Wdr45 (WD repeat domain 45) - Rat Genome Database

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Gene: Wdr45 (WD repeat domain 45) Rattus norvegicus
Analyze
Symbol: Wdr45
Name: WD repeat domain 45
RGD ID: 1359718
Description: Predicted to have phosphatidylinositol-3,5-bisphosphate binding activity; phosphatidylinositol-3-phosphate binding activity; and protein kinase binding activity. Predicted to be involved in several processes, including autophagy of mitochondrion; autophagy of nucleus; and protein localization to phagophore assembly site. Predicted to localize to cytosol; extrinsic component of membrane; and phagophore assembly site membrane. Human ortholog(s) of this gene implicated in neurodegeneration with brain iron accumulation 5. Orthologous to human WDR45 (WD repeat domain 45); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: LOC302559; similar to DNA segment, Chr X, Immunex 38, expressed; WD repeat domain phosphoinositide-interacting protein 4; WD repeat-containing protein 45; WIPI-4
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
mRatBN7.2X14,776,280 - 14,782,197 (-)NCBI
Rnor_6.0 EnsemblX15,621,209 - 15,627,235 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X15,621,249 - 15,627,159 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0X16,402,686 - 16,408,439 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X26,816,610 - 26,822,245 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1X26,870,079 - 26,875,714 (-)NCBI
CeleraX14,860,493 - 14,866,128 (-)NCBICelera
Cytogenetic MapXq12NCBI
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:15489334   PMID:23435086   PMID:28561066  


Genomics

Comparative Map Data
Wdr45
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X14,776,280 - 14,782,197 (-)NCBI
Rnor_6.0 EnsemblX15,621,209 - 15,627,235 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X15,621,249 - 15,627,159 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0X16,402,686 - 16,408,439 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X26,816,610 - 26,822,245 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1X26,870,079 - 26,875,714 (-)NCBI
CeleraX14,860,493 - 14,866,128 (-)NCBICelera
Cytogenetic MapXq12NCBI
WDR45
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 EnsemblX49,074,433 - 49,101,170 (-)EnsemblGRCh38hg38GRCh38
GRCh38X49,074,442 - 49,101,178 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37X48,932,101 - 48,958,116 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X48,819,036 - 48,845,003 (-)NCBINCBI36hg18NCBI36
Build 34X48,688,548 - 48,714,308NCBI
CeleraX52,706,432 - 52,732,399 (+)NCBI
Cytogenetic MapXp11.23NCBI
HuRefX46,588,725 - 46,614,834 (-)NCBIHuRef
CHM1_1X48,963,413 - 48,989,776 (-)NCBICHM1_1
Wdr45
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X7,588,193 - 7,594,440 (+)NCBIGRCm39mm39
GRCm39 EnsemblX7,580,572 - 7,594,445 (+)Ensembl
GRCm38X7,721,987 - 7,728,201 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX7,714,333 - 7,728,206 (+)EnsemblGRCm38mm10GRCm38
MGSCv37X7,299,375 - 7,305,327 (+)NCBIGRCm37mm9NCBIm37
MGSCv36X6,879,208 - 6,885,160 (+)NCBImm8
CeleraX3,742,357 - 3,748,359 (-)NCBICelera
Cytogenetic MapXA1.1NCBI
cM MapX3.48NCBI
Wdr45
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955543597,814 - 603,963 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955543597,796 - 604,163 (-)NCBIChiLan1.0ChiLan1.0
WDR45
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1X49,228,153 - 49,233,960 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX49,224,864 - 49,233,960 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0X41,372,722 - 41,400,441 (-)NCBIMhudiblu_PPA_v0panPan3
WDR45
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X42,221,261 - 42,237,535 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX42,218,046 - 42,226,422 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX16,596,869 - 16,613,180 (-)NCBI
ROS_Cfam_1.0X42,357,475 - 42,373,725 (-)NCBI
UMICH_Zoey_3.1X42,343,804 - 42,360,115 (-)NCBI
UNSW_CanFamBas_1.0X42,331,450 - 42,347,770 (-)NCBI
UU_Cfam_GSD_1.0X42,426,205 - 42,442,519 (-)NCBI
Wdr45
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X34,734,724 - 34,740,594 (-)NCBI
SpeTri2.0NW_004936721975,113 - 981,149 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
WDR45
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX43,147,476 - 43,156,195 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X43,150,691 - 43,155,981 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X47,998,631 - 48,003,934 (-)NCBISscrofa10.2Sscrofa10.2susScr3
WDR45
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X46,183,278 - 46,188,564 (-)NCBI
ChlSab1.1 EnsemblX46,183,443 - 46,188,536 (-)Ensembl
Vero_WHO_p1.0NW_02366607611,748,609 - 11,754,464 (-)NCBI
Wdr45
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624893845,689 - 852,221 (-)NCBI

Position Markers
MARC_3991-3992:996679250:1  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0X15,623,440 - 15,624,932NCBIRnor6.0
Rnor_5.0X16,404,889 - 16,406,381UniSTSRnor5.0
RGSC_v3.4X26,818,801 - 26,820,293UniSTSRGSC3.4
CeleraX14,862,684 - 14,864,176UniSTS
Cytogenetic MapXq13UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
731181Uae27Urinary albumin excretion QTL 272.70.0059urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)X144092703Rat
634325Bw13Body weight QTL 130body mass (VT:0001259)body weight (CMO:0000012)X166245321592783Rat
70165Bp64Blood pressure QTL 645.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)X166260933443848Rat
631204Gluco15Glucose level QTL 150.001blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)X183816624331837Rat
1298071Edpm12Estrogen-dependent pituitary mass QTL 123.2pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)X428214049282140Rat
631666Iddm5Insulin dependent diabetes mellitus QTL 5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)X595407850954078Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:75
Count of miRNA genes:64
Interacting mature miRNAs:71
Transcripts:ENSRNOT00000013369
Prediction methods:Miranda, Pita, 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 53 37 19 37 8 11 74 35 34 11 8
Low 4 4 4 7
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001013958 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006256710 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006256712 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006256713 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006256714 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008773071 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099632 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099633 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099634 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099635 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099636 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099637 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005497959 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005497960 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC130624 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC085816 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH474078 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225212 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232559 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233394 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000351 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000013369   ⟹   ENSRNOP00000013369
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX15,621,209 - 15,627,235 (-)Ensembl
RefSeq Acc Id: NM_001013958   ⟹   NP_001013980
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X14,776,292 - 14,781,927 (-)NCBI
Rnor_6.0X15,621,249 - 15,626,884 (-)NCBI
Rnor_5.0X16,402,686 - 16,408,439 (-)NCBI
RGSC_v3.4X26,816,610 - 26,822,245 (-)RGD
CeleraX14,860,493 - 14,866,128 (-)RGD
Sequence:
RefSeq Acc Id: XM_006256710   ⟹   XP_006256772
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X14,776,280 - 14,781,939 (-)NCBI
Rnor_6.0X15,621,249 - 15,626,900 (-)NCBI
Rnor_5.0X16,402,686 - 16,408,439 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006256712   ⟹   XP_006256774
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X14,776,280 - 14,782,181 (-)NCBI
Rnor_6.0X15,621,249 - 15,627,159 (-)NCBI
Rnor_5.0X16,402,686 - 16,408,439 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006256713   ⟹   XP_006256775
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X14,776,280 - 14,781,927 (-)NCBI
Rnor_6.0X15,621,249 - 15,626,883 (-)NCBI
Rnor_5.0X16,402,686 - 16,408,439 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006256714   ⟹   XP_006256776
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X14,776,280 - 14,781,960 (-)NCBI
Rnor_6.0X15,621,249 - 15,626,908 (-)NCBI
Rnor_5.0X16,402,686 - 16,408,439 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008773071   ⟹   XP_008771293
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X14,776,280 - 14,780,865 (-)NCBI
Rnor_6.0X15,621,249 - 15,625,474 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039099632   ⟹   XP_038955560
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X14,776,280 - 14,781,935 (-)NCBI
RefSeq Acc Id: XM_039099633   ⟹   XP_038955561
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X14,776,280 - 14,780,855 (-)NCBI
RefSeq Acc Id: XM_039099634   ⟹   XP_038955562
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X14,776,280 - 14,781,885 (-)NCBI
RefSeq Acc Id: XM_039099635   ⟹   XP_038955563
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X14,776,280 - 14,782,197 (-)NCBI
RefSeq Acc Id: XM_039099636   ⟹   XP_038955564
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X14,776,280 - 14,782,179 (-)NCBI
RefSeq Acc Id: XM_039099637   ⟹   XP_038955565
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X14,776,280 - 14,781,939 (-)NCBI
RefSeq Acc Id: XR_005497959
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X14,777,058 - 14,781,939 (-)NCBI
RefSeq Acc Id: XR_005497960
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X14,777,058 - 14,781,951 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001013980   ⟸   NM_001013958
- UniProtKB: Q5U2Y0 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006256774   ⟸   XM_006256712
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006256776   ⟸   XM_006256714
- Peptide Label: isoform X2
- UniProtKB: A0A140TAA5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006256772   ⟸   XM_006256710
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006256775   ⟸   XM_006256713
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008771293   ⟸   XM_008773071
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000013369   ⟸   ENSRNOT00000013369
RefSeq Acc Id: XP_038955563   ⟸   XM_039099635
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038955564   ⟸   XM_039099636
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038955565   ⟸   XM_039099637
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038955560   ⟸   XM_039099632
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038955562   ⟸   XM_039099634
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038955561   ⟸   XM_039099633
- Peptide Label: isoform X1

Transcriptome

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

Promoters
RGD ID:13701745
Promoter ID:EPDNEW_R12269
Type:single initiation site
Name:Wdr45_1
Description:WD repeat domain 45
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_6.0X15,627,152 - 15,627,212EPDNEW

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)
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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
LEW/NCrlBR (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
LH/MavRrrc (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
LL/MavRrrc (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
LN/MavRrrc (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
M520/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
MHS/Gib (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
MNS/Gib (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
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
X 16404679 16404680 C T snv GH/OmrMcwi (MCW), SBH/Ygl (MCW), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), SBN/Ygl (MCW), RCS/Kyo (KyushuU), SBH/Ygl (KNAW), SBN/Ygl (KNAW), FHH/EurMcwi (KNAW), FHL/EurMcwi (KNAW), MR/N (KNAW)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
X 15623230 15623231 C T snv GH/OmrMcwi (MCW), SBH/Ygl (MCW), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), SBN/Ygl (MCW), SBN/Ygl (RGD), MR/N (MCW), FHL/EurMcwi (RGD), FHH/EurMcwi (RGD), SBH/Ygl (RGD), CDS


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
X 26818591 26818592 C T snv FHH/EurMcwi (MDC), MR/N (KNAW), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), GH/OmrMcwi (MCW), HCR/2Mco (UMich), FHL/EurMcwi (ICL), SBH/Ygl (ICL), SBN/Ygl (ICL), HCR/1Mco (UMich), LCR/1Mco (UMich), FHH/EurMcwi (ICL)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1359718 AgrOrtholog
Ensembl Genes ENSRNOG00000009749 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000013369 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000013369 UniProtKB/TrEMBL
Gene3D-CATH 2.130.10.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7123612 IMAGE-MGC_LOAD
InterPro WD40/YVTN_repeat-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  WD40_repeat UniProtKB/TrEMBL
  WD40_repeat_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  WIPI4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:302559 UniProtKB/Swiss-Prot
MGC_CLONE MGC:94061 IMAGE-MGC_LOAD
NCBI Gene 302559 ENTREZGENE
PANTHER PTHR11227:SF44 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam WD40 UniProtKB/TrEMBL
PhenoGen Wdr45 PhenoGen
SMART WD40 UniProtKB/TrEMBL
Superfamily-SCOP SSF50978 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A140TAA5 ENTREZGENE, UniProtKB/TrEMBL
  Q5U2Y0 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2006-03-30 Wdr45  WD repeat domain 45  LOC302559  similar to DNA segment, Chr X, Immunex 38, expressed  Symbol and Name updated 1299863 APPROVED
2005-07-29 LOC302559  similar to DNA segment, Chr X, Immunex 38, expressed      Symbol and Name status set to provisional 70820 PROVISIONAL