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: Exhibits deacetylase activity. Involved in several processes, including generation of neurons; regulation of protein modification process; and response to glucocorticoid. Localizes to axon and centrosome. Predicted to colocalize with cytoplasmic microtubule and dynein complex. Used to study polycystic kidney disease and polycystic liver disease. Biomarker of hypertension and polycystic liver disease. 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
Also known as: histone deacetylase 6-like; LOC100911205
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
NCBI Annotation Information: Genome Annotation Status: not in current annotation release
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.0 EnsemblX15,295,473 - 15,316,671 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X15,295,372 - 15,316,673 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
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  (ISO)
axonal transport of mitochondrion  (IMP)
cellular response to hydrogen peroxide  (ISO)
cellular response to misfolded protein  (ISO)
cellular response to oxidative stress  (IEP)
cellular response to parathyroid hormone stimulus  (IEP)
cellular response to topologically incorrect protein  (ISO)
collateral sprouting  (ISO)
dendritic spine morphogenesis  (ISO)
histone deacetylation  (ISO)
Hsp90 deacetylation  (ISO)
intracellular protein transport  (ISO)
lysosome localization  (ISO)
mitochondrion localization  (ISO)
myotube differentiation  (ISO)
negative regulation of axon extension involved in axon guidance  (IMP)
negative regulation of microtubule depolymerization  (ISO)
negative regulation of neuron projection development  (IMP)
negative regulation of protein acetylation  (IMP)
negative regulation of protein-containing complex assembly  (ISO)
negative regulation of protein-containing complex disassembly  (ISO)
negative regulation of proteolysis  (ISO)
neuron differentiation  (IEP)
parkin-mediated stimulation of mitophagy in response to mitochondrial depolarization  (ISO)
peptidyl-lysine deacetylation  (ISO)
polyamine deacetylation  (ISO)
polyubiquitinated misfolded protein transport  (ISO)
positive regulation of cholangiocyte proliferation  (IMP)
positive regulation of dendrite morphogenesis  (IMP)
positive regulation of epithelial cell migration  (ISO)
positive regulation of hydrogen peroxide-mediated programmed cell death  (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  (ISO)
positive regulation of signaling receptor activity  (ISO)
positive regulation of synaptic transmission, glutamatergic  (IMP)
positive regulation of tubulin deacetylation  (IMP)
protein deacetylation  (ISO)
protein destabilization  (ISO)
protein polyubiquitination  (ISO)
protein quality control for misfolded or incompletely synthesized proteins  (ISO)
protein-containing complex disassembly  (ISO)
regulation of establishment of protein localization  (ISO)
regulation of fat cell differentiation  (ISO)
regulation of gene expression, epigenetic  (ISO)
regulation of macroautophagy  (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  (ISO)
response to immobilization stress  (IEP)
response to misfolded protein  (ISO)
skeletal muscle tissue development  (ISO)
spermidine deacetylation  (ISO)
tubulin deacetylation  (ISO)
ubiquitin-dependent protein catabolic process  (ISO)
ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway  (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: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:32653342  


Genomics

Comparative Map Data
Hdac6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.0 EnsemblX15,295,473 - 15,316,671 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X15,295,372 - 15,316,673 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
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
GRCh37X48,660,086 - 48,683,408 (+)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_1X48,690,928 - 48,714,536 (+)NCBICHM1_1
Hdac6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X7,796,355 - 7,814,284 (-)NCBIGRCm39mm39
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
CanFam3.1 EnsemblX42,004,591 - 42,024,427 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1X42,004,268 - 42,024,726 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Hdac6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
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 - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X45,927,625 - 45,951,636 (+)NCBI
ChlSab1.1 EnsemblX45,928,092 - 45,952,929 (+)Ensembl
Hdac6
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624893608,744 - 627,600 (+)NCBI

Position Markers
RH134245  
Rat AssemblyChrPosition (strand)SourceJBrowse
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 (Rnor_6.0)
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)X144092703Rat
634325Bw13Body weight QTL 130body mass (VT:0001259)body weight (CMO:0000012)X166245321592783Rat
70165Bp64Blood pressure QTL 645.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)X166260933443848Rat
631204Gluco15Glucose level QTL 150.001blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)X183816624331837Rat
1298071Edpm12Estrogen-dependent pituitary mass QTL 123.2pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)X428214049282140Rat
631666Iddm5Insulin dependent diabetes mellitus QTL 5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)X595407850954078Rat

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

Nucleotide Sequences
GenBank Nucleotide AF321134 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH474078 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000009295   ⟹   ENSRNOP00000009295
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX15,295,473 - 15,316,671 (+)Ensembl
RefSeq Acc Id: XM_001057931   ⟹   XP_001057931
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
CeleraX14,635,994 - 14,657,201 (+)NCBI
Sequence:
RefSeq Acc Id: XM_003754740   ⟹   XP_003754788
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
CeleraX14,635,994 - 14,657,201 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006227289   ⟹   XP_006227351
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
CeleraX14,635,909 - 14,657,201 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006256755   ⟹   XP_006256817
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X15,295,457 - 15,316,673 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006256756   ⟹   XP_006256818
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X15,295,372 - 15,316,673 (+)NCBI
Rnor_5.0X16,075,029 - 16,096,914 (+)NCBI
Sequence:
RefSeq Acc Id: XM_228753   ⟹   XP_228753
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X15,295,457 - 15,316,673 (+)NCBI
Rnor_5.0X16,075,029 - 16,096,914 (+)NCBI
RGSC_v3.4X26,585,852 - 26,606,999 (+)RGD
Sequence:
Protein Sequences
GenBank Protein AAK11187 (Get FASTA)   NCBI Sequence Viewer  
  EDL83809 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: XP_001057931   ⟸   XM_001057931
- Sequence:
RefSeq Acc Id: XP_228753   ⟸   XM_228753
- Sequence:
RefSeq Acc Id: XP_003754788   ⟸   XM_003754740
- Sequence:
RefSeq Acc Id: XP_006227351   ⟸   XM_006227289
- Sequence:
RefSeq Acc Id: XP_006256818   ⟸   XM_006256756
- Sequence:
RefSeq Acc Id: XP_006256817   ⟸   XM_006256755
- Sequence:
RefSeq Acc Id: ENSRNOP00000009295   ⟸   ENSRNOT00000009295
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 (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 (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/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 (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)
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
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
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/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
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 (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
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
LL/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
LN/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
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
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 (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
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)
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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
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)
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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/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
SHRSP/Gcrc (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
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)
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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/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 (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)
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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/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
WKY/Gcrc (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
WKY/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
WKY/NCrl (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
WKY/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
WN/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
Damaging Variants


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
X 26590033 26590034 G A snv SS/JrHsdMcwi (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:619981 AgrOrtholog
Ensembl Genes ENSRNOG00000048738 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000009295 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000009295 UniProtKB/TrEMBL
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
  rno:84581 UniProtKB/TrEMBL
NCBI Gene 84581 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_RAT UniProtKB/TrEMBL
  A0A1L5YJQ7_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
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