 Gene-Chemical Interaction Annotations | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Gene Ontology AnnotationsMolecular Pathway Annotations |
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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 |
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InterViewer (Protein-Protein Interactions) |
GViewer (Genome Viewer) |
Variant Visualizer (Damaging Variants) |
 Gene Annotator (Annotation Comparison) unavailable |
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Gene Annotator (Annotation Comparison) |
OLGA (Gene List Generator) |
Excel (Download) |
 MOET (Multi-Ontology Enrichement) unavailable |
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MOET (Multi-Ontology Enrichement) |
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. | Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27. |
| 2. | Pipeline to import SMPDB annotations from SMPDB into RGD |
| 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. | RGD comprehensive gene curation |
References - uncuratedGenomics
Comparative Map Data| Dera (Rattus norvegicus - Norway rat) |
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| DERA (Homo sapiens - human) |
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| Dera (Mus musculus - house mouse) |
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| Dera (Chinchilla lanigera - long-tailed chinchilla) |
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| DERA (Pan paniscus - bonobo/pygmy chimpanzee) |
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| DERA (Canis lupus familiaris - dog) |
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| Dera (Ictidomys tridecemlineatus - thirteen-lined ground squirrel) |
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| DERA (Sus scrofa - pig) |
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| DERA (Chlorocebus sabaeus - African green monkey) |
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| Dera (Heterocephalus glaber - naked mole-rat) |
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Position Markers| D4Rat69 |
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| RH132144 |
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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
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
| 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 | 35 | 57 | 41 | 19 | 41 | 5 | 8 | 66 | 35 | 34 | 11 | 5 |
| Low | 8 | 3 | 3 | 8 | 7 | 3 | |||||||
| Below cutoff |
View RNA-SEQ Expression Data
Sequence
Nucleotide Sequences| RefSeq Transcripts | XM_003749862 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles |
| XM_003753958 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| GenBank Nucleotide | AABR07062360 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles |
| AABR07062361 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| AAHX01033360 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| AAHX01033361 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| AAHX01033362 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| AAHX01033363 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| CH473964 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| FQ212862 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| FQ219539 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles |
Reference Sequences
| RefSeq Acc Id: | ENSRNOT00000009998 ⟹ ENSRNOP00000009998 | ||||||||
| RefSeq Status: | |||||||||
| Type: | CODING | ||||||||
| Position: |
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| RefSeq Acc Id: | XM_003749862 ⟹ XP_003749910 | ||||||||||||
| RefSeq Status: | |||||||||||||
| Type: | CODING | ||||||||||||
| Position: |
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| Sequence: |
CGTGGCTCAGGGCGGGCATTTGGCAGGAAGGAGGAAGACCAGGCCTGTGTGGCGCCCTACCCTGhide sequence |
| RefSeq Acc Id: | XM_003753958 ⟹ XP_003754006 | ||||||||
| RefSeq Status: | |||||||||
| Type: | CODING | ||||||||
| Position: |
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| Sequence: |
CGTGGCTCAGGGCGGGCATTTGGCAGGAAGGAGGAAGACCAGGCCTGTGTGGCGCCCTACCCTGhide sequence |
Protein Sequences| Protein RefSeqs | XP_003749910 | (Get FASTA) | NCBI Sequence Viewer |
| XP_003754006 | (Get FASTA) | NCBI Sequence Viewer | |
| GenBank Protein | EDM01579 | (Get FASTA) | NCBI Sequence Viewer |
Reference Sequences
| RefSeq Acc Id: | XP_003749910 ⟸ XM_003749862 |
| - UniProtKB: | F1M1H0 (UniProtKB/TrEMBL) |
| - Sequence: |
MAAHCRGTELDLSWVSRVQVNHAAVLRRAEQIQARRSVKKEWQAAWLLKAVTFIDLTTLSGDDThide sequence |
| RefSeq Acc Id: | XP_003754006 ⟸ XM_003753958 |
| - UniProtKB: | F1M1H0 (UniProtKB/TrEMBL) |
| - Sequence: |
MAAHCRGTELDLSWVSRVQVNHAAVLRRAEQIQARRSVKKEWQAAWLLKAVTFIDLTTLSGDDThide sequence |
| RefSeq Acc Id: | ENSRNOP00000009998 ⟸ ENSRNOT00000009998 |
TranscriptomePromoters| RGD ID: | 13693473 | ||||||||
| Promoter ID: | EPDNEW_R3996 | ||||||||
| Type: | initiation region | ||||||||
| Name: | Dera_1 | ||||||||
| Description: | deoxyribose-phosphate aldolase | ||||||||
| 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 |
| 4 | 236029592 | 236029593 | G | C | snv | NIG-III/Hok (KyushuU) |
Additional Information
External Database Links| Database | Acc Id | Source(s) |
| AGR Gene | RGD:1589836 | AgrOrtholog |
| Ensembl Genes | ENSRNOG00000007570 | Ensembl, ENTREZGENE, UniProtKB/TrEMBL |
| Ensembl Protein | ENSRNOP00000009998 | ENTREZGENE, UniProtKB/TrEMBL |
| Ensembl Transcript | ENSRNOT00000009998 | ENTREZGENE, UniProtKB/TrEMBL |
| Gene3D-CATH | 3.20.20.70 | UniProtKB/TrEMBL |
| InterPro | Aldolase_TIM | UniProtKB/TrEMBL |
| DeoC | UniProtKB/TrEMBL | |
| DeoC/FbaB/lacD_aldolase | UniProtKB/TrEMBL | |
| KEGG Report | rno:690945 | UniProtKB/TrEMBL |
| NCBI Gene | 690945 | ENTREZGENE |
| PANTHER | PTHR10889 | UniProtKB/TrEMBL |
| Pfam | DeoC | UniProtKB/TrEMBL |
| PhenoGen | Dera | PhenoGen |
| PIRSF | DeoC | UniProtKB/TrEMBL |
| SMART | DeoC | UniProtKB/TrEMBL |
| TIGRFAMs | deoC | UniProtKB/TrEMBL |
| UniGene | Rn.17191 | ENTREZGENE |
| UniProt | F1M1H0 | ENTREZGENE, UniProtKB/TrEMBL |
Nomenclature History| Date | Current Symbol | Current Name | Previous Symbol | Previous Name | Description | Reference | Status |
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| 2016-03-15 | Dera | deoxyribose-phosphate aldolase | Dera | deoxyribose-phosphate aldolase (putative) | Nomenclature updated to reflect human and mouse nomenclature | 1299863 | APPROVED |
| 2012-07-16 | Dera | deoxyribose-phosphate aldolase (putative) | Dera-ps1 | deoxyribose-phosphate aldolase, pseudogene 1 | Nomenclature updated to reflect human and mouse nomenclature | 1299863 | APPROVED |
| 2012-06-26 | Dera-ps1 | deoxyribose-phosphate aldolase, pseudogene 1 | Dera-ps1 | 2-deoxyribose-5-phosphate aldolase homolog (C. elegans), pseudogene 1 | Nomenclature updated to reflect human and mouse nomenclature | 1299863 | APPROVED |
| 2011-06-08 | Dera-ps1 | 2-deoxyribose-5-phosphate aldolase homolog (C. elegans), pseudogene 1 | Dera | 2-deoxyribose-5-phosphate aldolase homolog (C. elegans) | Nomenclature updated to reflect human and mouse nomenclature | 1299863 | APPROVED |
| 2008-11-21 | Dera | 2-deoxyribose-5-phosphate aldolase homolog (C. elegans) | LOC690945 | similar to Putative deoxyribose-phosphate aldolase (Phosphodeoxyriboaldolase) (Deoxyriboaldolase) (DERA) | Nomenclature updated to reflect human and mouse nomenclature | 1299863 | APPROVED |
| 2008-01-09 | LOC690945 | similar to Putative deoxyribose-phosphate aldolase (Phosphodeoxyriboaldolase) (Deoxyriboaldolase) (DERA) | LOC686184 | similar to Putative deoxyribose-phosphate aldolase (Phosphodeoxyriboaldolase) (Deoxyriboaldolase) (DERA) | Data Merged | 1643240 | APPROVED |
| 2006-11-20 | LOC690945 | similar to Putative deoxyribose-phosphate aldolase (Phosphodeoxyriboaldolase) (Deoxyriboaldolase) (DERA) | Symbol and Name status set to provisional | 70820 | PROVISIONAL | ||
| 2006-11-19 | LOC686184 | similar to Putative deoxyribose-phosphate aldolase (Phosphodeoxyriboaldolase) (Deoxyriboaldolase) (DERA) | Symbol and Name status set to provisional | 70820 | PROVISIONAL |
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| More on Dera | |
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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: | 1589836 |
| Created: | 2006-11-20 |
| Species: | Rattus norvegicus |
| Last Modified: | 2020-06-09 |
| Status: | ACTIVE |
