Wdr38 (WD repeat domain 38) - Rat Genome Database

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Gene: Wdr38 (WD repeat domain 38) Rattus norvegicus
Analyze
Symbol: Wdr38
Name: WD repeat domain 38
RGD ID: 1562587
Description: Predicted to act upstream of or within hematopoietic progenitor cell differentiation. Orthologous to human WDR38 (WD repeat domain 38); INTERACTS WITH amphetamine; bisphenol A; Cuprizon.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC366035; RGD1562587; similar to cis-Golgi matrix protein GM130; WD repeat-containing protein 38
RGD Orthologs
Human
Mouse
Bonobo
Dog
Squirrel
Pig
Green Monkey
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8343,158,737 - 43,169,466 (+)NCBIGRCr8
mRatBN7.2322,750,150 - 22,753,260 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl322,749,396 - 22,753,259 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx326,218,640 - 26,221,745 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0334,803,624 - 34,806,729 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0332,616,318 - 32,619,429 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0323,291,712 - 23,294,818 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl323,290,819 - 23,294,670 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0328,513,529 - 28,516,644 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4318,781,680 - 18,787,996 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera321,183,440 - 21,186,546 (+)NCBICelera
Cytogenetic Map3q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

References

References - curated
# Reference Title Reference Citation
1. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:24029230  


Genomics

Comparative Map Data
Wdr38
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8343,158,737 - 43,169,466 (+)NCBIGRCr8
mRatBN7.2322,750,150 - 22,753,260 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl322,749,396 - 22,753,259 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx326,218,640 - 26,221,745 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0334,803,624 - 34,806,729 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0332,616,318 - 32,619,429 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0323,291,712 - 23,294,818 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl323,290,819 - 23,294,670 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0328,513,529 - 28,516,644 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4318,781,680 - 18,787,996 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera321,183,440 - 21,186,546 (+)NCBICelera
Cytogenetic Map3q12NCBI
WDR38
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh389124,853,460 - 124,857,878 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl9124,853,417 - 124,857,890 (+)EnsemblGRCh38hg38GRCh38
GRCh379127,615,739 - 127,620,157 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 369126,655,576 - 126,659,981 (+)NCBINCBI36Build 36hg18NCBI36
Celera998,263,706 - 98,268,110 (+)NCBICelera
Cytogenetic Map9q33.3NCBI
HuRef997,228,194 - 97,232,664 (+)NCBIHuRef
CHM1_19127,764,472 - 127,768,945 (+)NCBICHM1_1
T2T-CHM13v2.09137,051,771 - 137,056,188 (+)NCBIT2T-CHM13v2.0
Wdr38
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39238,888,287 - 38,891,600 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl238,887,488 - 38,896,180 (+)EnsemblGRCm39 Ensembl
GRCm38238,998,309 - 39,001,584 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl238,997,476 - 39,006,168 (+)EnsemblGRCm38mm10GRCm38
MGSCv37238,853,829 - 38,857,104 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36238,819,485 - 38,828,177 (+)NCBIMGSCv36mm8
Celera240,724,185 - 40,727,330 (+)NCBICelera
Cytogenetic Map2BNCBI
cM Map224.42NCBI
WDR38
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21114,500,552 - 14,505,203 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1914,502,896 - 14,510,318 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0995,973,932 - 95,978,398 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.19124,491,753 - 124,496,140 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl9124,491,733 - 124,496,133 (+)Ensemblpanpan1.1panPan2
WDR38
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Dog10K_Boxer_Tasha957,357,579 - 57,362,824 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0959,079,201 - 59,084,446 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl959,079,362 - 59,084,388 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1957,838,176 - 57,843,421 (-)NCBIUMICH_Zoey_3.1
Wdr38
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947193,283,942 - 193,287,714 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493648713,052,665 - 13,056,014 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493648713,052,665 - 13,056,191 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
WDR38
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1265,633,564 - 265,637,267 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11265,632,153 - 265,637,098 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21299,458,604 - 299,462,243 (+)NCBISscrofa10.2Sscrofa10.2susScr3
WDR38
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11213,290,713 - 13,296,075 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1213,290,954 - 13,295,025 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660792,807,493 - 2,812,126 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Variants

.
Variants in Wdr38
10 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:97
Count of miRNA genes:79
Interacting mature miRNAs:81
Transcripts:ENSRNOT00000018921
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1358357Srcrtb1Stress Responsive Cort Basal QTL 16.360.002blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)3865816227494778Rat
6893355Bw101Body weight QTL 1010.40.38body mass (VT:0001259)body weight (CMO:0000012)31077870430357018Rat
634306Bp140Blood pressure QTL 1403.30.0013arterial blood pressure trait (VT:2000000)body weight (CMO:0000012)31737470335528639Rat
10401810Kidm53Kidney mass QTL 53kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)3822719447233430Rat
1298526Arunc3Aerobic running capacity QTL 32.2exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)3822719433703538Rat
8693641Alc30Alcohol consumption QTL 3020.739drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)31043430624512004Rat
2298542Neuinf11Neuroinflammation QTL 113.9nervous system integrity trait (VT:0010566)spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)31500542276927699Rat
1558657Cm43Cardiac mass QTL 436.63e-08heart mass (VT:0007028)heart wet weight (CMO:0000069)31077882330356773Rat
631568Bp92Blood pressure QTL 922.20.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3139874793Rat
6893363Bw105Body weight QTL 1052.60.0036body mass (VT:0001259)body weight (CMO:0000012)31077870430357018Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)pulse pressure (CMO:0000292)3133278763Rat
631831Alc8Alcohol consumption QTL 82.7consumption behavior trait (VT:0002069)calculated ethanol drink intake rate (CMO:0001615)3133230976Rat
1558647Cm46Cardiac mass QTL 465.40.0000055heart mass (VT:0007028)heart wet weight (CMO:0000069)31077882330356773Rat
4889966Bss95Bone structure and strength QTL 954.4tibia area (VT:1000281)tibia-fibula cross-sectional area (CMO:0001718)3136847613Rat
12879852Cm93Cardiac mass QTL 930.001heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)31831145447233430Rat
1558654Bw56Body weight QTL 564.50.0000171body mass (VT:0001259)body weight (CMO:0000012)31077870430357018Rat
12879853Am5Aortic mass QTL 50.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)31831145447233430Rat
12879854Kidm63Kidney mass QTL 630.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)31831145447233430Rat
10450804Scl70Serum cholesterol level QTL 704.70.001blood LDL cholesterol amount (VT:0000181)blood low density lipoprotein cholesterol level (CMO:0000053)32071409065714090Rat
1558650Cm48Cardiac mass QTL 4840.0001heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)31077882330356773Rat
1358905Hrtrt17Heart rate QTL 175.90.000014heart pumping trait (VT:2000009)heart rate (CMO:0000002)31086191289878372Rat
12879849Bw180Body weight QTL 1800.037body mass (VT:0001259)body weight (CMO:0000012)31831145447233430Rat
70191BpQTLcluster4Blood pressure QTL cluster 43arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)31077870450302886Rat
12879850Cm91Cardiac mass QTL 910.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)31831145447233430Rat
731172Bp151Blood pressure QTL 1510.04arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)31831145447233430Rat
12879851Cm92Cardiac mass QTL 920.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)31831145447233430Rat
631545Bp85Blood pressure QTL 853.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3133278763Rat
1358885Bp251Blood pressure QTL 2513.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)314489145121056321Rat
2325840Bp345Blood pressure QTL 3450.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)31831145428441896Rat
631676Cm8Cardiac mass QTL 87.030.0001aorta mass (VT:0002845)aorta weight (CMO:0000076)31695470861954708Rat
10450794Scl69Serum cholesterol level QTL 696.30.001blood LDL cholesterol amount (VT:0000181)blood low density lipoprotein cholesterol level (CMO:0000053)32071409065714090Rat
631679Cm10Cardiac mass QTL 107.340.0001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)3131158234Rat
2290452Scl56Serum cholesterol level QTL 562.26blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)3191609953Rat
70203Gcr2Gastric cancer resistance QTL 22.6stomach morphology trait (VT:0000470)stomach tumor susceptibility score (CMO:0002043)3865816227494778Rat
70202Alc19Alcohol consumption QTL 192.5drinking behavior trait (VT:0001422)ethanol intake volume to total fluid intake volume ratio (CMO:0001591)3127494778Rat
2312664Scl62Serum cholesterol level QTL 620.05blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)3138710544Rat
1358888Bp264Blood pressure QTL 2644.43arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)314489145121056321Rat


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
9 11 21 106 56 55 24 25 24 6 144 69 86 34 51 31

Sequence


Ensembl Acc Id: ENSRNOT00000018921   ⟹   ENSRNOP00000018921
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl322,749,396 - 22,753,259 (+)Ensembl
Rnor_6.0 Ensembl323,290,819 - 23,294,670 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000104343   ⟹   ENSRNOP00000087502
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl322,750,150 - 22,753,259 (+)Ensembl
RefSeq Acc Id: NM_001399335   ⟹   NP_001386264
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8343,159,856 - 43,162,965 (+)NCBI
mRatBN7.2322,750,150 - 22,753,260 (+)NCBI
RefSeq Acc Id: XM_063284264   ⟹   XP_063140334
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8343,158,737 - 43,162,965 (+)NCBI
RefSeq Acc Id: XR_010064673
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8343,159,844 - 43,169,466 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001386264 (Get FASTA)   NCBI Sequence Viewer  
  XP_063140334 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM00501 (Get FASTA)   NCBI Sequence Viewer  
  EDM00502 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000018921
  ENSRNOP00000018921.5
  ENSRNOP00000087502
  ENSRNOP00000087502.1
Ensembl Acc Id: ENSRNOP00000018921   ⟸   ENSRNOT00000018921
Ensembl Acc Id: ENSRNOP00000087502   ⟸   ENSRNOT00000104343
RefSeq Acc Id: NP_001386264   ⟸   NM_001399335
- UniProtKB: A0A8I6A5Y6 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063140334   ⟸   XM_063284264
- Peptide Label: isoform X1
- UniProtKB: F1LZZ1 (UniProtKB/TrEMBL)

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1LZZ1-F1-model_v2 AlphaFold F1LZZ1 1-295 view protein structure

Transcriptome

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

Promoters
RGD ID:13692059
Promoter ID:EPDNEW_R2579
Type:multiple initiation site
Name:Wdr38_1
Description:WD repeat domain 38
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_6.0323,290,835 - 23,290,895EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1562587 AgrOrtholog
BioCyc Gene G2FUF-49887 BioCyc
Ensembl Genes ENSRNOG00000014102 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000018921 ENTREZGENE
  ENSRNOT00000018921.7 UniProtKB/TrEMBL
  ENSRNOT00000104343 ENTREZGENE
  ENSRNOT00000104343.1 UniProtKB/TrEMBL
Gene3D-CATH 2.130.10.10 UniProtKB/TrEMBL
InterPro G-protein_beta_WD-40_rep UniProtKB/TrEMBL
  WD40/YVTN_repeat-like_dom_sf UniProtKB/TrEMBL
  WD40_repeat UniProtKB/TrEMBL
  WD40_repeat_CS UniProtKB/TrEMBL
  WD40_repeat_dom_sf UniProtKB/TrEMBL
NCBI Gene 366035 ENTREZGENE
PANTHER TRANSCRIPTION INITIATION FACTOR TFIID UniProtKB/TrEMBL
  TRANSCRIPTION INITIATION FACTOR TFIID SUBUNIT 5 UniProtKB/TrEMBL
Pfam WD40 UniProtKB/TrEMBL
PhenoGen Wdr38 PhenoGen
PRINTS GPROTEINBRPT UniProtKB/TrEMBL
PROSITE WD_REPEATS_1 UniProtKB/TrEMBL
  WD_REPEATS_2 UniProtKB/TrEMBL
  WD_REPEATS_REGION UniProtKB/TrEMBL
RatGTEx ENSRNOG00000014102 RatGTEx
SMART WD40 UniProtKB/TrEMBL
Superfamily-SCOP WD40_like UniProtKB/TrEMBL
UniProt A0A8I6A5Y6 ENTREZGENE, UniProtKB/TrEMBL
  F1LZZ1 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-02-29 Wdr38  WD repeat domain 38  RGD1562587_predicted  similar to cis-Golgi matrix protein GM130 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1562587_predicted  similar to cis-Golgi matrix protein GM130 (predicted)  LOC366035  similar to cis-Golgi matrix protein GM130  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC366035  similar to cis-Golgi matrix protein GM130      Symbol and Name status set to provisional 70820 PROVISIONAL