Wdr19 (WD repeat domain 19) - Rat Genome Database

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Gene: Wdr19 (WD repeat domain 19) Rattus norvegicus
Analyze
Symbol: Wdr19
Name: WD repeat domain 19
RGD ID: 1306997
Description: Predicted to be involved in cilium organization; protein localization to ciliary membrane; and protein-containing complex assembly. Predicted to act upstream of or within several processes, including chordate embryonic development; embryonic organ development; and myotome development. Predicted to be located in motile cilium and photoreceptor connecting cilium. Predicted to be part of intraciliary transport particle A. Predicted to be active in cilium. Human ortholog(s) of this gene implicated in several diseases, including Caroli disease; Senior-Loken syndrome; asphyxiating thoracic dystrophy 5; cranioectodermal dysplasia 4; and nephronophthisis 13. Orthologous to human WDR19 (WD repeat domain 19); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; acetamide.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC305349; RGD1306997; similar to WD repeat membrane protein; WD repeat-containing protein 19
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81443,396,130 - 43,460,012 (-)NCBIGRCr8
mRatBN7.21443,042,474 - 43,106,337 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1443,042,478 - 43,106,288 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1443,398,120 - 43,460,461 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01444,698,061 - 44,760,412 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01443,178,194 - 43,240,550 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01444,705,012 - 44,767,120 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1444,705,012 - 44,767,120 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01444,519,192 - 44,580,950 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41445,744,198 - 45,807,441 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11445,744,874 - 45,809,905 (-)NCBI
Celera1442,187,689 - 42,251,374 (-)NCBICelera
Cytogenetic Map14p11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Mutations in mouse Ift144 model the craniofacial, limb and rib defects in skeletal ciliopathies. Ashe A, etal., Hum Mol Genet. 2012 Apr 15;21(8):1808-23. doi: 10.1093/hmg/ddr613. Epub 2012 Jan 6.
2. Ciliopathies with skeletal anomalies and renal insufficiency due to mutations in the IFT-A gene WDR19. Bredrup C, etal., Am J Hum Genet. 2011 Nov 11;89(5):634-43. doi: 10.1016/j.ajhg.2011.10.001. Epub 2011 Oct 20.
3. WDR19: an ancient, retrograde, intraflagellar ciliary protein is mutated in autosomal recessive retinitis pigmentosa and in Senior-Loken syndrome. Coussa RG, etal., Clin Genet. 2013 Aug;84(2):150-9. doi: 10.1111/cge.12196.
4. 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.
5. Nephronophthisis 13: implications of its association with Caroli disease and altered intracellular localization of WDR19 in the kidney. Lee JM, etal., Pediatr Nephrol. 2015 Sep;30(9):1451-8. doi: 10.1007/s00467-015-3068-8. Epub 2015 Mar 1.
6. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
7. Hepatorenal fibrocystic diseases in children. Park E, etal., Pediatr Nephrol. 2016 Jan;31(1):113-9. doi: 10.1007/s00467-015-3185-4. Epub 2015 Aug 11.
8. GOA pipeline RGD automated data pipeline
9. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
10. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
11. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:16957054   PMID:19208653   PMID:20889716   PMID:22689656   PMID:25224227   PMID:27932497  


Genomics

Comparative Map Data
Wdr19
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81443,396,130 - 43,460,012 (-)NCBIGRCr8
mRatBN7.21443,042,474 - 43,106,337 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1443,042,478 - 43,106,288 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1443,398,120 - 43,460,461 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01444,698,061 - 44,760,412 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01443,178,194 - 43,240,550 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01444,705,012 - 44,767,120 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1444,705,012 - 44,767,120 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01444,519,192 - 44,580,950 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41445,744,198 - 45,807,441 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11445,744,874 - 45,809,905 (-)NCBI
Celera1442,187,689 - 42,251,374 (-)NCBICelera
Cytogenetic Map14p11NCBI
WDR19
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38439,182,529 - 39,285,810 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl439,182,504 - 39,285,810 (+)EnsemblGRCh38hg38GRCh38
GRCh37439,184,149 - 39,287,430 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36438,860,419 - 38,963,825 (+)NCBINCBI36Build 36hg18NCBI36
Build 34439,006,589 - 39,109,995NCBI
Celera439,621,888 - 39,725,263 (+)NCBICelera
Cytogenetic Map4p14NCBI
HuRef438,508,923 - 38,612,720 (+)NCBIHuRef
CHM1_1439,183,560 - 39,287,052 (+)NCBICHM1_1
T2T-CHM13v2.0439,152,167 - 39,255,444 (+)NCBIT2T-CHM13v2.0
Wdr19
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39565,357,039 - 65,417,758 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl565,357,039 - 65,417,758 (+)EnsemblGRCm39 Ensembl
GRCm38565,199,696 - 65,260,415 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl565,199,696 - 65,260,415 (+)EnsemblGRCm38mm10GRCm38
MGSCv37565,590,935 - 65,651,654 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36565,478,847 - 65,539,550 (+)NCBIMGSCv36mm8
Celera562,476,346 - 62,537,628 (+)NCBICelera
Cytogenetic Map5C3.1NCBI
cM Map533.58NCBI
Wdr19
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554438,053,847 - 8,123,110 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554438,053,847 - 8,122,918 (-)NCBIChiLan1.0ChiLan1.0
WDR19
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2339,371,162 - 39,477,207 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1439,563,751 - 39,669,617 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0433,511,283 - 33,616,946 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1439,365,204 - 39,470,074 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl439,365,276 - 39,462,903 (+)Ensemblpanpan1.1panPan2
WDR19
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1373,115,560 - 73,213,823 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl373,137,250 - 73,221,512 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha375,617,214 - 75,774,265 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0373,844,096 - 74,001,187 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl373,908,855 - 74,001,228 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1373,110,186 - 73,267,232 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0373,302,684 - 73,413,870 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0373,643,183 - 73,800,247 (-)NCBIUU_Cfam_GSD_1.0
Wdr19
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440528539,361,717 - 39,434,642 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364826,863,571 - 6,937,979 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364826,863,592 - 6,937,810 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
WDR19
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl830,463,862 - 30,553,703 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1830,453,969 - 30,553,699 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2832,078,753 - 32,168,583 (+)NCBISscrofa10.2Sscrofa10.2susScr3
WDR19
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12711,019,897 - 11,113,760 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2711,018,827 - 11,113,666 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604757,431,811 - 57,525,579 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Wdr19
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248407,624,687 - 7,699,997 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248407,624,744 - 7,702,283 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Wdr19
348 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:166
Count of miRNA genes:117
Interacting mature miRNAs:123
Transcripts:ENSRNOT00000003991
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
2313089Bss81Bone structure and strength QTL 813.40.0001body length (VT:0001256)body length, nose to rump (CMO:0000079)143766971982669719Rat
1581500Renag1Renal agenesis QTL 1kidney development trait (VT:0000527)percentage of study population developing unilateral renal agenesis during a period of time (CMO:0000940)14817066868298175Rat
10755459Coatc15Coat color QTL 150.01681coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)141983694464836944Rat
70214Niddm28Non-insulin dependent diabetes mellitus QTL 284.06blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)143999825175582726Rat
1300154Bp189Blood pressure QTL 1893.04arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)143088377768757901Rat
70187Pancm5Pancreatic morphology QTL 516.7pancreas mass (VT:0010144)pancreas weight to body weight ratio (CMO:0000630)143032009280829842Rat
631523Pia13Pristane induced arthritis QTL 133.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)144079346098037301Rat
1358296Ael3Aortic elastin QTL 33.70.00051aorta elastin amount (VT:0003905)aortic elastin14826709053267090Rat
2313100Bss82Bone structure and strength QTL 8230.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)143766971982669719Rat
7387267Uae42Urinary albumin excretion QTL 420.61urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)142216796767167967Rat
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141103062295876975Rat
2313397Coatc1Coat color QTL1coat/hair pigmentation trait (VT:0010463)coat/hair color measurement (CMO:0001808)141854133263541332Rat
2313048Bss84Bone structure and strength QTL 843.10.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)143766971982669719Rat
1300136Rf22Renal function QTL 223.9renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)144226252995023211Rat
2302045Pia39Pristane induced arthritis QTL 394.90.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G2a level (CMO:0002116)14826709053267090Rat
738037Hcas6Hepatocarcinoma susceptibility QTL 62.93liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)143905723783368335Rat
2313084Bss83Bone structure and strength QTL 832.90.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)143766971982669719Rat


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 49 113 91 90 59 25 59 6 218 97 93 45 60 31

Sequence


Ensembl Acc Id: ENSRNOT00000003991   ⟹   ENSRNOP00000003991
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1443,044,179 - 43,106,288 (-)Ensembl
Rnor_6.0 Ensembl1444,705,012 - 44,767,120 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000094871   ⟹   ENSRNOP00000091353
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1443,042,478 - 43,103,198 (-)Ensembl
RefSeq Acc Id: NM_001191679   ⟹   NP_001178608
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81443,397,835 - 43,459,939 (-)NCBI
mRatBN7.21443,044,179 - 43,106,288 (-)NCBI
Rnor_6.01444,705,012 - 44,767,120 (-)NCBI
Rnor_5.01444,519,192 - 44,580,950 (-)NCBI
Celera1442,187,689 - 42,251,374 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039091922   ⟹   XP_038947850
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81443,396,130 - 43,460,012 (-)NCBI
mRatBN7.21443,042,474 - 43,106,337 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001178608 (Get FASTA)   NCBI Sequence Viewer  
  XP_038947850 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL90074 (Get FASTA)   NCBI Sequence Viewer  
  EDL90075 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000003991.5
  ENSRNOP00000091353.1
RefSeq Acc Id: NP_001178608   ⟸   NM_001191679
- UniProtKB: F1LV01 (UniProtKB/TrEMBL),   A0A8I6GJJ5 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000003991   ⟸   ENSRNOT00000003991
RefSeq Acc Id: XP_038947850   ⟸   XM_039091922
- Peptide Label: isoform X1
- UniProtKB: A0A8I6GJJ5 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000091353   ⟸   ENSRNOT00000094871

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1LV01-F1-model_v2 AlphaFold F1LV01 1-1341 view protein structure

Transcriptome

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

Promoters
RGD ID:13699318
Promoter ID:EPDNEW_R9843
Type:multiple initiation site
Name:Wdr19_1
Description:WD repeat domain 19
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_6.01444,767,097 - 44,767,157EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1306997 AgrOrtholog
BioCyc Gene G2FUF-15737 BioCyc
Ensembl Genes ENSRNOG00000002932 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000003991.7 UniProtKB/TrEMBL
  ENSRNOT00000094871.1 UniProtKB/TrEMBL
Gene3D-CATH 1.25.40.470 UniProtKB/TrEMBL
  2.130.10.10 UniProtKB/TrEMBL
InterPro TPR-like_helical UniProtKB/TrEMBL
  WD40/YVTN_repeat-like_dom UniProtKB/TrEMBL
  WD40_repeat UniProtKB/TrEMBL
  WDR19/dyf-2 UniProtKB/TrEMBL
  WDR19_WD40_rpt UniProtKB/TrEMBL
KEGG Report rno:305349 UniProtKB/TrEMBL
NCBI Gene 305349 ENTREZGENE
PANTHER PTHR14920 UniProtKB/TrEMBL
  WD REPEAT-CONTAINING PROTEIN 19 UniProtKB/TrEMBL
Pfam WD40 UniProtKB/TrEMBL
  WD40_3 UniProtKB/TrEMBL
PhenoGen Wdr19 PhenoGen
RatGTEx ENSRNOG00000002932 RatGTEx
SMART WD40 UniProtKB/TrEMBL
Superfamily-SCOP DPP6 N-terminal domain-like UniProtKB/TrEMBL
  SSF48452 UniProtKB/TrEMBL
  Tricorn protease domain 2 UniProtKB/TrEMBL
UniProt A0A8I6GJJ5 ENTREZGENE, UniProtKB/TrEMBL
  F1LV01 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Wdr19  WD repeat domain 19   Wdr19_predicted  WD repeat domain 19 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Wdr19_predicted  WD repeat domain 19 (predicted)  RGD1306997_predicted  similar to WD repeat membrane protein (predicted)  Symbol and Name updated 1299863 APPROVED
2005-01-20 RGD1306997_predicted  similar to WD repeat membrane protein (predicted)  LOC305349_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC305349_predicted  similar to WD repeat membrane protein (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL