Hdac10 (histone deacetylase 10) - Rat Genome Database
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Gene: Hdac10 (histone deacetylase 10) Rattus norvegicus
Analyze
Symbol: Hdac10
Name: histone deacetylase 10
RGD ID: 1305874
Description: Predicted to have histone deacetylase activity; histone deacetylase binding activity; and zinc ion binding activity. Involved in oligodendrocyte development. Predicted to localize to cytoplasm and histone deacetylase complex. Orthologous to human HDAC10 (histone deacetylase 10); PARTICIPATES IN histone modification pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene; 2,6-dinitrotoluene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: HD10; LOC362981; polyamine deacetylase HDAC10
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
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.27120,199,126 - 120,205,850 (-)NCBI
Rnor_6.0 Ensembl7130,102,347 - 130,107,437 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.07130,102,335 - 130,109,036 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.07129,788,051 - 129,794,135 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47127,423,736 - 127,428,838 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.17127,459,992 - 127,462,839 (-)NCBI
Celera7116,673,021 - 116,678,123 (-)NCBICelera
Cytogenetic Map7q34NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:11726666   PMID:11739383   PMID:11861901   PMID:15489334   PMID:17172643   PMID:21247901   PMID:23801752   PMID:26221039   PMID:28516954  


Genomics

Comparative Map Data
Hdac10
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.27120,199,126 - 120,205,850 (-)NCBI
Rnor_6.0 Ensembl7130,102,347 - 130,107,437 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.07130,102,335 - 130,109,036 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.07129,788,051 - 129,794,135 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47127,423,736 - 127,428,838 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.17127,459,992 - 127,462,839 (-)NCBI
Celera7116,673,021 - 116,678,123 (-)NCBICelera
Cytogenetic Map7q34NCBI
HDAC10
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2250,245,183 - 50,251,405 (-)EnsemblGRCh38hg38GRCh38
GRCh382250,245,183 - 50,251,265 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh372250,683,612 - 50,689,694 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362249,025,739 - 49,031,941 (-)NCBINCBI36hg18NCBI36
Build 342248,986,071 - 48,992,271NCBI
Celera2234,558,514 - 34,564,737 (-)NCBI
Cytogenetic Map22q13.33NCBI
HuRef2233,581,335 - 33,587,801 (-)NCBIHuRef
CHM1_12250,642,365 - 50,648,588 (-)NCBICHM1_1
Hdac10
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391589,007,506 - 89,012,903 (-)NCBIGRCm39mm39
GRCm39 Ensembl1589,007,510 - 89,012,903 (-)Ensembl
GRCm381589,123,303 - 89,128,700 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1589,123,307 - 89,128,700 (-)EnsemblGRCm38mm10GRCm38
MGSCv371588,953,733 - 88,959,130 (-)NCBIGRCm37mm9NCBIm37
MGSCv361588,951,071 - 88,956,393 (-)NCBImm8
Celera1591,251,865 - 91,257,263 (-)NCBICelera
Cytogenetic Map15E3NCBI
Hdac10
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541333,272,714 - 33,277,686 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495541333,272,600 - 33,277,893 (-)NCBIChiLan1.0ChiLan1.0
HDAC10
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12249,473,369 - 49,479,251 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2249,473,369 - 49,479,216 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02230,473,753 - 30,481,369 (-)NCBIMhudiblu_PPA_v0panPan3
HDAC10
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl1016,995,762 - 17,078,262 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.11016,996,307 - 17,001,365 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Hdac10
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_004936629562,038 - 567,709 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
HDAC10
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl5439,805 - 445,340 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.15439,142 - 445,337 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.25110,662,633 - 110,668,163 (+)NCBISscrofa10.2Sscrofa10.2susScr3
HDAC10
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11932,735,091 - 32,741,200 (-)NCBI
ChlSab1.1 Ensembl1932,735,406 - 32,740,817 (-)Ensembl
Hdac10
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624752518,563 - 524,497 (+)NCBI

Position Markers
AW548891  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.07130,102,840 - 130,102,966NCBIRnor6.0
Rnor_5.07129,788,629 - 129,788,755UniSTSRnor5.0
RGSC_v3.47127,424,241 - 127,424,367UniSTSRGSC3.4
Celera7116,673,526 - 116,673,652UniSTS
Cytogenetic Map7q34UniSTS
RH139917  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.07130,103,223 - 130,103,433NCBIRnor6.0
Rnor_5.07129,789,012 - 129,789,222UniSTSRnor5.0
RGSC_v3.47127,424,624 - 127,424,834UniSTSRGSC3.4
Celera7116,673,909 - 116,674,119UniSTS
RH 3.4 Map7958.3UniSTS
Cytogenetic Map7q34UniSTS
RH128844  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.07130,109,244 - 130,109,428NCBIRnor6.0
Rnor_5.07129,795,033 - 129,795,217UniSTSRnor5.0
RGSC_v3.47127,430,645 - 127,430,829UniSTSRGSC3.4
Celera7116,679,930 - 116,680,114UniSTS
RH 3.4 Map7958.5UniSTS
Cytogenetic Map7q34UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1300179Kidm5Kidney mass QTL 53.51kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)751251919145729302Rat
70173Niddm19Non-insulin dependent diabetes mellitus QTL 194.330.00005blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)771448715145729302Rat
634331Pia17Pristane induced arthritis QTL 174.7joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)781645773140745067Rat
7411607Foco15Food consumption QTL 150.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)785595369130595369Rat
7411654Foco25Food consumption QTL 259.30.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)785595369130595369Rat
1331768Kidm10Kidney mass QTL 104.62096kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)788365265133365265Rat
1331728Bp214Blood pressure QTL 2142.825arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)788365265134673427Rat
2317052Aia17Adjuvant induced arthritis QTL 172.13joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)791018361136018361Rat
1358914Bp266Blood pressure QTL 266arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)791832949145158140Rat
1358891Bp265Blood pressure QTL 2652.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)791832949145158140Rat
71114Niddm14Non-insulin dependent diabetes mellitus QTL 144.5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)793726906138726906Rat
2298475Eau6Experimental allergic uveoretinitis QTL 60.0029uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)793726906138726906Rat
1558655Swd4Spike wave discharge measurement QTL 43.680.0002brain electrophysiology trait (VT:0010557)brain spike-and-wave discharge severity grade (CMO:0001988)796630946141630946Rat
2299163Iddm34Insulin dependent diabetes mellitus QTL 342.71blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)7100028953145729302Rat
631687Hcas1Hepatocarcinoma susceptibility QTL 13.90.001liver integrity trait (VT:0010547)liver tumorous lesion volume to total liver volume ratio (CMO:0001082)7100160423140335001Rat
1549899Stresp8Stress response QTL 84.370.0008stress-related behavior trait (VT:0010451)defensive burying duration (CMO:0001961)7100192194145192194Rat
731176Glom5Glomerulus QTL 52.50.0035kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)7106564316145729302Rat
1331731Bp216Blood pressure QTL 2162.851arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7111519266143965591Rat
731174Uae23Urinary albumin excretion QTL 232.40.0042urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)7114825174145729302Rat
2306821Bp335Blood pressure QTL 3350.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7115922628145729302Rat
631663Bw6Body weight QTL 63.4body mass (VT:0001259)body weight (CMO:0000012)7120746024145692398Rat
1300112Bp183Blood pressure QTL 1833.51arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)7121654760145729302Rat
1331748Bp215Blood pressure QTL 2154.043arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7121986439143965591Rat
1357339Stl14Serum triglyceride level QTL 143.450.0001blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)7122421276143965415Rat
1582240Sffal1Serum free fatty acids level QTL 13.40.0021blood free fatty acid amount (VT:0001553)serum free fatty acids level (CMO:0000547)7126463649134098026Rat
631201Panci1Pancreas inflammation QTL 100.001pancreas integrity trait (VT:0010560)percentage of study population displaying chronic pancreatitis at a point in time (CMO:0001214)7126463827137325116Rat
1354582Stl11Serum triglyceride level QTL 113.42blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)7129412003145729302Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:99
Count of miRNA genes:85
Interacting mature miRNAs:90
Transcripts:ENSRNOT00000055865
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 8 12 6 11 6 2 66 20 32 8
Low 35 45 35 8 35 8 9 8 15 9 3 8
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001035000 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006242218 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006242219 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079624 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079625 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079626 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079627 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079628 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079629 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079630 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079631 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079632 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079633 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079634 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC118923 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC092573 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH474027 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000187 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000055865   ⟹   ENSRNOP00000052717
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl7130,102,347 - 130,107,437 (-)Ensembl
RefSeq Acc Id: NM_001035000   ⟹   NP_001030172
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27120,199,126 - 120,204,228 (-)NCBI
Rnor_6.07130,102,335 - 130,107,437 (-)NCBI
Rnor_5.07129,788,051 - 129,794,135 (-)NCBI
RGSC_v3.47127,423,736 - 127,428,838 (-)RGD
Celera7116,673,021 - 116,678,123 (-)RGD
Sequence:
RefSeq Acc Id: XM_006242218   ⟹   XP_006242280
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27120,199,126 - 120,205,850 (-)NCBI
Rnor_6.07130,102,339 - 130,109,036 (-)NCBI
Rnor_5.07129,788,051 - 129,794,135 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006242219   ⟹   XP_006242281
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27120,199,126 - 120,205,850 (-)NCBI
Rnor_6.07130,102,339 - 130,109,036 (-)NCBI
Rnor_5.07129,788,051 - 129,794,135 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039079624   ⟹   XP_038935552
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27120,199,126 - 120,205,850 (-)NCBI
RefSeq Acc Id: XM_039079625   ⟹   XP_038935553
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27120,199,126 - 120,205,850 (-)NCBI
RefSeq Acc Id: XM_039079626   ⟹   XP_038935554
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27120,199,126 - 120,202,944 (-)NCBI
RefSeq Acc Id: XM_039079627   ⟹   XP_038935555
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27120,199,126 - 120,203,048 (-)NCBI
RefSeq Acc Id: XM_039079628   ⟹   XP_038935556
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27120,199,126 - 120,202,944 (-)NCBI
RefSeq Acc Id: XM_039079629   ⟹   XP_038935557
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27120,199,126 - 120,202,944 (-)NCBI
RefSeq Acc Id: XM_039079630   ⟹   XP_038935558
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27120,199,126 - 120,202,944 (-)NCBI
RefSeq Acc Id: XM_039079631   ⟹   XP_038935559
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27120,199,126 - 120,202,944 (-)NCBI
RefSeq Acc Id: XM_039079632   ⟹   XP_038935560
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27120,199,126 - 120,202,402 (-)NCBI
RefSeq Acc Id: XM_039079633   ⟹   XP_038935561
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27120,201,049 - 120,205,850 (-)NCBI
RefSeq Acc Id: XM_039079634   ⟹   XP_038935562
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27120,201,107 - 120,205,850 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001030172   ⟸   NM_001035000
- UniProtKB: Q569C4 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006242281   ⟸   XM_006242219
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006242280   ⟸   XM_006242218
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000052717   ⟸   ENSRNOT00000055865
RefSeq Acc Id: XP_038935553   ⟸   XM_039079625
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038935552   ⟸   XM_039079624
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038935555   ⟸   XM_039079627
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038935556   ⟸   XM_039079628
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038935559   ⟸   XM_039079631
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038935554   ⟸   XM_039079626
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038935558   ⟸   XM_039079630
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038935557   ⟸   XM_039079629
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038935560   ⟸   XM_039079632
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038935561   ⟸   XM_039079633
- Peptide Label: isoform X9
RefSeq Acc Id: XP_038935562   ⟸   XM_039079634
- Peptide Label: isoform X10

Transcriptome

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

Promoters
RGD ID:13695578
Promoter ID:EPDNEW_R6103
Type:initiation region
Name:Hdac10_1
Description:histone deacetylase 10
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.07130,107,413 - 130,107,473EPDNEW

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)
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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
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
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
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/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
LE/Stm (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
LEW/Crl (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
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
7 127425168 127425169 T C snv SS/JrHsdMcwi (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1305874 AgrOrtholog
Ensembl Genes ENSRNOG00000031915 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000052717 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000055865 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 3.40.800.20 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7323327 IMAGE-MGC_LOAD
InterPro His_deacetylse UniProtKB/Swiss-Prot
  His_deacetylse_dom UniProtKB/Swiss-Prot
  His_deacetylse_dom_sf UniProtKB/Swiss-Prot
  Ureohydrolase_dom_sf UniProtKB/Swiss-Prot
KEGG Report rno:362981 UniProtKB/Swiss-Prot
MGC_CLONE MGC:108767 IMAGE-MGC_LOAD
NCBI Gene 362981 ENTREZGENE
Pfam Hist_deacetyl UniProtKB/Swiss-Prot
PhenoGen Hdac10 PhenoGen
PRINTS HDASUPER UniProtKB/Swiss-Prot
Superfamily-SCOP SSF52768 UniProtKB/Swiss-Prot
UniProt HDA10_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-12-06 Hdac10  histone deacetylase 10  Hdac10_predicted  histone deacetylase 10 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Hdac10_predicted  histone deacetylase 10 (predicted)      Symbol and Name status set to approved 70820 APPROVED