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Analyze GeneStrainQTL List |
 Gene Annotator (Functional Annotation) unavailable |
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Variant Visualizer (Genomic Variants) |
 InterViewer (Protein-Protein Interactions) unavailable |
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 Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable |
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 Gene Annotator (Annotation Comparison) unavailable |
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Gene Annotator (Annotation Comparison) |
OLGA (Gene List Generator) |
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 MOET (Multi-Ontology Enrichement) unavailable |
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MOET (Multi-Ontology Enrichement) |
GOLF (Gene-Ortholog Location Finder) |
Imported Annotations - ClinVar | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Term | Qualifier | Evidence | With | Reference | Notes | Source | Original Reference(s) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| prostate cancer | ISO | RGD:1348952 | 8554872 | ClinVar Annotator: match by term: Prostate cancer | ClinVar | PMID:23265383 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Gene-Chemical Interaction AnnotationsGene Ontology AnnotationsMolecular Pathway AnnotationsDisease Annotations
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Gene-Chemical Interaction Annotations
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Gene Ontology Annotations
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Molecular Pathway AnnotationsReferences - curated| 1. | Boyken J, etal., Neuron. 2013 Apr 24;78(2):285-97. doi: 10.1016/j.neuron.2013.02.027. |
| 2. | Brini M and Carafoli E, Physiol Rev. 2009 Oct;89(4):1341-78. doi: 10.1152/physrev.00032.2008. |
| 3. | Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27. |
| 4. | Ghosh B, etal., J Neurosci. 2011 Feb 16;31(7):2361-70. |
| 5. | Husain M, etal., Am J Physiol. 1997 Jun;272(6 Pt 1):C1947-59. |
| 6. | Keeton TP and Shull GE, Biochem J 1995 Mar 15;306 ( Pt 3):779-85. |
| 7. | Kip SN, etal., Hippocampus. 2006;16(1):20-34. |
| 8. | MGD data from the GO Consortium |
| 9. | NCBI rat LocusLink and RefSeq merged data July 26, 2002 |
| 10. | Pipeline to import KEGG annotations from KEGG into RGD |
| 11. | Renteria RC, etal., Vis Neurosci. 2005 May-Jun;22(3):263-74. |
| 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. | Schuh K, etal., J Biol Chem 2003 Mar 14;278(11):9778-83. |
| 15. | Sgambato-Faure V, etal., Biochem Biophys Res Commun. 2006 May 5;343(2):630-7. Epub 2006 Mar 15. |
| 16. | Usachev YM, etal., Neuron 2002 Jan 3;33(1):113-22. |
| 17. | Wilhelm B, etal., Histochem Cell Biol. 2008 Mar;129(3):331-43. Epub 2007 Dec 4. |
| 18. | Wu X, etal., J Clin Invest. 2009 Apr;119(4):976-85. doi: 10.1172/JCI36693. Epub 2009 Mar 16. |
| 19. | Xiao J, etal., Neuroscience. 2007 Jan 19;144(2):439-61. Epub 2006 Nov 7. |
References - uncurated| PubMed | 7694502 7945253 8428948 8530416 11591728 15078889 15955804 16956963 17242280 18591664 19278978 19715754 19946888 21740891 22871113 23549614 24448801 25147342 25798335 29476059 |
Comparative Map Data| Atp2b4 (Rattus norvegicus - Norway rat) |
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| ATP2B4 (Homo sapiens - human) |
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| Atp2b4 (Mus musculus - house mouse) |
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| Atp2b4 (Chinchilla lanigera - long-tailed chinchilla) |
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| ATP2B4 (Pan paniscus - bonobo/pygmy chimpanzee) |
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| ATP2B4 (Canis lupus familiaris - dog) |
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| Atp2b4 (Ictidomys tridecemlineatus - thirteen-lined ground squirrel) |
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| ATP2B4 (Sus scrofa - pig) |
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| ATP2B4 (Chlorocebus sabaeus - African green monkey) |
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| Atp2b4 (Heterocephalus glaber - naked mole-rat) |
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Position Markers| D13Wox2 |
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QTLs in Region (Rnor_6.0)| The following QTLs overlap with this region. |  | Full Report | | CSV | | TAB | | Printer | | Gviewer |
miRNA Target Status
| 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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RNA-SEQ Expression| alimentary part of gastrointestinal system | circulatory system | endocrine system | exocrine system | hemolymphoid system | hepatobiliary system | integumental system | musculoskeletal system | nervous system | renal system | reproductive system | respiratory system | appendage | |
| High | |||||||||||||
| Medium | 3 | 30 | 28 | 22 | 17 | 22 | 1 | 1 | 72 | 34 | 40 | 11 | 1 |
| Low | 13 | 28 | 18 | 2 | 18 | 7 | 10 | 2 | 1 | 1 | 7 | ||
| Below cutoff | 1 | 1 | 1 |
Nucleotide Sequences| RefSeq Transcripts | NM_001005871 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles |
| XM_008769446 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| XM_008769447 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| XM_008769448 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| XM_008769449 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| XM_008769450 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| XM_017598773 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| GenBank Nucleotide | AAHX01075150 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles |
| AAHX01075151 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| AAHX01075152 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| AC105642 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| AH002538 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| U15408 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| X70978 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| X76452 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles |
| RefSeq Acc Id: | ENSRNOT00000004078 ⟹ ENSRNOP00000004078 | ||||||||
| RefSeq Status: | |||||||||
| Type: | CODING | ||||||||
| Position: |
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| RefSeq Acc Id: | ENSRNOT00000046273 ⟹ ENSRNOP00000039880 | ||||||||
| RefSeq Status: | |||||||||
| Type: | CODING | ||||||||
| Position: |
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| RefSeq Acc Id: | NM_001005871 ⟹ NP_001005871 | ||||||||||||||||||||
| RefSeq Status: | PROVISIONAL | ||||||||||||||||||||
| Type: | CODING | ||||||||||||||||||||
| Position: |
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| Sequence: |
GCTACTCTGAAACTTATTGCACAAGATATTGTCAATTTATCCCCTAACTGGGCTCCCAGAGAAGhide sequence |
| RefSeq Acc Id: | XM_008769446 ⟹ XP_008767668 | ||||||||
| RefSeq Status: | |||||||||
| Type: | CODING | ||||||||
| Position: |
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| Sequence: |
AACATAGAGCCCATCTACCACTGAGCTGCATCTCCAACCAGCAGTGTCTTCTGTATCCTAACCChide sequence |
| RefSeq Acc Id: | XM_008769447 ⟹ XP_008767669 | ||||||||
| RefSeq Status: | |||||||||
| Type: | CODING | ||||||||
| Position: |
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| Sequence: |
TCTGTTTATTACCCAGCCAATTGAAATGCCTTACCAGGCCCTGGCAGCATAAACCAATTGCAGGhide sequence |
| RefSeq Acc Id: | XM_008769448 ⟹ XP_008767670 | ||||||||
| RefSeq Status: | |||||||||
| Type: | CODING | ||||||||
| Position: |
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| Sequence: |
AACATAGAGCCCATCTACCACTGAGCTGCATCTCCAACCAGCAGTGTCTTCTGTATCCTAACCChide sequence |
| RefSeq Acc Id: | XM_008769449 ⟹ XP_008767671 | ||||||||
| RefSeq Status: | |||||||||
| Type: | CODING | ||||||||
| Position: |
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| Sequence: |
GAACATAGAGCCCATCTACCACTGAGCTGCATCTCCAACCAGCAGTGTCTTCTGTATCCTAACChide sequence |
| RefSeq Acc Id: | XM_008769450 ⟹ XP_008767672 | ||||||||
| RefSeq Status: | |||||||||
| Type: | CODING | ||||||||
| Position: |
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| Sequence: |
GAACATAGAGCCCATCTACCACTGAGCTGCATCTCCAACCAGCAGTGTCTTCTGTATCCTAACChide sequence |
| RefSeq Acc Id: | XM_017598773 ⟹ XP_017454262 | ||||||||
| RefSeq Status: | |||||||||
| Type: | CODING | ||||||||
| Position: |
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| Sequence: |
GAACATAGAGCCCATCTACCACTGAGCTGCATCTCCAACCAGCAGTGTCTTCTGTATCCTAACChide sequence |
Protein Sequences| Protein RefSeqs | NP_001005871 | (Get FASTA) | NCBI Sequence Viewer |
| XP_008767668 | (Get FASTA) | NCBI Sequence Viewer | |
| XP_008767669 | (Get FASTA) | NCBI Sequence Viewer | |
| XP_008767670 | (Get FASTA) | NCBI Sequence Viewer | |
| XP_008767671 | (Get FASTA) | NCBI Sequence Viewer | |
| XP_008767672 | (Get FASTA) | NCBI Sequence Viewer | |
| XP_017454262 | (Get FASTA) | NCBI Sequence Viewer | |
| GenBank Protein | AAA50820 | (Get FASTA) | NCBI Sequence Viewer |
| AAA81005 | (Get FASTA) | NCBI Sequence Viewer | |
| AAA81006 | (Get FASTA) | NCBI Sequence Viewer | |
| AAA81007 | (Get FASTA) | NCBI Sequence Viewer | |
| AAA81008 | (Get FASTA) | NCBI Sequence Viewer | |
| CAA53990 | (Get FASTA) | NCBI Sequence Viewer | |
| Q64542 | (Get FASTA) | NCBI Sequence Viewer |
| RefSeq Acc Id: | NP_001005871 ⟸ NM_001005871 |
| - UniProtKB: | Q64542 (UniProtKB/Swiss-Prot) |
| - Sequence: |
MTNPSGHNLPANSVAESYEGEFGCTLMDLRKLMELRAADAVTQISAHYGSVQEICARLKTSPVEhide sequence |
| RefSeq Acc Id: | XP_008767671 ⟸ XM_008769449 |
| - Peptide Label: | isoform X3 |
| - UniProtKB: | Q64542 (UniProtKB/Swiss-Prot) |
| - Sequence: |
MTNPSGHNLPANSVAESYEGEFGCTLMDLRKLMELRAADAVTQISAHYGSVQEICARLKTSPVEhide sequence |
| RefSeq Acc Id: | XP_008767672 ⟸ XM_008769450 |
| - Peptide Label: | isoform X4 |
| - UniProtKB: | Q64542 (UniProtKB/Swiss-Prot) |
| - Sequence: |
MTNPSGHNLPANSVAESYEGEFGCTLMDLRKLMELRAADAVTQISAHYGSVQEICARLKTSPVEhide sequence |
| RefSeq Acc Id: | XP_008767668 ⟸ XM_008769446 |
| - Peptide Label: | isoform X1 |
| - UniProtKB: | Q64542 (UniProtKB/Swiss-Prot) |
| - Sequence: |
MTNPSGHNLPANSVAESYEGEFGCTLMDLRKLMELRAADAVTQISAHYGSVQEICARLKTSPVEhide sequence |
| RefSeq Acc Id: | XP_008767670 ⟸ XM_008769448 |
| - Peptide Label: | isoform X2 |
| - UniProtKB: | Q64542 (UniProtKB/Swiss-Prot) |
| - Sequence: |
MTNPSGHNLPANSVAESYEGEFGCTLMDLRKLMELRAADAVTQISAHYGSVQEICARLKTSPVEhide sequence |
| RefSeq Acc Id: | XP_008767669 ⟸ XM_008769447 |
| - Peptide Label: | isoform X1 |
| - UniProtKB: | Q64542 (UniProtKB/Swiss-Prot) |
| - Sequence: |
MTNPSGHNLPANSVAESYEGEFGCTLMDLRKLMELRAADAVTQISAHYGSVQEICARLKTSPVEhide sequence |
| RefSeq Acc Id: | XP_017454262 ⟸ XM_017598773 |
| - Peptide Label: | isoform X5 |
| - Sequence: |
MTNPSGHNLPANSVAESYEGEFGCTLMDLRKLMELRAADAVTQISAHYGSVQEICARLKTSPVEhide sequence |
| RefSeq Acc Id: | ENSRNOP00000004078 ⟸ ENSRNOT00000004078 |
| RefSeq Acc Id: | ENSRNOP00000039880 ⟸ ENSRNOT00000046273 |
TranscriptomeStrain Sequence Variants (Rnor 6.0)
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Damaging Variants| Chromosome | Start Pos | End Pos | Reference Nucleotide | Variant Nucleotide | Variant Type | Strain |
| 13 | 50116624 | 50116625 | A | C | snv | MR/N (MCW) |
| 13 | 50125564 | 50125565 | T | C | snv | Buf/N (MCW) |
External Database Links| Database | Acc Id | Source(s) |
| AGR Gene | RGD:621305 | AgrOrtholog |
| Ensembl Genes | ENSRNOG00000003031 | Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot |
| Ensembl Protein | ENSRNOP00000004078 | ENTREZGENE, UniProtKB/Swiss-Prot |
| ENSRNOP00000039880 | ENTREZGENE, UniProtKB/Swiss-Prot | |
| Ensembl Transcript | ENSRNOT00000004078 | ENTREZGENE, UniProtKB/Swiss-Prot |
| ENSRNOT00000046273 | ENTREZGENE, UniProtKB/Swiss-Prot | |
| Gene3D-CATH | 3.40.1110.10 | UniProtKB/Swiss-Prot |
| 3.40.50.1000 | UniProtKB/Swiss-Prot | |
| InterPro | ATP2B4 | UniProtKB/Swiss-Prot |
| ATP_Ca_trans_C | UniProtKB/Swiss-Prot | |
| ATPase_P-typ_cation-transptr_C | UniProtKB/Swiss-Prot | |
| ATPase_P-typ_cation-transptr_N | UniProtKB/Swiss-Prot | |
| ATPase_P-typ_cyto_dom_N | UniProtKB/Swiss-Prot | |
| ATPase_P-typ_P_site | UniProtKB/Swiss-Prot | |
| ATPase_P-typ_TM_dom_sf | UniProtKB/Swiss-Prot | |
| ATPase_P-typ_transduc_dom_A_sf | UniProtKB/Swiss-Prot | |
| HAD-like_sf | UniProtKB/Swiss-Prot | |
| HAD_sf | UniProtKB/Swiss-Prot | |
| P-type_ATPase_IIB | UniProtKB/Swiss-Prot | |
| P_typ_ATPase | UniProtKB/Swiss-Prot | |
| KEGG Report | rno:29600 | UniProtKB/Swiss-Prot |
| NCBI Gene | 29600 | ENTREZGENE |
| PANTHER | PTHR24093:SF435 | UniProtKB/Swiss-Prot |
| Pfam | ATP_Ca_trans_C | UniProtKB/Swiss-Prot |
| Cation_ATPase_C | UniProtKB/Swiss-Prot | |
| Cation_ATPase_N | UniProtKB/Swiss-Prot | |
| PhenoGen | Atp2b4 | PhenoGen |
| PROSITE | ATPASE_E1_E2 | UniProtKB/Swiss-Prot |
| SMART | Cation_ATPase_N | UniProtKB/Swiss-Prot |
| Superfamily-SCOP | SSF56784 | UniProtKB/Swiss-Prot |
| SSF81653 | UniProtKB/Swiss-Prot | |
| SSF81660 | UniProtKB/Swiss-Prot | |
| SSF81665 | UniProtKB/Swiss-Prot | |
| TIGRFAMs | ATPase-IIB_Ca | UniProtKB/Swiss-Prot |
| ATPase_P-type | UniProtKB/Swiss-Prot | |
| UniGene | Rn.9986 | ENTREZGENE |
| UniProt | AT2B4_RAT | UniProtKB/Swiss-Prot, ENTREZGENE |
| UniProt Secondary | Q63127 | UniProtKB/Swiss-Prot |
| Q63445 | UniProtKB/Swiss-Prot | |
| Q64543 | UniProtKB/Swiss-Prot | |
| Q64544 | UniProtKB/Swiss-Prot | |
| Q64545 | UniProtKB/Swiss-Prot |
Nomenclature History| Date | Current Symbol | Current Name | Previous Symbol | Previous Name | Description | Reference | Status |
|---|---|---|---|---|---|---|---|
| 2016-02-17 | Atp2b4 | ATPase plasma membrane Ca2+ transporting 4 | Atp2b4 | ATPase, Ca++ transporting, plasma membrane 4 | Nomenclature updated to reflect human and mouse nomenclature | 1299863 | APPROVED |
| 2004-09-10 | Atp2b4 | ATPase, Ca++ transporting, plasma membrane 4 | Symbol and Name status set to approved | 1299863 | APPROVED | ||
| 2002-08-07 | Atp2b4 | ATPase, Ca++ transporting, plasma membrane 4 | Symbol and Name status set to provisional | 70820 | PROVISIONAL |
RGD Curation Notes| Note Type | Note | Reference |
|---|---|---|
| gene_cellular_localization | colocalizes with voltage-gated Ca2+ channels | 628395 |
| gene_function | binds to and extrudes Ca++ from neurons | 628395 |
| gene_process | meidates Ca2+ expulsion from the somata of dorsal root ganglion (DRG) neurons and from the presynaptic terminals of photoreceptors | 628395 |
| gene_regulation | removal of action potential-induced Ca2+ loads in sensory neurons is greatly enhanced by bradykinin and ATP; the carboxy-terminal domains are phosphorylated by protein kinase A (PKA) and protein kinase C (PKC) | 628395 |
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| More on Atp2b4 | |
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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: | 621305 |
| Created: | 2002-08-06 |
| Species: | Rattus norvegicus |
| Last Modified: | 2020-06-09 |
| Status: | ACTIVE |
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RGD is funded by grant HL64541 from the National Heart, Lung, and Blood Institute on behalf of the NIH.
