Hdac4 (histone deacetylase 4) - Rat Genome Database
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Gene: Hdac4 (histone deacetylase 4) Rattus norvegicus
Analyze
Symbol: Hdac4
Name: histone deacetylase 4
RGD ID: 619979
Description: Exhibits promoter-specific chromatin binding activity and transcription factor binding activity. Predicted to contribute to transcription regulatory region sequence-specific DNA binding activity. Involved in several processes, including cellular response to mechanical stimulus; cellular response to parathyroid hormone stimulus; and positive regulation of lamellipodium assembly. Localizes to several cellular components, including cytosol; nucleus; and sarcomere. Biomarker of middle cerebral artery infarction. Human ortholog(s) of this gene implicated in ataxia telangiectasia; chromosome 2q37 deletion syndrome; eating disorder; and retinal degeneration. Orthologous to human HDAC4 (histone deacetylase 4); PARTICIPATES IN calcium/calmodulin dependent kinase 2 signaling pathway; histone modification pathway; INTERACTS WITH (S)-nicotine; 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: HD4; LOC363287
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
Rnor_6.0999,052,945 - 99,299,715 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl999,057,089 - 99,299,715 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0998,727,262 - 98,973,829 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4991,147,435 - 91,389,810 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1991,421,635 - 91,447,796 (+)NCBI
Celera990,047,090 - 90,289,214 (-)NCBICelera
Cytogenetic Map9q36NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(S)-nicotine  (EXP,ISO)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
3,3',5,5'-tetrabromobisphenol A  (EXP)
5-aza-2'-deoxycytidine  (ISO)
5-fluorouracil  (ISO)
acetylsalicylic acid  (ISO)
aflatoxin B1  (ISO)
aflatoxin B2  (ISO)
ammonium chloride  (EXP)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
benzo[e]pyrene  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bis(2-ethylhexyl) phthalate  (EXP,ISO)
bisphenol A  (EXP,ISO)
bortezomib  (ISO)
ciguatoxin CTX1B  (ISO)
cisplatin  (ISO)
curcumin  (ISO)
cyclosporin A  (ISO)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
dicrotophos  (ISO)
dorsomorphin  (ISO)
endosulfan  (EXP,ISO)
ethanol  (EXP,ISO)
ethyl methanesulfonate  (ISO)
etoposide  (ISO)
fluoranthene  (ISO)
formaldehyde  (ISO)
gentamycin  (ISO)
indole-3-methanol  (ISO)
manganese(II) chloride  (EXP,ISO)
MC1568  (EXP,ISO)
methapyrilene  (ISO)
methotrexate  (ISO)
methyl methanesulfonate  (ISO)
methylmercury chloride  (EXP,ISO)
mitoxantrone  (ISO)
N-acetyl-1,4-benzoquinone imine  (ISO)
nicotine  (EXP,ISO)
nifedipine  (EXP)
O-methyleugenol  (ISO)
paclitaxel  (EXP)
paracetamol  (ISO)
paraquat  (EXP)
pelargonidin  (ISO)
phenylmercury acetate  (ISO)
quercetin  (ISO)
SB 431542  (ISO)
sodium arsenite  (ISO)
sunitinib  (ISO)
tamoxifen  (ISO)
tauroursodeoxycholic acid  (EXP)
tetrachloromethane  (EXP,ISO)
thimerosal  (EXP,ISO)
titanium dioxide  (ISO)
trichostatin A  (ISO)
valproic acid  (ISO)
vecuronium bromide  (ISO)
vinclozolin  (EXP)
vincristine  (EXP)
vorinostat  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
cellular response to mechanical stimulus  (IEP)
cellular response to parathyroid hormone stimulus  (IEP)
cellular response to tumor necrosis factor  (IEP)
chromatin remodeling  (ISO)
histone deacetylation  (ISO)
histone H3 deacetylation  (ISO)
histone H4 deacetylation  (ISO)
negative regulation of cell population proliferation  (ISO)
negative regulation of DNA-binding transcription factor activity  (ISO)
negative regulation of glycolytic process  (ISO)
negative regulation of myotube differentiation  (ISO)
negative regulation of osteoblast differentiation  (ISO)
negative regulation of pri-miRNA transcription by RNA polymerase II  (ISO)
negative regulation of transcription by RNA polymerase II  (ISO)
negative regulation of transcription, DNA-templated  (ISO)
osteoblast development  (ISO)
peptidyl-lysine deacetylation  (ISO)
positive regulation of cell population proliferation  (ISO)
positive regulation of DNA-binding transcription factor activity  (ISO)
positive regulation of lamellipodium assembly  (IMP)
positive regulation of male mating behavior  (IMP)
positive regulation of neuron apoptotic process  (IMP)
positive regulation of protein sumoylation  (ISO)
positive regulation of reactive oxygen species biosynthetic process  (IMP)
positive regulation of smooth muscle cell migration  (IMP)
positive regulation of smooth muscle cell proliferation  (IMP)
positive regulation of transcription by RNA polymerase II  (ISO)
positive regulation of transcription, DNA-templated  (ISO)
protein deacetylation  (ISO)
protein sumoylation  (IEA)
regulation of cardiac muscle contraction by calcium ion signaling  (ISO)
regulation of gene expression, epigenetic  (ISO)
regulation of protein binding  (ISO)
regulation of skeletal muscle fiber development  (ISO)
regulation of striated muscle cell differentiation  (ISO)
response to denervation involved in regulation of muscle adaptation  (ISO)
response to drug  (IDA)
response to interleukin-1  (ISO)
skeletal system development  (ISO)

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Abu-Farha M, etal., PLoS One. 2013 Sep 24;8(9):e75342. doi: 10.1371/journal.pone.0075342. eCollection 2013.
2. Backs J, etal., J Clin Invest. 2006 Jul;116(7):1853-64. Epub 2006 Jun 8.
3. Bers DM Heart Rhythm. 2011 Jul;8(7):1101-4. doi: 10.1016/j.hrthm.2011.01.030. Epub 2011 Jan 18.
4. Bricceno KV, etal., Hum Mol Genet. 2012 Oct 15;21(20):4448-59. Epub 2012 Jul 13.
5. Bruneteau G, etal., Brain. 2013 Aug;136(Pt 8):2359-68. doi: 10.1093/brain/awt164. Epub 2013 Jul 3.
6. Chen B and Cepko CL, Science. 2009 Jan 9;323(5911):256-9. doi: 10.1126/science.1166226.
7. Cui H, etal., J Clin Invest. 2013 Nov 1;123(11):4706-13.
8. Davis FJ, etal., J Biol Chem. 2003 May 30;278(22):20047-58. Epub 2003 Mar 26.
9. Ellis JJ, etal., Mol Cell Biochem 2003 Jan;242(1-2):153-61.
10. Fang J, etal., Neurol Sci. 2014 Feb;35(2):283-8. doi: 10.1007/s10072-013-1508-4. Epub 2013 Aug 8.
11. Ginnan R, etal., Biochem J. 2012 May 15;444(1):105-14. doi: 10.1042/BJ20120152.
12. Gordon JW, etal., J Biol Chem. 2009 Jul 10;284(28):19027-42. doi: 10.1074/jbc.M109.000539. Epub 2009 Apr 23.
13. Gruhn B, etal., Leuk Res. 2013 Oct;37(10):1200-7. doi: 10.1016/j.leukres.2013.07.016. Epub 2013 Aug 12.
14. Gupta MP, etal., J Biol Chem. 2008 Apr 11;283(15):10135-46. Epub 2008 Feb 4.
15. Hannan JL, etal., J Sex Med. 2014 Jun;11(6):1442-51. doi: 10.1111/jsm.12522. Epub 2014 Mar 18.
16. He M, etal., J Cell Mol Med. 2013 Apr;17(4):531-42. doi: 10.1111/jcmm.12040. Epub 2013 Mar 11.
17. Kao GD, etal., J Cell Biol 2003 Mar 31;160(7):1017-27.
18. Kassis H, etal., Neurochem Int. 2014 Nov;77:17-23. doi: 10.1016/j.neuint.2014.03.006. Epub 2014 Mar 19.
19. Kehat I, etal., J Cell Biol. 2011 Apr 4;193(1):21-9. doi: 10.1083/jcb.201101046.
20. Li J, etal., Nat Med. 2012 May;18(5):783-90. doi: 10.1038/nm.2709.
21. Matsuda KI, etal., Endocrinology. 2011 Jul;152(7):2760-7. doi: 10.1210/en.2011-0193. Epub 2011 May 17.
22. NCBI rat LocusLink and RefSeq merged data July 26, 2002
23. Noh H, etal., Am J Physiol Renal Physiol. 2009 Sep;297(3):F729-39. doi: 10.1152/ajprenal.00086.2009. Epub 2009 Jun 24.
24. OMIM Disease Annotation Pipeline
25. Peserico A and Simone C, J Biomed Biotechnol. 2011;2011:371832. doi: 10.1155/2011/371832. Epub 2010 Dec 5.
26. Rajan I, etal., PLoS One. 2009 Aug 12;4(8):e6612. doi: 10.1371/journal.pone.0006612.
27. RGD automated data pipeline
28. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
29. RGD automated import pipeline for gene-chemical interactions
30. RGD comprehensive gene curation
31. Shimizu E, etal., J Biol Chem. 2010 Mar 26;285(13):9616-26. doi: 10.1074/jbc.M109.094862. Epub 2010 Jan 22.
32. Sucharov CC, etal., Mol Biol Cell. 2008 Oct;19(10):4141-53. doi: 10.1091/mbc.E07-12-1217. Epub 2008 Jul 16.
33. Usui T, etal., Am J Physiol Heart Circ Physiol. 2012 May 1;302(9):H1894-904. doi: 10.1152/ajpheart.01039.2011. Epub 2012 Mar 2.
34. Usui T, etal., Hypertension. 2014 Feb;63(2):397-403. doi: 10.1161/HYPERTENSIONAHA.113.01843. Epub 2013 Oct 28.
35. Wang X, etal., Kidney Int. 2014 Oct;86(4):712-25. doi: 10.1038/ki.2014.111. Epub 2014 Apr 9.
36. Yan ZQ, etal., J Biomech. 2009 May 11;42(7):945-8. doi: 10.1016/j.jbiomech.2009.01.012. Epub 2009 Mar 3.
37. Yuan JH, etal., Hepatology. 2011 Dec;54(6):2025-35. doi: 10.1002/hep.24606.
38. Zhang CL, etal., Mol Cell Biol 2002 Oct;22(20):7302-12.
39. Zhao L, etal., Circulation. 2012 Jul 24;126(4):455-67. doi: 10.1161/CIRCULATIONAHA.112.103176. Epub 2012 Jun 18.
Additional References at PubMed
PMID:10220385   PMID:10748098   PMID:10869435   PMID:10983972   PMID:11804585   PMID:12477932   PMID:12590135   PMID:14576337   PMID:15057822   PMID:15537544   PMID:15601857   PMID:15743821  
PMID:15990875   PMID:16033423   PMID:16236793   PMID:16260608   PMID:17011572   PMID:17218271   PMID:17336904   PMID:17360518   PMID:17468767   PMID:17696781   PMID:17761942   PMID:17786239  
PMID:17873280   PMID:18614528   PMID:18850004   PMID:19071119   PMID:19109424   PMID:19276356   PMID:19281832   PMID:21554860   PMID:21590736   PMID:22318228   PMID:22357862   PMID:23271793  
PMID:23747726   PMID:23867755   PMID:24413532   PMID:24663010   PMID:24675724   PMID:24768298   PMID:24904057   PMID:24905014   PMID:25871743   PMID:25967576   PMID:26019235   PMID:26732138  
PMID:26759025   PMID:27660204   PMID:27706732   PMID:27708256   PMID:28127553   PMID:28157489   PMID:29393346   PMID:29529137   PMID:29614314   PMID:29845301   PMID:31009659  


Genomics

Comparative Map Data
Hdac4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.0999,052,945 - 99,299,715 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl999,057,089 - 99,299,715 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0998,727,262 - 98,973,829 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4991,147,435 - 91,389,810 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1991,421,635 - 91,447,796 (+)NCBI
Celera990,047,090 - 90,289,214 (-)NCBICelera
Cytogenetic Map9q36NCBI
HDAC4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2239,048,168 - 239,401,654 (-)EnsemblGRCh38hg38GRCh38
GRCh382239,048,168 - 239,401,649 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh372239,969,864 - 240,323,346 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362239,634,801 - 239,987,580 (-)NCBINCBI36hg18NCBI36
Build 342239,706,635 - 240,058,897NCBI
Celera2233,665,663 - 234,017,808 (-)NCBI
Cytogenetic Map2q37.3NCBI
HuRef2231,741,321 - 232,092,211 (-)NCBIHuRef
CHM1_12239,975,706 - 240,328,679 (-)NCBICHM1_1
Hdac4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39191,856,501 - 92,123,424 (-)NCBIGRCm39mm39
GRCm38191,928,779 - 92,195,702 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl191,928,779 - 92,195,699 (-)EnsemblGRCm38mm10GRCm38
MGSCv37193,829,311 - 94,044,970 (-)NCBIGRCm37mm9NCBIm37
MGSCv36193,763,140 - 93,978,799 (-)NCBImm8
Celera194,870,648 - 95,086,759 (-)NCBICelera
Cytogenetic Map1DNCBI
Hdac4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555421,629,691 - 1,886,210 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555421,629,691 - 1,886,160 (+)NCBIChiLan1.0ChiLan1.0
HDAC4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12B245,123,061 - 245,428,441 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2B245,123,061 - 245,427,054 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02B126,287,745 - 126,649,815 (-)NCBIMhudiblu_PPA_v0panPan3
HDAC4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl2549,317,349 - 49,453,478 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.12549,318,621 - 49,545,314 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Hdac4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049367451,730,743 - 1,942,071 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
HDAC4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl15138,381,627 - 138,614,301 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.115138,378,237 - 138,657,266 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.215152,920,983 - 153,035,106 (+)NCBISscrofa10.2Sscrofa10.2susScr3
HDAC4
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.110125,098,375 - 125,450,524 (-)NCBI
ChlSab1.1 Ensembl10125,098,366 - 125,403,227 (-)Ensembl
Hdac4
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248473,846,196 - 4,101,537 (-)NCBI

Position Markers
BG377748  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0999,136,097 - 99,136,241NCBIRnor6.0
Rnor_5.0998,810,211 - 98,810,355UniSTSRnor5.0
RGSC_v3.4991,226,223 - 91,226,367UniSTSRGSC3.4
Celera990,126,031 - 90,126,175UniSTS
Cytogenetic Map9q36UniSTS
RH 3.4 Map9786.7UniSTS
UniSTS:234174  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0999,057,013 - 99,057,143NCBIRnor6.0
Rnor_5.0998,731,330 - 98,731,460UniSTSRnor5.0
RGSC_v3.4991,147,481 - 91,147,611UniSTSRGSC3.4
Celera990,047,032 - 90,047,162UniSTS
Cytogenetic Map9q36UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724544Uae9Urinary albumin excretion QTL 94.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)929075079122095297Rat
731164Uae25Urinary albumin excretion QTL 253.50.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)929466970107878528Rat
2290450Scl57Serum cholesterol level QTL 574.15blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)941261034102531865Rat
631656Bp108Blood pressure QTL 1085.970.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)95417754299177542Rat
1578760Cm53Cardiac mass QTL 533.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)961186278106186278Rat
724515Uae16Urinary albumin excretion QTL 168urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)963270073107878387Rat
1300134Bp185Blood pressure QTL 1853.73arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)966757444112943287Rat
1581580Uae34Urinary albumin excretion QTL 34urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)96745166499920892Rat
1578757Pur6Proteinuria QTL 63.30.005total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)96745166499920892Rat
61385Edpm9Estrogen-dependent pituitary mass QTL 93.430.05pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)970241351115241351Rat
731171Glom6Glomerulus QTL 62.80.0003kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)970942881115942881Rat
1354626Bvd1Brain ventricular dilatation QTL 13.730.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)981411073119983851Rat
724547Cm21Cardiac mass QTL 212.7heart mass (VT:0007028)calculated heart weight (CMO:0000073)983686153111609081Rat
4889852Pur26Proteinuria QTL 26150.001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)990024661107199079Rat
7794784Mcs31Mammary carcinoma susceptibility QTL 312.98mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)990024661119983851Rat
1582203Gluco19Glucose level QTL 193.30.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)999041068107878528Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:54
Count of miRNA genes:53
Interacting mature miRNAs:53
Transcripts:ENSRNOT00000027622
Prediction methods:Microtar, Miranda, Rnahybrid
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 18 2 16 2 4 4 70 22 37 9 4
Low 3 43 39 39 3 39 4 7 4 13 4 2 4
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_053449 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006245438 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006245440 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006245441 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006245442 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006245443 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008767278 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008767279 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017596541 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AABR07068327 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01061501 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01061502 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01061503 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF321132 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC158868 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473997 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000027622   ⟹   ENSRNOP00000027622
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl999,057,089 - 99,299,715 (-)Ensembl
RefSeq Acc Id: NM_053449   ⟹   NP_445901
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0999,057,071 - 99,299,715 (-)NCBI
Rnor_5.0998,727,262 - 98,973,829 (-)NCBI
Celera990,047,090 - 90,289,214 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006245438   ⟹   XP_006245500
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0999,052,945 - 99,299,667 (-)NCBI
Rnor_5.0998,727,262 - 98,973,829 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006245440   ⟹   XP_006245502
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0999,052,945 - 99,299,667 (-)NCBI
Rnor_5.0998,727,262 - 98,973,829 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006245441   ⟹   XP_006245503
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0999,052,945 - 99,299,667 (-)NCBI
Rnor_5.0998,727,262 - 98,973,829 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006245442   ⟹   XP_006245504
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0999,052,945 - 99,299,667 (-)NCBI
Rnor_5.0998,727,262 - 98,973,829 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006245443   ⟹   XP_006245505
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0999,052,945 - 99,299,708 (-)NCBI
Rnor_5.0998,727,262 - 98,973,829 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008767278   ⟹   XP_008765500
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0999,052,945 - 99,247,058 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008767279   ⟹   XP_008765501
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0999,052,945 - 99,236,673 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017596541   ⟹   XP_017452030
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0999,052,945 - 99,178,367 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_445901   ⟸   NM_053449
- UniProtKB: Q99P99 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006245505   ⟸   XM_006245443
- Peptide Label: isoform X8
- Sequence:
RefSeq Acc Id: XP_006245504   ⟸   XM_006245442
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_006245502   ⟸   XM_006245440
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006245503   ⟸   XM_006245441
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_006245500   ⟸   XM_006245438
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008765500   ⟸   XM_008767278
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: XP_008765501   ⟸   XM_008767279
- Peptide Label: isoform X7
- Sequence:
RefSeq Acc Id: XP_017452030   ⟸   XM_017596541
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: ENSRNOP00000027622   ⟸   ENSRNOT00000027622
Protein Domains
HDAC4_Gln

Transcriptome

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

Promoters
RGD ID:13696865
Promoter ID:EPDNEW_R7389
Type:initiation region
Name:Hdac4_1
Description:histone deacetylase 4
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_6.0999,299,679 - 99,299,739EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/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)
ACI/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
ACI/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
BBDP/Wor (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
BN/SsN (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
Buf/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
COP/CrCrl (MCW & UW)
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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: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
9 98790154 98790155 C T snv IS-Tlk/Kyo (KyushuU)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
9 99072260 99072261 C T snv CDS


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:619979 AgrOrtholog
Ensembl Genes ENSRNOG00000020372 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000027622 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000027622 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 3.40.800.20 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7929963 IMAGE-MGC_LOAD
InterPro HDAC4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  His_deacetylse UniProtKB/Swiss-Prot
  His_deacetylse_dom UniProtKB/Swiss-Prot
  His_deacetylse_dom_sf UniProtKB/Swiss-Prot
  Hist_deacetylase_Gln_rich_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Histone_deAcase_II_euk UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ureohydrolase_dom_sf UniProtKB/Swiss-Prot
KEGG Report rno:363287 UniProtKB/Swiss-Prot
MGC_CLONE MGC:188501 IMAGE-MGC_LOAD
NCBI Gene 363287 ENTREZGENE
PANTHER PTHR45364 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR45364:SF3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam HDAC4_Gln UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Hist_deacetyl UniProtKB/Swiss-Prot
PhenoGen Hdac4 PhenoGen
PIRSF HDAC_II_euk UniProtKB/Swiss-Prot
PRINTS HDASUPER UniProtKB/Swiss-Prot
Superfamily-SCOP SSF52768 UniProtKB/Swiss-Prot
UniGene Rn.23483 ENTREZGENE
UniProt B0BNL3_RAT UniProtKB/TrEMBL
  HDAC4_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2007-10-22 Hdac4  histone deacetylase 4  Hdac4_predicted  histone deacetylase 4 (predicted)  Data Merged 737654 APPROVED
2005-01-12 Hdac4_predicted  histone deacetylase 4 (predicted)      Symbol and Name status set to approved 70820 APPROVED
2002-08-07 Hdac4  histone deacetylase 4      Symbol and Name status set to provisional 70820 PROVISIONAL