Jph1 (junctophilin 1) - Rat Genome Database

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Gene: Jph1 (junctophilin 1) Rattus norvegicus
Analyze
Symbol: Jph1
Name: junctophilin 1
RGD ID: 1308789
Description: Predicted to be a structural constituent of muscle. Predicted to act upstream of or within muscle organ development. Predicted to be located in Z disc; junctional sarcoplasmic reticulum membrane; and nucleoplasm. Predicted to be part of junctional membrane complex. Predicted to be active in endoplasmic reticulum membrane; plasma membrane; and sarcoplasmic reticulum. Human ortholog(s) of this gene implicated in Charcot-Marie-Tooth disease axonal type 2K. Orthologous to human JPH1 (junctophilin 1); INTERACTS WITH 2,6-dinitrotoluene; 6-propyl-2-thiouracil; aconitine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: junctophilin-1; LOC297748
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
GRCr856,813,553 - 6,920,488 (+)NCBIGRCr8
mRatBN7.252,030,227 - 2,137,171 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl52,030,281 - 2,125,284 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx54,146,657 - 4,241,653 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.055,785,523 - 5,880,520 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.055,473,359 - 5,568,364 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.051,417,414 - 1,511,754 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl51,417,478 - 1,511,416 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.051,413,646 - 1,507,659 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.451,110,289 - 1,207,092 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.151,110,442 - 1,204,716 (+)NCBI
Celera51,665,186 - 1,760,181 (+)NCBICelera
Cytogenetic Map5q11NCBI
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. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
5. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:10949023   PMID:12135771   PMID:12729900   PMID:22206666   PMID:22927069   PMID:23148318   PMID:31315980  


Genomics

Comparative Map Data
Jph1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr856,813,553 - 6,920,488 (+)NCBIGRCr8
mRatBN7.252,030,227 - 2,137,171 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl52,030,281 - 2,125,284 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx54,146,657 - 4,241,653 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.055,785,523 - 5,880,520 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.055,473,359 - 5,568,364 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.051,417,414 - 1,511,754 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl51,417,478 - 1,511,416 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.051,413,646 - 1,507,659 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.451,110,289 - 1,207,092 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.151,110,442 - 1,204,716 (+)NCBI
Celera51,665,186 - 1,760,181 (+)NCBICelera
Cytogenetic Map5q11NCBI
JPH1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38874,234,700 - 74,321,540 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl874,234,700 - 74,321,540 (-)EnsemblGRCh38hg38GRCh38
GRCh37875,146,935 - 75,233,775 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36875,309,493 - 75,396,117 (-)NCBINCBI36Build 36hg18NCBI36
Build 34875,311,996 - 75,396,117NCBI
Celera871,144,786 - 71,231,414 (-)NCBICelera
Cytogenetic Map8q21.11NCBI
HuRef870,637,846 - 70,724,493 (-)NCBIHuRef
CHM1_1875,198,909 - 75,285,541 (-)NCBICHM1_1
T2T-CHM13v2.0874,663,960 - 74,750,834 (-)NCBIT2T-CHM13v2.0
Jph1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39117,012,328 - 17,168,132 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl117,034,784 - 17,168,113 (-)EnsemblGRCm39 Ensembl
GRCm38116,942,104 - 17,097,922 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl116,964,560 - 17,097,889 (-)EnsemblGRCm38mm10GRCm38
MGSCv37116,987,545 - 17,087,879 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36116,982,678 - 17,083,012 (-)NCBIMGSCv36mm8
Celera116,921,250 - 17,021,597 (-)NCBICelera
Cytogenetic Map1A3NCBI
cM Map15.17NCBI
Jph1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554446,108,312 - 6,176,814 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554446,108,312 - 6,176,430 (+)NCBIChiLan1.0ChiLan1.0
JPH1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2789,977,880 - 90,064,163 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1865,605,684 - 65,691,948 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0870,768,560 - 70,855,068 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1872,413,794 - 72,500,252 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl872,413,794 - 72,505,309 (-)Ensemblpanpan1.1panPan2
JPH1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12922,701,531 - 22,785,712 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2922,703,647 - 22,785,415 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2922,966,671 - 23,050,394 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02922,813,226 - 22,897,018 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2922,815,346 - 22,897,353 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12922,872,083 - 22,956,225 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02922,907,073 - 22,990,897 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02923,190,302 - 23,274,157 (-)NCBIUU_Cfam_GSD_1.0
Jph1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440530356,492,214 - 56,580,189 (+)NCBIHiC_Itri_2
SpeTri2.0NW_0049366482,868,419 - 2,956,370 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
JPH1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl461,628,299 - 61,716,544 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1461,628,304 - 61,716,550 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2467,369,034 - 67,423,314 (+)NCBISscrofa10.2Sscrofa10.2susScr3
JPH1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1869,839,696 - 69,919,915 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl869,839,460 - 69,919,950 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603971,452,965 - 71,533,094 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Jph1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474416,937,092 - 17,013,862 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474416,937,138 - 17,013,765 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Jph1
276 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:23
Count of miRNA genes:22
Interacting mature miRNAs:23
Transcripts:ENSRNOT00000008153
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
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)51131345958Rat
1331756Rf34Renal function QTL 344.16275kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5190450412Rat
1331771Rf35Renal function QTL 354.36965kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)572947086724018Rat


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
9 11 49 113 78 77 46 24 46 6 204 96 93 45 58 31

Sequence


Ensembl Acc Id: ENSRNOT00000008153   ⟹   ENSRNOP00000008153
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl52,030,281 - 2,125,284 (+)Ensembl
Rnor_6.0 Ensembl51,417,478 - 1,511,416 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000085564   ⟹   ENSRNOP00000075672
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl51,417,505 - 1,509,052 (+)Ensembl
RefSeq Acc Id: NM_001106630   ⟹   NP_001100100
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr856,813,603 - 6,908,601 (+)NCBI
mRatBN7.252,030,281 - 2,125,284 (+)NCBI
Rnor_6.051,417,478 - 1,511,416 (+)NCBI
Rnor_5.051,413,646 - 1,507,659 (+)NCBI
RGSC_v3.451,110,289 - 1,207,092 (+)RGD
Celera51,665,186 - 1,760,181 (+)RGD
Sequence:
RefSeq Acc Id: XM_006237719   ⟹   XP_006237781
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr856,813,553 - 6,906,241 (+)NCBI
mRatBN7.252,030,227 - 2,122,924 (+)NCBI
Rnor_6.051,417,414 - 1,509,056 (+)NCBI
Rnor_5.051,413,646 - 1,507,659 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006237720   ⟹   XP_006237782
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr856,813,553 - 6,906,241 (+)NCBI
mRatBN7.252,030,227 - 2,122,924 (+)NCBI
Rnor_6.051,417,414 - 1,509,056 (+)NCBI
Rnor_5.051,413,646 - 1,507,659 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006237721   ⟹   XP_006237783
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr856,813,553 - 6,906,241 (+)NCBI
mRatBN7.252,030,227 - 2,122,924 (+)NCBI
Rnor_6.051,417,414 - 1,509,056 (+)NCBI
Rnor_5.051,413,646 - 1,507,659 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006237722   ⟹   XP_006237784
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr856,813,553 - 6,906,241 (+)NCBI
mRatBN7.252,030,227 - 2,122,924 (+)NCBI
Rnor_6.051,417,414 - 1,509,056 (+)NCBI
Rnor_5.051,413,646 - 1,507,659 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006237723   ⟹   XP_006237785
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr856,813,553 - 6,920,488 (+)NCBI
mRatBN7.252,030,227 - 2,127,319 (+)NCBI
Rnor_6.051,417,414 - 1,511,754 (+)NCBI
Rnor_5.051,413,646 - 1,507,659 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039109388   ⟹   XP_038965316
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr856,813,553 - 6,906,241 (+)NCBI
mRatBN7.252,030,227 - 2,122,924 (+)NCBI
RefSeq Acc Id: NP_001100100   ⟸   NM_001106630
- UniProtKB: D3ZQ55 (UniProtKB/TrEMBL),   A6JF93 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006237785   ⟸   XM_006237723
- Peptide Label: isoform X1
- UniProtKB: D3ZQ55 (UniProtKB/TrEMBL),   A6JF93 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006237781   ⟸   XM_006237719
- Peptide Label: isoform X1
- UniProtKB: D3ZQ55 (UniProtKB/TrEMBL),   A6JF93 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006237783   ⟸   XM_006237721
- Peptide Label: isoform X1
- UniProtKB: D3ZQ55 (UniProtKB/TrEMBL),   A6JF93 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006237782   ⟸   XM_006237720
- Peptide Label: isoform X1
- UniProtKB: D3ZQ55 (UniProtKB/TrEMBL),   A6JF93 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006237784   ⟸   XM_006237722
- Peptide Label: isoform X1
- UniProtKB: D3ZQ55 (UniProtKB/TrEMBL),   A6JF93 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000008153   ⟸   ENSRNOT00000008153
Ensembl Acc Id: ENSRNOP00000075672   ⟸   ENSRNOT00000085564
RefSeq Acc Id: XP_038965316   ⟸   XM_039109388
- Peptide Label: isoform X1
- UniProtKB: D3ZQ55 (UniProtKB/TrEMBL),   A6JF93 (UniProtKB/TrEMBL)

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZQ55-F1-model_v2 AlphaFold D3ZQ55 1-660 view protein structure

Transcriptome

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

Promoters
RGD ID:13693521
Promoter ID:EPDNEW_R4045
Type:single initiation site
Name:Jph1_1
Description:junctophilin 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.051,417,434 - 1,417,494EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1308789 AgrOrtholog
BioCyc Gene G2FUF-42323 BioCyc
Ensembl Genes ENSRNOG00000006110 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000008153.6 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:297748 UniProtKB/TrEMBL
NCBI Gene 297748 ENTREZGENE
PANTHER JUNCTOPHILIN-1 UniProtKB/TrEMBL
  PTHR23085 UniProtKB/TrEMBL
Pfam MORN UniProtKB/TrEMBL
PhenoGen Jph1 PhenoGen
PIRSF Junctophilin UniProtKB/TrEMBL
RatGTEx ENSRNOG00000006110 RatGTEx
SMART MORN UniProtKB/TrEMBL
Superfamily-SCOP Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain UniProtKB/TrEMBL
UniProt A6JF93 ENTREZGENE, UniProtKB/TrEMBL
  D3ZQ55 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Jph1  junctophilin 1   Jph1_predicted  junctophilin 1 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Jph1_predicted  junctophilin 1 (predicted)      Symbol and Name status set to approved 70820 APPROVED