Cdc42bpb (CDC42 binding protein kinase beta) - Rat Genome Database
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Gene: Cdc42bpb (CDC42 binding protein kinase beta) Rattus norvegicus
Analyze
Symbol: Cdc42bpb
Name: CDC42 binding protein kinase beta
RGD ID: 621753
Description: Exhibits Rho GTPase binding activity and protein serine/threonine kinase activity. Involved in actomyosin structure organization; cell migration; and protein phosphorylation. Localizes to actomyosin. Orthologous to human CDC42BPB (CDC42 binding protein kinase beta); INTERACTS WITH 2,4-dinitrotoluene; 2,6-dinitrotoluene; 3H-1,2-dithiole-3-thione.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: CDC42 binding protein kinase beta (DMPK-like); Cdc42-binding protein kinase beta; DMPK-like beta; MRCK beta; myotonic dystrophy kinase-related CDC42-binding kinase beta; myotonic dystrophy protein kinase-like beta; serine/threonine-protein kinase MRCK beta
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
mRatBN7.26130,333,712 - 130,416,631 (-)NCBI
Rnor_6.0 Ensembl6135,746,754 - 135,830,086 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.06135,746,743 - 135,830,144 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.06144,585,365 - 144,667,686 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.46136,053,885 - 136,136,234 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.16136,061,068 - 136,142,380 (-)NCBI
Celera6127,890,990 - 127,973,161 (-)NCBICelera
Cytogenetic Map6q32NCBI
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
actomyosin  (IBA,IDA,ISO)
cell leading edge  (ISS)
cell-cell junction  (ISS)
cytoplasm  (IBA,IEA)
cytoskeleton  (IBA)
lamellipodium  (IEA,ISS)
membrane  (IEA)
plasma membrane  (IEA)

References

Additional References at PubMed
PMID:19056867   PMID:21949762   PMID:25743393  


Genomics

Comparative Map Data
Cdc42bpb
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.26130,333,712 - 130,416,631 (-)NCBI
Rnor_6.0 Ensembl6135,746,754 - 135,830,086 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.06135,746,743 - 135,830,144 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.06144,585,365 - 144,667,686 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.46136,053,885 - 136,136,234 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.16136,061,068 - 136,142,380 (-)NCBI
Celera6127,890,990 - 127,973,161 (-)NCBICelera
Cytogenetic Map6q32NCBI
CDC42BPB
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl14102,932,380 - 103,057,549 (-)EnsemblGRCh38hg38GRCh38
GRCh3814102,932,380 - 103,057,549 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh3714103,398,717 - 103,523,886 (-)NCBIGRCh37GRCh37hg19GRCh37
GRCh3714103,398,716 - 103,523,742 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3614102,468,469 - 102,593,495 (-)NCBINCBI36hg18NCBI36
Build 3414102,468,469 - 102,593,552NCBI
Celera1483,452,838 - 83,577,854 (-)NCBI
Cytogenetic Map14q32.32NCBI
HuRef1483,573,751 - 83,698,598 (-)NCBIHuRef
CHM1_114103,336,156 - 103,461,595 (-)NCBICHM1_1
Cdc42bpb
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3912111,259,406 - 111,347,985 (-)NCBIGRCm39mm39
GRCm3812111,292,972 - 111,379,313 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl12111,292,976 - 111,377,718 (-)EnsemblGRCm38mm10GRCm38
MGSCv3712112,531,183 - 112,615,929 (-)NCBIGRCm37mm9NCBIm37
MGSCv3612111,740,787 - 111,825,167 (-)NCBImm8
Celera12112,487,034 - 112,573,080 (-)NCBICelera
Cytogenetic Map12F1NCBI
cM Map1260.94NCBI
Cdc42bpb
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555382,024,776 - 2,113,211 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555382,023,681 - 2,113,213 (-)NCBIChiLan1.0ChiLan1.0
CDC42BPB
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.114103,367,060 - 103,447,382 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl14103,367,060 - 103,451,989 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01483,551,870 - 83,679,888 (-)NCBIMhudiblu_PPA_v0panPan3
CDC42BPB
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl870,811,023 - 71,033,324 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1870,809,943 - 70,915,922 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Cdc42bpb
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_004936835975,941 - 1,026,046 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CDC42BPB
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa10.27128,824,316 - 128,887,793 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CDC42BPB
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12480,894,777 - 81,024,998 (-)NCBI
Cdc42bpb
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247341,624,001 - 1,718,427 (+)NCBI

Position Markers
RH127478  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.06135,747,029 - 135,747,213NCBIRnor6.0
Rnor_5.06144,667,216 - 144,667,400UniSTSRnor5.0
RGSC_v3.46136,054,171 - 136,054,355UniSTSRGSC3.4
Celera6127,891,276 - 127,891,460UniSTS
RH 3.4 Map6781.0UniSTS
Cytogenetic Map6q32UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
731173Uae22Urinary albumin excretion QTL 2210.1urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)668781170147991367Rat
2290393Uae37Urinary albumin excretion QTL 370.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)668781170147991367Rat
724536Uae7Urinary albumin excretion QTL 73.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)675623277136143011Rat
1331799Bp211Blood pressure QTL 2113.66407arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)675623277136426962Rat
1581550Pur8Proteinuria QTL 8total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)675623393136142742Rat
1581563Uae33Urinary albumin excretion QTL 33urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)675623393136142742Rat
724513Uae14Urinary albumin excretion QTL 146.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)688996335139410483Rat
1300076Glom8Glomerulus QTL 870.000000009kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli directly contacting the kidney surface (CMO:0001001)691703409136703409Rat
2303624Vencon5Ventilatory control QTL 54.45respiration trait (VT:0001943)minute ventilation (VE) (CMO:0000132)692879510137879510Rat
12801411Schws8Schwannoma susceptibility QTL 8nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)699273921144273921Rat
61414Pia3Pristane induced arthritis QTL 34.5joint integrity trait (VT:0010548)post-insult time to onset of experimental arthritis (CMO:0001450)699273921144792678Rat
8552796Vie3Viral induced encephalitis QTL 32.6brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)6101207574147991367Rat
1358355Srcrt4Stress Responsive Cort QTL 46.39blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)6104363890147991367Rat
2313399Anxrr28Anxiety related response QTL 28aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)6104381930138066274Rat
4145118Mcs26Mammary carcinoma susceptibility QTL 260.0001mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)6111134524138065254Rat
737976Pia24Pristane induced arthritis QTL 24joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)6117355600147991367Rat
1641917Colcr5Colorectal carcinoma resistance QTL 53.180.0009intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)6127286494144745573Rat
2293085Iddm29Insulin dependent diabetes mellitus QTL 297.66blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)6127286494147249902Rat
61329Eae9Experimental allergic encephalomyelitis QTL 93.7body mass (VT:0001259)change in body weight (CMO:0002045)6127286494147991367Rat
2312560Pur20Proteinuria QTL 202.10.005total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)6130561943144745573Rat
71111Iddm8Insulin dependent diabetes mellitus QTL 81.90.002blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)6132652096138068606Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:168
Count of miRNA genes:105
Interacting mature miRNAs:137
Transcripts:ENSRNOT00000039059
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


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 38 44 34 13 34 1 3 74 35 40 11 1
Low 5 13 7 6 7 7 8 1 7
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000039059   ⟹   ENSRNOP00000036487
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl6135,746,754 - 135,830,086 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000080623   ⟹   ENSRNOP00000075663
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl6135,747,740 - 135,829,953 (-)Ensembl
RefSeq Acc Id: NM_053620   ⟹   NP_446072
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26130,333,712 - 130,416,377 (-)NCBI
Rnor_6.06135,746,743 - 135,829,994 (-)NCBI
Rnor_5.06144,585,365 - 144,667,686 (+)NCBI
RGSC_v3.46136,053,885 - 136,136,234 (-)RGD
Celera6127,890,990 - 127,973,161 (-)RGD
Sequence:
RefSeq Acc Id: XM_006240562   ⟹   XP_006240624
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26130,333,712 - 130,416,631 (-)NCBI
Rnor_6.06135,746,744 - 135,830,144 (-)NCBI
Rnor_5.06144,585,365 - 144,667,686 (+)NCBI
Sequence:
RefSeq Acc Id: XR_005505433
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26130,334,848 - 130,416,289 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_446072   ⟸   NM_053620
- UniProtKB: Q7TT49 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006240624   ⟸   XM_006240562
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000075663   ⟸   ENSRNOT00000080623
RefSeq Acc Id: ENSRNOP00000036487   ⟸   ENSRNOT00000039059
Protein Domains
AGC-kinase C-terminal   CNH   CRIB   PH   Phorbol-ester/DAG-type   Protein kinase

Transcriptome

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

Promoters
RGD ID:13694839
Promoter ID:EPDNEW_R5361
Type:initiation region
Name:Cdc42bpb_1
Description:CDC42 binding protein kinase beta
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_6.06135,830,085 - 135,830,145EPDNEW

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)
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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
6 144636393 144636394 G A snv ACI/EurMcwi (MCW), WAG/Rij (KNAW), ACI/N (KNAW), ACI/EurMcwi (KNAW), Crl:SD (UDEL), LEW/Crl (KNAW), LEW/NCrl (KNAW), WN/N (KNAW), LE/OrlBarth (UDEL), DA/BklArbNsi (KNAW)


Assembly: Rnor_6.0
Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
6 135778036 135778037 C T snv ACI/EurMcwi (MCW), ACI/N (MCW), WN/N (MCW), WAG/Rij (RGD), LEW/Crl (RGD), LEW/NCrlBR (RGD), ACI/EurMcwi (RGD)


Assembly: RGSC_v3.4
Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
6 136062348 136062349 T G snv SR/JrHsd (MCW)
6 136085178 136085179 C T snv WN/N (KNAW), ACI/EurMcwi (MCW), ACI/EurMcwi (ICL), LEW/Crl (ICL), DA/BklArbNsi (ICAHN), WAG/Rij (ICL), HCR/1Mco (UMich), LCR/1Mco (UMich), HCR/2Mco (UMich), LCR/2Mco (UMich), ACI/N (KNAW), LEW/NCrl (ICL)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621753 AgrOrtholog
Ensembl Genes ENSRNOG00000009675 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000036487 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000075663 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000039059 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000080623 UniProtKB/TrEMBL
Gene3D-CATH 2.30.29.30 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro AGC-kinase_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CNH_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CRIB_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  DAG/PE-bd UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  KELK UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Kinase-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MRCK_beta UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MRCKB_STKc UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Myotonic_dystrophy_kinase_coil UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PE/DAG-bd UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PH-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PH_domain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Prot_kinase_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Protein_kinase_ATP_BS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ser/Thr_kinase_AS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:113960 UniProtKB/Swiss-Prot
NCBI Gene 113960 ENTREZGENE
PANTHER PTHR22988:SF34 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam C1_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CNH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  DMPK_coil UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  KELK UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Pkinase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Cdc42bpb PhenoGen
PRINTS DAGPEDOMAIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE AGC_KINASE_CTER UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CNH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CRIB UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PH_DOMAIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PROTEIN_KINASE_ATP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PROTEIN_KINASE_DOM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PROTEIN_KINASE_ST UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZF_DAG_PE_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZF_DAG_PE_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART CNH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PBD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  S_TK_X UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  S_TKc UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SM00109 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SM00233 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF56112 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2KB58_RAT UniProtKB/TrEMBL
  MRCKB_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary O54875 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-01-13 Cdc42bpb  CDC42 binding protein kinase beta  Cdc42bpb  CDC42 binding protein kinase beta (DMPK-like)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-26 Cdc42bpb  CDC42 binding protein kinase beta (DMPK-like)  Cdc42bpb  Cdc42 binding protein kinase beta  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-12-14 Cdc42bpb  Cdc42-binding protein kinase beta      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Cdc42bpb        Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_domains contains a kinase domain, cysteine-rich domain, pleckstrin-like domain, and p21 GTPase binding domain 632451