 Gene Ontology Annotations | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Cellular Component
Molecular Function
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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 |
 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 |
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Gene Annotator (Annotation Comparison) |
OLGA (Gene List Generator) |
Excel (Download) |
 MOET (Multi-Ontology Enrichement) unavailable |
 GOLF (Gene-Ortholog Location Finder) unavailable |
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MOET (Multi-Ontology Enrichement) |
GOLF (Gene-Ortholog Location Finder) |
Cellular Component
Molecular Function
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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References - curated| 1. | Kalashnikova E, etal., Neuron. 2010 Jan 14;65(1):80-93. doi: 10.1016/j.neuron.2009.12.021. |
| 2. | RGD automated data pipeline |
| 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| Syndig1 (Rattus norvegicus - Norway rat) |
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| SYNDIG1 (Homo sapiens - human) |
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| Syndig1 (Mus musculus - house mouse) |
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| Syndig1 (Chinchilla lanigera - long-tailed chinchilla) |
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| SYNDIG1 (Pan paniscus - bonobo/pygmy chimpanzee) |
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| SYNDIG1 (Canis lupus familiaris - dog) |
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| Syndig1 (Ictidomys tridecemlineatus - thirteen-lined ground squirrel) |
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| SYNDIG1 (Sus scrofa - pig) |
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| SYNDIG1 (Chlorocebus sabaeus - African green monkey) |
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| Syndig1 (Heterocephalus glaber - naked mole-rat) |
No map positions available. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 | exocrine system | hemolymphoid system | hepatobiliary system | integumental system | musculoskeletal system | nervous system | renal system | reproductive system | respiratory system | appendage | |
| High | |||||||||||||
| Medium | 50 | 7 | |||||||||||
| Low | 3 | 43 | 12 | 4 | 8 | 10 | 24 | 28 | 29 | 11 | 8 | ||
| Below cutoff | 23 | 19 | 15 | 19 | 1 | 6 | 5 |
View RNA-SEQ Expression Data
Sequence
Nucleotide Sequences| RefSeq Transcripts | NM_001025020 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles |
| XM_017591912 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| XM_017591913 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| XM_017591914 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| XM_017591915 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| XM_017591916 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| XM_017591917 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| XM_017591918 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| XM_017591919 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| XM_017591920 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| XM_017591921 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| XM_017591922 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| GenBank Nucleotide | AABR07054244 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles |
| AAHX01025750 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| AAHX01025751 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| AAHX01025752 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| AAHX01025753 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| AAHX01025754 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| BC092131 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| CH474026 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| FQ214215 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles |
Reference Sequences
| RefSeq Acc Id: | ENSRNOT00000068210 ⟹ ENSRNOP00000060788 | ||||||||
| RefSeq Status: | |||||||||
| Type: | CODING | ||||||||
| Position: |
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| RefSeq Acc Id: | NM_001025020 ⟹ NP_001020191 | ||||||||||||||||||||
| RefSeq Status: | PROVISIONAL | ||||||||||||||||||||
| Type: | CODING | ||||||||||||||||||||
| Position: |
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| Sequence: |
GCTCCGCGCCCCGCACGCTCCCTGGCTCTCGAGACGCGCGGGCGACAGCCTGGGCGCACCAGCChide sequence |
| RefSeq Acc Id: | XM_017591912 ⟹ XP_017447401 | ||||||||
| RefSeq Status: | |||||||||
| Type: | CODING | ||||||||
| Position: |
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| Sequence: |
CCTAGAGGGTAGCAGTGGCCGGGCCAGGGAGACACAGAGTCGCCCCCGAGAGAGGGGAGATGGChide sequence |
| RefSeq Acc Id: | XM_017591913 ⟹ XP_017447402 | ||||||||
| RefSeq Status: | |||||||||
| Type: | CODING | ||||||||
| Position: |
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| Sequence: |
CCTAGAGGGTAGCAGTGGCCGGGCCAGGGAGACACAGAGTCGCCCCCGAGAGAGGGGAGATGGChide sequence |
| RefSeq Acc Id: | XM_017591914 ⟹ XP_017447403 | ||||||||
| RefSeq Status: | |||||||||
| Type: | CODING | ||||||||
| Position: |
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| Sequence: |
AGCAAGGAAGAAAAGAATCTTTGAGTCATCCAGTAAATTGATCTCTGGTCATCTGAGGAGCAGGhide sequence |
| RefSeq Acc Id: | XM_017591915 ⟹ XP_017447404 | ||||||||
| RefSeq Status: | |||||||||
| Type: | CODING | ||||||||
| Position: |
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| Sequence: |
TGTGTGTGTGTGTGTGTAGATTTTCTTTTCCACTTAGAACTCAATATATTTCCTCTGGTTAATAhide sequence |
| RefSeq Acc Id: | XM_017591916 ⟹ XP_017447405 | ||||||||
| RefSeq Status: | |||||||||
| Type: | CODING | ||||||||
| Position: |
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| Sequence: |
GGAGGATGCCCTGGCGCAGGCGGGCGTCCTGCTCCGCCTCGCAGCGCGCAGACCAGGCGGCGGThide sequence |
| RefSeq Acc Id: | XM_017591917 ⟹ XP_017447406 | ||||||||
| RefSeq Status: | |||||||||
| Type: | CODING | ||||||||
| Position: |
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| Sequence: |
CCTAGAGGGTAGCAGTGGCCGGGCCAGGGAGACACAGAGTCGCCCCCGAGAGAGGGGAGATGGChide sequence |
| RefSeq Acc Id: | XM_017591918 ⟹ XP_017447407 | ||||||||
| RefSeq Status: | |||||||||
| Type: | CODING | ||||||||
| Position: |
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| Sequence: |
CAGTTTCCTTCCAACAGCAACTACCATGGGGCCACCCGCAGTGCACCTGCGCTGGTGTTGGCCThide sequence |
| RefSeq Acc Id: | XM_017591919 ⟹ XP_017447408 | ||||||||
| RefSeq Status: | |||||||||
| Type: | CODING | ||||||||
| Position: |
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| Sequence: |
CCTAGAGGGTAGCAGTGGCCGGGCCAGGGAGACACAGAGTCGCCCCCGAGAGAGGGGAGATGGChide sequence |
| RefSeq Acc Id: | XM_017591920 ⟹ XP_017447409 | ||||||||
| RefSeq Status: | |||||||||
| Type: | CODING | ||||||||
| Position: |
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| Sequence: |
CCTAGAGGGTAGCAGTGGCCGGGCCAGGGAGACACAGAGTCGCCCCCGAGAGAGGGGAGATGGChide sequence |
| RefSeq Acc Id: | XM_017591921 ⟹ XP_017447410 | ||||||||
| RefSeq Status: | |||||||||
| Type: | CODING | ||||||||
| Position: |
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| Sequence: |
CCTAGAGGGTAGCAGTGGCCGGGCCAGGGAGACACAGAGTCGCCCCCGAGAGAGGGGAGATGGChide sequence |
| RefSeq Acc Id: | XM_017591922 ⟹ XP_017447411 | ||||||||
| RefSeq Status: | |||||||||
| Type: | CODING | ||||||||
| Position: |
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| Sequence: |
GGAGGATGCCCTGGCGCAGGCGGGCGTCCTGCTCCGCCTCGCAGCGCGCAGACCAGGCGGCGGThide sequence |
Protein Sequences| Protein RefSeqs | NP_001020191 | (Get FASTA) | NCBI Sequence Viewer |
| XP_017447401 | (Get FASTA) | NCBI Sequence Viewer | |
| XP_017447402 | (Get FASTA) | NCBI Sequence Viewer | |
| XP_017447403 | (Get FASTA) | NCBI Sequence Viewer | |
| XP_017447404 | (Get FASTA) | NCBI Sequence Viewer | |
| XP_017447405 | (Get FASTA) | NCBI Sequence Viewer | |
| XP_017447406 | (Get FASTA) | NCBI Sequence Viewer | |
| XP_017447407 | (Get FASTA) | NCBI Sequence Viewer | |
| XP_017447408 | (Get FASTA) | NCBI Sequence Viewer | |
| XP_017447409 | (Get FASTA) | NCBI Sequence Viewer | |
| XP_017447410 | (Get FASTA) | NCBI Sequence Viewer | |
| XP_017447411 | (Get FASTA) | NCBI Sequence Viewer | |
| GenBank Protein | AAH92131 | (Get FASTA) | NCBI Sequence Viewer |
| EDL95059 | (Get FASTA) | NCBI Sequence Viewer | |
| Q58DZ9 | (Get FASTA) | NCBI Sequence Viewer |
Reference Sequences
| RefSeq Acc Id: | NP_001020191 ⟸ NM_001025020 |
| - UniProtKB: | Q58DZ9 (UniProtKB/Swiss-Prot) |
| - Sequence: |
MDGIVEQKSVLVHSKIGDAGKRNGLINTRNFMAESRDGLVSVYPAPQYQSHRLVASAAPGSLEGhide sequence |
| RefSeq Acc Id: | XP_017447407 ⟸ XM_017591918 |
| - Peptide Label: | isoform X1 |
| - UniProtKB: | Q58DZ9 (UniProtKB/Swiss-Prot) |
| - Sequence: |
MDGIVEQKSVLVHSKIGDAGKRNGLINTRNFMAESRDGLVSVYPAPQYQSHRLVASAAPGSLEGhide sequence |
| RefSeq Acc Id: | XP_017447405 ⟸ XM_017591916 |
| - Peptide Label: | isoform X1 |
| - UniProtKB: | Q58DZ9 (UniProtKB/Swiss-Prot) |
| - Sequence: |
MDGIVEQKSVLVHSKIGDAGKRNGLINTRNFMAESRDGLVSVYPAPQYQSHRLVASAAPGSLEGhide sequence |
| RefSeq Acc Id: | XP_017447411 ⟸ XM_017591922 |
| - Peptide Label: | isoform X1 |
| - UniProtKB: | Q58DZ9 (UniProtKB/Swiss-Prot) |
| - Sequence: |
MDGIVEQKSVLVHSKIGDAGKRNGLINTRNFMAESRDGLVSVYPAPQYQSHRLVASAAPGSLEGhide sequence |
| RefSeq Acc Id: | XP_017447401 ⟸ XM_017591912 |
| - Peptide Label: | isoform X1 |
| - UniProtKB: | Q58DZ9 (UniProtKB/Swiss-Prot) |
| - Sequence: |
MDGIVEQKSVLVHSKIGDAGKRNGLINTRNFMAESRDGLVSVYPAPQYQSHRLVASAAPGSLEGhide sequence |
| RefSeq Acc Id: | XP_017447408 ⟸ XM_017591919 |
| - Peptide Label: | isoform X1 |
| - UniProtKB: | Q58DZ9 (UniProtKB/Swiss-Prot) |
| - Sequence: |
MDGIVEQKSVLVHSKIGDAGKRNGLINTRNFMAESRDGLVSVYPAPQYQSHRLVASAAPGSLEGhide sequence |
| RefSeq Acc Id: | XP_017447410 ⟸ XM_017591921 |
| - Peptide Label: | isoform X1 |
| - UniProtKB: | Q58DZ9 (UniProtKB/Swiss-Prot) |
| - Sequence: |
MDGIVEQKSVLVHSKIGDAGKRNGLINTRNFMAESRDGLVSVYPAPQYQSHRLVASAAPGSLEGhide sequence |
| RefSeq Acc Id: | XP_017447402 ⟸ XM_017591913 |
| - Peptide Label: | isoform X1 |
| - UniProtKB: | Q58DZ9 (UniProtKB/Swiss-Prot) |
| - Sequence: |
MDGIVEQKSVLVHSKIGDAGKRNGLINTRNFMAESRDGLVSVYPAPQYQSHRLVASAAPGSLEGhide sequence |
| RefSeq Acc Id: | XP_017447409 ⟸ XM_017591920 |
| - Peptide Label: | isoform X1 |
| - UniProtKB: | Q58DZ9 (UniProtKB/Swiss-Prot) |
| - Sequence: |
MDGIVEQKSVLVHSKIGDAGKRNGLINTRNFMAESRDGLVSVYPAPQYQSHRLVASAAPGSLEGhide sequence |
| RefSeq Acc Id: | XP_017447406 ⟸ XM_017591917 |
| - Peptide Label: | isoform X1 |
| - UniProtKB: | Q58DZ9 (UniProtKB/Swiss-Prot) |
| - Sequence: |
MDGIVEQKSVLVHSKIGDAGKRNGLINTRNFMAESRDGLVSVYPAPQYQSHRLVASAAPGSLEGhide sequence |
| RefSeq Acc Id: | XP_017447404 ⟸ XM_017591915 |
| - Peptide Label: | isoform X1 |
| - UniProtKB: | Q58DZ9 (UniProtKB/Swiss-Prot) |
| - Sequence: |
MDGIVEQKSVLVHSKIGDAGKRNGLINTRNFMAESRDGLVSVYPAPQYQSHRLVASAAPGSLEGhide sequence |
| RefSeq Acc Id: | XP_017447403 ⟸ XM_017591914 |
| - Peptide Label: | isoform X1 |
| - UniProtKB: | Q58DZ9 (UniProtKB/Swiss-Prot) |
| - Sequence: |
MDGIVEQKSVLVHSKIGDAGKRNGLINTRNFMAESRDGLVSVYPAPQYQSHRLVASAAPGSLEGhide sequence |
| RefSeq Acc Id: | ENSRNOP00000060788 ⟸ ENSRNOT00000068210 |
TranscriptomePromoters| RGD ID: | 13692512 | ||||||||
| Promoter ID: | EPDNEW_R3037 | ||||||||
| Type: | initiation region | ||||||||
| Name: | Syndig1_1 | ||||||||
| Description: | synapse differentiation inducing 1 | ||||||||
| 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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Additional Information
External Database Links| Database | Acc Id | Source(s) |
| AGR Gene | RGD:1310753 | AgrOrtholog |
| Ensembl Genes | ENSRNOG00000031536 | Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot |
| Ensembl Protein | ENSRNOP00000060788 | ENTREZGENE, UniProtKB/Swiss-Prot |
| Ensembl Transcript | ENSRNOT00000068210 | ENTREZGENE, UniProtKB/Swiss-Prot |
| IMAGE_CLONE | IMAGE:7312153 | IMAGE-MGC_LOAD |
| InterPro | CD225/Dispanin_fam | UniProtKB/Swiss-Prot |
| KEGG Report | rno:362235 | UniProtKB/Swiss-Prot |
| MGC_CLONE | MGC:105581 | IMAGE-MGC_LOAD |
| NCBI Gene | 362235 | ENTREZGENE |
| Pfam | CD225 | UniProtKB/Swiss-Prot |
| PhenoGen | Syndig1 | PhenoGen |
| Transposagen | RGD1310753 |
Transposagen |
| UniGene | Rn.162709 | ENTREZGENE |
| UniProt | Q58DZ9 | ENTREZGENE, UniProtKB/Swiss-Prot |
Nomenclature History| Date | Current Symbol | Current Name | Previous Symbol | Previous Name | Description | Reference | Status |
|---|---|---|---|---|---|---|---|
| 2005-12-06 | RGD1310753 | similar to chromosome 20 open reading frame 39 | RGD1310753_predicted | similar to chromosome 20 open reading frame 39 (predicted) | Symbol and Name updated | 1559027 | APPROVED |
| 2005-01-20 | RGD1310753_predicted | similar to chromosome 20 open reading frame 39 (predicted) | LOC362235_predicted | Symbol and Name status set to approved | 1331353 | APPROVED | |
| 2005-01-12 | LOC362235_predicted | similar to chromosome 20 open reading frame 39 (predicted) | Symbol and Name status set to provisional | 70820 | PROVISIONAL |
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| More on Syndig1 | |
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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: | 1310753 |
| Created: | 2005-01-12 |
| Species: | Rattus norvegicus |
| Last Modified: | 2020-03-04 |
| Status: | ACTIVE |
