Prkcsh (protein kinase C substrate 80K-H) - Rat Genome Database

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Gene: Prkcsh (protein kinase C substrate 80K-H) Rattus norvegicus
Analyze
Symbol: Prkcsh
Name: protein kinase C substrate 80K-H
RGD ID: 1309628
Description: Predicted to have several functions, including calcium ion binding activity; ion channel binding activity; and protein kinase C binding activity. Predicted to be involved in several processes, including N-glycan processing; liver development; and negative regulation of neuron projection development. Predicted to localize to glucosidase II complex. Human ortholog(s) of this gene implicated in liver disease and polycystic liver disease. Orthologous to human PRKCSH (protein kinase C substrate 80K-H); PARTICIPATES IN Endoplasmic Reticulum-associated degradation pathway; INTERACTS WITH 2,5-hexanedione; bisphenol A; Brodifacoum.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: glucosidase 2 subunit beta; LOC300445
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2820,534,787 - 20,546,493 (+)NCBI
Rnor_6.0 Ensembl823,014,956 - 23,026,503 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0823,014,802 - 23,026,507 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0823,069,586 - 23,081,291 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4821,107,041 - 21,144,270 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1821,106,881 - 21,117,476 (+)NCBI
Celera821,925,450 - 21,937,160 (+)NCBICelera
Cytogenetic Map8q13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:8702988   PMID:9148925   PMID:10929008   PMID:12477932   PMID:16706842   PMID:19801576   PMID:21685914   PMID:22337885   PMID:27462106  


Genomics

Comparative Map Data
Prkcsh
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2820,534,787 - 20,546,493 (+)NCBI
Rnor_6.0 Ensembl823,014,956 - 23,026,503 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0823,014,802 - 23,026,507 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0823,069,586 - 23,081,291 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4821,107,041 - 21,144,270 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1821,106,881 - 21,117,476 (+)NCBI
Celera821,925,450 - 21,937,160 (+)NCBICelera
Cytogenetic Map8q13NCBI
PRKCSH
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1911,435,284 - 11,450,968 (+)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl1911,435,288 - 11,450,968 (+)EnsemblGRCh38hg38GRCh38
GRCh381911,435,290 - 11,450,968 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371911,546,456 - 11,561,783 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361911,407,269 - 11,422,783 (+)NCBINCBI36hg18NCBI36
Build 341911,407,268 - 11,422,783NCBI
Celera1911,441,004 - 11,456,521 (+)NCBI
Cytogenetic Map19p13.2NCBI
HuRef1911,121,465 - 11,136,774 (+)NCBIHuRef
CHM1_11911,546,100 - 11,561,813 (+)NCBICHM1_1
Prkcsh
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39921,914,284 - 21,925,541 (+)NCBIGRCm39mm39
GRCm39 Ensembl921,914,102 - 21,925,518 (+)Ensembl
GRCm38922,002,988 - 22,014,245 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl922,002,806 - 22,014,222 (+)EnsemblGRCm38mm10GRCm38
MGSCv37921,807,479 - 21,818,666 (+)NCBIGRCm37mm9NCBIm37
MGSCv36921,753,437 - 21,764,624 (+)NCBImm8
Celera919,272,723 - 19,283,910 (+)NCBICelera
Cytogenetic Map9A3NCBI
cM Map98.04NCBI
Prkcsh
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554952,331,569 - 2,337,946 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554952,331,075 - 2,338,479 (+)NCBIChiLan1.0ChiLan1.0
PRKCSH
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11911,693,620 - 11,707,610 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1911,693,620 - 11,707,728 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01910,981,398 - 10,997,062 (+)NCBIMhudiblu_PPA_v0panPan3
PRKCSH
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12049,905,246 - 49,916,551 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2049,905,248 - 49,916,463 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2049,775,959 - 49,787,692 (-)NCBI
ROS_Cfam_1.02050,423,129 - 50,434,871 (-)NCBI
UMICH_Zoey_3.12049,633,425 - 49,645,158 (-)NCBI
UNSW_CanFamBas_1.02050,059,568 - 50,071,314 (-)NCBI
UU_Cfam_GSD_1.02050,302,755 - 50,314,497 (-)NCBI
Prkcsh
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118208,843,072 - 208,853,320 (-)NCBI
SpeTri2.0NW_0049366591,501,425 - 1,511,634 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PRKCSH
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl270,097,444 - 70,114,446 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1270,097,424 - 70,114,460 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2270,332,429 - 70,349,468 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PRKCSH
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1610,360,392 - 10,375,785 (+)NCBI
ChlSab1.1 Ensembl610,360,751 - 10,374,208 (+)Ensembl
Prkcsh
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248283,219,105 - 3,227,369 (+)NCBI

Position Markers
RH128469  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0823,026,353 - 23,026,502NCBIRnor6.0
Rnor_5.0823,081,137 - 23,081,286UniSTSRnor5.0
Celera821,937,008 - 21,937,157UniSTS
Cytogenetic Map8q13UniSTS
RH129453  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0823,026,320 - 23,026,479NCBIRnor6.0
Rnor_5.0823,081,104 - 23,081,263UniSTSRnor5.0
Celera821,936,975 - 21,937,134UniSTS
RH 3.4 Map8183.7UniSTS
Cytogenetic Map8q13UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2302367Slep5Serum leptin concentration QTL 53.43blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)81137350945712344Rat
631650Stl6Serum triglyceride level QTL 640.0019blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)810938911120496129Rat
2317882Alcrsp24Alcohol response QTL 243.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)8125942267Rat
731182Uae24Urinary albumin excretion QTL 246.4urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)821813070100873963Rat
631271Lecl1Lens clarity QTL 10.001lens clarity trait (VT:0001304)age of onset/diagnosis of cataract (CMO:0001584)82146491991140553Rat
1581557Eae16Experimental allergic encephalomyelitis QTL 163.8nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)89531047119211942Rat
1598824Memor4Memory QTL 42.5exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)81137326757541668Rat
2301416Bp315Blood pressure QTL 3150.008arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)8873867753738677Rat
1357398Slep3Serum leptin concentration QTL 33.43blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)81137350945712344Rat
1354595Despr4Despair related QTL 42.160.0036locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)81038843955388439Rat
1354627Despr14Despair related QTL 140.0056locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)81038843955388439Rat
1558646Swd5Spike wave discharge measurement QTL 53.450.00036brain electrophysiology trait (VT:0010557)brain spike-and-wave discharge frequency (CMO:0001742)81766655562666555Rat
2317030Wbc5White blood cell count QTL 53.210.005leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)81144825156448251Rat
2317032Ginf2Gastrointestinal inflammation QTL 23.210.005liver integrity trait (VT:0010547)liver granuloma severity score (CMO:0002157)8736807652368076Rat
2317036Livw3Liver weight QTL 32.430.01liver mass (VT:0003402)liver weight to body weight ratio (CMO:0000633)8736807652368076Rat
2317048Ginf1Gastrointestinal inflammation QTL 13.520.005cecum mucosa thickness (VT:0010234)enterocolitis severity score (CMO:0002138)8736807652368076Rat
2317051Aia18Adjuvant induced arthritis QTL 182.42joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)81144825156448251Rat
61373Mcs4Mammary carcinoma susceptibility QTL 41.1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)82071759265717592Rat
9590084Insglur5Insulin/glucose ratio QTL 518.540.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)8124608226Rat
12880044Am9Aortic mass QTL 90.007aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)8210812847108128Rat
12880023Bw184Body weight QTL 1840.001body mass (VT:0001259)body weight (CMO:0000012)8210812847108128Rat
12880025Cm102Cardiac mass QTL 1020.044heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)8210812847108128Rat
12880028Cm103Cardiac mass QTL 1030.02heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)8210812847108128Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:205
Count of miRNA genes:127
Interacting mature miRNAs:143
Transcripts:ENSRNOT00000018009
Prediction methods:Microtar, 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.


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 3 43 57 41 19 41 8 11 74 35 41 11 8
Low
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000018009   ⟹   ENSRNOP00000018009
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl823,014,956 - 23,026,503 (+)Ensembl
RefSeq Acc Id: NM_001106806   ⟹   NP_001100276
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2820,534,941 - 20,546,491 (+)NCBI
Rnor_6.0823,014,956 - 23,026,505 (+)NCBI
Rnor_5.0823,069,586 - 23,081,291 (+)NCBI
RGSC_v3.4821,107,041 - 21,144,270 (+)RGD
Celera821,925,450 - 21,937,160 (+)RGD
Sequence:
RefSeq Acc Id: XM_006242633   ⟹   XP_006242695
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2820,534,881 - 20,546,493 (+)NCBI
Rnor_6.0823,014,907 - 23,026,507 (+)NCBI
Rnor_5.0823,069,586 - 23,081,291 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006242634   ⟹   XP_006242696
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2820,534,787 - 20,546,493 (+)NCBI
Rnor_6.0823,014,802 - 23,026,507 (+)NCBI
Rnor_5.0823,069,586 - 23,081,291 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001100276 (Get FASTA)   NCBI Sequence Viewer  
  XP_006242695 (Get FASTA)   NCBI Sequence Viewer  
  XP_006242696 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI61987 (Get FASTA)   NCBI Sequence Viewer  
  EDL78242 (Get FASTA)   NCBI Sequence Viewer  
  EDL78243 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001100276   ⟸   NM_001106806
- Peptide Label: precursor
- UniProtKB: B1WC34 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006242696   ⟸   XM_006242634
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006242695   ⟸   XM_006242633
- Peptide Label: isoform X1
- UniProtKB: B1WC34 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000018009   ⟸   ENSRNOT00000018009
Protein Domains
EF-hand

Transcriptome

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

Promoters
RGD ID:13695802
Promoter ID:EPDNEW_R6324
Type:multiple initiation site
Name:Prkcsh_1
Description:protein kinase C substrate 80K-H
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R6325  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0823,014,905 - 23,014,965EPDNEW
RGD ID:13695801
Promoter ID:EPDNEW_R6325
Type:multiple initiation site
Name:Prkcsh_2
Description:protein kinase C substrate 80K-H
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R6324  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0823,015,312 - 23,015,372EPDNEW

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)
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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
SBH/Ygl (MCW)
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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)
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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
SBN/Ygl (MCW)
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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)
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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
SHR/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
SHRSP/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
SR/JrHsd (MCW)
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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)
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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
SS/Jr (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
SS/JrHsdMcwi (MCW)
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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
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
8 23077401 23077402 C G snv BN/SsNSlc (KyushuU)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1309628 AgrOrtholog
Ensembl Genes ENSRNOG00000013360 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000018009 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000018009 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 2.70.130.10 UniProtKB/TrEMBL
  4.10.400.10 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:9030870 IMAGE-MGC_LOAD
InterPro EF-hand-dom_pair UniProtKB/TrEMBL
  EF_Hand_1_Ca_BS UniProtKB/TrEMBL
  EF_hand_Ca-bd UniProtKB/TrEMBL
  Gtb1-like UniProtKB/TrEMBL
  LDL_receptor-like_sf UniProtKB/TrEMBL
  Man6P_isomerase_rcpt_bd UniProtKB/TrEMBL
  PRKCSH UniProtKB/TrEMBL
  PRKCSH_N UniProtKB/TrEMBL
KEGG Report rno:300445 UniProtKB/TrEMBL
MGC_CLONE MGC:187806 IMAGE-MGC_LOAD
NCBI Gene 300445 ENTREZGENE
PANTHER PTHR12630 UniProtKB/TrEMBL
Pfam EF_hand_3 UniProtKB/TrEMBL
  PRKCSH-like UniProtKB/TrEMBL
  PRKCSH_1 UniProtKB/TrEMBL
PhenoGen Prkcsh PhenoGen
PROSITE EF_HAND_1 UniProtKB/TrEMBL
  EF_HAND_2 UniProtKB/TrEMBL
Superfamily-SCOP SSF47473 UniProtKB/TrEMBL
UniProt B1WC34 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Prkcsh  protein kinase C substrate 80K-H   Prkcsh_predicted  protein kinase C substrate 80K-H (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Prkcsh_predicted  protein kinase C substrate 80K-H (predicted)      Symbol and Name status set to approved 70820 APPROVED