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: Enables promoter-specific chromatin binding activity. Involved in several processes, including cellular response to mechanical stimulus; cellular response to parathyroid hormone stimulus; and positive regulation of lamellipodium assembly. Located in cytosol; nucleus; and sarcomere. Part of protein-containing complex. 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
Previously 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: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2992,503,467 - 92,750,164 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl992,507,611 - 92,750,164 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx9100,941,905 - 101,184,435 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.09106,077,667 - 106,320,195 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.09104,435,308 - 104,677,856 (-)NCBIRnor_WKY
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 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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)
acrylamide  (ISO)
aflatoxin B1  (ISO)
Aflatoxin B2 alpha  (ISO)
all-trans-retinoic acid  (ISO)
allethrin  (EXP)
ammonium chloride  (EXP)
aristolochic acid A  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
benzene  (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)
caffeine  (ISO)
ciguatoxin CTX1B  (ISO)
cisplatin  (ISO)
curcumin  (ISO)
cyclosporin A  (ISO)
cyhalothrin  (EXP)
cypermethrin  (EXP)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
dicrotophos  (ISO)
dorsomorphin  (ISO)
endosulfan  (EXP,ISO)
ethanol  (EXP,ISO)
ethyl methanesulfonate  (ISO)
etoposide  (ISO)
fenvalerate  (EXP)
fluoranthene  (ISO)
formaldehyde  (ISO)
fulvestrant  (ISO)
gentamycin  (EXP,ISO)
indole-3-methanol  (ISO)
lead diacetate  (EXP)
lead(0)  (EXP)
lead(2+)  (EXP)
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  (EXP,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)
thioacetamide  (EXP)
titanium dioxide  (ISO)
trichloroethene  (EXP)
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
cell population proliferation  (ISO)
cellular response to mechanical stimulus  (IEP)
cellular response to parathyroid hormone stimulus  (IEP)
cellular response to tumor necrosis factor  (IEP)
chromatin organization  (IEA)
chromatin remodeling  (ISO)
epigenetic regulation of gene expression  (ISO)
histone deacetylation  (IBA,IEA,ISO)
histone H3 deacetylation  (ISO)
histone H4 deacetylation  (IBA,ISO)
negative regulation of cell population proliferation  (ISO)
negative regulation of DNA-binding transcription factor activity  (ISO)
negative regulation of DNA-templated transcription  (ISO)
negative regulation of glycolytic process  (ISO)
negative regulation of miRNA transcription  (ISO)
negative regulation of myotube differentiation  (ISO)
negative regulation of osteoblast differentiation  (ISO)
negative regulation of transcription by RNA polymerase II  (IBA,IEA,ISO)
osteoblast development  (ISO)
osteoblast differentiation  (ISO)
peptidyl-lysine deacetylation  (ISO)
positive regulation of cell population proliferation  (ISO)
positive regulation of DNA-binding transcription factor activity  (ISO)
positive regulation of DNA-templated transcription  (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)
protein deacetylation  (ISO)
protein sumoylation  (IEA)
regulation of cardiac muscle contraction by calcium ion signaling  (ISO)
regulation of multicellular organismal process  (IEA)
regulation of protein binding  (ISO)
regulation of skeletal muscle fiber development  (ISO)
regulation of skeletal muscle fiber differentiation  (ISO)
regulation of striated muscle cell differentiation  (ISO)
response to denervation involved in regulation of muscle adaptation  (ISO)
response to interleukin-1  (ISO)
response to xenobiotic stimulus  (IDA)
skeletal system development  (ISO)

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Proteomics analysis of human obesity reveals the epigenetic factor HDAC4 as a potential target for obesity. Abu-Farha M, etal., PLoS One. 2013 Sep 24;8(9):e75342. doi: 10.1371/journal.pone.0075342. eCollection 2013.
2. CaM kinase II selectively signals to histone deacetylase 4 during cardiomyocyte hypertrophy. Backs J, etal., J Clin Invest. 2006 Jul;116(7):1853-64. Epub 2006 Jun 8.
3. Ca(2)(+)-calmodulin-dependent protein kinase II regulation of cardiac excitation-transcription coupling. Bers DM Heart Rhythm. 2011 Jul;8(7):1101-4. doi: 10.1016/j.hrthm.2011.01.030. Epub 2011 Jan 18.
4. Histone deacetylase inhibition suppresses myogenin-dependent atrogene activation in spinal muscular atrophy mice. Bricceno KV, etal., Hum Mol Genet. 2012 Oct 15;21(20):4448-59. Epub 2012 Jul 13.
5. Muscle histone deacetylase 4 upregulation in amyotrophic lateral sclerosis: potential role in reinnervation ability and disease progression. Bruneteau G, etal., Brain. 2013 Aug;136(Pt 8):2359-68. doi: 10.1093/brain/awt164. Epub 2013 Jul 3.
6. HDAC4 regulates neuronal survival in normal and diseased retinas. Chen B and Cepko CL, Science. 2009 Jan 9;323(5911):256-9. doi: 10.1126/science.1166226.
7. Eating disorder predisposition is associated with ESRRA and HDAC4 mutations. Cui H, etal., J Clin Invest. 2013 Nov 1;123(11):4706-13.
8. Calcium/calmodulin-dependent protein kinase activates serum response factor transcription activity by its dissociation from histone deacetylase, HDAC4. Implications in cardiac muscle gene regulation during hypertrophy. Davis FJ, etal., J Biol Chem. 2003 May 30;278(22):20047-58. Epub 2003 Mar 26.
9. CaM kinase IIdeltaC phosphorylation of 14-3-3beta in vascular smooth muscle cells: activation of class II HDAC repression. Ellis JJ, etal., Mol Cell Biochem 2003 Jan;242(1-2):153-61.
10. Epigenetic modulation of neuronal apoptosis and cognitive functions in sepsis-associated encephalopathy. Fang J, etal., Neurol Sci. 2014 Feb;35(2):283-8. doi: 10.1007/s10072-013-1508-4. Epub 2013 Aug 8.
11. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
12. MEF2 is regulated by CaMKIIdelta2 and a HDAC4-HDAC5 heterodimer in vascular smooth muscle cells. Ginnan R, etal., Biochem J. 2012 May 15;444(1):105-14. doi: 10.1042/BJ20120152.
13. Protein kinase A-regulated assembly of a MEF2{middle dot}HDAC4 repressor complex controls c-Jun expression in vascular smooth muscle cells. Gordon JW, etal., J Biol Chem. 2009 Jul 10;284(28):19027-42. doi: 10.1074/jbc.M109.000539. Epub 2009 Apr 23.
14. The expression of histone deacetylase 4 is associated with prednisone poor-response in childhood acute lymphoblastic leukemia. Gruhn B, etal., Leuk Res. 2013 Oct;37(10):1200-7. doi: 10.1016/j.leukres.2013.07.016. Epub 2013 Aug 12.
15. HDAC4 and PCAF bind to cardiac sarcomeres and play a role in regulating myofilament contractile activity. Gupta MP, etal., J Biol Chem. 2008 Apr 11;283(15):10135-46. Epub 2008 Feb 4.
16. Valproic acid prevents penile fibrosis and erectile dysfunction in cavernous nerve-injured rats. Hannan JL, etal., J Sex Med. 2014 Jun;11(6):1442-51. doi: 10.1111/jsm.12522. Epub 2014 Mar 18.
17. HDAC4/5-HMGB1 signalling mediated by NADPH oxidase activity contributes to cerebral ischaemia/reperfusion injury. He M, etal., J Cell Mol Med. 2013 Apr;17(4):531-42. doi: 10.1111/jcmm.12040. Epub 2013 Mar 11.
18. Histone deacetylase 4 interacts with 53BP1 to mediate the DNA damage response. Kao GD, etal., J Cell Biol 2003 Mar 31;160(7):1017-27.
19. Histone deacetylase expression in white matter oligodendrocytes after stroke. Kassis H, etal., Neurochem Int. 2014 Nov;77:17-23. doi: 10.1016/j.neuint.2014.03.006. Epub 2014 Mar 19.
20. Modulation of chromatin position and gene expression by HDAC4 interaction with nucleoporins. Kehat I, etal., J Cell Biol. 2011 Apr 4;193(1):21-9. doi: 10.1083/jcb.201101046.
21. Nuclear accumulation of HDAC4 in ATM deficiency promotes neurodegeneration in ataxia telangiectasia. Li J, etal., Nat Med. 2012 May;18(5):783-90. doi: 10.1038/nm.2709.
22. Histone deacetylation during brain development is essential for permanent masculinization of sexual behavior. Matsuda KI, etal., Endocrinology. 2011 Jul;152(7):2760-7. doi: 10.1210/en.2011-0193. Epub 2011 May 17.
23. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
24. Histone deacetylase-2 is a key regulator of diabetes- and transforming growth factor-beta1-induced renal injury. Noh H, etal., Am J Physiol Renal Physiol. 2009 Sep;297(3):F729-39. doi: 10.1152/ajprenal.00086.2009. Epub 2009 Jun 24.
25. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
26. Physical and functional HAT/HDAC interplay regulates protein acetylation balance. Peserico A and Simone C, J Biomed Biotechnol. 2011;2011:371832. doi: 10.1155/2011/371832. Epub 2010 Dec 5.
27. Loss of the putative catalytic domain of HDAC4 leads to reduced thermal nociception and seizures while allowing normal bone development. Rajan I, etal., PLoS One. 2009 Aug 12;4(8):e6612. doi: 10.1371/journal.pone.0006612.
28. GOA pipeline RGD automated data pipeline
29. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
30. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
31. Comprehensive gene review and curation RGD comprehensive gene curation
32. HDAC4 represses matrix metalloproteinase-13 transcription in osteoblastic cells, and parathyroid hormone controls this repression. Shimizu E, etal., J Biol Chem. 2010 Mar 26;285(13):9616-26. doi: 10.1074/jbc.M109.094862. Epub 2010 Jan 22.
33. YY1 protects cardiac myocytes from pathologic hypertrophy by interacting with HDAC5. Sucharov CC, etal., Mol Biol Cell. 2008 Oct;19(10):4141-53. doi: 10.1091/mbc.E07-12-1217. Epub 2008 Jul 16.
34. HDAC4 mediates development of hypertension via vascular inflammation in spontaneous hypertensive rats. 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.
35. Histone deacetylase 4 controls neointimal hyperplasia via stimulating proliferation and migration of vascular smooth muscle cells. Usui T, etal., Hypertension. 2014 Feb;63(2):397-403. doi: 10.1161/HYPERTENSIONAHA.113.01843. Epub 2013 Oct 28.
36. Histone deacetylase 4 selectively contributes to podocyte injury in diabetic nephropathy. Wang X, etal., Kidney Int. 2014 Oct;86(4):712-25. doi: 10.1038/ki.2014.111. Epub 2014 Apr 9.
37. Histone deacetylases modulate vascular smooth muscle cell migration induced by cyclic mechanical strain. Yan ZQ, etal., J Biomech. 2009 May 11;42(7):945-8. doi: 10.1016/j.jbiomech.2009.01.012. Epub 2009 Mar 3.
38. The histone deacetylase 4/SP1/microrna-200a regulatory network contributes to aberrant histone acetylation in hepatocellular carcinoma. Yuan JH, etal., Hepatology. 2011 Dec;54(6):2025-35. doi: 10.1002/hep.24606.
39. Association of class II histone deacetylases with heterochromatin protein 1: potential role for histone methylation in control of muscle differentiation. Zhang CL, etal., Mol Cell Biol 2002 Oct;22(20):7302-12.
40. Histone deacetylation inhibition in pulmonary hypertension: therapeutic potential of valproic acid and suberoylanilide hydroxamic acid. 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   PMID:31696766  
PMID:31960421   PMID:32646070   PMID:33276563   PMID:33375628   PMID:33999989   PMID:34118928   PMID:35408999  


Genomics

Comparative Map Data
Hdac4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2992,503,467 - 92,750,164 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl992,507,611 - 92,750,164 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx9100,941,905 - 101,184,435 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.09106,077,667 - 106,320,195 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.09104,435,308 - 104,677,856 (-)NCBIRnor_WKY
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 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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
GRCh382239,048,168 - 239,401,649 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl2239,048,168 - 239,401,654 (-)EnsemblGRCh38hg38GRCh38
GRCh372239,969,864 - 240,323,343 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362239,634,801 - 239,987,580 (-)NCBINCBI36Build 36hg18NCBI36
Build 342239,706,635 - 240,058,897NCBI
Celera2233,665,663 - 234,017,808 (-)NCBICelera
Cytogenetic Map2q37.3NCBI
HuRef2231,741,321 - 232,092,211 (-)NCBIHuRef
CHM1_12239,975,706 - 240,328,679 (-)NCBICHM1_1
T2T-CHM13v2.02239,539,541 - 239,892,233 (-)NCBIT2T-CHM13v2.0
Hdac4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39191,856,501 - 92,123,424 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl191,856,501 - 92,123,421 (-)EnsemblGRCm39 Ensembl
GRCm38191,928,779 - 92,195,702 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl191,928,779 - 92,195,699 (-)EnsemblGRCm38mm10GRCm38
MGSCv37193,829,311 - 94,044,970 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36193,763,140 - 93,978,799 (-)NCBIMGSCv36mm8
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_v0Mhudiblu_PPA_v0panPan3
HDAC4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12549,318,621 - 49,545,314 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2549,317,349 - 49,453,478 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2549,810,705 - 50,083,929 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02549,702,537 - 49,976,665 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2549,706,181 - 49,977,414 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12549,576,470 - 49,848,695 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02549,364,978 - 49,638,565 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02549,597,454 - 49,869,914 (-)NCBIUU_Cfam_GSD_1.0
Hdac4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405303191,277,349 - 191,488,700 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049367451,730,694 - 1,942,074 (+)EnsemblSpeTri2.0
SpeTri2.0NW_0049367451,730,743 - 1,942,071 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
HDAC4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl15138,381,635 - 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 - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.110125,098,375 - 125,450,524 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl10125,098,366 - 125,403,227 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604073,947,227 - 74,329,237 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Hdac4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248473,845,858 - 4,101,487 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248473,846,196 - 4,101,537 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Hdac4
1180 total Variants
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.


QTLs in Region (mRatBN7.2)
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)925268044114175309Rat
731164Uae25Urinary albumin excretion QTL 253.50.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)925661188100929786Rat
2290450Scl57Serum cholesterol level QTL 574.15blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)93696235995410867Rat
631656Bp108Blood pressure QTL 1085.970.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)94859825193598251Rat
1578760Cm53Cardiac mass QTL 533.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)956771635101771635Rat
724515Uae16Urinary albumin excretion QTL 168urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)958163035100929646Rat
1300134Bp185Blood pressure QTL 1853.73arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)961381434104821652Rat
1581580Uae34Urinary albumin excretion QTL 34urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)96207227596470995Rat
1578757Pur6Proteinuria QTL 63.30.005urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)96207227596470995Rat
61385Edpm9Estrogen-dependent pituitary mass QTL 93.430.05pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)963869687108869687Rat
731171Glom6Glomerulus QTL 62.80.0003kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)964573531109573531Rat
1354626Bvd1Brain ventricular dilatation QTL 13.730.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)975712843111552878Rat
4889852Pur26Proteinuria QTL 26150.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)977813894101597663Rat
7794784Mcs31Mammary carcinoma susceptibility QTL 312.98mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)977813894111552878Rat
724547Cm21Cardiac mass QTL 212.7heart mass (VT:0007028)calculated heart weight (CMO:0000073)979271511102910209Rat
1582203Gluco19Glucose level QTL 193.30.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)992491589100929786Rat

Markers in Region
BG377748  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2992,586,549 - 92,586,694 (+)MAPPERmRatBN7.2
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
RH 3.4 Map9786.7UniSTS
Cytogenetic Map9q36UniSTS
UniSTS:234174  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2992,507,534 - 92,507,665 (+)MAPPERmRatBN7.2
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


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
  XM_039083927 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083928 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083929 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083930 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083931 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide 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
  JACYVU010000215 (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
mRatBN7.2 Ensembl992,507,611 - 92,750,164 (-)Ensembl
Rnor_6.0 Ensembl999,057,089 - 99,299,715 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000107908   ⟹   ENSRNOP00000079742
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl992,507,611 - 92,629,160 (-)Ensembl
RefSeq Acc Id: NM_053449   ⟹   NP_445901
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2992,507,593 - 92,750,164 (-)NCBI
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
mRatBN7.2992,503,467 - 92,750,121 (-)NCBI
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
mRatBN7.2992,503,467 - 92,750,156 (-)NCBI
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
mRatBN7.2992,503,467 - 92,697,288 (-)NCBI
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
mRatBN7.2992,503,467 - 92,687,196 (-)NCBI
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
mRatBN7.2992,503,467 - 92,623,222 (-)NCBI
Rnor_6.0999,052,945 - 99,178,367 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039083927   ⟹   XP_038939855
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2992,503,467 - 92,697,291 (-)NCBI
RefSeq Acc Id: XM_039083928   ⟹   XP_038939856
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2992,503,467 - 92,697,287 (-)NCBI
RefSeq Acc Id: XM_039083929   ⟹   XP_038939857
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2992,503,467 - 92,697,288 (-)NCBI
RefSeq Acc Id: XM_039083930   ⟹   XP_038939858
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2992,503,467 - 92,697,287 (-)NCBI
RefSeq Acc Id: XM_039083931   ⟹   XP_038939859
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2992,503,467 - 92,603,315 (-)NCBI
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 X5
- UniProtKB: A0A8L2UKG8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006245500   ⟸   XM_006245438
- Peptide Label: isoform X5
- UniProtKB: A0A8L2UKG8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008765500   ⟸   XM_008767278
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008765501   ⟸   XM_008767279
- Peptide Label: isoform X7
- Sequence:
RefSeq Acc Id: XP_017452030   ⟸   XM_017596541
- Peptide Label: isoform X8
- Sequence:
RefSeq Acc Id: ENSRNOP00000027622   ⟸   ENSRNOT00000027622
RefSeq Acc Id: XP_038939855   ⟸   XM_039083927
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038939857   ⟸   XM_039083929
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038939858   ⟸   XM_039083930
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038939856   ⟸   XM_039083928
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038939859   ⟸   XM_039083931
- Peptide Label: isoform X9
RefSeq Acc Id: ENSRNOP00000079742   ⟸   ENSRNOT00000107908
Protein Domains
HDAC4_Gln   Hist_deacetyl

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q99P99-F1-model_v2 AlphaFold Q99P99 1-1077 view protein structure

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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:619979 AgrOrtholog
BioCyc Gene G2FUF-26695 BioCyc
Ensembl Genes ENSRNOG00000020372 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000027622 ENTREZGENE
  ENSRNOP00000027622.6 UniProtKB/TrEMBL
  ENSRNOP00000079742 ENTREZGENE
  ENSRNOP00000079742.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000027622 ENTREZGENE
  ENSRNOT00000027622.7 UniProtKB/TrEMBL
  ENSRNOT00000107908 ENTREZGENE
  ENSRNOT00000107908.1 UniProtKB/TrEMBL
Gene3D-CATH 3.40.800.20 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7929963 IMAGE-MGC_LOAD
InterPro HDAC4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  His_deacetylse UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  His_deacetylse_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  His_deacetylse_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  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, UniProtKB/TrEMBL
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, UniProtKB/TrEMBL
PhenoGen Hdac4 PhenoGen
PIRSF HDAC_II_euk UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PRINTS HDASUPER UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF52768 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A8I5ZP14_RAT UniProtKB/TrEMBL
  A0A8L2UKG8 ENTREZGENE, UniProtKB/TrEMBL
  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