Uty (ubiquitously transcribed tetratricopeptide repeat containing, Y-linked) - Rat Genome Database

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Gene: Uty (ubiquitously transcribed tetratricopeptide repeat containing, Y-linked) Rattus norvegicus
Analyze
Symbol: Uty
Name: ubiquitously transcribed tetratricopeptide repeat containing, Y-linked
RGD ID: 1565481
Description: Enables chromatin binding activity. Predicted to act upstream of or within several processes, including animal organ development; cardiac muscle cell contraction; and regulation of chromatin silencing. Located in nucleus; PARTICIPATES IN histone modification pathway; renal cell carcinoma pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 8-Br-cAMP (ortholog); aflatoxin B1 (ortholog).
Type: protein-coding
RefSeq Status: MODEL
Also known as: histone demethylase UTY; histone demethylase UTY-like; Kdm6a; LOC103694558; LOC317178; lysine (K)-specific demethylase 6A; lysine demethylase 6A; lysine-specific demethylase 6A; RGD1565481; ubiquitously transcribed tetratricopeptide repeat gene, X chromosome; ubiquitously transcribed tetratricopeptide repeat gene, Y chromosome; ubiquitously transcribed tetratricopeptide repeat, X chromosome; Utx
RGD Orthologs
Human
Mouse
Pig
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2Y942,838 - 1,105,313 (-)NCBImRatBN7.2
mRatBN7.2 EnsemblY924,168 - 1,103,422 (-)Ensembl
Rnor_6.0Y1,065,274 - 1,206,127 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblY989,240 - 1,206,096 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X5,591,847 - 5,731,843 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
CeleraX4,851,606 - 4,991,287 (-)NCBICelera
Cytogenetic MapYq11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Audenet F, etal., BJU Int. 2012 Jun;109(12):1864-70. doi: 10.1111/j.1464-410X.2011.10661.x. Epub 2011 Oct 28.
2. Black JC, etal., Mol Cell. 2012 Nov 30;48(4):491-507. doi: 10.1016/j.molcel.2012.11.006.
3. Gao YB, etal., Nat Genet. 2014 Oct;46(10):1097-102. doi: 10.1038/ng.3076. Epub 2014 Aug 24.
4. Henriquez B, etal., Mol Cell Neurosci. 2013 Nov;57:130-43. doi: 10.1016/j.mcn.2013.07.012. Epub 2013 Aug 8.
5. Komers R, etal., Lab Invest. 2013 May;93(5):543-52. doi: 10.1038/labinvest.2013.47. Epub 2013 Mar 18.
6. Mar BG, etal., Leukemia. 2012 Aug;26(8):1881-3. doi: 10.1038/leu.2012.56. Epub 2012 Mar 1.
7. OMIM Disease Annotation Pipeline
8. Paolicchi E, etal., Crit Rev Oncol Hematol. 2013 May;86(2):97-103. doi: 10.1016/j.critrevonc.2012.11.008. Epub 2012 Dec 23.
9. Patani N, etal., Anticancer Res. 2011 Dec;31(12):4115-25.
10. RGD automated data pipeline
11. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
12. RGD automated import pipeline for gene-chemical interactions
13. RGD comprehensive gene curation
14. Shen Y, etal., BMC Cancer. 2012 Oct 12;12:470. doi: 10.1186/1471-2407-12-470.
15. Shilatifard A Annu Rev Biochem. 2012;81:65-95. doi: 10.1146/annurev-biochem-051710-134100.
16. Vieira FQ, etal., Endocr Relat Cancer. 2013 Dec 16;21(1):51-61. doi: 10.1530/ERC-13-0375. Print 2014 Feb.
17. Wilson BG and Roberts CW, Nat Rev Cancer. 2011 Jun 9;11(7):481-92. doi: 10.1038/nrc3068.
Additional References at PubMed
PMID:20333173   PMID:22192413   PMID:22949634   PMID:23028370   PMID:24759410  


Genomics

Comparative Map Data
Uty
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2Y942,838 - 1,105,313 (-)NCBImRatBN7.2
mRatBN7.2 EnsemblY924,168 - 1,103,422 (-)Ensembl
Rnor_6.0Y1,065,274 - 1,206,127 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblY989,240 - 1,206,096 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X5,591,847 - 5,731,843 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
CeleraX4,851,606 - 4,991,287 (-)NCBICelera
Cytogenetic MapYq11NCBI
UTY
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 EnsemblY13,234,577 - 13,480,673 (-)EnsemblGRCh38hg38GRCh38
GRCh38Y13,231,827 - 13,480,670 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37Y15,360,259 - 15,592,550 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36Y13,869,657 - 14,101,944 (-)NCBINCBI36hg18NCBI36
Build 34Y13,873,045 - 14,030,681NCBI
CeleraX2,342,975 - 2,575,256 (-)NCBI
Cytogenetic MapYq11.221NCBI
HuRefY10,010,130 - 10,240,194 (-)NCBIHuRef
Uty
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39Y1,085,187 - 1,245,787 (-)NCBIGRCm39mm39
GRCm39 EnsemblY1,096,861 - 1,245,759 (-)Ensembl
GRCm38Y1,085,187 - 1,245,773 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblY1,096,861 - 1,245,759 (-)EnsemblGRCm38mm10GRCm38
MGSCv37Y433,587 - 582,181 (-)NCBIGRCm37mm9NCBIm37
MGSCv36Y439,206 - 582,063 (-)NCBImm8
CeleraY3,928,367 - 4,071,302 (-)NCBICelera
Cytogenetic MapYpterNCBI
LOC110255320
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1Y8,937,949 - 9,087,971 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1

Position Markers
G34976  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X4,377,831 - 4,377,925 (+)MAPPERmRatBN7.2
Rnor_6.0X4,846,526 - 4,846,619NCBIRnor6.0
Rnor_5.0X5,632,569 - 5,632,662UniSTSRnor5.0
RGSC_v3.4X15,954,008 - 15,954,101UniSTSRGSC3.4
CeleraX4,892,712 - 4,892,805UniSTS

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:317
Count of miRNA genes:138
Interacting mature miRNAs:162
Transcripts:ENSRNOT00000005742, ENSRNOT00000071375, ENSRNOT00000073473, ENSRNOT00000075712
Prediction methods:Microtar, Miranda, Pita, 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 4 12 4 10 4 3 3 4 4 4 6 3
Low 3 31 31 31 1 31 1 3 57 27 18 1 1
Below cutoff 2 12 5 6 5 2 3 3 3 3 4 2

Sequence

Nucleotide Sequences
RefSeq Transcripts XM_008773695 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008773696 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017602447 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017602449 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039100671 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039100672 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039100673 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039100674 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039100675 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039100676 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039100677 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039100678 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039100679 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039100680 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039100682 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039100683 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039100684 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039100685 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005498739 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC241873 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC242055 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FJ775728 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225011 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232470 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  GAPM01000002 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  GATN01000009 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000495 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000082648
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblY946,608 - 1,103,401 (-)Ensembl
Rnor_6.0 EnsemblY989,957 - 1,206,096 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000093013
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblY945,299 - 1,103,324 (-)Ensembl
Rnor_6.0 EnsemblY989,240 - 1,206,026 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000119067   ⟹   ENSRNOP00000097587
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblY924,168 - 1,103,422 (-)Ensembl
RefSeq Acc Id: XM_008773695   ⟹   XP_008771917
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2Y943,152 - 1,103,529 (-)NCBI
Rnor_6.0Y1,065,274 - 1,206,127 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008773696   ⟹   XP_008771918
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2Y943,152 - 1,103,518 (-)NCBI
Rnor_6.0Y1,065,274 - 1,206,127 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017602447   ⟹   XP_017457936
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2Y943,152 - 1,103,065 (-)NCBI
Rnor_6.0Y1,065,274 - 1,205,762 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017602449   ⟹   XP_017457938
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2Y943,152 - 1,103,065 (-)NCBI
Rnor_6.0Y1,065,274 - 1,205,762 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039100671   ⟹   XP_038956599
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2Y943,152 - 1,103,530 (-)NCBI
RefSeq Acc Id: XM_039100672   ⟹   XP_038956600
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2Y943,152 - 1,103,525 (-)NCBI
RefSeq Acc Id: XM_039100673   ⟹   XP_038956601
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2Y943,152 - 1,103,529 (-)NCBI
RefSeq Acc Id: XM_039100674   ⟹   XP_038956602
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2Y943,152 - 1,103,530 (-)NCBI
RefSeq Acc Id: XM_039100675   ⟹   XP_038956603
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2Y943,152 - 1,103,521 (-)NCBI
RefSeq Acc Id: XM_039100676   ⟹   XP_038956604
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2Y943,152 - 1,103,544 (-)NCBI
RefSeq Acc Id: XM_039100677   ⟹   XP_038956605
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2Y943,152 - 1,103,523 (-)NCBI
RefSeq Acc Id: XM_039100678   ⟹   XP_038956606
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2Y943,152 - 1,103,520 (-)NCBI
RefSeq Acc Id: XM_039100679   ⟹   XP_038956607
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2Y943,152 - 1,065,382 (-)NCBI
RefSeq Acc Id: XM_039100680   ⟹   XP_038956608
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2Y943,152 - 1,048,814 (-)NCBI
RefSeq Acc Id: XM_039100682   ⟹   XP_038956610
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2Y942,838 - 1,103,517 (-)NCBI
RefSeq Acc Id: XM_039100683   ⟹   XP_038956611
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2Y942,838 - 1,037,927 (-)NCBI
RefSeq Acc Id: XM_039100684   ⟹   XP_038956612
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2Y942,838 - 1,014,658 (-)NCBI
RefSeq Acc Id: XM_039100685   ⟹   XP_038956613
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2Y991,077 - 1,105,313 (-)NCBI
RefSeq Acc Id: XR_005498739
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2Y989,677 - 1,105,313 (-)NCBI
Reference Sequences
RefSeq Acc Id: XP_008771918   ⟸   XM_008773696
- Peptide Label: isoform X7
- Sequence:
RefSeq Acc Id: XP_008771917   ⟸   XM_008773695
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017457936   ⟸   XM_017602447
- Peptide Label: isoform X14
- Sequence:
RefSeq Acc Id: XP_017457938   ⟸   XM_017602449
- Peptide Label: isoform X15
- Sequence:
RefSeq Acc Id: XP_038956610   ⟸   XM_039100682
- Peptide Label: isoform X13
RefSeq Acc Id: XP_038956611   ⟸   XM_039100683
- Peptide Label: isoform X16
RefSeq Acc Id: XP_038956612   ⟸   XM_039100684
- Peptide Label: isoform X17
RefSeq Acc Id: XP_038956604   ⟸   XM_039100676
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038956599   ⟸   XM_039100671
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038956602   ⟸   XM_039100674
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038956601   ⟸   XM_039100673
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038956600   ⟸   XM_039100672
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038956605   ⟸   XM_039100677
- Peptide Label: isoform X9
RefSeq Acc Id: XP_038956603   ⟸   XM_039100675
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038956606   ⟸   XM_039100678
- Peptide Label: isoform X10
RefSeq Acc Id: XP_038956607   ⟸   XM_039100679
- Peptide Label: isoform X11
RefSeq Acc Id: XP_038956608   ⟸   XM_039100680
- Peptide Label: isoform X12
RefSeq Acc Id: XP_038956613   ⟸   XM_039100685
- Peptide Label: isoform X18
RefSeq Acc Id: ENSRNOP00000097587   ⟸   ENSRNOT00000119067
Protein Domains
JmjC   TPR_REGION

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
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/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
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
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
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
Sequenced By: MCW
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
Sequenced By: MCW
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
Sequenced By: MCW
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/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
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
Sequenced By: MCW
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
Sequenced By: MCW
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
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
Visual CSV TAB Printer
Sequenced By: MCW
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
Sequenced By: MCW
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
Sequenced By: MCW
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
Sequenced By: MCW
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/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
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Sequenced By: MCW
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
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
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Sequenced By: MCW
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
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
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Sequenced By: MCW
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/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
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Sequenced By: MCW
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/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
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
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
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Sequenced By: MCW
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
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
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Sequenced By: MCW
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
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
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Sequenced By: MCW
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
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
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Sequenced By: MCW
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/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
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/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
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Sequenced By: MCW
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/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
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
WN/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1565481 AgrOrtholog
Ensembl Genes ENSRNOG00000060617 Ensembl
Gene3D-CATH 1.25.40.10 UniProtKB/TrEMBL
InterPro JmjC_dom UniProtKB/TrEMBL
  TPR-contain_dom UniProtKB/TrEMBL
  TPR-like_helical_dom_sf UniProtKB/TrEMBL
  TPR_repeat UniProtKB/TrEMBL
NCBI Gene 100310845 ENTREZGENE
Pfam JmjC UniProtKB/TrEMBL
  TPR_8 UniProtKB/TrEMBL
PhenoGen Uty PhenoGen
PROSITE JMJC UniProtKB/TrEMBL
  TPR UniProtKB/TrEMBL
  TPR_REGION UniProtKB/TrEMBL
SMART JmjC UniProtKB/TrEMBL
  TPR UniProtKB/TrEMBL
Superfamily-SCOP SSF48452 UniProtKB/TrEMBL
UniProt C9WPN3_RAT UniProtKB/TrEMBL
  W8C8I9_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Uty  ubiquitously transcribed tetratricopeptide repeat containing, Y-linked  LOC103694558  histone demethylase UTY-like  Data Merged 737654 PROVISIONAL
2020-01-17 Uty  ubiquitously transcribed tetratricopeptide repeat containing, Y-linked  Uty  ubiquitously transcribed tetratricopeptide repeat gene, Y chromosome  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2017-03-27 Uty  ubiquitously transcribed tetratricopeptide repeat gene, Y chromosome  Uty  ubiquitously transcribed tetratricopeptide repeat containing, Y-linked  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2016-10-20 Uty  ubiquitously transcribed tetratricopeptide repeat containing, Y-linked  Kdm6a  lysine demethylase 6A  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2016-02-17 Kdm6a  lysine demethylase 6A  Kdm6a  lysine (K)-specific demethylase 6A  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2014-08-25 LOC103694558  histone demethylase UTY-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2011-09-08 Kdm6a  lysine (K)-specific demethylase 6A  Uty  ubiquitously transcribed tetratricopeptide repeat gene, Y chromosome  Data Merged 737654 APPROVED
2010-05-05 Kdm6a  lysine (K)-specific demethylase 6A  Utx  ubiquitously transcribed tetratricopeptide repeat, X chromosome  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-04-29 Uty  ubiquitously transcribed tetratricopeptide repeat gene, Y chromosome      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-10-23 Utx  ubiquitously transcribed tetratricopeptide repeat, X chromosome  Utx  ubiquitously transcribed tetratricopeptide repeat gene, X chromosome   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Utx  ubiquitously transcribed tetratricopeptide repeat gene, X chromosome   Utx_predicted  ubiquitously transcribed tetratricopeptide repeat gene, X chromosome (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Utx_predicted  ubiquitously transcribed tetratricopeptide repeat gene, X chromosome (predicted)  RGD1565481_predicted  similar to ubiquitously transcribed tetratricopeptide repeat gene, X chromosome (predicted)  Symbol and Name updated 1299863 APPROVED
2006-03-07 RGD1565481_predicted  similar to ubiquitously transcribed tetratricopeptide repeat gene, X chromosome (predicted)  LOC317178  similar to ubiquitously transcribed tetratricopeptide repeat gene, X chromosome  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC317178  similar to ubiquitously transcribed tetratricopeptide repeat gene, X chromosome      Symbol and Name status set to provisional 70820 PROVISIONAL