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 ncRNA 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
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr88131,235,714 - 131,290,359 (+)NCBIGRCr8
mRatBN7.28122,358,243 - 122,412,875 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl8122,358,243 - 122,412,875 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx8127,952,043 - 128,007,121 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.08126,150,983 - 126,206,061 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.08123,977,202 - 124,031,791 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.08131,788,816 - 131,843,668 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8131,789,575 - 131,843,713 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.08130,944,799 - 130,998,710 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48127,448,509 - 127,502,514 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera8121,473,442 - 121,530,654 (+)NCBICelera
Cytogenetic Map8q32NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

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 (+)NCBIGRCr8
mRatBN7.28122,358,243 - 122,412,875 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl8122,358,243 - 122,412,875 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx8127,952,043 - 128,007,121 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.08126,150,983 - 126,206,061 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.08123,977,202 - 124,031,791 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.08131,788,816 - 131,843,668 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8131,789,575 - 131,843,713 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.08130,944,799 - 130,998,710 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48127,448,509 - 127,502,514 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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 (+)EnsemblGRCh38hg38GRCh38
GRCh37344,283,378 - 44,373,590 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36344,258,382 - 44,348,594 (+)NCBINCBI36Build 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 Ensembl
GRCm389122,747,199 - 122,802,135 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl9122,747,346 - 122,802,135 (+)EnsemblGRCm38mm10GRCm38
MGSCv379122,656,464 - 122,711,253 (+)NCBIGRCm37MGSCv37mm9NCBIm37
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 (-)EnsemblChiLan1.0
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 (+)Ensemblpanpan1.1panPan2
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 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha232,044,773 - 2,122,720 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0232,256,165 - 2,334,127 (-)NCBIROS_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_1.0
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 (-)EnsemblSpeTri2.0SpeTri2.0 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 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
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 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
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_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473076,011,384 - 76,083,927 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Topaz1
318 total Variants
miRNA Target Status

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 (mRatBN7.2)
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)893535351123900184Rat
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
1554321Bmd3Bone mineral density QTL 37.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)840952565123900184Rat
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
61437Cia6Collagen induced arthritis QTL 6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)882460758122812818Rat
2300182Bmd56Bone mineral density QTL 565.4femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)895718998123900184Rat

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
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 17 4
Low 12 7 7 1 1 7 14 19 8 1
Below cutoff 2 6 19 8 18 8 7 8 6 2 12 3 7

Sequence


RefSeq Acc Id: ENSRNOT00000036545   ⟹   ENSRNOP00000032345
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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
- UniProtKB: R9PXW9 (UniProtKB/Swiss-Prot),   D3ZUC6 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_008764950   ⟸   XM_008766728
- Peptide Label: isoform X2
- UniProtKB: R9PXW9 (UniProtKB/Swiss-Prot),   D3ZUC6 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000032345   ⟸   ENSRNOT00000036545
RefSeq Acc Id: NP_001363842   ⟸   NM_001376913
- UniProtKB: R9PXW9 (UniProtKB/Swiss-Prot),   D3ZUC6 (UniProtKB/Swiss-Prot),   A0A8L2QH74 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063121377   ⟸   XM_063265307
- Peptide Label: isoform X3
RefSeq Acc Id: XP_063121378   ⟸   XM_063265308
- Peptide Label: isoform X4
Protein Domains
Protein TOPAZ1

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, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000036545 ENTREZGENE
  ENSRNOT00000036545.6 UniProtKB/TrEMBL
InterPro TOPAZ1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TOPAZ1_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 301075 ENTREZGENE
PANTHER PROTEIN TOPAZ1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR35671 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Asp_Glu_race_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
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