Phka1 (phosphorylase kinase regulatory subunit alpha 1) - Rat Genome Database

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Gene: Phka1 (phosphorylase kinase regulatory subunit alpha 1) Rattus norvegicus
Analyze
Symbol: Phka1
Name: phosphorylase kinase regulatory subunit alpha 1
RGD ID: 621522
Description: Predicted to enable choline-phosphate cytidylyltransferase activity. Involved in protein autophosphorylation. Part of phosphorylase kinase complex. Used to study hypothyroidism. Human ortholog(s) of this gene implicated in glycogen storage disease and glycogen storage disease IXd. Orthologous to human PHKA1 (phosphorylase kinase regulatory subunit alpha 1); PARTICIPATES IN glycogen degradation pathway; calcium/calcium-mediated signaling pathway; insulin signaling pathway; INTERACTS WITH (+)-schisandrin B; acrylamide; ammonium chloride.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: Pcyt1b; PhK-alpha-subunit; phosphorylase B kinase alpha subunit; phosphorylase b kinase regulatory subunit alpha, skeletal muscle isoform; phosphorylase kinase alpha 1; phosphorylase kinase alpha M subunit; phosphorylase kinase alpha-subunit; phosphorylase kinase, alpha 1
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
mRatBN7.2X67,601,302 - 67,738,504 (-)NCBI
Rnor_6.0 EnsemblX72,377,021 - 72,515,366 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X72,377,020 - 72,515,385 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0X73,218,886 - 73,356,004 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X90,553,527 - 90,692,073 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1X90,626,959 - 90,765,506 (-)NCBI
CeleraX67,954,686 - 68,091,557 (-)NCBICelera
Cytogenetic MapXq22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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:1512265   PMID:3362857  


Genomics

Comparative Map Data
Phka1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X67,601,302 - 67,738,504 (-)NCBI
Rnor_6.0 EnsemblX72,377,021 - 72,515,366 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X72,377,020 - 72,515,385 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0X73,218,886 - 73,356,004 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X90,553,527 - 90,692,073 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1X90,626,959 - 90,765,506 (-)NCBI
CeleraX67,954,686 - 68,091,557 (-)NCBICelera
Cytogenetic MapXq22NCBI
PHKA1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 EnsemblX72,578,814 - 72,714,319 (-)EnsemblGRCh38hg38GRCh38
GRCh38X72,578,814 - 72,714,306 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37X71,798,664 - 71,934,154 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X71,717,203 - 71,850,612 (-)NCBINCBI36hg18NCBI36
Build 34X71,583,501 - 71,716,903NCBI
CeleraX72,141,887 - 72,277,747 (-)NCBI
Cytogenetic MapXq13.1NCBI
HuRefX65,553,170 - 65,688,660 (-)NCBIHuRef
CHM1_1X71,691,651 - 71,827,294 (-)NCBICHM1_1
Phka1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X101,557,581 - 101,687,907 (-)NCBIGRCm39mm39
GRCm39 EnsemblX101,557,581 - 101,687,852 (-)Ensembl
GRCm38X102,513,975 - 102,644,301 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX102,513,975 - 102,644,246 (-)EnsemblGRCm38mm10GRCm38
MGSCv37X99,709,314 - 99,839,585 (-)NCBIGRCm37mm9NCBIm37
MGSCv36X98,718,393 - 98,846,917 (-)NCBImm8
CeleraX89,425,232 - 89,555,150 (-)NCBICelera
Cytogenetic MapXDNCBI
cM MapX45.47NCBI
Phka1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495547512,020,629 - 12,172,443 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495547512,020,278 - 12,172,427 (-)NCBIChiLan1.0ChiLan1.0
PHKA1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1X71,900,762 - 72,033,055 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX71,900,762 - 72,033,055 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0X61,816,613 - 61,949,179 (-)NCBIMhudiblu_PPA_v0panPan3
PHKA1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X56,579,538 - 56,758,293 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX56,581,435 - 56,757,905 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX47,405,712 - 47,585,405 (-)NCBI
ROS_Cfam_1.0X57,633,970 - 57,778,843 (-)NCBI
UMICH_Zoey_3.1X55,549,695 - 55,732,132 (-)NCBI
UNSW_CanFamBas_1.0X56,945,562 - 57,125,410 (-)NCBI
UU_Cfam_GSD_1.0X56,794,558 - 56,974,936 (-)NCBI
Phka1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X45,213,224 - 45,321,344 (+)NCBI
SpeTri2.0NW_0049367621,657,778 - 1,766,592 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PHKA1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX58,455,938 - 58,583,216 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X58,456,097 - 58,583,216 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X66,182,346 - 66,288,186 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PHKA1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X62,397,726 - 62,528,695 (-)NCBI
ChlSab1.1 EnsemblX62,397,739 - 62,528,708 (-)Ensembl
Vero_WHO_p1.0NW_0236660654,273,916 - 4,405,596 (-)NCBI
Phka1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046249032,859,252 - 3,068,516 (-)NCBI

Position Markers
RH142784  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X67,733,046 - 67,733,167 (+)MAPPER
Rnor_6.0X72,509,921 - 72,510,041NCBIRnor6.0
Rnor_5.0X73,350,562 - 73,350,682UniSTSRnor5.0
RGSC_v3.4X90,686,937 - 90,687,057UniSTSRGSC3.4
CeleraX68,086,431 - 68,086,551UniSTS
Cytogenetic MapXq31UniSTS
AU022198  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2687,791,311 - 87,791,510 (+)MAPPER
mRatBN7.2X67,673,699 - 67,673,898 (+)MAPPER
Rnor_6.0X72,449,832 - 72,450,030NCBIRnor6.0
Rnor_6.0691,610,683 - 91,610,881NCBIRnor6.0
Rnor_5.06101,068,322 - 101,068,520UniSTSRnor5.0
Rnor_5.0X73,291,717 - 73,291,915UniSTSRnor5.0
RGSC_v3.4X90,625,288 - 90,625,486UniSTSRGSC3.4
RGSC_v3.4691,274,523 - 91,274,721UniSTSRGSC3.4
Celera686,288,663 - 86,288,861UniSTS
CeleraX68,027,084 - 68,027,282UniSTS
Cytogenetic MapXq31UniSTS
Cytogenetic Map6q24UniSTS
UniSTS:236937  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X67,672,892 - 67,673,043 (+)MAPPER
Rnor_6.0X72,449,025 - 72,449,175NCBIRnor6.0
Rnor_5.0X73,290,910 - 73,291,060UniSTSRnor5.0
RGSC_v3.4X90,624,481 - 90,624,631UniSTSRGSC3.4
CeleraX68,026,277 - 68,026,427UniSTS
Cytogenetic MapXq31UniSTS
Cytogenetic Map6q24UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X15688119127888215Rat
1598837Memor13Memory QTL 133.2exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X44320616158345622Rat
738035Stresp1Stress response QTL 14.960.000011stress-related behavior trait (VT:0010451)defensive burying - copingX44557974120045269Rat
61431Cia19Collagen induced arthritis QTL 194.4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X70352120127888215Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:85
Count of miRNA genes:75
Interacting mature miRNAs:78
Transcripts:ENSRNOT00000041138
Prediction methods:Microtar, 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 1 8 8 11 43 1 24 6 8
Low 2 43 49 41 19 41 31 34 17 5
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000041138   ⟹   ENSRNOP00000046508
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX72,379,037 - 72,515,144 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000075929
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX72,416,426 - 72,515,366 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000076235
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX72,509,687 - 72,510,085 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000076725   ⟹   ENSRNOP00000068281
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX72,378,867 - 72,515,320 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000076850   ⟹   ENSRNOP00000068112
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX72,377,021 - 72,515,057 (-)Ensembl
RefSeq Acc Id: NM_022626   ⟹   NP_072148
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X67,601,302 - 67,738,185 (-)NCBI
Rnor_6.0X72,378,434 - 72,515,057 (-)NCBI
Rnor_5.0X73,218,886 - 73,356,004 (-)NCBI
RGSC_v3.4X90,553,527 - 90,692,073 (-)RGD
CeleraX67,954,686 - 68,091,557 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006257102   ⟹   XP_006257164
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X67,601,935 - 67,738,504 (-)NCBI
Rnor_6.0X72,377,020 - 72,515,385 (-)NCBI
Rnor_5.0X73,218,886 - 73,356,004 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_072148   ⟸   NM_022626
- UniProtKB: A0A096MJF7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006257164   ⟸   XM_006257102
- Peptide Label: isoform X1
- UniProtKB: A0A096MJV9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000046508   ⟸   ENSRNOT00000041138
RefSeq Acc Id: ENSRNOP00000068112   ⟸   ENSRNOT00000076850
RefSeq Acc Id: ENSRNOP00000068281   ⟸   ENSRNOT00000076725
Protein Domains
Glyco_hydro_15

Transcriptome

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

Promoters
RGD ID:13701888
Promoter ID:EPDNEW_R12409
Type:initiation region
Name:Phka1_1
Description:phosphorylase kinase regulatory subunit alpha 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_6.0X72,515,343 - 72,515,403EPDNEW

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)
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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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621522 AgrOrtholog
Ensembl Genes ENSRNOG00000003063 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000046508 UniProtKB/TrEMBL
  ENSRNOP00000068112 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000068281 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000041138 UniProtKB/TrEMBL
  ENSRNOT00000076725 UniProtKB/TrEMBL
  ENSRNOT00000076850 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 1.50.10.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro 6-hairpin_glycosidase_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  6hp_glycosidase-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  GH15-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PHK_A/B_su UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:64561 UniProtKB/TrEMBL
NCBI Gene 64561 ENTREZGENE
PANTHER PTHR10749 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Glyco_hydro_15 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Phka1 PhenoGen
Superfamily-SCOP SSF48208 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A096MJF7 ENTREZGENE, UniProtKB/TrEMBL
  A0A096MJV9 ENTREZGENE, UniProtKB/TrEMBL
  F1LLZ7_RAT UniProtKB/TrEMBL
  KPB1_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q64650 UniProtKB/Swiss-Prot
  Q64651 UniProtKB/Swiss-Prot
  Q9QZ77 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-05-18 Phka1  phosphorylase kinase regulatory subunit alpha 1  Phka1  phosphorylase kinase, alpha 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-02-25 Phka1  phosphorylase kinase, alpha 1  Phka1  phosphorylase kinase alpha 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 Phka1  phosphorylase kinase alpha 1  Pcyt1b  phosphorylase B kinase alpha subunit  Symbol and Name updated 1299863 APPROVED
2002-08-07 Pcyt1b  phosphorylase B kinase alpha subunit      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_regulation translocation to membranes in vivo increases as a function of anionic lipid content 724642