Hdac4 (histone deacetylase 4) - Rat Genome Database

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Gene: Hdac4 (histone deacetylase 4) Ictidomys tridecemlineatus
Analyze
Symbol: Hdac4
Name: histone deacetylase 4
RGD ID: 12647806
Description: ENCODES a protein that exhibits histone binding (ortholog); histone deacetylase binding (ortholog); identical protein binding (ortholog); INVOLVED IN cell population proliferation (ortholog); cellular response to mechanical stimulus (ortholog); cellular response to parathyroid hormone stimulus (ortholog); PARTICIPATES IN calcium/calmodulin dependent kinase 2 signaling pathway; histone modification pathway; ASSOCIATED WITH acute lymphoblastic leukemia (ortholog); amyotrophic lateral sclerosis (ortholog); aortic aneurysm (ortholog); FOUND IN A band (ortholog); chromatin (ortholog); histone deacetylase complex (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: histone deacetylase 4, transcript variant X1; histone deacetylase 4, transcript variant X2; histone deacetylase 4, transcript variant X3; histone deacetylase 4, transcript variant X4
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: SpeTri2.0 - Squirrel SpeTri2.0 Assembly
Position:
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 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049367451,730,743 - 1,942,071 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
cell population proliferation  (IEA,ISO)
cellular response to mechanical stimulus  (ISO)
cellular response to parathyroid hormone stimulus  (ISO)
cellular response to tumor necrosis factor  (ISO)
chromatin organization  (IEA)
chromatin remodeling  (ISO)
negative regulation of cell population proliferation  (IEA,ISO)
negative regulation of DNA-binding transcription factor activity  (ISO)
negative regulation of DNA-templated transcription  (IEA,ISO)
negative regulation of gene expression, epigenetic  (ISO)
negative regulation of glycolytic process  (IEA)
negative regulation of miRNA transcription  (IEA)
negative regulation of myotube differentiation  (ISO)
negative regulation of osteoblast differentiation  (IEA,ISO)
negative regulation of transcription by competitive promoter binding  (ISO)
negative regulation of transcription by RNA polymerase II  (IEA,ISO)
osteoblast development  (IEA,ISO)
osteoblast differentiation  (IEA,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  (IEA)
positive regulation of lamellipodium assembly  (ISO)
positive regulation of male mating behavior  (ISO)
positive regulation of neuron apoptotic process  (ISO)
positive regulation of protein sumoylation  (ISO)
positive regulation of reactive oxygen species biosynthetic process  (ISO)
positive regulation of smooth muscle cell migration  (ISO)
positive regulation of smooth muscle cell proliferation  (ISO)
positive regulation of transcription by RNA polymerase II  (IEA)
protein deacetylation  (ISO)
regulation of biosynthetic process  (IEA)
regulation of cardiac muscle contraction by calcium ion signaling  (IEA,ISO)
regulation of skeletal muscle fiber development  (IEA,ISO)
regulation of skeletal muscle fiber differentiation  (IEA,ISO)
response to alcohol  (ISO)
response to denervation involved in regulation of muscle adaptation  (IEA)
response to interleukin-1  (ISO)
response to xenobiotic stimulus  (ISO)
skeletal system development  (IEA,ISO)
type I interferon-mediated signaling pathway  (ISO)

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References
Additional References at PubMed
PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
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 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049367451,730,743 - 1,942,071 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
HDAC4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382239,048,168 - 239,401,649 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 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
cM Map146.24NCBI
Hdac4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8999,950,972 - 100,200,994 (-)NCBIGRCr8
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_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.09106,077,667 - 106,320,195 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.09104,435,308 - 104,677,856 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
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
(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
NHGRI_mPanPan1-v213141,692,632 - 142,055,693 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12B141,707,597 - 142,070,660 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02B126,287,745 - 126,649,815 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12B245,123,061 - 245,428,441 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2B245,123,061 - 245,427,054 (-)Ensemblpanpan1.1panPan2
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
(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


Expression

RNA-SEQ Expression


Sequence


Ensembl Acc Id: ENSSTOT00000011129   ⟹   ENSSTOP00000009983
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
SpeTri2.0 EnsemblNW_0049367451,811,097 - 1,937,714 (+)Ensembl
Ensembl Acc Id: ENSSTOT00000035996   ⟹   ENSSTOP00000026706
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
SpeTri2.0 EnsemblNW_0049367451,730,694 - 1,942,074 (+)Ensembl
Ensembl Acc Id: ENSSTOT00000041311   ⟹   ENSSTOP00000027584
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
SpeTri2.0 EnsemblNW_0049367451,730,694 - 1,942,074 (+)Ensembl
RefSeq Acc Id: XM_013364898   ⟹   XP_013220352
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
HiC_Itri_2NW_024405303191,277,349 - 191,488,700 (-)NCBI
SpeTri2.0NW_0049367451,730,743 - 1,942,071 (+)NCBI
Sequence:
RefSeq Acc Id: XM_021719627   ⟹   XP_021575302
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
HiC_Itri_2NW_024405303191,277,349 - 191,488,700 (-)NCBI
SpeTri2.0NW_0049367451,730,743 - 1,942,071 (+)NCBI
Sequence:
RefSeq Acc Id: XM_021719628   ⟹   XP_021575303
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
HiC_Itri_2NW_024405303191,277,349 - 191,488,700 (-)NCBI
SpeTri2.0NW_0049367451,730,743 - 1,942,071 (+)NCBI
Sequence:
RefSeq Acc Id: XM_021719629   ⟹   XP_021575304
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
HiC_Itri_2NW_024405303191,277,349 - 191,488,700 (-)NCBI
SpeTri2.0NW_0049367451,730,743 - 1,942,071 (+)NCBI
Sequence:
RefSeq Acc Id: XM_040268140   ⟹   XP_040124074
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
HiC_Itri_2NW_024405303191,277,349 - 191,488,700 (-)NCBI
RefSeq Acc Id: XM_040268141   ⟹   XP_040124075
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
HiC_Itri_2NW_024405303191,277,349 - 191,488,700 (-)NCBI
RefSeq Acc Id: XM_040268142   ⟹   XP_040124076
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
HiC_Itri_2NW_024405303191,277,349 - 191,433,732 (-)NCBI
RefSeq Acc Id: XM_040268143   ⟹   XP_040124077
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
HiC_Itri_2NW_024405303191,277,349 - 191,382,771 (-)NCBI
RefSeq Acc Id: XP_013220352   ⟸   XM_013364898
- Peptide Label: isoform X3
- UniProtKB: A0A287CZK7 (UniProtKB/TrEMBL),   A0A287D219 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_021575302   ⟸   XM_021719627
- Peptide Label: isoform X1
- UniProtKB: A0A287D219 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_021575303   ⟸   XM_021719628
- Peptide Label: isoform X4
- UniProtKB: A0A287D219 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_021575304   ⟸   XM_021719629
- Peptide Label: isoform X6
- UniProtKB: A0A287D219 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_040124075   ⟸   XM_040268141
- Peptide Label: isoform X5
- UniProtKB: A0A287D219 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_040124074   ⟸   XM_040268140
- Peptide Label: isoform X2
- UniProtKB: A0A287D219 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_040124076   ⟸   XM_040268142
- Peptide Label: isoform X7
- UniProtKB: A0A287D219 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_040124077   ⟸   XM_040268143
- Peptide Label: isoform X8
- UniProtKB: A0A287D219 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSSTOP00000009983   ⟸   ENSSTOT00000011129
Ensembl Acc Id: ENSSTOP00000026706   ⟸   ENSSTOT00000035996
Ensembl Acc Id: ENSSTOP00000027584   ⟸   ENSSTOT00000041311

Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSSTOG00000011115 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSSTOT00000011129.3 UniProtKB/TrEMBL
  ENSSTOT00000035996.1 UniProtKB/TrEMBL
  ENSSTOT00000041311.1 UniProtKB/TrEMBL
Gene3D-CATH 3.40.800.20 UniProtKB/TrEMBL
  6.10.250.1550 UniProtKB/TrEMBL
InterPro HDAC4/5/7/9 UniProtKB/TrEMBL
  His_deacetylse UniProtKB/TrEMBL
  His_deacetylse_dom UniProtKB/TrEMBL
  His_deacetylse_dom_sf UniProtKB/TrEMBL
  Hist_deacetylase_Gln_rich_N UniProtKB/TrEMBL
  Ureohydrolase_dom_sf UniProtKB/TrEMBL
NCBI Gene Hdac4 ENTREZGENE
PANTHER HISTONE DEACETYLASE UniProtKB/TrEMBL
  PTHR45364 UniProtKB/TrEMBL
Pfam HDAC4_Gln UniProtKB/TrEMBL
  Hist_deacetyl UniProtKB/TrEMBL
PIRSF HDAC_II_euk UniProtKB/TrEMBL
PRINTS HDASUPER UniProtKB/TrEMBL
Superfamily-SCOP SSF52768 UniProtKB/TrEMBL
UniProt A0A287CZK7 ENTREZGENE, UniProtKB/TrEMBL
  A0A287D219 ENTREZGENE, UniProtKB/TrEMBL
  I3MGR1_ICTTR UniProtKB/TrEMBL