LOC103690878 (syntaxin-3-like) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models   new Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Gene: LOC103690878 (syntaxin-3-like) Rattus norvegicus
Analyze
No known orthologs.
Symbol: LOC103690878
Name: syntaxin-3-like
RGD ID: 9098358
Description: Predicted to enable SNAP receptor activity and SNARE binding activity. Predicted to be involved in intracellular protein transport; synaptic vesicle fusion to presynaptic active zone membrane; and vesicle docking. Predicted to be part of SNARE complex. Predicted to be active in presynaptic active zone membrane and synaptic vesicle.
Type: protein-coding
RefSeq Status: MODEL
Previously known as: LOC302365; RGD1564704; similar to syntaxin 3A
RGD Orthologs
Alliance Genes
More Info homologs ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X77,770,801 - 77,771,694 (-)NCBIGRCr8
mRatBN7.2X73,695,215 - 73,696,108 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX73,695,215 - 73,696,108 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.0X79,742,224 - 79,743,117 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX79,742,224 - 79,743,117 (-)EnsemblRnor6.0rn6Rnor6.0
RGSC_v3.4X96,922,170 - 96,923,063 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX74,973,921 - 74,974,814 (-)NCBICelera
Cytogenetic MapXq22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Variants

.
Variants in LOC103690878
2 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:10
Count of miRNA genes:10
Interacting mature miRNAs:10
Transcripts:ENSRNOT00000044808
Prediction methods:Miranda, Rnahybrid
Result types:miRGate_prediction

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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X14843113120568734Rat
1598837Memor13Memory QTL 133.2exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X41052407146860749Rat
738035Stresp1Stress response QTL 14.960.000011stress-related behavior trait (VT:0010451)defensive burying - copingX41304447112935181Rat
61431Cia19Collagen induced arthritis QTL 194.4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X65612192120568734Rat


Expression


RNA-SEQ Expression
High: > 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 nervous system reproductive system respiratory system
High
Medium 2 2 2
Low 3 14 14 14
Below cutoff 1 19 17 2 17 3 4 5

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000044808   ⟹   ENSRNOP00000051292
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX73,695,215 - 73,696,108 (-)Ensembl
Rnor_6.0 EnsemblX79,742,224 - 79,743,117 (-)Ensembl
RefSeq Acc Id: XM_008773369   ⟹   XP_008771591
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X77,770,801 - 77,771,694 (-)NCBI
mRatBN7.2X73,695,215 - 73,696,108 (-)NCBI
Rnor_6.0X79,742,224 - 79,743,117 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs XP_008771591 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000051292
  ENSRNOP00000051292.4
Reference Protein Sequences
RefSeq Acc Id: XP_008771591   ⟸   XM_008773369
- UniProtKB: D3ZUH2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000051292   ⟸   ENSRNOT00000044808
Protein Domains
t-SNARE coiled-coil homology

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZUH2-F1-model_v2 AlphaFold D3ZUH2 1-297 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:9098358 AgrOrtholog
BioCyc Gene G2FUF-1881 BioCyc
Ensembl Genes ENSRNOG00000031283 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000044808 ENTREZGENE
  ENSRNOT00000044808.5 UniProtKB/TrEMBL
Gene3D-CATH 1.20.5.110 UniProtKB/TrEMBL
  1.20.58.70 UniProtKB/TrEMBL
InterPro Syntaxin UniProtKB/TrEMBL
  Syntaxin/epimorphin_CS UniProtKB/TrEMBL
  Syntaxin_N UniProtKB/TrEMBL
  t-SNARE UniProtKB/TrEMBL
  T_SNARE_dom UniProtKB/TrEMBL
KEGG Report rno:103690878 UniProtKB/TrEMBL
NCBI Gene LOC103690878 ENTREZGENE
PANTHER PTHR19957 UniProtKB/TrEMBL
  SYNTAXIN-3-LIKE UniProtKB/TrEMBL
Pfam SNARE UniProtKB/TrEMBL
  Syntaxin UniProtKB/TrEMBL
PhenoGen LOC103690878 PhenoGen
PROSITE SYNTAXIN UniProtKB/TrEMBL
  T_SNARE UniProtKB/TrEMBL
RatGTEx ENSRNOG00000031283 RatGTEx
SMART t_SNARE UniProtKB/TrEMBL
Superfamily-SCOP t-snare UniProtKB/TrEMBL
UniProt D3ZUH2 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-07-29 LOC103690878  syntaxin-3-like  RGD1564704  similar to syntaxin 3A  Data merged from RGD:1564704 737654 PROVISIONAL
2014-08-25 LOC103690878  syntaxin-3-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-04-30 RGD1564704  similar to syntaxin 3A   RGD1564704_predicted  similar to syntaxin 3A (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-07 RGD1564704_predicted  similar to syntaxin 3A (predicted)  LOC302365  similar to syntaxin 3A  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC302365  similar to syntaxin 3A      Symbol and Name status set to provisional 70820 PROVISIONAL