Topaz1 (testis and ovary specific TOPAZ 1) - Rat Genome Database

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Gene: Topaz1 (testis and ovary specific TOPAZ 1) Rattus norvegicus
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Symbol: Topaz1
Name: testis and ovary specific TOPAZ 1
RGD ID: 1563398
Description: Predicted to be involved in spermatocyte division. Predicted to act upstream of or within apoptotic process; ectopic germ cell programmed cell death; and lncRNA transcription. Predicted to be located in cytosol. Orthologous to human TOPAZ1 (testis and ovary specific TOPAZ 1); INTERACTS WITH 1-naphthyl isothiocyanate; bisphenol A; perfluorooctanoic acid.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: hypothetical LOC301075; LOC301075; RGD1563398; testis and ovary specific PAZ domain containing 1; testis- and ovary-specific PAZ domain-containing protein 1
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
GRCr88131,235,714 - 131,290,359 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl8131,236,522 - 131,290,342 (+)EnsemblGRCr8
mRatBN7.28122,358,243 - 122,412,875 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl8122,358,243 - 122,412,875 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx8127,952,043 - 128,007,121 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.08126,150,983 - 126,206,061 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.08123,977,202 - 124,031,791 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.08131,788,816 - 131,843,668 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8131,789,575 - 131,843,713 (+)Ensemblrn6Rnor6.0
Rnor_5.08130,944,799 - 130,998,710 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.48127,448,509 - 127,502,514 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera8121,473,442 - 121,530,654 (+)NCBICelera
Cytogenetic Map8q32NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
cytosol  (IEA)

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. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:26358182  


Genomics

Comparative Map Data
Topaz1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr88131,235,714 - 131,290,359 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl8131,236,522 - 131,290,342 (+)EnsemblGRCr8
mRatBN7.28122,358,243 - 122,412,875 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl8122,358,243 - 122,412,875 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx8127,952,043 - 128,007,121 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.08126,150,983 - 126,206,061 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.08123,977,202 - 124,031,791 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.08131,788,816 - 131,843,668 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8131,789,575 - 131,843,713 (+)Ensemblrn6Rnor6.0
Rnor_5.08130,944,799 - 130,998,710 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.48127,448,509 - 127,502,514 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera8121,473,442 - 121,530,654 (+)NCBICelera
Cytogenetic Map8q32NCBI
TOPAZ1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38344,241,886 - 44,336,689 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl344,241,886 - 44,332,098 (+)Ensemblhg38GRCh38
GRCh37344,283,378 - 44,373,590 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36344,258,382 - 44,348,594 (+)NCBIBuild 36Build 36hg18NCBI36
Celera344,221,424 - 44,311,638 (+)NCBICelera
Cytogenetic Map3p21.31NCBI
HuRef344,326,973 - 44,417,182 (+)NCBIHuRef
CHM1_1344,233,507 - 44,323,686 (+)NCBICHM1_1
T2T-CHM13v2.0344,257,474 - 44,352,542 (+)NCBIT2T-CHM13v2.0
Topaz1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm399122,576,264 - 122,631,200 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl9122,576,411 - 122,631,200 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm389122,747,199 - 122,802,135 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl9122,747,346 - 122,802,135 (+)Ensemblmm10GRCm38
MGSCv379122,656,464 - 122,711,253 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv369122,680,835 - 122,711,253 (+)NCBIMGSCv36mm8
Celera9123,196,291 - 123,251,031 (+)NCBICelera
Cytogenetic Map9F4NCBI
cM Map973.1NCBI
Topaz1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542027,048,713 - 27,107,006 (-)Ensembl
ChiLan1.0NW_00495542027,048,650 - 27,106,983 (-)NCBIChiLan1.0ChiLan1.0
TOPAZ1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2244,188,877 - 44,279,430 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1344,193,643 - 44,284,197 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0344,131,729 - 44,221,846 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1345,190,901 - 45,280,601 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl345,190,960 - 45,280,601 (+)EnsemblpanPan2panpan1.1
TOPAZ1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1232,009,526 - 2,086,669 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl232,009,613 - 2,086,697 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha232,044,773 - 2,122,720 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0232,256,165 - 2,334,127 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
UMICH_Zoey_3.1232,096,692 - 2,174,636 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0232,221,131 - 2,299,082 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0232,189,445 - 2,267,387 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Topaz1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118198,785,413 - 198,853,817 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366951,137,867 - 1,206,152 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049366951,137,867 - 1,206,152 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TOPAZ1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1327,574,767 - 27,643,980 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.11327,574,718 - 27,644,009 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
TOPAZ1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1225,665,735 - 5,757,697 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl225,666,215 - 5,757,697 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_023666041161,424,967 - 161,523,855 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Topaz1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473076,010,503 - 76,068,979 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462473076,011,384 - 76,083,927 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Topaz1
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v18113,854,527 - 113,909,620 (+)NCBIRrattus_CSIRO_v1

miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:144
Count of miRNA genes:119
Interacting mature miRNAs:126
Transcripts:ENSRNOT00000036545
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
738011Anxrr9Anxiety related response QTL 96.1exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)8102413464132782436Rat
2303171Bp331Blood pressure QTL 3315.570.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)8105462581132782436Rat
634332Pia18Pristane induced arthritis QTL 184joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)884192326132782436Rat
1300171Bp184Blood pressure QTL 1843.66arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)879394435132782436Rat
61437Cia6Collagen induced arthritis QTL 6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)891340911131690273Rat

Markers in Region
AI010851  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.28122,359,889 - 122,359,979 (+)MAPPERmRatBN7.2
Rnor_6.08131,790,463 - 131,790,552NCBIRnor6.0
Rnor_5.08130,945,505 - 130,945,594UniSTSRnor5.0
RGSC_v3.48127,449,211 - 127,449,300UniSTSRGSC3.4
Celera8121,476,265 - 121,476,354UniSTS
RH 3.4 Map81273.8UniSTS
Cytogenetic Map8q32UniSTS


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
sensory system
visual system
15 9 22 51 65 64 33 35 33 6 213 78 1 34 79 68 31 1 1

Sequence


Ensembl Acc Id: ENSRNOT00000036545   ⟹   ENSRNOP00000032345
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl8131,236,522 - 131,290,342 (+)Ensembl
mRatBN7.2 Ensembl8122,358,243 - 122,412,875 (+)Ensembl
Rnor_6.0 Ensembl8131,789,575 - 131,843,713 (+)Ensembl
RefSeq Acc Id: NM_001376913   ⟹   NP_001363842
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88131,235,714 - 131,290,342 (+)NCBI
mRatBN7.28122,358,243 - 122,412,875 (+)NCBI
RefSeq Acc Id: XM_006244204   ⟹   XP_006244266
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88131,236,666 - 131,290,359 (+)NCBI
mRatBN7.28122,359,195 - 122,412,875 (+)NCBI
Rnor_6.08131,788,816 - 131,843,668 (+)NCBI
Rnor_5.08130,944,799 - 130,998,710 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008766728   ⟹   XP_008764950
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88131,236,666 - 131,290,359 (+)NCBI
mRatBN7.28122,359,195 - 122,412,875 (+)NCBI
Rnor_6.08131,788,816 - 131,843,668 (+)NCBI
Sequence:
RefSeq Acc Id: XM_063265307   ⟹   XP_063121377
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88131,236,666 - 131,290,359 (+)NCBI
RefSeq Acc Id: XM_063265308   ⟹   XP_063121378
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88131,236,666 - 131,284,534 (+)NCBI
RefSeq Acc Id: XP_006244266   ⟸   XM_006244204
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008764950   ⟸   XM_008766728
- Peptide Label: isoform X2
- Sequence:
Ensembl Acc Id: ENSRNOP00000032345   ⟸   ENSRNOT00000036545
RefSeq Acc Id: NP_001363842   ⟸   NM_001376913
- UniProtKB: A0A8L2QH74 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063121377   ⟸   XM_063265307
- Peptide Label: isoform X3
- UniProtKB: R9PXW9 (UniProtKB/Swiss-Prot),   D3ZUC6 (UniProtKB/Swiss-Prot)
RefSeq Acc Id: XP_063121378   ⟸   XM_063265308
- Peptide Label: isoform X4

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZUC6-F1-model_v2 AlphaFold D3ZUC6 1-1646 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:1563398 AgrOrtholog
BioCyc Gene G2FUF-28639 BioCyc
Ensembl Genes ENSRNOG00000025601 Ensembl, ENTREZGENE
Ensembl Transcript ENSRNOT00000036545 ENTREZGENE
InterPro TOPAZ1 UniProtKB/Swiss-Prot
  TOPAZ1_dom UniProtKB/Swiss-Prot
NCBI Gene 301075 ENTREZGENE
PANTHER PROTEIN TOPAZ1 UniProtKB/Swiss-Prot
  PTHR35671 UniProtKB/Swiss-Prot
Pfam Asp_Glu_race_2 UniProtKB/Swiss-Prot
PhenoGen Topaz1 PhenoGen
RatGTEx ENSRNOG00000025601 RatGTEx
UniProt A0A8L2QH74 ENTREZGENE, UniProtKB/TrEMBL
  D3ZUC6 ENTREZGENE
  R9PXW9 ENTREZGENE
  TOPZ1_RAT UniProtKB/Swiss-Prot
UniProt Secondary R9PXW9 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-06-17 Topaz1  testis and ovary specific TOPAZ 1  Topaz1  testis and ovary specific PAZ domain containing 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-10-17 Topaz1  testis and ovary specific PAZ domain containing 1  RGD1563398  RGD1563398  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1563398  RGD1563398   RGD1563398_predicted  RGD1563398 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-07 RGD1563398_predicted  RGD1563398 (predicted)  LOC301075  hypothetical LOC301075  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC301075  hypothetical LOC301075      Symbol and Name status set to provisional 70820 PROVISIONAL