Ptprd Gene Detail

Summary

• Symbol
  Ptprd
• Name
  protein tyrosine phosphatase receptor type D
• Synonyms
  1110002J03Rik, 3000002J10Rik, B230219D21Rik, MGC:36851

• Feature Type
  protein coding gene
• IDs
  MGI:97812
  NCBI Gene: 19266
• Alliance
  gene page
• Transcription Start Sites
  63 TSS
• Candidate for QTL
  1 QTL

Location &
Maps

• Sequence Map
  Chr4:75859475-78130198 bp, - strand

  From Ensembl annotation of GRCm39
  

• View this region in JBrowse
  

• Genome Browsers
  Ensembl | UCSC | NCBI

• Genetic Map
  Chromosome 4, 36.94 cM
• Mapping Data
  5 experiments

Strain
Comparison

• SNPs within 2kb
  70341 from dbSNP Build 142
• Strain Annotations
  18
• RFLP
  1

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_97812	protein coding gene	Chr4:75859474-78132282 (-)
129S1/SvImJ	MGP_129S1SvImJ_G0028392	protein coding gene	Chr4:75237187-77646721 (-)
A/J	MGP_AJ_G0028352	protein coding gene	Chr4:72705182-74984755 (-)
AKR/J	MGP_AKRJ_G0028301	protein coding gene	Chr4:74517745-76852467 (-)
BALB/cJ	MGP_BALBcJ_G0028372	protein coding gene	Chr4:72847103-75132008 (-)
C3H/HeJ	MGP_C3HHeJ_G0028087	protein coding gene	Chr4:75091034-77478187 (-)
C57BL/6NJ	MGP_C57BL6NJ_G0028812	protein coding gene	Chr4:78207980-80692465 (-)
CAROLI/EiJ	MGP_CAROLIEiJ_G0026114	protein coding gene	Chr4:69004232-71215865 (-)
CAST/EiJ	MGP_CASTEiJ_G0027528	protein coding gene	Chr4:73065992-75466621 (-)
CBA/J	MGP_CBAJ_G0028056	protein coding gene	Chr4:80568511-83167016 (-)
DBA/2J	MGP_DBA2J_G0028205	protein coding gene	Chr4:72443264-74719110 (-)
FVB/NJ	MGP_FVBNJ_G0028171	protein coding gene	Chr4:71517686-73788298 (-)
LP/J	MGP_LPJ_G0028305	protein coding gene	Chr4:75636017-78023002 (-)
NOD/ShiLtJ	MGP_NODShiLtJ_G0028200	protein coding gene	Chr4:84803329-87662170 (-)
NZO/HlLtJ	MGP_NZOHlLtJ_G0028848	protein coding gene	Chr4:74591136-76985941 (-)
PWK/PhJ	MGP_PWKPhJ_G0027254	protein coding gene	Chr4:70872234-73160319 (-)
SPRET/EiJ	MGP_SPRETEiJ_G0027079	protein coding gene	Chr4:72095005-74481219 (-)
WSB/EiJ	MGP_WSBEiJ_G0027604	protein coding gene	Chr4:74740677-77105876 (-)

Homology

• Human Ortholog
  PTPRD, protein tyrosine phosphatase receptor type D

• Vertebrate Orthologs
  3

Vertebrate Orthology Source

Alliance of Genome Resources

• Human Ortholog
  PTPRD, protein tyrosine phosphatase receptor type D
  
• Synonyms
  HPTP, HPTPD, HPTPDELTA, PTPD, R-PTP-delta, RPTPDELTA
• Links
  HGNC:9668

  NCBI Gene ID: 5789

  neXtProt AC: NX_P23468

  UniProt: P23468

  
  
• Chr Location
  9p24.1-p23; chr9:8314246-10613002 (-)  GRCh38

---

• MGI Vertebrate Homology
  Ptprd stringent orthology
  1 human;1 mouse;1 rat;1 zebrafish
  
• HCOP
  vertebrate homology predictions: PTPRD
• Gene Tree
  Ptprd
  

Human Diseases

• Diseases
  4 with human PTPRD associations

				Human Disease	Mouse Models
				coronary artery disease IDs coronary artery disease       DOID:3393 DOID:10506 DOID:3363 DOID:3394 DOID:9420 EFO:0001645 ICD10CM:I20-I25 ICD10CM:I25 ICD10CM:I25.10 ICD9CM:410-414.99 ICD9CM:414.0 ICD9CM:414.9 MESH:D003324 MESH:D003327 MESH:D017202 NCI:C35505 NCI:C50625 OMIM:300464 OMIM:607339 OMIM:608316 OMIM:608318 OMIM:608320 OMIM:610947 OMIM:611139 OMIM:612030 OMIM:614293 UMLS_CUI:C0010054 UMLS_CUI:C0010068 UMLS_CUI:C0151744 UMLS_CUI:C0264694
				diabetes mellitus IDs diabetes mellitus       DOID:9351 ICD10CM:E08-E13 ICD9CM:250 MESH:D003920 NCI:C2985 UMLS_CUI:C0011849
				hypertension IDs hypertension       DOID:10763 EFO:0000537 ICD10CM:I10 ICD9CM:401-405.99 ICD9CM:997.91 MESH:D006973 NCI:C3117 UMLS_CUI:C0020538
				type 2 diabetes mellitus IDs type 2 diabetes mellitus       DOID:9352 ICD10CM:E11 KEGG:04930 MESH:D003924 NCI:C26747 OMIM:125853 OMIM:601283 OMIM:601407 OMIM:603694 OMIM:608036 UMLS_CUI:C0011860

Click on a disease name to see all genes associated with that disease.

Mutations,
Alleles, and
Phenotypes

• Phenotype Summary
  15 phenotypes from 2 alleles in 2 genetic backgrounds
  16 phenotypes from multigenic genotypes
  39 phenotype references
  

• All Mutations and Alleles
  14
• Chemically induced (other)
  2
• Endonuclease-mediated
  2
• Gene trapped
  4
• Radiation induced
  1
• Targeted
  5
• Genomic Mutations
  3 involving Ptprd
• Incidental Mutations
  Mutagenetix , APF , CvDC
• Find Mice (IMSR)
  121 strains or lines available
• Comparison Matrix
  Gene Expression + Phenotype

Homozygotes for a targeted null mutation exhibit impaired learning of spatial tasks, enhanced long-term potentiation at hippocampal synapses, and high mortality associated with reduced food intake.

Gene Ontology
(GO)
Classifications

• All GO Annotations
  50
• GO References
  15

Expression

• Assay Results
  891
• Tissues
  156
• cDNA Data
  35
• Literature Summary
  27

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

• Other Mouse Links
  Allen Institute
  GEO
  Expression Atlas
• Other Vertebrate Links
  GEISHA PTPRS
  Xenbase ptprd

Sequences &
Gene Models

• All Sequences
  211
• RefSeq
  105
• UniProt
  19
• CCDS
  CCDS18289.1, CCDS57280.1

• Ensembl
  ENSMUSG00000028399 (Evidence)
• NCBI Gene
  19266

Representative Sequences			Length	Strain/Species
genomic	ENSMUSG00000028399	Ensembl Gene Model | MGI Sequence Detail	2270724	C57BL/6J
transcript	ENSMUST00000107289	Ensembl | MGI Sequence Detail	9899	Not Applicable
polypeptide	ENSMUSP00000102910	Ensembl | MGI Sequence Detail	1912	Not Applicable

Protein
Information

• UniProt
  19 Sequences
• Protein Ontology
  PR:000013467 receptor-type tyrosine-protein phosphatase delta
  (term hierarchy)
• PDB
  4Y61, 4YFD, 4YFE, 4YFG, 4YH7, 5XWT, 5XWU, 5Y32, 6KIP, 7CEG
• EC
  3.1.3.48
• InterPro Domains
  IPR003961 Fibronectin type III
  IPR036116 Fibronectin type III superfamily
  IPR013098 Immunoglobulin I-set
  IPR007110 Immunoglobulin-like domain
  IPR036179 Immunoglobulin-like domain superfamily
  IPR013783 Immunoglobulin-like fold
  IPR003599 Immunoglobulin subtype
  IPR003598 Immunoglobulin subtype 2
  IPR050348 Protein-Tyrosine Phosphatase
  IPR016130 Protein-tyrosine phosphatase, active site
  IPR003595 Protein-tyrosine phosphatase, catalytic
  IPR029021 Protein-tyrosine phosphatase-like
  IPR045905 Receptor-type tyrosine-protein phosphatase delta, PTPase domain, repeat 1
  IPR050713 Receptor-type Tyrosine-protein Phosphatases/Ushers
  IPR000242 Tyrosine-specific protein phosphatase, PTPase domain
  IPR000387 Tyrosine-specific protein phosphatases domain
• GlyGen
  Q64487 4 sites, 8 N-linked glycans (2 sites)

Molecular
Reagents

• All nucleic 45

  cDNA 38

  Primer pair 4

  Other 3

  
  

  Microarray probesets 12

Other
Accession IDs

MGD-MRK-13681, MGI:1917472, MGI:1919036, MGI:2444522

References

• Summaries
  All 104

  Developmental Gene Expression 27

  Gene Ontology 15

  Phenotypes 39
• Earliest
  J:14172 Mizuno K, et al., MPTP delta, a putative murine homolog of HPTP delta, is expressed in specialized regions of the brain and in the B-cell lineage. Mol Cell Biol. 1993 Sep;13(9):5513-23
• Latest
  J:358058 Emperador-Melero J, et al., Distinct active zone protein machineries mediate Ca(2+) channel clustering and vesicle priming at hippocampal synapses. Nat Neurosci. 2024 Sep;27(9):1680-1694

TSS for Ptprd:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr42212	Chr4:78130186-78130236 (-)	-13 bp
Tssr42211	Chr4:78130064-78130126 (-)	103 bp
Tssr42210	Chr4:78129995-78130027 (-)	187 bp
Tssr42209	Chr4:78129969-78129991 (-)	218 bp
Tssr42208	Chr4:78129922-78129933 (-)	270 bp
Tssr42207	Chr4:78099126-78099129 (-)	31,070 bp
Tssr1209	Chr4:78010445-78010449 (-)	119,751 bp
Tssr42206	Chr4:77996671-77996691 (-)	133,517 bp
Tssr42205	Chr4:77987721-77987733 (-)	142,471 bp
Tssr42204	Chr4:77978650-77978655 (-)	151,545 bp
Tssr42203	Chr4:77967133-77967144 (-)	163,059 bp
Tssr42202	Chr4:77962048-77962057 (-)	168,145 bp
Tssr42201	Chr4:77921820-77921823 (-)	208,376 bp
Tssr42200	Chr4:77834261-77834285 (-)	295,925 bp
Tssr42199	Chr4:77823255-77823268 (-)	306,936 bp
Tssr42198	Chr4:77811634-77811638 (-)	318,562 bp
Tssr42197	Chr4:77809935-77809936 (-)	320,262 bp
Tssr42196	Chr4:77775013-77775019 (-)	355,182 bp
Tssr42195	Chr4:77744483-77744497 (-)	385,708 bp
Tssr42194	Chr4:77741801-77741804 (-)	388,395 bp
Tssr42193	Chr4:77741154-77741156 (-)	389,043 bp
Tssr42192	Chr4:77706804-77706808 (-)	423,392 bp
Tssr42191	Chr4:77705400-77705415 (-)	424,790 bp
Tssr42190	Chr4:77702988-77703014 (-)	427,197 bp
Tssr42189	Chr4:77693565-77693570 (-)	436,630 bp
Tssr42188	Chr4:77682612-77682616 (-)	447,584 bp
Tssr42187	Chr4:77619310-77619337 (-)	510,874 bp
Tssr42186	Chr4:77444199-77444203 (-)	685,997 bp
Tssr42185	Chr4:77372413-77372421 (-)	757,781 bp
Tssr42184	Chr4:77372346-77372357 (-)	757,846 bp
Tssr42183	Chr4:77345223-77345225 (-)	784,974 bp
Tssr42182	Chr4:77087059-77087073 (-)	1,043,132 bp
Tssr42181	Chr4:77086985-77087020 (-)	1,043,195 bp
Tssr42180	Chr4:77072978-77072987 (-)	1,057,215 bp
Tssr42179	Chr4:77072842-77072855 (-)	1,057,349 bp
Tssr42178	Chr4:77070198-77070211 (-)	1,059,993 bp
Tssr42177	Chr4:77056067-77056068 (-)	1,074,130 bp
Tssr42175	Chr4:76832943-76832992 (-)	1,297,230 bp
Tssr42174	Chr4:76795810-76795813 (-)	1,334,386 bp
Tssr1207	Chr4:76782417-76782423 (-)	1,347,778 bp
Tssr42173	Chr4:76772720-76772722 (-)	1,357,477 bp
Tssr42172	Chr4:76772553-76772557 (-)	1,357,643 bp
Tssr42171	Chr4:76718912-76718918 (-)	1,411,283 bp
Tssr42170	Chr4:76666465-76666481 (-)	1,463,725 bp
Tssr42169	Chr4:76488584-76488588 (-)	1,641,612 bp
Tssr42168	Chr4:76477284-76477308 (-)	1,652,902 bp
Tssr42167	Chr4:76475274-76475277 (-)	1,654,922 bp
Tssr42166	Chr4:76454648-76454652 (-)	1,675,548 bp
Tssr42165	Chr4:76405593-76405604 (-)	1,724,599 bp
Tssr42164	Chr4:76368827-76368852 (-)	1,761,358 bp
Tssr42163	Chr4:76368715-76368733 (-)	1,761,474 bp
Tssr42162	Chr4:76368005-76368022 (-)	1,762,184 bp
Tssr42161	Chr4:76354100-76354115 (-)	1,776,090 bp
Tssr42160	Chr4:76354029-76354033 (-)	1,776,167 bp
Tssr42159	Chr4:76276468-76276471 (-)	1,853,728 bp
Tssr42158	Chr4:76262464-76262487 (-)	1,867,722 bp
Tssr42157	Chr4:76262399-76262458 (-)	1,867,769 bp
Tssr42156	Chr4:76250702-76250704 (-)	1,879,495 bp
Tssr42155	Chr4:76140796-76140803 (-)	1,989,398 bp
Tssr42154	Chr4:76060312-76060323 (-)	2,069,880 bp
Tssr42153	Chr4:76022593-76022605 (-)	2,107,599 bp
Tssr42152	Chr4:76021081-76021086 (-)	2,109,114 bp
Tssr42151	Chr4:75901002-75901025 (-)	2,229,184 bp

Ptprd is Candidate Gene for:

QTL	Genetic Location*	Genome Location (GRCm39)	Reference	QTL Note
Papg1	Chr4, 47.21 cM	Chr4:102781167-102781279	J:78525	Microarray gene expression analysis was used to identify candidate genes for tumor resistant and tumor susceptibility QTLs Par8,2,3,4 and and Pas1-4, respectively. Transcripts found within the flanking markers of each QTL were identified and matched to transcripts from Affymetrix probe sets. RNA from A/J, BALB/cJ, C57BL/6J, and SM/J were used for analysis. Pas1 is located between 48.2 cM and 75 cM on mouse Chromosome 6 and was identified in a cross between A/J and C57BL/6J. Candidate oncogenic genes identified by microarray analysis are hes related protein (**Note- this gene is not found in MGD), Ppih (cyclophilin H **Note-this gene is positioned on mouse Chromosome 4 in MGD), Ptpro, Mglap, Recql, and Bcat1 (ECA39). Other candidate genes identified via differential expression are Ccnd2 (cyclin D2) and high mobility group protein 2A,4 (**Note-this gene is not found in MGD). K-ras, a positional candidate gene, did not show significantly different expression between A/J and C57BL/6J. Pas2 is located between 17 cMand 23.2 cM on mouse Chromosome 17 and was identified in crosses involving A/J and C57BL/6J. Candidate oncogenic genes identified by microarray analysis are Notch4, Hnrpk (**Note-this gene is positioned on mouse Chromosome 13 in MGD), and Enpp4. Other candidate genes identified via differential expression are Cdc5l, Tapbp (tapasin), H2-Ke2, Rbx1 (regulator of cullins 1 **Note- this gene is found on mouse Chromosome 15 in MGD), Psors1c2, H2-Ke6, and H2-M9. Positional candidate genes Tnf (Tnfa) and Lta (Tnfb) did not show significantly different expression between A/J and C57BL/6J. Pas3 is located between 2 cM and 25 cM on mouse Chromosome 19 and was identified in a cross between A/J and C57BL/6J. Candidate oncogenic genes identified by microarray analysis are golgi specific Gbf1 (brefeldin A resistance factor 1) and Sema4g. Other candidate genes identified via differential expression are Pdcd4, Adrb1, and Cdc25l. Pas4 is located between 42 cM and 72 cM on mouse Chromosome 9 and was identified in a cross between A/J and C57BL/6J. Candidate oncogenic genes identified by microarray analysis are Nck1, Pthr1, and Topbp1. Candidate tumor suppressor genes for Pas4 are G protein alpha I 2 (**Note-this gene is not found in MGD), Cdk5 (**Note-this gene is positioned on mouse Chromosome 5 in MGD), Smarcd3 (**Note-this gene is positioned on mouse Chromosome 5 in MGD), and Nckipsd. Another candidate gene identified via differential expression is Stag1. Par1 is located between 37 cM and 59 cM on mouse Chromosome 11 and was identified in a cross between A/J and SM/J. Candidate oncogenic genes identified by microarray analysis are Alox12 (12-lipoxygenase), Zfp617 (zinc finger protein s11-6), Grn, and Rpl29 (**Note-this gene is positioned on mouse Chromosome 9 in MGD). A tumor suppressor candidate gene for Par1 is Spop. 02.05.2016 Curator Note: Becasue Par1 was originally mapped in J:32079 using an (A/J x M. spretus) x C57BL/6J interspecific backcross, which differs from the cross used here, we have equated this QTL with Par8 which was mapped using A/J and SM/J mice, see J:41849. Par2 is located between 32 cM and 57 cM on mouse Chromosome 18 and was identified in a cross between A/J and BALB/cJ. Candidate oncogenic genes identified by microarray analysis are Adrb2, Mbd2, Htr4, Hmgb1-rs12, and Iigp1. Dcc is an expected candidate gene of Par2 but its expression pattern (A/J=high expression) is not consistent with its effect on tumor resistance/susceptibility. Mc2r is another candidate gene identified via differential gene expression between A/J and SM/J. Par3 is located between 13 cM and 44 cM on mouse Chromosome 12 and was identified in a cross between A/J and SM/J. Only one candidate oncogenic gene was identified for Par3. This is placental growth factor, Pgf. Par4 is located between 10.6 cM and 42.5 cM on mouse Chromosome 4 and was identified in a cross between A/J and BALB/cJ. Candidate tumor suppressor genes identified via differential gene expression are Cdkn2a, Egfl5, Ambp (bikunin), Pole3, Tyrp1, Ifnab, and Igfbpl1.Candidate oncogenes are T complex protein 1 alpha (**Note-this gene is not found in MGD) and Stmn1. Another candidate gene identified via differential expression between A/J and SM/J is Ptprd.

*cM position of peak correlated region/marker