Jph3 (junctophilin 3) - 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: Jph3 (junctophilin 3) Rattus norvegicus
Analyze
Symbol: Jph3
Name: junctophilin 3
RGD ID: 1308416
Description: Predicted to be involved in exploration behavior; memory; and regulation of synaptic plasticity. Predicted to act upstream of or within several processes, including learning; neuromuscular process controlling balance; and regulation of neuronal synaptic plasticity. Predicted to be located in endoplasmic reticulum. Predicted to be part of junctional membrane complex. Predicted to be active in endoplasmic reticulum membrane and plasma membrane. Human ortholog(s) of this gene implicated in Huntington's disease-like 2. Orthologous to human JPH3 (junctophilin 3); INTERACTS WITH 1-naphthyl isothiocyanate; 17beta-estradiol 3-benzoate; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: junctophilin-3; LOC307916
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81966,702,497 - 66,763,948 (+)NCBIGRCr8
mRatBN7.21949,793,967 - 49,855,338 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1949,793,092 - 49,855,338 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1956,586,342 - 56,647,708 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01957,269,286 - 57,330,287 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01959,484,882 - 59,546,252 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01954,553,419 - 54,613,477 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1954,553,419 - 54,613,477 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01965,267,451 - 65,327,679 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41951,975,477 - 52,037,634 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11951,963,537 - 52,041,163 (+)NCBI
Celera1949,040,036 - 49,100,583 (+)NCBICelera
Cytogenetic Map19q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
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. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. Homer1a is a core brain molecular correlate of sleep loss. Maret S, etal., Proc Natl Acad Sci U S A. 2007 Dec 11;104(50):20090-5. Epub 2007 Dec 6.
4. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
5. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
6. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
7. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:11906164   PMID:16809425   PMID:17347645  


Genomics

Comparative Map Data
Jph3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81966,702,497 - 66,763,948 (+)NCBIGRCr8
mRatBN7.21949,793,967 - 49,855,338 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1949,793,092 - 49,855,338 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1956,586,342 - 56,647,708 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01957,269,286 - 57,330,287 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01959,484,882 - 59,546,252 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01954,553,419 - 54,613,477 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1954,553,419 - 54,613,477 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01965,267,451 - 65,327,679 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41951,975,477 - 52,037,634 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11951,963,537 - 52,041,163 (+)NCBI
Celera1949,040,036 - 49,100,583 (+)NCBICelera
Cytogenetic Map19q12NCBI
JPH3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381687,601,835 - 87,698,156 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1687,601,835 - 87,698,156 (+)EnsemblGRCh38hg38GRCh38
GRCh371687,635,441 - 87,731,762 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361686,194,000 - 86,289,263 (+)NCBINCBI36Build 36hg18NCBI36
Build 341686,193,999 - 86,289,263NCBI
Celera1671,933,529 - 72,028,806 (+)NCBICelera
Cytogenetic Map16q24.2NCBI
HuRef1673,376,273 - 73,472,834 (+)NCBIHuRef
CHM1_11689,047,216 - 89,143,211 (+)NCBICHM1_1
T2T-CHM13v2.01693,673,276 - 93,769,801 (+)NCBIT2T-CHM13v2.0
Jph3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm398122,457,298 - 122,517,822 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl8122,456,362 - 122,521,015 (+)EnsemblGRCm39 Ensembl
GRCm388121,730,559 - 121,791,083 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl8121,729,623 - 121,794,276 (+)EnsemblGRCm38mm10GRCm38
MGSCv378124,254,463 - 124,314,721 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv368124,616,653 - 124,676,911 (+)NCBIMGSCv36mm8
Celera8125,951,307 - 126,011,917 (+)NCBICelera
Cytogenetic Map8E1NCBI
cM Map870.73NCBI
Jph3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555411,969,194 - 2,017,588 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555411,969,197 - 2,020,868 (+)NCBIChiLan1.0ChiLan1.0
JPH3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21897,363,464 - 97,469,048 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan116103,279,757 - 103,383,259 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01668,276,459 - 68,379,909 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11687,596,820 - 87,698,034 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1687,596,814 - 87,700,235 (+)Ensemblpanpan1.1panPan2
JPH3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1565,445,329 - 65,530,288 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl565,451,050 - 65,530,294 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha565,461,589 - 65,542,450 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0565,671,280 - 65,752,276 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl565,666,918 - 65,751,998 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1565,696,410 - 65,777,258 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0565,528,138 - 65,609,065 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0565,935,516 - 66,022,935 (-)NCBIUU_Cfam_GSD_1.0
Jph3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934925,866,093 - 25,914,934 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366411,620,652 - 1,668,486 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366411,619,640 - 1,668,480 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
JPH3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.161,677,132 - 1,767,010 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.261,765,733 - 1,855,707 (-)NCBISscrofa10.2Sscrofa10.2susScr3
JPH3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1572,972,373 - 73,095,710 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl572,972,361 - 73,094,231 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660472,615,479 - 2,721,312 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Jph3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247463,193,687 - 3,242,444 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247463,193,695 - 3,243,916 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Jph3
327 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:236
Count of miRNA genes:141
Interacting mature miRNAs:192
Transcripts:ENSRNOT00000025392
Prediction methods:Miranda, 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

Markers in Region
D19Got112  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21949,851,618 - 49,851,746 (+)MAPPERmRatBN7.2
Rnor_6.01954,609,758 - 54,609,885NCBIRnor6.0
Rnor_5.01965,323,960 - 65,324,087UniSTSRnor5.0
RGSC_v3.41952,033,915 - 52,034,042UniSTSRGSC3.4
Celera1949,096,864 - 49,096,991UniSTS
Cytogenetic Map19q12UniSTS
BF392976  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21949,821,734 - 49,821,900 (+)MAPPERmRatBN7.2
Rnor_6.01954,580,946 - 54,581,111NCBIRnor6.0
Rnor_5.01965,294,978 - 65,295,143UniSTSRnor5.0
RGSC_v3.41952,002,814 - 52,002,979UniSTSRGSC3.4
Celera1949,067,017 - 49,067,182UniSTS
RH 3.4 Map19682.8UniSTS
Cytogenetic Map19q12UniSTS


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 64
Low 3 14 4 14 4 10 6 36 6
Below cutoff 35 40 34 5 34 8 11 24 5 5 8

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000025392   ⟹   ENSRNOP00000025392
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1949,793,092 - 49,855,338 (+)Ensembl
Rnor_6.0 Ensembl1954,553,419 - 54,613,477 (+)Ensembl
RefSeq Acc Id: NM_001107437   ⟹   NP_001100907
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81966,702,943 - 66,763,948 (+)NCBI
mRatBN7.21949,794,323 - 49,855,338 (+)NCBI
Rnor_6.01954,553,419 - 54,613,477 (+)NCBI
Rnor_5.01965,267,451 - 65,327,679 (+)NCBI
RGSC_v3.41951,975,477 - 52,037,634 (+)RGD
Celera1949,040,036 - 49,100,583 (+)RGD
Sequence:
RefSeq Acc Id: XM_039097780   ⟹   XP_038953708
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81966,702,497 - 66,754,615 (+)NCBI
mRatBN7.21949,793,967 - 49,846,002 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001100907 (Get FASTA)   NCBI Sequence Viewer  
  XP_038953708 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL92729 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000025392
  ENSRNOP00000025392.4
Reference Protein Sequences
RefSeq Acc Id: NP_001100907   ⟸   NM_001107437
- UniProtKB: D3ZWH2 (UniProtKB/TrEMBL),   A6IZQ1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000025392   ⟸   ENSRNOT00000025392
RefSeq Acc Id: XP_038953708   ⟸   XM_039097780
- Peptide Label: isoform X1

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZWH2-F1-model_v2 AlphaFold D3ZWH2 1-749 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:1308416 AgrOrtholog
BioCyc Gene G2FUF-5418 BioCyc
Ensembl Genes ENSRNOG00000018784 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000025392 ENTREZGENE
  ENSRNOT00000025392.6 UniProtKB/TrEMBL
Gene3D-CATH Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain UniProtKB/TrEMBL
InterPro Junctophilin UniProtKB/TrEMBL
  MORN UniProtKB/TrEMBL
KEGG Report rno:307916 UniProtKB/TrEMBL
NCBI Gene 307916 ENTREZGENE
PANTHER JUNCTOPHILIN-3 UniProtKB/TrEMBL
  PTHR23085 UniProtKB/TrEMBL
Pfam MORN UniProtKB/TrEMBL
PhenoGen Jph3 PhenoGen
PIRSF Junctophilin UniProtKB/TrEMBL
RatGTEx ENSRNOG00000018784 RatGTEx
SMART MORN UniProtKB/TrEMBL
Superfamily-SCOP Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain UniProtKB/TrEMBL
UniProt A6IZQ1 ENTREZGENE, UniProtKB/TrEMBL
  D3ZWH2 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Jph3  junctophilin 3   Jph3_predicted  junctophilin 3 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Jph3_predicted  junctophilin 3 (predicted)      Symbol and Name status set to approved 70820 APPROVED