Hdac6 (histone deacetylase 6) - Rat Genome Database

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Gene: Hdac6 (histone deacetylase 6) Rattus norvegicus
Analyze
Symbol: Hdac6
Name: histone deacetylase 6
RGD ID: 619981
Description: Enables deacetylase activity. Involved in several processes, including generation of neurons; regulation of protein modification process; and response to glucocorticoid. Located in axon and centrosome. Used to study polycystic kidney disease and polycystic liver disease. Biomarker of hypertension and polycystic liver disease. Human ortholog(s) of this gene implicated in chondrodysplasia with platyspondyly, distinctive brachydactyly, hydrocephaly, and microphthalmia. Orthologous to human HDAC6 (histone deacetylase 6); PARTICIPATES IN histone modification pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene; 2,6-dinitrotoluene.
Type: protein-coding
RefSeq Status: MODEL
Also known as: histone deacetylase 6-like; LOC100911205; LOC108348065
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
mRatBN7.2X14,550,645 - 14,572,445 (+)NCBImRatBN7.2
mRatBN7.2 EnsemblX14,551,044 - 14,572,441 (+)Ensembl
Rnor_6.0X15,396,185 - 15,417,486 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX15,396,895 - 15,417,146 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 EnsemblX15,295,473 - 15,316,671 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X16,075,029 - 16,096,914 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X26,585,852 - 26,606,999 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1X26,658,892 - 26,659,565 (+)NCBI
CeleraX14,635,909 - 14,657,201 (+)NCBICelera
Cytogenetic MapXq12NCBI
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
aggresome assembly  (IEA,ISO)
axonal transport of mitochondrion  (IEA,IMP,ISO)
cellular response to hydrogen peroxide  (IEA,ISO)
cellular response to misfolded protein  (IEA,ISO)
cellular response to oxidative stress  (IEP)
cellular response to parathyroid hormone stimulus  (IEP)
cellular response to topologically incorrect protein  (ISO)
collateral sprouting  (IEA,ISO)
dendritic spine morphogenesis  (IEA,ISO)
histone deacetylation  (IEA,ISO)
Hsp90 deacetylation  (IEA,ISO)
intracellular protein transport  (ISO)
lysosome localization  (IEA,ISO)
mitochondrion localization  (ISO)
myotube differentiation  (ISO)
negative regulation of axon extension involved in axon guidance  (IMP)
negative regulation of microtubule depolymerization  (IEA,ISO)
negative regulation of neuron projection development  (IMP)
negative regulation of protein acetylation  (IMP)
negative regulation of protein-containing complex assembly  (IEA,ISO)
negative regulation of protein-containing complex disassembly  (ISO)
negative regulation of proteolysis  (IEA,ISO)
neuron differentiation  (IEP)
parkin-mediated stimulation of mitophagy in response to mitochondrial depolarization  (IEA,ISO)
peptidyl-lysine deacetylation  (IEA,ISO)
polyamine deacetylation  (ISO)
polyubiquitinated misfolded protein transport  (IEA,ISO)
positive regulation of cholangiocyte proliferation  (IMP)
positive regulation of dendrite morphogenesis  (IMP)
positive regulation of epithelial cell migration  (IEA,ISO)
positive regulation of hydrogen peroxide-mediated programmed cell death  (IEA,ISO)
positive regulation of mitophagy in response to mitochondrial depolarization  (ISO)
positive regulation of oxidative stress-induced neuron death  (IMP)
positive regulation of peptidyl-serine phosphorylation  (IEA,ISO)
positive regulation of signaling receptor activity  (IEA,ISO)
positive regulation of synaptic transmission, glutamatergic  (IMP)
positive regulation of tubulin deacetylation  (IMP)
protein deacetylation  (ISO)
protein destabilization  (IEA,ISO)
protein polyubiquitination  (IEA,ISO)
protein quality control for misfolded or incompletely synthesized proteins  (IEA,ISO)
protein-containing complex disassembly  (IEA,ISO)
regulation of establishment of protein localization  (IEA,ISO)
regulation of fat cell differentiation  (IEA,ISO)
regulation of gene expression, epigenetic  (IEA,ISO)
regulation of macroautophagy  (IEA,ISO)
regulation of microtubule cytoskeleton organization  (IMP)
regulation of mitochondrion organization  (IMP)
regulation of protein phosphorylation  (IMP)
regulation of protein stability  (ISO)
response to amphetamine  (IEP)
response to corticosterone  (IMP)
response to dexamethasone  (IEP)
response to growth factor  (IEA,ISO)
response to immobilization stress  (IEP)
response to misfolded protein  (ISO)
skeletal muscle tissue development  (ISO)
spermidine deacetylation  (ISO)
tubulin deacetylation  (IEA,ISO)
ubiquitin-dependent protein catabolic process  (ISO)
ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway  (IEA,ISO)

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Ajamian F, etal., Neurosci Lett 2003 Jul 31;346(1-2):57-60.
2. Alamdari N, etal., Am J Physiol Regul Integr Comp Physiol. 2010 Aug;299(2):R509-20. doi: 10.1152/ajpregu.00858.2009. Epub 2010 Jun 10.
3. Gradilone SA, etal., Am J Pathol. 2014 Mar;184(3):600-8. doi: 10.1016/j.ajpath.2013.11.027. Epub 2014 Jan 13.
4. Gradilone SA, etal., Cancer Res. 2013 Apr 1;73(7):2259-70. doi: 10.1158/0008-5472.CAN-12-2938. Epub 2013 Jan 31.
5. Kee HJ, etal., Kidney Blood Press Res. 2013;37(4-5):229-39. doi: 10.1159/000350148. Epub 2013 Jul 8.
6. Kim AH, etal., Cell. 2009 Jan 23;136(2):322-36.
7. Kim C, etal., PLoS One. 2012;7(8):e42983. doi: 10.1371/journal.pone.0042983. Epub 2012 Aug 22.
8. Kim JW, etal., Differentiation. 2007 Feb;75(2):147-57.
9. Lee JB, etal., J Physiol. 2012 Apr 1;590(Pt 7):1535-46. doi: 10.1113/jphysiol.2011.224907. Epub 2012 Feb 13.
10. Lin Z, etal., Clin Cancer Res. 2009 Jan 15;15(2):570-7.
11. MGD data from the GO Consortium
12. NCBI rat LocusLink and RefSeq merged data July 26, 2002
13. Noack M, etal., Glia. 2014 Apr;62(4):535-47. doi: 10.1002/glia.22624. Epub 2014 Jan 24.
14. OMIM Disease Annotation Pipeline
15. Omonijo O, etal., Neurotoxicology. 2014 Oct 27;45C:178-184. doi: 10.1016/j.neuro.2014.10.008.
16. Peserico A and Simone C, J Biomed Biotechnol. 2011;2011:371832. doi: 10.1155/2011/371832. Epub 2010 Dec 5.
17. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
18. RGD automated import pipeline for gene-chemical interactions
19. Rivieccio MA, etal., Proc Natl Acad Sci U S A. 2009 Nov 17;106(46):19599-604. doi: 10.1073/pnas.0907935106. Epub 2009 Nov 2.
20. Shimizu E, etal., J Biol Chem. 2010 Mar 26;285(13):9616-26. doi: 10.1074/jbc.M109.094862. Epub 2010 Jan 22.
21. Vishwakarma S, etal., Int Immunopharmacol. 2013 May;16(1):72-8. doi: 10.1016/j.intimp.2013.03.016. Epub 2013 Mar 27.
22. Zhang Y, etal., EMBO J 2003 Mar 3;22(5):1168-79.
Additional References at PubMed
PMID:9891014   PMID:10220385   PMID:11689694   PMID:11948178   PMID:12024216   PMID:12486003   PMID:12620231   PMID:14675537   PMID:15632090   PMID:15916966   PMID:16192271   PMID:16810319  
PMID:16933150   PMID:17785525   PMID:18316616   PMID:18356165   PMID:18606987   PMID:18636984   PMID:19228685   PMID:19457097   PMID:19893491   PMID:20308065   PMID:20457763   PMID:21539845  
PMID:21753002   PMID:22792322   PMID:23093407   PMID:23126280   PMID:23322205   PMID:23580651   PMID:23962722   PMID:24113571   PMID:24413532   PMID:24687993   PMID:24882211   PMID:24909686  
PMID:25411052   PMID:26401643   PMID:26765925   PMID:26975406   PMID:27430620   PMID:28516954   PMID:29201907   PMID:31068376   PMID:31251981   PMID:31432127   PMID:31775910   PMID:32453021  
PMID:32592806   PMID:32653342   PMID:32711564   PMID:33999989  


Genomics

Comparative Map Data
Hdac6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X14,550,645 - 14,572,445 (+)NCBImRatBN7.2
mRatBN7.2 EnsemblX14,551,044 - 14,572,441 (+)Ensembl
Rnor_6.0X15,396,185 - 15,417,486 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX15,396,895 - 15,417,146 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 EnsemblX15,295,473 - 15,316,671 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X16,075,029 - 16,096,914 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X26,585,852 - 26,606,999 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1X26,658,892 - 26,659,565 (+)NCBI
CeleraX14,635,909 - 14,657,201 (+)NCBICelera
Cytogenetic MapXq12NCBI
HDAC6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 EnsemblX48,801,377 - 48,824,982 (+)EnsemblGRCh38hg38GRCh38
GRCh38X48,801,398 - 48,824,982 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37X48,659,805 - 48,683,392 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X48,545,431 - 48,568,324 (+)NCBINCBI36hg18NCBI36
Build 34X48,416,735 - 48,439,629NCBI
CeleraX52,980,148 - 53,003,041 (-)NCBI
Cytogenetic MapXp11.23NCBI
HuRefX46,319,662 - 46,343,018 (+)NCBIHuRef
CHM1_1X48,691,631 - 48,714,524 (+)NCBICHM1_1
Hdac6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X7,796,355 - 7,814,284 (-)NCBIGRCm39mm39
GRCm39 EnsemblX7,796,359 - 7,814,128 (-)Ensembl
GRCm38X7,930,116 - 7,948,047 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX7,930,120 - 7,947,889 (-)EnsemblGRCm38mm10GRCm38
MGSCv37X7,507,248 - 7,525,015 (-)NCBIGRCm37mm9NCBIm37
MGSCv36X7,087,085 - 7,104,203 (-)NCBImm8
CeleraX3,521,555 - 3,539,209 (+)NCBICelera
Cytogenetic MapXA1.1NCBI
cM MapX3.58NCBI
Hdac6
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955543348,019 - 378,071 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955543348,314 - 378,391 (+)NCBIChiLan1.0ChiLan1.0
HDAC6
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1X48,960,181 - 48,982,648 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX48,960,430 - 48,982,642 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0X41,099,539 - 41,122,650 (+)NCBIMhudiblu_PPA_v0panPan3
HDAC6
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X42,004,268 - 42,024,726 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX42,004,591 - 42,024,427 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX16,379,688 - 16,400,160 (+)NCBI
ROS_Cfam_1.0X42,140,437 - 42,160,915 (+)NCBI
ROS_Cfam_1.0 EnsemblX42,140,480 - 42,160,909 (+)Ensembl
UMICH_Zoey_3.1X42,126,695 - 42,147,162 (+)NCBI
UNSW_CanFamBas_1.0X42,114,965 - 42,135,438 (+)NCBI
UU_Cfam_GSD_1.0X42,209,124 - 42,229,594 (+)NCBI
Hdac6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X34,517,114 - 34,538,029 (+)NCBI
SpeTri2.0NW_004936721757,500 - 778,416 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
HDAC6
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX42,917,960 - 42,941,890 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X42,917,911 - 42,941,894 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X47,858,997 - 47,883,202 (+)NCBISscrofa10.2Sscrofa10.2susScr3
HDAC6
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X45,927,625 - 45,951,636 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 EnsemblX45,928,092 - 45,952,929 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366607611,407,911 - 11,431,438 (+)NCBIVero_WHO_p1.0
Hdac6
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624893608,744 - 627,600 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
RH134245  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X14,572,163 - 14,572,372 (+)MAPPERmRatBN7.2
Rnor_6.0X15,316,392 - 15,316,600NCBIRnor6.0
Rnor_6.0X15,417,205 - 15,417,413NCBIRnor6.0
Rnor_5.0X16,198,440 - 16,198,648UniSTSRnor5.0
Rnor_5.0X16,096,633 - 16,096,841UniSTSRnor5.0
RGSC_v3.4X26,606,714 - 26,606,922UniSTSRGSC3.4
CeleraX14,656,920 - 14,657,128UniSTS
RH 3.4 MapX164.6UniSTS
Cytogenetic MapXq13UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
731181Uae27Urinary albumin excretion QTL 272.70.0059urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)X143491017Rat
634325Bw13Body weight QTL 130body mass (VT:0001259)body weight (CMO:0000012)X144797220991088Rat
70165Bp64Blood pressure QTL 645.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)X144812931706553Rat
631204Gluco15Glucose level QTL 150.001blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)X162371522646544Rat
1298071Edpm12Estrogen-dependent pituitary mass QTL 123.2pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)X292789847927898Rat
10755455Coatc13Coat color QTL 130coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7440600049406000Rat
631666Iddm5Insulin dependent diabetes mellitus QTL 5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)X449454949494549Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:148
Count of miRNA genes:67
Interacting mature miRNAs:71
Transcripts:ENSRNOT00000009295, ENSRNOT00000064924
Prediction methods: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 53 27 16
Low 3 39 57 41 19 41 1 4 21 8 25 11 1
Below cutoff 4 7 7 7

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000009295   ⟹   ENSRNOP00000009295
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX14,551,296 - 14,572,439 (+)Ensembl
Rnor_6.0 EnsemblX15,295,473 - 15,316,671 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000064924   ⟹   ENSRNOP00000063689
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX14,551,044 - 14,572,441 (+)Ensembl
Rnor_6.0 EnsemblX15,396,895 - 15,417,146 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000116471   ⟹   ENSRNOP00000096671
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX14,551,296 - 14,572,439 (+)Ensembl
RefSeq Acc Id: XM_003752010   ⟹   XP_003752058
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X14,551,246 - 14,572,445 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006256758   ⟹   XP_006256820
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X14,551,246 - 14,572,445 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006256759   ⟹   XP_006256821
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X14,551,152 - 14,572,445 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039100468   ⟹   XP_038956396
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X14,550,645 - 14,572,445 (+)NCBI
Reference Sequences
RefSeq Acc Id: ENSRNOP00000009295   ⟸   ENSRNOT00000009295
RefSeq Acc Id: ENSRNOP00000063689   ⟸   ENSRNOT00000064924
RefSeq Acc Id: XP_038956396   ⟸   XM_039100468
RefSeq Acc Id: XP_006256821   ⟸   XM_006256759
- UniProtKB: A0A0G2QC41 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006256820   ⟸   XM_006256758
- UniProtKB: A0A0G2QC41 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_003752058   ⟸   XM_003752010
- UniProtKB: A0A0G2QC41 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000096671   ⟸   ENSRNOT00000116471
Protein Domains
UBP-type

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)
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
F344/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/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
FHH/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)
FHH/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
FHL/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)
FHL/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
FXLE16/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (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)
GK/FarMcwi (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
GK/Ox (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
HXB10/IpcvMcwi (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
HXB2/IpcvMcwi (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
HXB20/IpcvMcwi (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
HXB31/IpcvMcwi (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
HXB4/IpcvMcwi (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
LE/Stm (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: 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)
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
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)
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
LEXF10A/StmMcwi (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
LEXF11/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/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
LH/MavRrrcAek (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: 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)
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: 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)
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: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/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
M520/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
M520/NRrrcMcwi (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
MHS/Gib (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
MNS/Gib (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
MR/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
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)
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
PVG/Seac (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (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: 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)
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: 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)
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/OlalpcvMcwi (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
SHRSP/A3NCrl (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
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)
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
SR/JrHsd (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: 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)
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/JrHsdMcwi (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
SS/JrHsdMcwi (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)
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)
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/RijCrl (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: 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)
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
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:619981 AgrOrtholog
Ensembl Genes ENSRNOG00000047281 Ensembl, UniProtKB/TrEMBL
  ENSRNOG00000048738 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000009295 UniProtKB/TrEMBL
  ENSRNOP00000063689 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000096671 ENTREZGENE
Ensembl Transcript ENSRNOT00000009295 UniProtKB/TrEMBL
  ENSRNOT00000064924 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000116471 ENTREZGENE
Gene3D-CATH 3.30.40.10 UniProtKB/TrEMBL
  3.40.800.20 UniProtKB/TrEMBL
InterPro His_deacetylse UniProtKB/TrEMBL
  His_deacetylse_dom UniProtKB/TrEMBL
  His_deacetylse_dom_sf UniProtKB/TrEMBL
  Ureohydrolase_domain UniProtKB/TrEMBL
  Znf_RING/FYVE/PHD UniProtKB/TrEMBL
  Znf_UBP UniProtKB/TrEMBL
KEGG Report rno:108348065 UniProtKB/TrEMBL
NCBI Gene Hdac6 ENTREZGENE
Pfam Hist_deacetyl UniProtKB/TrEMBL
  zf-UBP UniProtKB/TrEMBL
PhenoGen Hdac6 PhenoGen
PRINTS HDASUPER UniProtKB/TrEMBL
PROSITE ZF_UBP UniProtKB/TrEMBL
SMART ZnF_UBP UniProtKB/TrEMBL
Superfamily-SCOP SSF52768 UniProtKB/TrEMBL
UniProt A0A0G2QC41 ENTREZGENE, UniProtKB/TrEMBL
  A0A1L5YJQ7_RAT UniProtKB/TrEMBL
  D3ZVD8_RAT UniProtKB/TrEMBL
UniProt Secondary F1LSE3 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Hdac6  histone deacetylase 6  LOC108348065  histone deacetylase 6  Data Merged 737654 PROVISIONAL
2016-08-02 LOC108348065  histone deacetylase 6      Symbol and Name status set to provisional 70820 PROVISIONAL
2015-07-29 Hdac6  histone deacetylase 6  LOC100911205  histone deacetylase 6-like  Data Merged 737654 PROVISIONAL
2012-07-05 LOC100911205  histone deacetylase 6-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2004-09-10 Hdac6  histone deacetylase 6      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Hdac6  histone deacetylase 6      Symbol and Name status set to provisional 70820 PROVISIONAL