 Gene-Chemical Interaction Annotations | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Gene Ontology AnnotationsMolecular Pathway Annotations |
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Analyze GeneStrainQTL List |
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Gene Annotator (Functional Annotation) |
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InterViewer (Protein-Protein Interactions) |
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Gene Annotator (Annotation Comparison) |
OLGA (Gene List Generator) |
Excel (Download) |
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MOET (Multi-Ontology Enrichement) |
GOLF (Gene-Ortholog Location Finder) |
Gene Ontology AnnotationsMolecular Pathway AnnotationsDisease AnnotationsGene-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. | MGD data from the GO Consortium |
| 3. | Pipeline to import KEGG annotations from KEGG into RGD |
| 4. | RGD automated data pipeline |
| 5. | RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations |
| 6. | RGD automated import pipeline for gene-chemical interactions |
| 7. | RGD comprehensive gene curation |
References - uncuratedGenomics
Comparative Map Data| Sptlc3 (Rattus norvegicus - Norway rat) |
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| SPTLC3 (Homo sapiens - human) |
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| Sptlc3 (Mus musculus - house mouse) |
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| Sptlc3 (Chinchilla lanigera - long-tailed chinchilla) |
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| SPTLC3 (Pan paniscus - bonobo/pygmy chimpanzee) |
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| SPTLC3 (Canis lupus familiaris - dog) |
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| Sptlc3 (Ictidomys tridecemlineatus - thirteen-lined ground squirrel) |
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| SPTLC3 (Sus scrofa - pig) |
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| SPTLC3 (Chlorocebus sabaeus - African green monkey) |
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| Sptlc3 (Heterocephalus glaber - naked mole-rat) |
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Position Markers| D3Rat14 |
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| D3Got236 |
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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
| alimentary part of gastrointestinal system | circulatory system | endocrine system | hemolymphoid system | integumental system | musculoskeletal system | nervous system | renal system | reproductive system | respiratory system | appendage | |
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| Low | 1 | 1 | 1 | 12 | 10 | 11 | 8 | ||||
| Below cutoff | 2 | 12 | 5 | 3 | 3 | 34 | 22 | 21 | 2 | 3 |
View RNA-SEQ Expression Data
Sequence
Nucleotide Sequences| RefSeq Transcripts | NM_001106517 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles |
| GenBank Nucleotide | AABR07053885 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles |
| AABR07053886 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| AABR07053887 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| AAHX01025358 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| AAHX01025359 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| AAHX01025360 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| AAHX01025361 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| AAHX01025362 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| AAHX01025363 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| AAHX01025364 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| AAHX01025365 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| CH473949 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles |
Reference Sequences
| RefSeq Acc Id: | ENSRNOT00000005920 ⟹ ENSRNOP00000005920 | ||||||||
| RefSeq Status: | |||||||||
| Type: | CODING | ||||||||
| Position: |
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| RefSeq Acc Id: | NM_001106517 ⟹ NP_001099987 | ||||||||||||||||||||
| RefSeq Status: | PROVISIONAL | ||||||||||||||||||||
| Type: | CODING | ||||||||||||||||||||
| Position: |
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| Sequence: |
CCTCAGCCTCAAAAGGCAGCTAGCAAGGCAAATTCTCTTTGTAGTTTCAGAACAGGTTTGTTGChide sequence |
Protein Sequences| Protein RefSeqs | NP_001099987 | (Get FASTA) | NCBI Sequence Viewer |
| GenBank Protein | EDL80317 | (Get FASTA) | NCBI Sequence Viewer |
Reference Sequences
| RefSeq Acc Id: | NP_001099987 ⟸ NM_001106517 |
| - UniProtKB: | D4A9V0 (UniProtKB/TrEMBL) |
| - Sequence: |
MANPRDSAVTNGTLRNPKTQPGKRQSTDCVKNGISKEAQQNRKAEEDDKLVFKPYPEPPLYVFVhide sequence |
| RefSeq Acc Id: | ENSRNOP00000005920 ⟸ ENSRNOT00000005920 |
Protein Domains
Aminotran_1_2
TranscriptomeStrain Variation
Strain Sequence Variants (Rnor 6.0)
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Additional Information
External Database Links| Database | Acc Id | Source(s) |
| AGR Gene | RGD:1310030 | AgrOrtholog |
| Ensembl Genes | ENSRNOG00000004443 | Ensembl, ENTREZGENE, UniProtKB/TrEMBL |
| Ensembl Protein | ENSRNOP00000005920 | ENTREZGENE, UniProtKB/TrEMBL |
| Ensembl Transcript | ENSRNOT00000005920 | ENTREZGENE, UniProtKB/TrEMBL |
| Gene3D-CATH | 3.40.640.10 | UniProtKB/TrEMBL |
| 3.90.1150.10 | UniProtKB/TrEMBL | |
| InterPro | Aminotrans_II_pyridoxalP_BS | UniProtKB/TrEMBL |
| Aminotransferase_I/II | UniProtKB/TrEMBL | |
| PyrdxlP-dep_Trfase_major_dom | UniProtKB/TrEMBL | |
| PyrdxlP-dep_Trfase_major_sub1 | UniProtKB/TrEMBL | |
| PyrdxlP-dep_Trfase_major_sub2 | UniProtKB/TrEMBL | |
| KEGG Report | rno:296188 | UniProtKB/TrEMBL |
| NCBI Gene | 296188 | ENTREZGENE |
| Pfam | Aminotran_1_2 | UniProtKB/TrEMBL |
| PhenoGen | Sptlc3 | PhenoGen |
| PROSITE | AA_TRANSFER_CLASS_2 | UniProtKB/TrEMBL |
| Superfamily-SCOP | PyrdxlP-dep_Trfase_major | UniProtKB/TrEMBL |
| Transposagen | Sptlc3 |
Transposagen |
| UniGene | Rn.218183 | ENTREZGENE |
| UniProt | D4A9V0 | ENTREZGENE, UniProtKB/TrEMBL |
Nomenclature History| Date | Current Symbol | Current Name | Previous Symbol | Previous Name | Description | Reference | Status |
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| 2008-02-27 | Sptlc3 | serine palmitoyltransferase, long chain base subunit 3 | RGD1310030_predicted | similar to RIKEN cDNA C130053K05 gene; similar to dJ718P11.1.1 (novel class II aminotransferase similar to serine palmotyltransferase (isoform 1)) (predicted) | Nomenclature updated to reflect human and mouse nomenclature | 1299863 | APPROVED |
| 2005-01-20 | RGD1310030_predicted | similar to RIKEN cDNA C130053K05 gene; similar to dJ718P11.1.1 (novel class II aminotransferase similar to serine palmotyltransferase (isoform 1)) (predicted) | LOC296188_predicted | Symbol and Name status set to approved | 1331353 | APPROVED | |
| 2005-01-12 | LOC296188_predicted | similar to RIKEN cDNA C130053K05 gene; similar to dJ718P11.1.1 (novel class II aminotransferase similar to serine palmotyltransferase (isoform 1)) (predicted) | Symbol and Name status set to provisional | 70820 | PROVISIONAL |
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| More on Sptlc3 | |
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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: | 1310030 |
| Created: | 2005-01-12 |
| Species: | Rattus norvegicus |
| Last Modified: | 2020-08-20 |
| Status: | ACTIVE |
