Jph1 (junctophilin 1) - Chinchilla Research Resource Database
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Gene: Jph1 (junctophilin 1) Rattus norvegicus
Analyze
Symbol: Jph1
Name: junctophilin 1
CRRD ID: 1308789
Description: Predicted to be a structural constituent of muscle. Predicted to be involved in muscle organ development. Predicted to localize to several cellular components, including Z disc; junctional membrane complex; and junctional sarcoplasmic reticulum membrane. 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; acrylamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: junctophilin-1; LOC297748
Orthologs:
Homo sapiens (human) : JPH1 (junctophilin 1)  HGNC  Alliance
Mus musculus (house mouse) : Jph1 (junctophilin 1)  MGI  Alliance
Chinchilla lanigera (long-tailed chinchilla) : Jph1 (junctophilin 1)
Pan paniscus (bonobo/pygmy chimpanzee) : JPH1 (junctophilin 1)
Canis lupus familiaris (dog) : JPH1 (junctophilin 1)
Ictidomys tridecemlineatus (thirteen-lined ground squirrel) : Jph1 (junctophilin 1)
Sus scrofa (pig) : JPH1 (junctophilin 1)
Chlorocebus sabaeus (African green monkey) : JPH1 (junctophilin 1)
Heterocephalus glaber (naked mole-rat) : Jph1 (junctophilin 1)
more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
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 (+)NCBIRGSC3.4rn4RGSC3.4
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 Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

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
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 (+)NCBIRGSC3.4rn4RGSC3.4
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
GRCh38.p13 Ensembl874,234,700 - 74,321,540 (-)EnsemblGRCh38hg38GRCh38
GRCh38874,234,700 - 74,321,540 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37875,146,935 - 75,233,721 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36875,309,493 - 75,396,117 (-)NCBINCBI36hg18NCBI36
Build 34875,311,996 - 75,396,117NCBI
Celera871,144,786 - 71,231,414 (-)NCBI
Cytogenetic Map8q21.11NCBI
HuRef870,637,846 - 70,724,493 (-)NCBIHuRef
CHM1_1875,198,905 - 75,285,575 (-)NCBICHM1_1
Jph1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39117,012,328 - 17,168,132 (-)NCBI
GRCm38116,942,104 - 17,097,922 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl116,964,560 - 17,097,889 (-)EnsemblGRCm38mm10GRCm38
MGSCv37116,987,545 - 17,087,879 (-)NCBIGRCm37mm9NCBIm37
MGSCv36116,982,678 - 17,083,012 (-)NCBImm8
Celera116,921,250 - 17,021,597 (-)NCBICelera
Cytogenetic Map1A3NCBI
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
PanPan1.1872,413,794 - 72,500,252 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl872,413,794 - 72,505,309 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0870,768,560 - 70,855,068 (-)NCBIMhudiblu_PPA_v0panPan3
JPH1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl2922,703,647 - 22,785,415 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.12922,701,531 - 22,785,712 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Jph1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
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 - 61,716,546 (+)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 - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1 Ensembl869,839,460 - 69,919,950 (-)Ensembl
ChlSab1.1869,839,696 - 69,919,915 (-)NCBI
Jph1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474416,937,138 - 17,013,765 (+)NCBI


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
CRRD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1331771Rf35Renal function QTL 354.36965kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5189432042Rat
1331756Rf34Renal function QTL 344.16275kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5193273395Rat
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)51136640934Rat

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.


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 8 11 4 8
Low 3 43 31 16 9 16 70 22 34 11
Below cutoff 17 16 9 16 13 5

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000008153   ⟹   ENSRNOP00000008153
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl51,417,478 - 1,511,416 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000085564   ⟹   ENSRNOP00000075672
RefSeq Status:
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
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
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.051,417,414 - 1,511,754 (+)NCBI
Rnor_5.051,413,646 - 1,507,659 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008763475   ⟹   XP_008761697
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.051,417,414 - 1,509,056 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_001100100   ⟸   NM_001106630
- UniProtKB: D3ZQ55 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006237785   ⟸   XM_006237723
- Peptide Label: isoform X1
- UniProtKB: D3ZQ55 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006237781   ⟸   XM_006237719
- Peptide Label: isoform X1
- UniProtKB: D3ZQ55 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006237783   ⟸   XM_006237721
- Peptide Label: isoform X1
- UniProtKB: D3ZQ55 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006237782   ⟸   XM_006237720
- Peptide Label: isoform X1
- UniProtKB: D3ZQ55 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006237784   ⟸   XM_006237722
- Peptide Label: isoform X1
- UniProtKB: D3ZQ55 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008761697   ⟸   XM_008763475
- Peptide Label: isoform X1
- UniProtKB: D3ZQ55 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000008153   ⟸   ENSRNOT00000008153
RefSeq Acc Id: ENSRNOP00000075672   ⟸   ENSRNOT00000085564

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

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1308789 AgrOrtholog
Ensembl Genes ENSRNOG00000006110 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000008153 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000075672 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000008153 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000085564 ENTREZGENE, UniProtKB/TrEMBL
InterPro Junctophilin UniProtKB/TrEMBL
  MORN UniProtKB/TrEMBL
KEGG Report rno:297748 UniProtKB/TrEMBL
NCBI Gene 297748 ENTREZGENE
PANTHER PTHR23085 UniProtKB/TrEMBL
Pfam MORN UniProtKB/TrEMBL
PhenoGen Jph1 PhenoGen
PIRSF Junctophilin UniProtKB/TrEMBL
SMART MORN UniProtKB/TrEMBL
UniGene Rn.152547 ENTREZGENE
UniProt 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