBroadEn_01341 PTPN4 gene, encodes complete protein. CU679793 - Synthetic construct Homo sapiens gateway clone IMAGE:100020512 5' read PTPN4 mRNA. JF432311 - Synthetic construct Homo sapiens clone IMAGE:100073495 protein tyrosine phosphatase, non-receptor type 4 (megakaryocyte) (PTPN4) gene, encodes complete protein. MA619214 - JP 2018138019-A/191140: Polycomb-Associated Non-Coding RNAs. BX648614 - Homo sapiens mRNA; cDNA DKFZp686P05224 (from clone DKFZp686P05224). AK301218 - Homo sapiens cDNA FLJ53929 complete cds, highly similar to Tyrosine-protein phosphatase non-receptor type4 (EC 3.1.3.48). JD118615 - Sequence 99639 from Patent EP1572962. JD549955 - Sequence 530979 from Patent EP1572962. JD514804 - Sequence 495828 from Patent EP1572962. JD209491 - Sequence 190515 from Patent EP1572962. JD479758 - Sequence 460782 from Patent EP1572962. JD407081 - Sequence 388105 from Patent EP1572962. JD407082 - Sequence 388106 from Patent EP1572962. JD186946 - Sequence 167970 from Patent EP1572962. LF319312 - JP 2014500723-A/126815: Polycomb-Associated Non-Coding RNAs. LF319304 - JP 2014500723-A/126807: Polycomb-Associated Non-Coding RNAs. LF213455 - JP 2014500723-A/20958: Polycomb-Associated Non-Coding RNAs. LF319301 - JP 2014500723-A/126804: Polycomb-Associated Non-Coding RNAs. LF319299 - JP 2014500723-A/126802: Polycomb-Associated Non-Coding RNAs. LF319298 - JP 2014500723-A/126801: Polycomb-Associated Non-Coding RNAs. LF319297 - JP 2014500723-A/126800: Polycomb-Associated Non-Coding RNAs. LF319295 - JP 2014500723-A/126798: Polycomb-Associated Non-Coding RNAs. MA554889 - JP 2018138019-A/126815: Polycomb-Associated Non-Coding RNAs. MA554881 - JP 2018138019-A/126807: Polycomb-Associated Non-Coding RNAs. MA449032 - JP 2018138019-A/20958: Polycomb-Associated Non-Coding RNAs. MA554878 - JP 2018138019-A/126804: Polycomb-Associated Non-Coding RNAs. MA554876 - JP 2018138019-A/126802: Polycomb-Associated Non-Coding RNAs. MA554875 - JP 2018138019-A/126801: Polycomb-Associated Non-Coding RNAs. MA554874 - JP 2018138019-A/126800: Polycomb-Associated Non-Coding RNAs. MA554872 - JP 2018138019-A/126798: Polycomb-Associated Non-Coding RNAs. LF319290 - JP 2014500723-A/126793: Polycomb-Associated Non-Coding RNAs. LF319287 - JP 2014500723-A/126790: Polycomb-Associated Non-Coding RNAs. JD306148 - Sequence 287172 from Patent EP1572962. JD051235 - Sequence 32259 from Patent EP1572962. BC037838 - Homo sapiens cDNA clone IMAGE:4813920. AK025546 - Homo sapiens cDNA: FLJ21893 fis, clone HEP03412. MA554867 - JP 2018138019-A/126793: Polycomb-Associated Non-Coding RNAs. MA554864 - JP 2018138019-A/126790: Polycomb-Associated Non-Coding RNAs.

Biochemical and Signaling Pathways


	Reactome (by CSHL, EBI, and GO) Protein P29074 (Reactome details) participates in the following event(s): R-HSA-9008059 Interleukin-37 signaling R-HSA-446652 Interleukin-1 family signaling R-HSA-449147 Signaling by Interleukins R-HSA-1280215 Cytokine Signaling in Immune system R-HSA-168256 Immune System

Other Names for This Gene


	Alternate Gene Symbols: B2RBV8, ENST00000263708.1, ENST00000263708.2, ENST00000263708.3, ENST00000263708.4, ENST00000263708.5, ENST00000263708.6, NM_002830, P29074, PTN4_HUMAN, Q9UDA7, uc317hlv.1, uc317hlv.2 UCSC ID: ENST00000263708.7_4 RefSeq Accession: NM_002830.4 Protein: P29074 (aka PTN4_HUMAN)

Gene Model Information


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Methods, Credits, and Use Restrictions


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