Wdr75 (WD repeat domain 75) - Rat Genome Database

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Gene: Wdr75 (WD repeat domain 75) Rattus norvegicus
Analyze
Symbol: Wdr75
Name: WD repeat domain 75
RGD ID: 1564869
Description: Predicted to enable RNA binding activity. Predicted to be involved in positive regulation of rRNA processing and positive regulation of transcription by RNA polymerase I. Predicted to be active in nucleolus. Orthologous to human WDR75 (WD repeat domain 75); PARTICIPATES IN ribosome biogenesis pathway; INTERACTS WITH (+)-schisandrin B; 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC314545; LRRG00118; similar to CG12050-PA; WD repeat-containing protein 75
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2947,903,166 - 47,933,399 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl947,903,200 - 47,933,399 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx956,429,616 - 56,459,789 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0961,552,439 - 61,582,612 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0959,848,437 - 59,878,610 (+)NCBIRnor_WKY
Rnor_6.0952,687,845 - 52,717,808 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl952,687,868 - 52,717,809 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0952,353,665 - 52,383,624 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4944,849,323 - 44,873,180 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera945,578,427 - 45,602,289 (+)NCBICelera
Cytogenetic Map9q22NCBI
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
nucleolus  (IBA,ISO)

Molecular Function
RNA binding  (IBA)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:17699751   PMID:22658674   PMID:22681889   PMID:24912190  


Genomics

Comparative Map Data
Wdr75
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2947,903,166 - 47,933,399 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl947,903,200 - 47,933,399 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx956,429,616 - 56,459,789 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0961,552,439 - 61,582,612 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0959,848,437 - 59,878,610 (+)NCBIRnor_WKY
Rnor_6.0952,687,845 - 52,717,808 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl952,687,868 - 52,717,809 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0952,353,665 - 52,383,624 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4944,849,323 - 44,873,180 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera945,578,427 - 45,602,289 (+)NCBICelera
Cytogenetic Map9q22NCBI
WDR75
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382189,441,474 - 189,475,552 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl2189,441,446 - 189,475,552 (+)EnsemblGRCh38hg38GRCh38
GRCh372190,306,200 - 190,340,278 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362190,014,404 - 190,048,509 (+)NCBINCBI36Build 36hg18NCBI36
Celera2183,901,218 - 183,935,325 (+)NCBICelera
Cytogenetic Map2q32.2NCBI
HuRef2182,165,790 - 182,199,902 (+)NCBIHuRef
CHM1_12190,312,056 - 190,346,161 (+)NCBICHM1_1
T2T-CHM13v2.02189,930,767 - 189,964,846 (+)NCBIT2T-CHM13v2.0
Wdr75
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39145,834,313 - 45,862,798 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl145,834,326 - 45,862,779 (+)EnsemblGRCm39 Ensembl
GRCm38145,795,153 - 45,823,638 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl145,795,166 - 45,823,619 (+)EnsemblGRCm38mm10GRCm38
MGSCv37145,852,346 - 45,880,458 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36145,740,047 - 45,768,159 (+)NCBIMGSCv36mm8
Celera146,127,754 - 46,155,866 (+)NCBICelera
Cytogenetic Map1C1.1NCBI
Wdr75
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554039,352,615 - 9,383,206 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554039,352,615 - 9,383,206 (-)NCBIChiLan1.0ChiLan1.0
WDR75
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12B194,668,211 - 194,702,343 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2B194,668,211 - 194,702,343 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02B76,748,487 - 76,782,649 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
WDR75
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.137157,400 - 191,127 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl37157,455 - 190,916 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha371,127,984 - 1,162,166 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.03746,253 - 80,392 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3746,310 - 80,394 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.13758,984 - 93,113 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03726,641 - 61,083 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03755,367 - 89,511 (+)NCBIUU_Cfam_GSD_1.0
Wdr75
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405303148,308,723 - 148,335,802 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365068,500,752 - 8,529,698 (-)EnsemblSpeTri2.0
SpeTri2.0NW_0049365068,502,795 - 8,529,305 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
WDR75
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1593,981,215 - 94,026,707 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11593,981,054 - 94,026,479 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.215104,503,605 - 104,547,626 (+)NCBISscrofa10.2Sscrofa10.2susScr3
WDR75
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11074,953,086 - 74,989,662 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1074,953,072 - 74,991,458 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666040124,487,868 - 124,524,883 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Wdr75
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624899785,343 - 818,855 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624899786,447 - 818,310 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Wdr75
415 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:10
Count of miRNA genes:10
Interacting mature miRNAs:10
Transcripts:ENSRNOT00000050275
Prediction methods:Miranda, Rnahybrid
Result types:miRGate_prediction

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

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


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
10054125Srcrt7Stress Responsive Cort QTL 73.330.0011blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)9187073594Rat
1331757Cdexp1CD45RC expression in CD8 T cells QTL 14.3CD8-positive T cell quantity (VT:0008077)blood CD45RC(high) CD8 T cell count to CD45RC(low) CD8 T cell count ratio (CMO:0001990)9102453767509080Rat
631211Bw4Body weight QTL45.31retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)9510982650109826Rat
11353947Bp392Blood pressure QTL 392arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)9728325252283252Rat
9589133Insul26Insulin level QTL 2617.960.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)9895256053952560Rat
7411609Foco16Food consumption QTL 1625.60.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)9895256053952560Rat
631680Cm11Cardiac mass QTL 113.10.00089heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)92043051965430519Rat
70186Niddm26Non-insulin dependent diabetes mellitus QTL 263.87blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)92207116986369743Rat
631643Bp120Blood pressure QTL 12030.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)92207120067071200Rat
1598823Memor16Memory QTL 161.9exploratory 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)92213332249968732Rat
7207805Bmd88Bone mineral density QTL 884femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)92375402458157242Rat
1300180Bw14Body weight QTL 143.776body mass (VT:0001259)body weight (CMO:0000012)92375402461381613Rat
7207814Bmd91Bone mineral density QTL 913.5femur size trait (VT:1000369)femoral neck cross-sectional area (CMO:0001697)92375414483851531Rat
70218Cm28Cardiac mass QTL 288.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)92526804479271759Rat
724544Uae9Urinary albumin excretion QTL 94.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)925268044114175309Rat
731164Uae25Urinary albumin excretion QTL 253.50.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)925661188100929786Rat
1641894Alcrsp12Alcohol response QTL 12response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)92746863972468639Rat
7411656Foco26Food consumption QTL 269.80.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)93253550577535505Rat
7411571Bw138Body weight QTL 13814.30.001body mass (VT:0001259)body weight gain (CMO:0000420)93253550577535505Rat
1598834Memor11Memory QTL 112.5exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)93696235977814038Rat
8662828Vetf6Vascular elastic tissue fragility QTL 63.9artery integrity trait (VT:0010639)patent ductus arteriosus score (CMO:0002566)93696235992058970Rat
2290450Scl57Serum cholesterol level QTL 574.15blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)93696235995410867Rat
6903941Pur31Proteinuria QTL 310.036urine total protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)94019418885194188Rat
11353949Bp393Blood pressure QTL 393arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)94019418885194188Rat
61352Bp34Blood pressure QTL 345arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)94249534379271511Rat
10058949Gmadr5Adrenal mass QTL 520.014adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)94279151387976209Rat
11353951Bp394Blood pressure QTL 394arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)94464992189649921Rat
12879506Pur33Proteinuria QTL 33urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)94464992189649921Rat
11353957Bmd92Bone mineral density QTL 920.01tibia mineral mass (VT:1000283)volumetric bone mineral density (CMO:0001553)94611419991114199Rat
6903937Bp356Blood pressure QTL 3560.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)94790220852283252Rat

Markers in Region
RH130012  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2947,933,085 - 47,933,276 (+)MAPPERmRatBN7.2
Rnor_6.0952,717,495 - 52,717,685NCBIRnor6.0
Rnor_5.0952,383,311 - 52,383,501UniSTSRnor5.0
RGSC_v3.4944,872,987 - 44,873,177UniSTSRGSC3.4
Celera945,602,096 - 45,602,286UniSTS
Cytogenetic Map9q22UniSTS


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 46 30 19 30 8 8 74 34 35 11 8
Low 5 11 11 11 3 1 6
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000050275   ⟹   ENSRNOP00000044241
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl947,909,212 - 47,933,399 (+)Ensembl
Rnor_6.0 Ensembl952,693,831 - 52,717,688 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000083864   ⟹   ENSRNOP00000074925
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl947,903,200 - 47,933,399 (+)Ensembl
Rnor_6.0 Ensembl952,687,868 - 52,717,809 (+)Ensembl
RefSeq Acc Id: NM_001047889   ⟹   NP_001041354
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2947,909,416 - 47,933,279 (+)NCBI
Rnor_6.0952,693,831 - 52,717,688 (+)NCBI
Rnor_5.0952,353,665 - 52,383,624 (+)NCBI
RGSC_v3.4944,849,323 - 44,873,180 (+)RGD
Celera945,578,427 - 45,602,289 (+)RGD
Sequence:
RefSeq Acc Id: XM_006244892   ⟹   XP_006244954
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2947,903,166 - 47,933,399 (+)NCBI
Rnor_6.0952,687,845 - 52,717,808 (+)NCBI
Rnor_5.0952,353,665 - 52,383,624 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_001041354   ⟸   NM_001047889
- Sequence:
RefSeq Acc Id: XP_006244954   ⟸   XM_006244892
- Peptide Label: isoform X1
- UniProtKB: A0A0G2K9A7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000074925   ⟸   ENSRNOT00000083864
RefSeq Acc Id: ENSRNOP00000044241   ⟸   ENSRNOT00000050275

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A0G2K9A7-F1-model_v2 AlphaFold A0A0G2K9A7 1-829 view protein structure

Transcriptome

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

Promoters
RGD ID:13696648
Promoter ID:EPDNEW_R7172
Type:multiple initiation site
Name:Wdr75_1
Description:WD repeat domain 75
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_6.0952,687,867 - 52,687,927EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1564869 AgrOrtholog
BioCyc Gene G2FUF-27636 BioCyc
Ensembl Genes ENSRNOG00000003825 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000044241.1 UniProtKB/TrEMBL
  ENSRNOP00000074925 ENTREZGENE
  ENSRNOP00000074925.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000050275.2 UniProtKB/TrEMBL
  ENSRNOT00000083864 ENTREZGENE
  ENSRNOT00000083864.2 UniProtKB/TrEMBL
Gene3D-CATH 2.130.10.10 UniProtKB/TrEMBL
InterPro Quinonprotein_ADH-like_supfam UniProtKB/TrEMBL
  WD40/YVTN_repeat-like_dom UniProtKB/TrEMBL
  WD40_repeat UniProtKB/TrEMBL
  WD40_repeat_dom_sf UniProtKB/TrEMBL
KEGG Report rno:314545 UniProtKB/TrEMBL
NCBI Gene 314545 ENTREZGENE
Pfam WD40 UniProtKB/TrEMBL
PhenoGen Wdr75 PhenoGen
PROSITE WD_REPEATS_2 UniProtKB/TrEMBL
SMART WD40 UniProtKB/TrEMBL
Superfamily-SCOP SSF50998 UniProtKB/TrEMBL
  WD40_like UniProtKB/TrEMBL
UniProt A0A0G2K9A7 ENTREZGENE, UniProtKB/TrEMBL
  Q6QI90_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2006-03-30 Wdr75  WD repeat domain 75  LOC314545  similar to CG12050-PA  Symbol and Name updated 1299863 APPROVED
2006-02-09 LOC314545  similar to CG12050-PA      Symbol and Name status set to provisional 70820 PROVISIONAL