 Gene-Chemical Interaction Annotations | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Gene Ontology AnnotationsMolecular Pathway Annotations |
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Analyze GeneStrainQTL List |
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Gene Annotator (Annotation Comparison) |
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GOLF (Gene-Ortholog Location Finder) |
Gene Ontology AnnotationsMolecular Pathway AnnotationsDisease Annotations
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Gene-Chemical Interaction Annotations
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Gene Ontology AnnotationsBiological Process
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Cellular Component
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Molecular Function
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Molecular Pathway AnnotationsReferences - curated| 1. | Calera MR, etal., J Biol Chem. 2000 Mar 3;275(9):6308-12. |
| 2. | Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27. |
| 3. | GOA data from the GO Consortium |
| 4. | Helmke S, etal., J Cell Sci. 1998 Aug;111 ( Pt 16):2465-75. |
| 5. | Lei G, etal., EMBO J. 2002 Jun 17;21(12):2977-89. |
| 6. | Lin D, etal., J Biol Chem. 2008 Mar 21;283(12):7674-81. Epub 2008 Jan 22. |
| 7. | MGD data from the GO Consortium |
| 8. | Moriyama T, etal., Biochem Biophys Res Commun 1992 Oct 15;188(1):34-9. |
| 9. | NCBI rat LocusLink and RefSeq merged data July 26, 2002 |
| 10. | Pipeline to import Pathway Interaction Database annotations from NCI into RGD |
| 11. | RGD automated data pipeline |
| 12. | RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations |
| 13. | RGD automated import pipeline for gene-chemical interactions |
| 14. | Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11. |
| 15. | Su J, etal., J Biol Chem. 1994 Jul 22;269(29):18731-4. |
| 16. | Tentative Sequence Data IDs. TIGR Gene Index, Rat Data |
| 17. | Wang PS, etal., J Biol Chem. 2009 Oct 6. |
References - uncuratedGenomics
Comparative Map Data| Ptpra (Rattus norvegicus - Norway rat) |
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| PTPRA (Homo sapiens - human) |
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| Ptpra (Mus musculus - house mouse) |
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| Ptpra (Chinchilla lanigera - long-tailed chinchilla) |
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| PTPRA (Pan paniscus - bonobo/pygmy chimpanzee) |
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| PTPRA (Canis lupus familiaris - dog) |
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| Ptpra (Ictidomys tridecemlineatus - thirteen-lined ground squirrel) |
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| PTPRA (Sus scrofa - pig) |
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| PTPRA (Chlorocebus sabaeus - green monkey) |
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| Ptpra (Heterocephalus glaber - naked mole-rat) |
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Position Markers| BE108511 |
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| AU047115 |
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| RH134950 |
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QTLs in Region (Rnor_6.0)| The following QTLs overlap with this region. |  | Full Report | | CSV | | TAB | | Printer | | Gviewer |
Genetic ModelsmiRNA Target Status
Predicted Target Of
| The detailed report is available here: | | Full Report | | CSV | | TAB | | Printer |
miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/). For more information about miRGate, see PMID:25858286 or access the full paper here. |
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Expression
RNA-SEQ ExpressionHigh: > 1000 TPM value Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM Below Cutoff: < 0.5 TPM
| testis | heart | brain | ovary | uterus | skeletal muscle tissue | colon | gastrocnemius | forebrain | hindbrain | lung | spleen | liver | kidney | adrenal gland | thymus | |
| High | ||||||||||||||||
| Medium | 19 | 43 | 23 | 15 | 4 | 3 | 6 | 26 | 25 | 11 | 11 | 40 | 35 | 8 | 8 | |
| Low | 3 | 3 | 2 | 1 | ||||||||||||
| Below cutoff |
View RNA-SEQ Expression Data
Sequence
Nucleotide Sequences| RefSeq Transcripts | NM_012763 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles |
| XM_006235006 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| XM_006235007 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| GenBank Nucleotide | AABR07053738 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles |
| AABR07053739 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| AAHX01025049 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| AAHX01025050 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| AAHX01025051 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| AAHX01025052 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| BC081828 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| L01702 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| U57500 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles |
Reference Sequences
| RefSeq Acc Id: | ENSRNOT00000055801 ⟹ ENSRNOP00000052657 | |||||||||
| RefSeq Status: | ||||||||||
| Type: | CODING | |||||||||
| Position: |
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| RefSeq Acc Id: | ENSRNOT00000080379 ⟹ ENSRNOP00000069583 | |||||||||
| RefSeq Status: | ||||||||||
| Type: | CODING | |||||||||
| Position: |
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| RefSeq Acc Id: | NM_012763 ⟹ NP_036895 | ||||||||||||||||||||||||
| RefSeq Status: | PROVISIONAL | ||||||||||||||||||||||||
| Type: | CODING | ||||||||||||||||||||||||
| Position: |
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| Sequence: |
CGGCGAGTGAGGCGCTGACAGGGACTCACGGGGGCATCTTGCACAGACCCCTGGACCACGCCGChide sequence |
| RefSeq Acc Id: | XM_006235006 ⟹ XP_006235068 | ||||||||||||||
| RefSeq Status: | |||||||||||||||
| Type: | CODING | ||||||||||||||
| Position: |
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| Sequence: |
AGCGCCTTACAGCCCAGGCCGCGTTGGGAGTGAGGCTGCGGCGAGTGAGGCGCTGACAGGGACThide sequence |
| RefSeq Acc Id: | XM_006235007 ⟹ XP_006235069 | ||||||||||||||
| RefSeq Status: | |||||||||||||||
| Type: | CODING | ||||||||||||||
| Position: |
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| Sequence: |
ACTGAGCTAAATCCCCAGCCTCATTTCTGTGCTTATGAATAAGAAAATGATACTTTGTGGGAGThide sequence |
Protein Sequences| Protein RefSeqs | NP_036895 | (Get FASTA) | NCBI Sequence Viewer |
| XP_006235068 | (Get FASTA) | NCBI Sequence Viewer | |
| XP_006235069 | (Get FASTA) | NCBI Sequence Viewer | |
| GenBank Protein | AAA41983 | (Get FASTA) | NCBI Sequence Viewer |
| AAB02230 | (Get FASTA) | NCBI Sequence Viewer | |
| AAH81828 | (Get FASTA) | NCBI Sequence Viewer | |
| Q03348 | (Get FASTA) | NCBI Sequence Viewer |
Reference Sequences
| RefSeq Acc Id: | NP_036895 ⟸ NM_012763 |
| - Peptide Label: | precursor |
| - UniProtKB: | Q66HJ7 (UniProtKB/TrEMBL) |
| - Sequence: |
MDSWFILILFGSGLIHISANNTTTVSPSLGTTRLIKTSTTESAKEENKTSNSTSSVISLSVTPThide sequence |
| RefSeq Acc Id: | XP_006235068 ⟸ XM_006235006 |
| - Peptide Label: | isoform X1 |
| - Sequence: |
MDSWFILILFGSGLIHISANNTTTVSPSLGTTRLIKTSTTESAKEENKTSNSTSSVISLSVTPThide sequence |
| RefSeq Acc Id: | XP_006235069 ⟸ XM_006235007 |
| - Peptide Label: | isoform X1 |
| - Sequence: |
MDSWFILILFGSGLIHISANNTTTVSPSLGTTRLIKTSTTESAKEENKTSNSTSSVISLSVTPThide sequence |
| RefSeq Acc Id: | ENSRNOP00000069583 ⟸ ENSRNOT00000080379 |
| RefSeq Acc Id: | ENSRNOP00000052657 ⟸ ENSRNOT00000055801 |
Protein Domains
TYR_PHOSPHATASE_2 Tyrosine-protein phosphatase
TranscriptomePromoters| RGD ID: | 13692434 | |||||||||
| Promoter ID: | EPDNEW_R2958 | |||||||||
| Type: | multiple initiation site | |||||||||
| Name: | Ptpra_1 | |||||||||
| Description: | protein tyrosine phosphatase, receptor type, A | |||||||||
| SO ACC ID: | SO:0000170 | |||||||||
| Source: | EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/) | |||||||||
| Experiment Methods: | Single-end sequencing. | |||||||||
| Position: |
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Strain Variation
Strain Sequence Variants (Rnor 6.0)
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Damaging VariantsAssembly: Rnor_5.0
| Chromosome | Start Pos | End Pos | Reference Nucleotide | Variant Nucleotide | Variant Type | Strain |
| 3 | 129571241 | 129571242 | T | C | snv | FHL/EurMcwi (MCW), IS-Tlk/Kyo (KyushuU), KFRS3B/Kyo (KyushuU), SBH/Ygl (MCW), F344/Jcl (KyushuU), SDLEF7/Barth (UDEL), LE/Stm (KyushuU), HTX/Kyo (KyushuU), F344/Stm (KyushuU), BDIX.Cg-Tal/NemOda (KyushuU), COP/CrCrl (MCW & UW), BUF/MNa (KyushuU), HWY/Slc (KyushuU), GH/OmrMcwi (MCW), SR/JrHsd (MCW), F344/NSlc (KyushuU), DOB/Oda (KyushuU), F344/DuCrlCrlj (KyushuU), RCS/Kyo (KyushuU), BDIX/NemOda (KyushuU), LE/OrlBarth (UDEL), Crl:SD (UDEL), IS/Kyo (KyushuU), ZF (KyushuU), ZFDM (KyushuU), ACI/EurMcwi (MCW), FHH/EurMcwi (MCW), NIG-III/Hok (KyushuU) |
Assembly: Rnor_6.0
| Chromosome | Start Pos | End Pos | Reference Nucleotide | Variant Nucleotide | Variant Type | Strain |
| 3 | 123073113 | 123073114 | T | C | snv | CDS, MNS/Gib (RGD), LEW/NCrlBR (RGD), SHRSP/Gcrc (RGD), SHR/NHsd (RGD), FHH/EurMcwi (RGD), SBH/Ygl (RGD), SR/JrHsd (RGD), ACI/N (MCW), ACI/EurMcwi (RGD), LE/Stm (RGD), Buf/N (MCW), MR/N (MCW), WKY/N (MCW), FHL/EurMcwi (RGD), LEW/Crl (RGD), WKY/Gcrc (RGD), WKY/NHsd (RGD), M520/N (MCW), WAG/Rij (RGD), BBDP/Wor (RGD), WKY/NCrl (RGD), F344/NRrrc (MCW), F344/NCrl (RGD) |
Assembly: RGSC_v3.4
| Chromosome | Start Pos | End Pos | Reference Nucleotide | Variant Nucleotide | Variant Type | Strain |
| 3 | 118157700 | 118157701 | G | A | snv | SS/JrHsdMcwi (MCW) |
| 3 | 118158825 | 118158826 | T | C | snv | MHS/Gib (ICL), FHL/EurMcwi (ICL), LEW/Crl (ICL), SHRSP/Gcrc (ICL), WKY/Gcrc (ICL), ACI/N (KNAW), F344/NRrrc (KNAW), ACI/EurMcwi (ICL), SBH/Ygl (ICL), WAG/Rij (ICL), DA/BklArbNsi (ICAHN), FHH/EurMcwi (MDC), LE/Stm (ICL), SR/JrHsd (ICL), HCR/1Mco (UMich), MR/N (KNAW), FHL/EurMcwi (MCW), SHR/OlaIpcv (ICL), SHR/NHsd (ICL), SHR/OlaIpcv (ICL), BUF/N (KNAW), M520/N (KNAW), FHH/EurMcwi (MCW), COP/CrCrl (MCW & UW), BBDP/WorN (ICL), FHH/EurMcwi (ICL), LEW/NCrl (ICL), WKY/NHsd (ICL), LCR/1Mco (UMich), HCR/2Mco (UMich), F344/NHsd (ICAHN), WKY/N (KNAW), SR/JrHsd (MCW), F344/NCrl (ICL), MNS/Gib (ICL), WKY/NCrl (ICL), LCR/2Mco (UMich), SHRSP/Gcrc (MDC), LE/Stm (KNAW), ACI/EurMcwi (MCW), SHR/OlaIpcv (KNAW), GH/OmrMcwi (MCW) |
Additional Information
External Database Links| Database | Acc Id | Source(s) |
| AGR Gene | RGD:3450 | AgrOrtholog |
| Ensembl Genes | ENSRNOG00000021223 | Ensembl, ENTREZGENE, UniProtKB/TrEMBL |
| Ensembl Protein | ENSRNOP00000052657 | ENTREZGENE, UniProtKB/TrEMBL |
| ENSRNOP00000069583 | UniProtKB/TrEMBL | |
| Ensembl Transcript | ENSRNOT00000055801 | ENTREZGENE, UniProtKB/TrEMBL |
| ENSRNOT00000080379 | UniProtKB/TrEMBL | |
| Gene3D-CATH | 3.90.190.10 | UniProtKB/Swiss-Prot |
| IMAGE_CLONE | IMAGE:7107006 | IMAGE-MGC_LOAD |
| InterPro | Prot-tyrosine_phosphatase-like | UniProtKB/Swiss-Prot |
| PTPase_domain | UniProtKB/Swiss-Prot | |
| Tyr_Pase_AS | UniProtKB/Swiss-Prot | |
| Tyr_Pase_cat | UniProtKB/Swiss-Prot | |
| Tyr_Pase_rcpt_a/e-type | UniProtKB/Swiss-Prot | |
| Tyr_Pase_rcpt_alpha | UniProtKB/Swiss-Prot | |
| TYR_PHOSPHATASE_dom | UniProtKB/Swiss-Prot | |
| KEGG Report | rno:25167 | UniProtKB/TrEMBL |
| MGC_CLONE | MGC:93561 | IMAGE-MGC_LOAD |
| NCBI Gene | 25167 | ENTREZGENE |
| PANTHER | PTHR19134:SF433 | UniProtKB/Swiss-Prot |
| Pfam | Y_phosphatase | UniProtKB/Swiss-Prot |
| PhenoGen | Ptpra | PhenoGen |
| PIRSF | PTPR_alpha | UniProtKB/Swiss-Prot |
| PTPR_alpha_epsilon | UniProtKB/Swiss-Prot | |
| PRINTS | PRTYPHPHTASE | UniProtKB/Swiss-Prot |
| PROSITE | TYR_PHOSPHATASE_1 | UniProtKB/Swiss-Prot |
| TYR_PHOSPHATASE_2 | UniProtKB/Swiss-Prot | |
| TYR_PHOSPHATASE_PTP | UniProtKB/Swiss-Prot | |
| SMART | PTPc | UniProtKB/Swiss-Prot |
| PTPc_motif | UniProtKB/Swiss-Prot | |
| Superfamily-SCOP | SSF52799 | UniProtKB/Swiss-Prot |
| TIGR | TC229590 | |
| Transposagen | Ptpra |
Transposagen |
| UniGene | Rn.18043 | ENTREZGENE |
| UniProt | A0A0G2JVR0_RAT | UniProtKB/TrEMBL |
| PTPRA_RAT | UniProtKB/Swiss-Prot, ENTREZGENE | |
| Q66HJ7 | ENTREZGENE, UniProtKB/TrEMBL | |
| UniProt Secondary | F1M833 | UniProtKB/TrEMBL |
Nomenclature History| Date | Current Symbol | Current Name | Previous Symbol | Previous Name | Description | Reference | Status |
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| 2002-06-10 | Ptpra | Protein tyrosine phosphatase, receptor type, A | Symbol and Name status set to approved | 70586 | APPROVED |
RGD Curation Notes| Note Type | Note | Reference |
|---|---|---|
| gene_domains | has two intracellular PTPase domains | 633823 |
| gene_regulation | expression is inhibited by treatment with Il6 or Il1 | 633823 |
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| More on Ptpra | |
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Alliance Gene |
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NCBI Gene |
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Ensembl Gene |
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JBrowse: rn5 rn6 |
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NCBI Genome Data Viewer |
| RGD Object Information | |
| RGD ID: | 3450 |
| Created: | 2000-05-25 |
| Species: | Rattus norvegicus |
| Last Modified: | 2019-11-27 |
| Status: | ACTIVE |
