Wdr48 (WD repeat domain 48) - Rat Genome Database

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Gene: Wdr48 (WD repeat domain 48) Rattus norvegicus
Analyze
Symbol: Wdr48
Name: WD repeat domain 48
RGD ID: 1309702
Description: Predicted to enable DNA binding activity; deubiquitinase activator activity; and ubiquitin binding activity. Predicted to be involved in double-strand break repair via homologous recombination; positive regulation of nitrogen compound metabolic process; and protein deubiquitination. Predicted to act upstream of or within several processes, including positive regulation of epithelial cell proliferation; regulation of protein monoubiquitination; and seminiferous tubule development. Predicted to be located in nucleus. Orthologous to human WDR48 (WD repeat domain 48); INTERACTS WITH 3,4-methylenedioxymethamphetamine; acrylamide; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC363164; RGD1309702; similar to WD repeat endosomal protein; WD repeat-containing protein 48
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
mRatBN7.28119,622,053 - 119,655,264 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl8119,622,048 - 119,655,264 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx8125,203,504 - 125,236,737 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.08123,402,547 - 123,435,784 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.08121,235,273 - 121,268,518 (+)NCBIRnor_WKY
Rnor_6.08128,577,080 - 128,610,287 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8128,577,080 - 128,610,287 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.08127,778,763 - 127,811,970 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48124,850,235 - 124,883,442 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.18124,869,881 - 124,902,301 (+)NCBI
Celera8118,769,024 - 118,802,212 (+)NCBICelera
Cytogenetic Map8q32NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease 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. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:18082604   PMID:19075014   PMID:24001775   PMID:24145035  


Genomics

Comparative Map Data
Wdr48
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.28119,622,053 - 119,655,264 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl8119,622,048 - 119,655,264 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx8125,203,504 - 125,236,737 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.08123,402,547 - 123,435,784 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.08121,235,273 - 121,268,518 (+)NCBIRnor_WKY
Rnor_6.08128,577,080 - 128,610,287 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8128,577,080 - 128,610,287 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.08127,778,763 - 127,811,970 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48124,850,235 - 124,883,442 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.18124,869,881 - 124,902,301 (+)NCBI
Celera8118,769,024 - 118,802,212 (+)NCBICelera
Cytogenetic Map8q32NCBI
WDR48
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38339,052,016 - 39,096,664 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl339,052,013 - 39,096,671 (+)EnsemblGRCh38hg38GRCh38
GRCh37339,093,507 - 39,138,155 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36339,068,511 - 39,112,886 (+)NCBINCBI36Build 36hg18NCBI36
Build 34339,068,510 - 39,112,883NCBI
Celera339,033,745 - 39,078,385 (+)NCBICelera
Cytogenetic Map3p22.2NCBI
HuRef339,135,626 - 39,179,803 (+)NCBIHuRef
CHM1_1339,044,573 - 39,088,966 (+)NCBICHM1_1
T2T-CHM13v2.0339,064,178 - 39,108,828 (+)NCBIT2T-CHM13v2.0
Wdr48
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm399119,723,943 - 119,755,652 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl9119,723,944 - 119,755,653 (+)EnsemblGRCm39 Ensembl
GRCm389119,894,895 - 119,926,586 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl9119,894,878 - 119,926,587 (+)EnsemblGRCm38mm10GRCm38
MGSCv379119,804,013 - 119,835,697 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv369119,743,593 - 119,775,277 (+)NCBIMGSCv36mm8
Celera9120,362,077 - 120,393,799 (+)NCBICelera
Cytogenetic Map9F4NCBI
Wdr48
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542724,873,616 - 24,917,691 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495542724,873,616 - 24,917,691 (-)NCBIChiLan1.0ChiLan1.0
WDR48
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1339,228,920 - 39,273,300 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl339,228,920 - 39,273,300 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0338,948,440 - 38,992,872 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
WDR48
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1238,716,598 - 8,766,242 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl238,715,700 - 8,764,678 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha238,756,451 - 8,805,903 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0239,005,151 - 9,054,838 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl239,004,578 - 9,054,838 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1238,818,871 - 8,868,534 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0238,961,107 - 9,010,791 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0238,954,513 - 9,004,213 (+)NCBIUU_Cfam_GSD_1.0
Wdr48
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118195,169,311 - 195,213,154 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647328,307,875 - 28,354,279 (+)EnsemblSpeTri2.0
SpeTri2.0NW_00493647328,307,913 - 28,351,727 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
WDR48
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1323,735,567 - 23,786,308 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11323,735,566 - 23,786,312 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21325,995,433 - 26,045,850 (+)NCBISscrofa10.2Sscrofa10.2susScr3
WDR48
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.115319,589 - 366,265 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl15319,810 - 366,246 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660639,046,714 - 9,093,695 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Wdr48
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247311,884,666 - 1,934,754 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247311,884,660 - 1,934,818 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Wdr48
155 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:570
Count of miRNA genes:267
Interacting mature miRNAs:344
Transcripts:ENSRNOT00000024172
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1554321Bmd3Bone mineral density QTL 37.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)840952565123900184Rat
2300181Bmd55Bone mineral density QTL 555.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)876468691121468691Rat
61437Cia6Collagen induced arthritis QTL 6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)882460758122812818Rat
738011Anxrr9Anxiety related response QTL 96.1exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)893535351123900184Rat
1358893Bp263Blood pressure QTL 2635.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)893965141123900184Rat
1358903Bp252Blood pressure QTL 25270.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)893965141123900184Rat
738014Anxrr15Anxiety related response QTL 153.60.005locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)895718998123900184Rat
2300182Bmd56Bone mineral density QTL 565.4femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)895718998123900184Rat
724539Cm19Cardiac mass QTL 192.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)8100149864120994388Rat

Markers in Region
RH127721  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.28119,655,296 - 119,655,480 (+)MAPPERmRatBN7.2
Rnor_6.08128,610,320 - 128,610,503NCBIRnor6.0
Rnor_5.08127,812,003 - 127,812,186UniSTSRnor5.0
RGSC_v3.48124,883,475 - 124,883,658UniSTSRGSC3.4
Celera8118,802,245 - 118,802,428UniSTS
RH 3.4 Map81285.99UniSTS
Cytogenetic Map8q32UniSTS
BE101118  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.28119,654,311 - 119,654,467 (+)MAPPERmRatBN7.2
Rnor_6.08128,609,335 - 128,609,490NCBIRnor6.0
Rnor_5.08127,811,018 - 127,811,173UniSTSRnor5.0
RGSC_v3.48124,882,490 - 124,882,645UniSTSRGSC3.4
Celera8118,801,260 - 118,801,415UniSTS
RH 3.4 Map81286.29UniSTS
Cytogenetic Map8q32UniSTS
BE110354  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.28119,637,287 - 119,637,487 (+)MAPPERmRatBN7.2
Rnor_6.08128,592,311 - 128,592,510NCBIRnor6.0
Rnor_5.08127,793,994 - 127,794,193UniSTSRnor5.0
RGSC_v3.48124,865,466 - 124,865,665UniSTSRGSC3.4
Celera8118,784,251 - 118,784,450UniSTS
RH 3.4 Map81315.0UniSTS
Cytogenetic Map8q32UniSTS


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 36 45 29 19 29 1 1 74 35 41 11 1
Low 7 12 12 12 7 10 7
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000024172   ⟹   ENSRNOP00000024172
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl8119,630,416 - 119,655,264 (+)Ensembl
Rnor_6.0 Ensembl8128,577,080 - 128,610,287 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000082356   ⟹   ENSRNOP00000075552
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl8119,622,129 - 119,655,264 (+)Ensembl
Rnor_6.0 Ensembl8128,577,345 - 128,608,739 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000114700   ⟹   ENSRNOP00000088537
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl8119,622,048 - 119,655,263 (+)Ensembl
RefSeq Acc Id: NM_001135895   ⟹   NP_001129367
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28119,622,053 - 119,655,264 (+)NCBI
Rnor_6.08128,577,080 - 128,610,287 (+)NCBI
Rnor_5.08127,778,763 - 127,811,970 (+)NCBI
RGSC_v3.48124,850,235 - 124,883,442 (+)RGD
Celera8118,769,024 - 118,802,212 (+)RGD
Sequence:
RefSeq Acc Id: XM_017595770   ⟹   XP_017451259
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28119,622,345 - 119,655,264 (+)NCBI
Rnor_6.08128,577,318 - 128,610,287 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001129367 (Get FASTA)   NCBI Sequence Viewer  
  XP_017451259 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL76897 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001129367   ⟸   NM_001135895
- UniProtKB: D3Z8C7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017451259   ⟸   XM_017595770
- Peptide Label: isoform X1
- UniProtKB: A0A0G2KAW5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000075552   ⟸   ENSRNOT00000082356
RefSeq Acc Id: ENSRNOP00000024172   ⟸   ENSRNOT00000024172
RefSeq Acc Id: ENSRNOP00000088537   ⟸   ENSRNOT00000114700

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A0G2KAW5-F1-model_v2 AlphaFold A0A0G2KAW5 1-691 view protein structure

Transcriptome

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

Promoters
RGD ID:13696374
Promoter ID:EPDNEW_R6899
Type:multiple initiation site
Name:Wdr48_1
Description:WD repeat domain 48
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R6900  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.08128,577,086 - 128,577,146EPDNEW
RGD ID:13696376
Promoter ID:EPDNEW_R6900
Type:multiple initiation site
Name:Wdr48_2
Description:WD repeat domain 48
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R6899  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.08128,577,367 - 128,577,427EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1309702 AgrOrtholog
BioCyc Gene G2FUF-28777 BioCyc
Ensembl Genes ENSRNOG00000016942 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000024172.6 UniProtKB/TrEMBL
  ENSRNOP00000075552 ENTREZGENE
  ENSRNOP00000075552.1 UniProtKB/TrEMBL
  ENSRNOP00000088537 ENTREZGENE
  ENSRNOP00000088537.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000024172.8 UniProtKB/TrEMBL
  ENSRNOT00000082356 ENTREZGENE
  ENSRNOT00000082356.2 UniProtKB/TrEMBL
  ENSRNOT00000114700 ENTREZGENE
  ENSRNOT00000114700.1 UniProtKB/TrEMBL
Gene3D-CATH 2.130.10.10 UniProtKB/TrEMBL
InterPro DUF3337 UniProtKB/TrEMBL
  G-protein_beta_WD-40_rep_reg UniProtKB/TrEMBL
  WD40/YVTN_repeat-like_dom UniProtKB/TrEMBL
  WD40_repeat UniProtKB/TrEMBL
  WD40_repeat_CS UniProtKB/TrEMBL
  WD40_repeat_dom_sf UniProtKB/TrEMBL
KEGG Report rno:363164 UniProtKB/TrEMBL
NCBI Gene 363164 ENTREZGENE
Pfam DUF3337 UniProtKB/TrEMBL
  WD40 UniProtKB/TrEMBL
PhenoGen Wdr48 PhenoGen
PRINTS GPROTEINBRPT UniProtKB/TrEMBL
PROSITE WD_REPEATS_1 UniProtKB/TrEMBL
  WD_REPEATS_2 UniProtKB/TrEMBL
SMART WD40 UniProtKB/TrEMBL
Superfamily-SCOP WD40_like UniProtKB/TrEMBL
UniProt A0A0G2KAW5 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6AA52_RAT UniProtKB/TrEMBL
  D3Z8C7 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Wdr48  WD repeat domain 48   Wdr48_predicted  WD repeat domain 48 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Wdr48_predicted  WD repeat domain 48 (predicted)  RGD1309702_predicted  similar to WD repeat endosomal protein (predicted)  Symbol and Name updated 1299863 APPROVED
2005-01-20 RGD1309702_predicted  similar to WD repeat endosomal protein (predicted)  LOC363164_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC363164_predicted  similar to WD repeat endosomal protein (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL