Upk3a (uroplakin 3A) - Rat Genome Database

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Gene: Upk3a (uroplakin 3A) Rattus norvegicus
Analyze
Symbol: Upk3a
Name: uroplakin 3A
RGD ID: 1310633
Description: Predicted to be involved in epithelial cell differentiation; urea transport; and water transport. Predicted to act upstream of or within several processes, including potassium ion homeostasis; sodium ion homeostasis; and urinary bladder development. Predicted to be located in apical plasma membrane. Predicted to be active in apical plasma membrane urothelial plaque. Orthologous to human UPK3A (uroplakin 3A); INTERACTS WITH 6-propyl-2-thiouracil; alpha-Zearalanol; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC315190; uroplakin-3a
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr87118,008,898 - 118,019,865 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl7118,014,108 - 118,019,870 (+)EnsemblGRCr8
mRatBN7.27116,128,981 - 116,139,950 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7116,134,874 - 116,139,948 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx7117,885,813 - 117,890,893 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.07120,111,548 - 120,116,628 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.07120,080,987 - 120,086,067 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.07125,920,357 - 125,925,430 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7125,920,357 - 125,925,430 (+)Ensemblrn6Rnor6.0
Rnor_5.07125,634,480 - 125,639,553 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.47123,032,773 - 123,037,846 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera7112,433,330 - 112,438,403 (+)NCBICelera
RGSC_v3.17123,066,999 - 123,071,942 (+)NCBI
Cytogenetic Map7q34NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

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. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
5. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:8175808   PMID:10514386   PMID:12388410   PMID:19056867   PMID:21301865   PMID:22323295   PMID:23376485   PMID:23533145   PMID:26046524  


Genomics

Comparative Map Data
Upk3a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr87118,008,898 - 118,019,865 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl7118,014,108 - 118,019,870 (+)EnsemblGRCr8
mRatBN7.27116,128,981 - 116,139,950 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7116,134,874 - 116,139,948 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx7117,885,813 - 117,890,893 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.07120,111,548 - 120,116,628 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.07120,080,987 - 120,086,067 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.07125,920,357 - 125,925,430 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7125,920,357 - 125,925,430 (+)Ensemblrn6Rnor6.0
Rnor_5.07125,634,480 - 125,639,553 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.47123,032,773 - 123,037,846 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera7112,433,330 - 112,438,403 (+)NCBICelera
RGSC_v3.17123,066,999 - 123,071,942 (+)NCBI
Cytogenetic Map7q34NCBI
UPK3A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382245,284,949 - 45,295,874 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2245,284,924 - 45,295,874 (+)Ensemblhg38GRCh38
GRCh372245,680,830 - 45,691,755 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362244,059,553 - 44,070,419 (+)NCBIBuild 36Build 36hg18NCBI36
Build 342244,001,425 - 44,012,291NCBI
Celera2229,592,413 - 29,603,314 (+)NCBICelera
Cytogenetic Map22q13.31NCBI
HuRef2228,626,095 - 28,636,548 (+)NCBIHuRef
CHM1_12245,639,576 - 45,650,477 (+)NCBICHM1_1
T2T-CHM13v2.02245,770,156 - 45,781,101 (+)NCBIT2T-CHM13v2.0
Upk3a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391584,901,342 - 84,906,761 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1584,901,342 - 84,906,748 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm381585,017,141 - 85,022,560 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1585,017,141 - 85,022,547 (+)Ensemblmm10GRCm38
MGSCv371584,847,571 - 84,852,990 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361584,844,986 - 84,850,300 (+)NCBIMGSCv36mm8
Celera1587,149,444 - 87,154,863 (+)NCBICelera
Cytogenetic Map15E2NCBI
cM Map1540.25NCBI
Upk3a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541329,672,970 - 29,682,245 (+)Ensembl
ChiLan1.0NW_00495541329,673,160 - 29,679,604 (+)NCBIChiLan1.0ChiLan1.0
UPK3A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22355,109,776 - 55,121,690 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12257,805,230 - 57,817,146 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02226,170,186 - 26,182,100 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12244,351,511 - 44,362,863 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2244,351,511 - 44,362,863 (+)EnsemblpanPan2panpan1.1
UPK3A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11020,747,139 - 20,755,131 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1020,747,140 - 20,755,162 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha1020,667,736 - 20,675,741 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.01021,479,967 - 21,487,971 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1021,479,968 - 21,488,054 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11021,200,536 - 21,208,489 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01021,514,037 - 21,522,000 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01021,694,579 - 21,702,582 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Upk3a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244049454,421,977 - 4,427,783 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366294,421,966 - 4,427,312 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049366294,421,977 - 4,427,783 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
UPK3A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl54,109,938 - 4,119,289 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.154,109,985 - 4,122,272 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.251,324,192 - 1,387,438 (-)NCBISscrofa10.2Sscrofa10.2susScr3
UPK3A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11927,749,232 - 27,761,309 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1927,750,876 - 27,761,295 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366604597,572,811 - 97,586,937 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Upk3a
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247524,351,164 - 4,361,235 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046247524,354,415 - 4,361,250 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Upk3a
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11254,393,989 - 254,399,035 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Upk3a
72 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:36
Count of miRNA genes:31
Interacting mature miRNAs:36
Transcripts:ENSRNOT00000018365
Prediction methods: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
1300179Kidm5Kidney mass QTL 53.51kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)792388565119280177Rat
1331728Bp214Blood pressure QTL 2142.825arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)782111245123048330Rat
1331731Bp216Blood pressure QTL 2162.851arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7104186212135371468Rat
70159Bp61Blood pressure QTL 610.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)773618702118618702Rat
631687Hcas1Hepatocarcinoma susceptibility QTL 13.90.001liver integrity trait (VT:0010547)liver tumorous lesion volume to total liver volume ratio (CMO:0001082)793302009131686183Rat
61397Bw17Body weight QTL 176.3body mass (VT:0001259)body weight (CMO:0000012)795485047137014596Rat
1358914Bp266Blood pressure QTL 266arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7115313999136544683Rat
631504Cm27Cardiac mass QTL 273.45heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)746307490127866166Rat
634322Bw12Body weight QTL 120body mass (VT:0001259)body weight (CMO:0000012)785043242130043242Rat
70173Niddm19Non-insulin dependent diabetes mellitus QTL 194.330.00005blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)785497398130497398Rat
1549899Stresp8Stress response QTL 84.370.0008stress-related behavior trait (VT:0010451)defensive burying duration (CMO:0001961)792362341137014596Rat
2317052Aia17Adjuvant induced arthritis QTL 172.13joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)783626689128626689Rat
631529Tls2T-lymphoma susceptibility QTL 200.001thymus integrity trait (VT:0010555)percentage of study population developing T-cell lymphomas during a period of time (CMO:0001911)782111382132099989Rat
731176Glom5Glomerulus QTL 52.50.0035kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)798549867137014596Rat
7411607Foco15Food consumption QTL 150.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)777807807122807807Rat
631201Panci1Pancreas inflammation QTL 100.001pancreas integrity trait (VT:0010560)percentage of study population displaying chronic pancreatitis at a point in time (CMO:0001214)773557047118557047Rat
1331768Kidm10Kidney mass QTL 104.62096kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)782111245123048330Rat
2313102Bmd79Bone mineral density QTL 792.30.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)796700404118618702Rat
61357Bp38Blood pressure QTL 381.60.052arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)740540077123682549Rat
1331748Bp215Blood pressure QTL 2154.043arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7110725024135371468Rat
61428Scl3Serum cholesterol level QTL 33.2blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)7100548246137014596Rat
1331746Kidm9Kidney mass QTL 93.934kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)782111245134948181Rat
7411654Foco25Food consumption QTL 259.30.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)777807807122807807Rat
2299163Iddm34Insulin dependent diabetes mellitus QTL 342.71blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)7116269196132020414Rat
10402855Bp379Blood pressure QTL 3790.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)778682549123682549Rat
631540Bw9Body weight QTL 94.5body mass (VT:0001259)body weight (CMO:0000012)771621154119349044Rat
1358891Bp265Blood pressure QTL 2652.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)771827901136544683Rat


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
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
16 1 3 77 24 35 10 32 10 1 133 36 1 75 70 60 25

Sequence


Ensembl Acc Id: ENSRNOT00000018365   ⟹   ENSRNOP00000018365
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl7118,014,968 - 118,019,870 (+)Ensembl
mRatBN7.2 Ensembl7116,134,874 - 116,139,948 (+)Ensembl
Rnor_6.0 Ensembl7125,920,357 - 125,925,430 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000123772   ⟹   ENSRNOP00000111621
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl7118,014,108 - 118,019,863 (+)Ensembl
RefSeq Acc Id: NM_001130507   ⟹   NP_001123979
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr87118,014,790 - 118,019,863 (+)NCBI
mRatBN7.27116,134,874 - 116,139,948 (+)NCBI
Rnor_6.07125,920,357 - 125,925,430 (+)NCBI
Rnor_5.07125,634,480 - 125,639,553 (+)NCBI
RGSC_v3.47123,032,773 - 123,037,846 (+)RGD
Celera7112,433,330 - 112,438,403 (+)RGD
Sequence:
RefSeq Acc Id: XM_039079296   ⟹   XP_038935224
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr87118,008,898 - 118,019,865 (+)NCBI
mRatBN7.27116,128,981 - 116,139,950 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001123979 (Get FASTA)   NCBI Sequence Viewer  
  XP_038935224 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM15591 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000018365
  ENSRNOP00000018365.6
  ENSRNOP00000111621.1
RefSeq Acc Id: NP_001123979   ⟸   NM_001130507
- Peptide Label: precursor
- UniProtKB: D3ZZ76 (UniProtKB/TrEMBL),   A6HTD1 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000018365   ⟸   ENSRNOT00000018365
RefSeq Acc Id: XP_038935224   ⟸   XM_039079296
- Peptide Label: isoform X1
Ensembl Acc Id: ENSRNOP00000111621   ⟸   ENSRNOT00000123772

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZZ76-F1-model_v2 AlphaFold D3ZZ76 1-287 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1310633 AgrOrtholog
BioCyc Gene G2FUF-32564 BioCyc
Ensembl Genes ENSRNOG00000013593 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000018365 ENTREZGENE
  ENSRNOT00000018365.7 UniProtKB/TrEMBL
  ENSRNOT00000123772.1 UniProtKB/TrEMBL
InterPro Uroplakin-3 UniProtKB/TrEMBL
  Uroplakin-3a UniProtKB/TrEMBL
KEGG Report rno:315190 UniProtKB/TrEMBL
NCBI Gene 315190 ENTREZGENE
PANTHER PTHR15446 UniProtKB/TrEMBL
  PTHR15446:SF17 UniProtKB/TrEMBL
PhenoGen Upk3a PhenoGen
RatGTEx ENSRNOG00000013593 RatGTEx
UniProt A0ABK0M7U1_RAT UniProtKB/TrEMBL
  A6HTD1 ENTREZGENE, UniProtKB/TrEMBL
  D3ZZ76 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Upk3a  uroplakin 3A   Upk3a_predicted  uroplakin 3A (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Upk3a_predicted  uroplakin 3A (predicted)      Symbol and Name status set to approved 70820 APPROVED