 Gene-Chemical Interaction Annotations | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Gene Ontology Annotations |
Welcome {{ username}}
Message Center
{{ messageCount }} Messages
Watched Genes
{{$index + 1}}. {{ watchedObject.symbol }} (RGD ID:{{watchedObject.rgdId}})
Watched Ontology Terms
{{gene.symbol}}: {{ gene.description }}
Save List to My RGD
| Create Name: | |
| Description: |
|
| Save what matters to you |
| {{ loginError }} |
| Sign in with your RGD account |
| Create New Account | Recover Password |
{{ watchLinkText }}
Select categories you would like to watch. Updates to this gene will be send to {{ username }}
Analyze GeneStrainQTL List |
 Gene Annotator (Functional Annotation) unavailable |
 Gene Annotator (Annotation Distribution) unavailable |
 Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable |
Gene Annotator (Functional Annotation) |
Gene Annotator (Annotation Distribution) |
Variant Visualizer (Genomic Variants) |
 InterViewer (Protein-Protein Interactions) unavailable |
 Gviewer (Genome Viewer) unavailable |
 Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable |
InterViewer (Protein-Protein Interactions) |
GViewer (Genome Viewer) |
Variant Visualizer (Damaging Variants) |
 Gene Annotator (Annotation Comparison) unavailable |
 OLGA (Gene List Generator) unavailable |
 |
Gene Annotator (Annotation Comparison) |
OLGA (Gene List Generator) |
Excel (Download) |
 MOET (Multi-Ontology Enrichement) unavailable |
 GOLF (Gene-Ortholog Location Finder) unavailable |
|
MOET (Multi-Ontology Enrichement) |
GOLF (Gene-Ortholog Location Finder) |
Gene Ontology AnnotationsDisease Annotations
|
Gene-Chemical Interaction Annotations
|
|
|
Gene Ontology AnnotationsBiological Process
|
Cellular Component
|
|
Molecular Function
|
References - curated| 1. | GOA data from the GO Consortium |
| 2. | NCBI rat LocusLink and RefSeq merged data July 26, 2002 |
| 3. | RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations |
| 4. | RGD automated import pipeline for gene-chemical interactions |
| 5. | Schoch S, etal., Nature 2002 Jan 17;415(6869):321-6. |
| 6. | Wyszynski M, etal., Neuron 2002 Mar 28;34(1):39-52. |
References - uncuratedGenomics
Comparative Map Data| Ppfia4 (Rattus norvegicus - Norway rat) |
|
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| PPFIA4 (Homo sapiens - human) |
|
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Ppfia4 (Mus musculus - house mouse) |
|
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Ppfia4 (Chinchilla lanigera - long-tailed chinchilla) |
|
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| PPFIA4 (Pan paniscus - bonobo/pygmy chimpanzee) |
|
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| PPFIA4 (Canis lupus familiaris - dog) |
|
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Ppfia4 (Ictidomys tridecemlineatus - thirteen-lined ground squirrel) |
|
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| PPFIA4 (Sus scrofa - pig) |
|
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Position Markers| D13Hmgc23 |
|
|||||||||||||||||||||||||||||||||||
| AI448359 |
|
|||||||||||||||||||||||||||||||||||
| RH127096 |
|
|||||||||||||||||||||||||||||||||||
| BF405092 |
|
QTLs in Region (Rnor_6.0)| The following QTLs overlap with this region. |  | Full Report | | CSV | | TAB | | Printer | | Gviewer |
miRNA 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. |
||||||||
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 | 3 | 14 | 11 | 1 | 22 | 23 | 1 | |||||||||
| Low | 19 | 29 | 12 | 15 | 3 | 3 | 3 | 8 | 4 | 2 | 11 | 11 | 29 | 34 | 8 | 8 |
| Below cutoff | 12 |
View RNA-SEQ Expression Data
Sequence
Nucleotide Sequences| RefSeq Transcripts | NM_080409 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles |
| XM_008769529 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| XM_017598653 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| XR_001840768 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| XR_358905 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| GenBank Nucleotide | AAHX01075171 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles |
| AAHX01075172 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| AC117152 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| AY057064 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| BC092640 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| BF285985 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| CB584337 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| CH473958 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles |
Reference Sequences
| RefSeq Acc Id: | NM_080409 ⟹ NP_536334 | ||||||||||||||||||||||||
| RefSeq Status: | VALIDATED | ||||||||||||||||||||||||
| Type: | CODING | ||||||||||||||||||||||||
| Position: |
|
||||||||||||||||||||||||
| Sequence: |
GCTACCTTTGCGGGCTTGCCTCTAGGACGCTTCGCACTGCCGAGGTCGGGGGCGGCGCCCTGCThide sequence |
| RefSeq Acc Id: | XM_008769529 ⟹ XP_008767751 | |||||||||
| RefSeq Status: | ||||||||||
| Type: | CODING | |||||||||
| Position: |
|
|||||||||
| Sequence: |
TATCCGCGGAGGAAGGGGGCGGGTCCTTCGGGCCACGGTACTGGGCGGTGGAGGCTGCAGCTAChide sequence |
| RefSeq Acc Id: | XM_017598653 ⟹ XP_017454142 | |||||||||
| RefSeq Status: | ||||||||||
| Type: | CODING | |||||||||
| Position: |
|
|||||||||
| Sequence: |
TATCCGCGGAGGAAGGGGGCGGGTCCTTCGGGCCACGGTACTGGGCGGTGGAGGCTGCAGCTAChide sequence |
| RefSeq Acc Id: | XR_001840768 | |||||||||
| RefSeq Status: | ||||||||||
| Type: | NON-CODING | |||||||||
| Position: |
|
|||||||||
| Sequence: |
TATCCGCGGAGGAAGGGGGCGGGTCCTTCGGGCCACGGTACTGGGCGGTGGAGGCTGCAGCTAChide sequence |
| RefSeq Acc Id: | XR_358905 | ||||||||||||||
| RefSeq Status: | |||||||||||||||
| Type: | NON-CODING | ||||||||||||||
| Position: |
|
||||||||||||||
| Sequence: |
TATCCGCGGAGGAAGGGGGCGGGTCCTTCGGGCCACGGTACTGGGCGGTGGAGGCTGCAGCTAChide sequence |
Protein Sequences| Protein RefSeqs | NP_536334 | (Get FASTA) | NCBI Sequence Viewer |
| XP_008767751 | (Get FASTA) | NCBI Sequence Viewer | |
| XP_017454142 | (Get FASTA) | NCBI Sequence Viewer | |
| GenBank Protein | AAH92640 | (Get FASTA) | NCBI Sequence Viewer |
| AAL23695 | (Get FASTA) | NCBI Sequence Viewer | |
| EDM09734 | (Get FASTA) | NCBI Sequence Viewer | |
| Q91Z80 | (Get FASTA) | NCBI Sequence Viewer |
Reference Sequences
| RefSeq Acc Id: | NP_536334 ⟸ NM_080409 |
| - UniProtKB: | Q91Z80 (UniProtKB/Swiss-Prot) |
| - Sequence: |
MCEVMPTINEGDPLGPPHGADADANFEQLMVNMLDEREKLLESLRESQETLVATQSRLQDALHEhide sequence |
| RefSeq Acc Id: | XP_008767751 ⟸ XM_008769529 |
| - Peptide Label: | isoform X1 |
| - UniProtKB: | F1M863 (UniProtKB/TrEMBL) |
| - Sequence: |
MCEVMPTINEGDPLGPPHGADADANFEQLMVNMLDEREKLLESLRESQETLVATQSRLQDALHEhide sequence |
| RefSeq Acc Id: | XP_017454142 ⟸ XM_017598653 |
| - Peptide Label: | isoform X2 |
| - Sequence: |
MCEVMPTINEGDPLGPPHGADADANFEQLMVNMLDEREKLLESLRESQETLVATQSRLQDALHEhide sequence |
TranscriptomeStrain Variation
Strain Sequence Variants (Rnor 6.0)
|
||||||||||||||||||||
|
||||||||||||||||||||
|
||||||||||||||||||||
|
||||||||||||||||||||
|
||||||||||||||||||||
|
||||||||||||||||||||
|
||||||||||||||||||||
|
||||||||||||||||||||
|
||||||||||||||||||||
|
||||||||||||||||||||
|
||||||||||||||||||||
|
||||||||||||||||||||
|
||||||||||||||||||||
|
||||||||||||||||||||
|
||||||||||||||||||||
|
||||||||||||||||||||
|
||||||||||||||||||||
|
||||||||||||||||||||
|
||||||||||||||||||||
|
||||||||||||||||||||
|
||||||||||||||||||||
|
||||||||||||||||||||
|
||||||||||||||||||||
|
||||||||||||||||||||
|
||||||||||||||||||||
|
||||||||||||||||||||
|
||||||||||||||||||||
|
||||||||||||||||||||
|
||||||||||||||||||||
|
||||||||||||||||||||
|
||||||||||||||||||||
|
||||||||||||||||||||
|
||||||||||||||||||||
|
||||||||||||||||||||
|
||||||||||||||||||||
|
||||||||||||||||||||
|
||||||||||||||||||||
|
||||||||||||||||||||
|
||||||||||||||||||||
|
||||||||||||||||||||
|
||||||||||||||||||||
|
||||||||||||||||||||
Additional Information
External Database Links| Database | Acc Id | Source(s) |
| AGR Gene | RGD:620055 | AgrOrtholog |
| Ensembl Genes | ENSRNOG00000003494 | ENTREZGENE, UniProtKB/TrEMBL |
| Ensembl Protein | ENSRNOP00000033209 | ENTREZGENE, UniProtKB/TrEMBL |
| Ensembl Transcript | ENSRNOT00000039540 | ENTREZGENE, UniProtKB/TrEMBL |
| Gene3D-CATH | 1.10.150.50 | UniProtKB/Swiss-Prot |
| IMAGE_CLONE | IMAGE:7316820 | IMAGE-MGC_LOAD |
| InterPro | Liprin | UniProtKB/Swiss-Prot |
| Liprin-alpha_SAM_rpt_1 | UniProtKB/Swiss-Prot | |
| Liprin-alpha_SAM_rpt_2 | UniProtKB/Swiss-Prot | |
| Liprin-alpha_SAM_rpt_3 | UniProtKB/Swiss-Prot | |
| PPFIA4 | UniProtKB/Swiss-Prot | |
| SAM | UniProtKB/Swiss-Prot | |
| SAM/pointed_sf | UniProtKB/Swiss-Prot | |
| KEGG Report | rno:140592 | UniProtKB/Swiss-Prot |
| MGC_CLONE | MGC:109376 | IMAGE-MGC_LOAD |
| NCBI Gene | 140592 | ENTREZGENE |
| PANTHER | PTHR12587 | UniProtKB/Swiss-Prot |
| PTHR12587:SF5 | UniProtKB/Swiss-Prot | |
| Pfam | SAM_1 | UniProtKB/Swiss-Prot |
| SAM_2 | UniProtKB/Swiss-Prot | |
| PhenoGen | Ppfia4 | PhenoGen |
| PROSITE | SAM_DOMAIN | UniProtKB/Swiss-Prot |
| SMART | SAM | UniProtKB/Swiss-Prot |
| Superfamily-SCOP | SSF47769 | UniProtKB/Swiss-Prot |
| UniGene | Rn.105913 | ENTREZGENE |
| UniProt | F1M863 | ENTREZGENE, UniProtKB/TrEMBL |
| LIPA4_RAT | UniProtKB/Swiss-Prot | |
| Q562A3_RAT | UniProtKB/TrEMBL | |
| Q91Z80 | ENTREZGENE |
Nomenclature History| Date | Current Symbol | Current Name | Previous Symbol | Previous Name | Description | Reference | Status |
|---|---|---|---|---|---|---|---|
| 2016-02-17 | Ppfia4 | PTPRF interacting protein alpha 4 | Ppfia4 | protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 4 | Nomenclature updated to reflect human and mouse nomenclature | 1299863 | APPROVED |
| 2015-07-29 | Ppfia4 | protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 4 | LOC685423 | hypothetical protein LOC685423 | Data Merged | 737654 | PROVISIONAL |
| 2006-11-20 | LOC685423 | hypothetical protein LOC685423 | Symbol and Name status set to provisional | 70820 | PROVISIONAL | ||
| 2004-02-26 | Ppfia4 | protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 4 | Symbol and Name status set to approved | 625702 | APPROVED | ||
| 2002-08-07 | Ppfia4 | protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 4 | Symbol and Name status set to provisional | 70820 | PROVISIONAL |
RGD Curation Notes| Note Type | Note | Reference |
|---|---|---|
| gene_physical_interaction | binds to RIM-BPs, cyclic-AMP-GEFII, and Munc13-1 | 633666 |
 |
| More on Ppfia4 | |
|
Alliance Gene |
|
NCBI Gene |
|
Ensembl Gene |
|
|
JBrowse: rn5 rn6 |
|
NCBI Genome Data Viewer |
| RGD Object Information | |
| RGD ID: | 620055 |
| Created: | 2002-08-06 |
| Species: | Rattus norvegicus |
| Last Modified: | 2019-08-20 |
| Status: | ACTIVE |
