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

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Gene: Topaz1 (testis and ovary specific TOPAZ 1) Rattus norvegicus
Analyze
Symbol: Topaz1
Name: testis and ovary specific TOPAZ 1
RGD ID: 1563398
Description: Predicted to be involved in spermatid development and spermatocyte division. Predicted to act upstream of or within apoptotic process; ncRNA transcription; and positive regulation of meiotic cell cycle phase transition. 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
mRatBN7.28122,358,243 - 122,412,875 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl8122,358,243 - 122,412,875 (+)Ensembl
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 (+)NCBIRGSC3.4rn4RGSC3.4
Celera8121,473,442 - 121,530,654 (+)NCBICelera
Cytogenetic Map8q32NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction 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
mRatBN7.28122,358,243 - 122,412,875 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl8122,358,243 - 122,412,875 (+)Ensembl
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 (+)NCBIRGSC3.4rn4RGSC3.4
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.p13 Ensembl344,241,886 - 44,332,098 (+)EnsemblGRCh38hg38GRCh38
GRCh37344,283,378 - 44,373,590 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36344,258,382 - 44,348,594 (+)NCBINCBI36hg18NCBI36
Celera344,221,424 - 44,311,638 (+)NCBI
Cytogenetic Map3p21.31NCBI
HuRef344,326,973 - 44,417,182 (+)NCBIHuRef
CHM1_1344,233,507 - 44,323,686 (+)NCBICHM1_1
T2T-CHM13v2.0344,257,474 - 44,347,952 (+)NCBI
Topaz1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm399122,576,264 - 122,631,200 (+)NCBIGRCm39mm39
GRCm39 Ensembl9122,576,411 - 122,631,200 (+)Ensembl
GRCm389122,747,199 - 122,802,135 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl9122,747,346 - 122,802,135 (+)EnsemblGRCm38mm10GRCm38
MGSCv379122,656,464 - 122,711,253 (+)NCBIGRCm37mm9NCBIm37
MGSCv369122,680,835 - 122,711,253 (+)NCBImm8
Celera9123,196,291 - 123,251,031 (+)NCBICelera
Cytogenetic Map9F4NCBI
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
PanPan1.1345,190,901 - 45,280,601 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl345,190,960 - 45,280,601 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0344,131,729 - 44,221,846 (+)NCBIMhudiblu_PPA_v0panPan3
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 (-)NCBI
ROS_Cfam_1.0232,256,165 - 2,334,127 (-)NCBI
UMICH_Zoey_3.1232,096,692 - 2,174,636 (-)NCBI
UNSW_CanFamBas_1.0232,221,131 - 2,299,082 (-)NCBI
UU_Cfam_GSD_1.0232,189,445 - 2,267,387 (-)NCBI
Topaz1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118198,785,413 - 198,853,817 (-)NCBI
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 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl225,666,215 - 5,757,697 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666041161,424,967 - 161,523,855 (-)NCBIVero_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_1.0hetGla2
HetGla 1.0NW_00462473076,011,384 - 76,083,927 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
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


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1554321Bmd3Bone mineral density QTL 37.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)840952565123900184Rat
61437Cia6Collagen induced arthritis QTL 6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)882460758122812818Rat
738011Anxrr9Anxiety related response QTL 96.1exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)893535351123900184Rat
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
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
2300182Bmd56Bone mineral density QTL 565.4femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)895718998123900184Rat

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.


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


Reference Sequences
RefSeq Acc Id: ENSRNOT00000036545   ⟹   ENSRNOP00000032345
RefSeq Status:
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
mRatBN7.28122,358,243 - 122,412,875 (+)NCBI
RefSeq Acc Id: XM_006244204   ⟹   XP_006244266
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28122,359,195 - 122,412,875 (+)NCBI
Rnor_6.08131,788,816 - 131,843,668 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001363842 (Get FASTA)   NCBI Sequence Viewer  
  XP_006244266 (Get FASTA)   NCBI Sequence Viewer  
  XP_008764950 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein D3ZUC6 (Get FASTA)   NCBI Sequence Viewer  
  EDL76794 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: XP_006244266   ⟸   XM_006244204
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008764950   ⟸   XM_008766728
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSRNOP00000032345   ⟸   ENSRNOT00000036545
RefSeq Acc Id: NP_001363842   ⟸   NM_001376913

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


Strain Variation

Strain Sequence Variants (MRatBN7.2)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BUF/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
DA/OlaHsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE16/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/FarMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/NRrrcMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MWF/Hsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHR/OlalpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WAG/RijCrl (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Damaging Variants


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
8 131791112 131791113 A G snv WKY/N (MCW), WKY/NCrl (RGD), WKY/N (2020), WKY/NHsd (RGD), WKY/NCrl (2019), WKY/Gcrc (RGD)


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
8 130946154 130946155 A G snv WKY/NCrl (KNAW), WKY/N (KNAW), WKY/Gcrc (KNAW), WKY/NHsd (KNAW)
8 130947559 130947560 C T snv ACI/N (KNAW), ACI/EurMcwi (KNAW), DA/BklArbNsi (KNAW), F344/NRrrc (SOLiD) (KNAW), F344/NCrl (KNAW), F344/NHsd (KNAW), LEW/Crl (KNAW), LEW/NCrl (KNAW), MNS/Gib (KNAW), SBH/Ygl (KNAW), SBN/Ygl (KNAW), F344/NRrrc (Illumina) (KNAW), SDLEF7/Barth (UDEL), LE/OrlBarth (UDEL), F344/DuCrlCrlj (KyushuU), F344/NSlc (KyushuU), F344/Stm (KyushuU), HWY/Slc (KyushuU), F344/Jcl (KyushuU), ZFDM (KyushuU), MHS/Gib (KNAW), WN/N (KNAW), SBN/Ygl (MCW), ACI/EurMcwi (MCW), SBH/Ygl (MCW)


Assembly: mRatBN7.2

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
8 122360539 122360540 A G snv WKY/N (2020), WKY/NCrl (2019)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1563398 AgrOrtholog
BioCyc Gene G2FUF-28639 BioCyc
Ensembl Genes ENSRNOG00000025601 Ensembl, ENTREZGENE
Ensembl Protein ENSRNOP00000032345 ENTREZGENE
Ensembl Transcript ENSRNOT00000036545 ENTREZGENE
InterPro TOPAZ1 UniProtKB/Swiss-Prot
  TOPAZ1_dom UniProtKB/Swiss-Prot
NCBI Gene 301075 ENTREZGENE
PANTHER PTHR35671 UniProtKB/Swiss-Prot
Pfam Asp_Glu_race_2 UniProtKB/Swiss-Prot
PhenoGen Topaz1 PhenoGen
UniProt D3ZUC6 ENTREZGENE, 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