Mir3564 (microRNA 3564) - 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: Mir3564 (microRNA 3564) Rattus norvegicus
Analyze
Symbol: Mir3564
Name: microRNA 3564
RGD ID: 4888596
Description: INTERACTS WITH bisphenol A; chlorpyrifos
Type: ncrna (Ensembl: miRNA)
RefSeq Status: PROVISIONAL
Previously known as: rno-mir-3564
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81966,782,208 - 66,782,319 (+)NCBIGRCr8
mRatBN7.21949,873,603 - 49,873,714 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1949,873,603 - 49,873,714 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1956,666,067 - 56,666,178 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01957,348,545 - 57,348,656 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01959,564,615 - 59,564,726 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01954,632,008 - 54,632,119 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1954,632,008 - 54,632,119 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01965,346,120 - 65,346,231 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera1949,118,809 - 49,118,920 (+)NCBICelera
Cytogenetic Map19q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
References
Additional References at PubMed
PMID:16381832   PMID:20403161  


Genomics

miRNA Target Status

Predicted Targets
Summary Value
Count of predictions:9120
Count of gene targets:5443
Count of transcripts:5813
Interacting mature miRNAs:rno-miR-3564
Prediction methods:Microtar, Miranda, Pita, Rnahybrid, Targetscan
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
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19218792756457239Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19409615555283277Rat
7411549Bw130Body weight QTL 13050.001body mass (VT:0001259)body weight gain (CMO:0000420)191545586057337602Rat
1578764Stresp19Stress response QTL 193.60.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)191563020157337602Rat
2298478Eau8Experimental allergic uveoretinitis QTL 80.0163uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)191715443357337602Rat
61350Bp32Blood pressure QTL 320.012arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)192048357557337602Rat
724546Kidm3Kidney mass QTL 33.1kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)192932249057337602Rat
1358200Insglur2Insulin/glucose ratio QTL 24.1blood glucose amount (VT:0000188)serum insulin level (CMO:0000358)193383821455283146Rat
1358200Insglur2Insulin/glucose ratio QTL 24.1blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)193383821455283146Rat
5135224Leukc1Leukocyte quantity QTL 1eosinophil quantity (VT:0002602)blood eosinophil count (CMO:0000033)194434021455283277Rat


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 integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium
Low 2 3 16 17 2 2 8 8 8 9 2
Below cutoff 1 2 1 1 1 1 2 1 1 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000072413
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1949,873,603 - 49,873,714 (+)Ensembl
Rnor_6.0 Ensembl1954,632,008 - 54,632,119 (+)Ensembl
RefSeq Acc Id: NR_037347
RefSeq Status: PROVISIONAL
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81966,782,208 - 66,782,319 (+)NCBI
mRatBN7.21949,873,603 - 49,873,714 (+)NCBI
Rnor_6.01954,632,008 - 54,632,119 (+)NCBI
Rnor_5.01965,346,120 - 65,346,231 (+)NCBI
Celera1949,118,809 - 49,118,920 (+)NCBI
Sequence:
Transcriptome

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


Additional Information

Database Acc Id Source(s)
BioCyc Gene G2FUF-5415 BioCyc
Ensembl Genes ENSRNOG00000046739 Ensembl, ENTREZGENE
Ensembl Transcript ENSRNOT00000072413 ENTREZGENE
miRBase MI0015427 ENTREZGENE
NCBI Gene 100526579 ENTREZGENE
PhenoGen Mir3564 PhenoGen
RatGTEx ENSRNOG00000046739 RatGTEx
RNAcentral URS000075C16E RNACentral
  URS000075E46A RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-04-09 Mir3564  microRNA 3564  Mir3564  microRNA mir-3564  Name updated 61478 APPROVED
2010-11-23 Mir3564  microRNA mir-3564      Symbol and Name status set to provisional 70820 PROVISIONAL