HDAC1 (histone deacetylase 1) - Rat Genome Database

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Gene: HDAC1 (histone deacetylase 1) Canis lupus familiaris
Analyze
Symbol: HDAC1
Name: histone deacetylase 1
RGD ID: 12415746
Description: ENCODES a protein that exhibits chromatin binding (ortholog); deacetylase activity (ortholog); protein-containing complex binding (ortholog); INVOLVED IN cellular response to oxidative stress (ortholog); cellular response to platelet-derived growth factor stimulus (ortholog); cellular response to tumor necrosis factor (ortholog); PARTICIPATES IN CHD family mediated chromatin remodeling pathway; Hedgehog signaling pathway; histone modification pathway; ASSOCIATED WITH acute lymphoblastic leukemia (ortholog); alopecia areata (ortholog); breast carcinoma (ortholog); FOUND IN chromatin (ortholog); nucleus (ortholog); perinuclear region of cytoplasm (ortholog)
Type: protein-coding
RefSeq Status: MODEL
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: CanFam3.1 - Dog CanFam3.1 Assembly
Position:
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1268,901,339 - 68,936,473 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl268,901,651 - 68,936,186 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha265,482,127 - 65,517,259 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0269,467,855 - 69,503,012 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl269,467,851 - 69,502,759 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1266,304,797 - 66,339,911 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0267,300,918 - 67,335,502 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0268,299,008 - 68,334,559 (-)NCBIUU_Cfam_GSD_1.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
cellular response to oxidative stress  (ISO)
cellular response to platelet-derived growth factor stimulus  (ISO)
cellular response to tumor necrosis factor  (ISO)
chromatin organization  (IEA)
chromatin remodeling  (IEA)
circadian regulation of gene expression  (IEA)
circadian rhythm  (IEA)
DNA methylation-dependent heterochromatin formation  (IEA)
embryonic digit morphogenesis  (IEA)
endoderm development  (IEA,ISO)
epidermal cell differentiation  (IEA)
eyelid development in camera-type eye  (IEA)
fungiform papilla formation  (IEA)
hair follicle placode formation  (IEA)
hippocampus development  (IEA,ISO)
negative regulation by host of viral transcription  (IEA)
negative regulation of androgen receptor signaling pathway  (IEA)
negative regulation of apoptotic process  (IEA)
negative regulation of canonical NF-kappaB signal transduction  (IEA,ISO)
negative regulation of canonical Wnt signaling pathway  (IEA,ISO)
negative regulation of cell population proliferation  (ISO)
negative regulation of DNA-templated transcription  (IEA,ISO)
negative regulation of gene expression  (IEA)
negative regulation of gene expression, epigenetic  (ISO)
negative regulation of insulin secretion  (ISO)
negative regulation of intrinsic apoptotic signaling pathway  (IEA,ISO)
negative regulation of myotube differentiation  (ISO)
negative regulation of neuron apoptotic process  (ISO)
negative regulation of peptidyl-lysine acetylation  (ISO)
negative regulation of transcription by RNA polymerase II  (IEA,ISO)
neuron differentiation  (IEA,ISO)
odontogenesis of dentin-containing tooth  (IEA)
oligodendrocyte differentiation  (IEA,ISO)
positive regulation of cell population proliferation  (IEA,ISO)
positive regulation of chemokine (C-X-C motif) ligand 2 production  (ISO)
positive regulation of DNA-templated transcription  (IEA)
positive regulation of gene expression  (ISO)
positive regulation of interleukin-1 production  (ISO)
positive regulation of oligodendrocyte differentiation  (IEA,ISO)
positive regulation of smooth muscle cell proliferation  (ISO)
positive regulation of transcription by RNA polymerase II  (IEA)
positive regulation of tumor necrosis factor production  (ISO)
positive regulation of type B pancreatic cell apoptotic process  (ISO)
positive regulation of tyrosine phosphorylation of STAT protein  (ISO)
regulation of transcription by RNA polymerase II  (IEA)
response to amphetamine  (ISO)
response to caffeine  (ISO)
response to hyperoxia  (ISO)
response to lipopolysaccharide  (ISO)
response to xenobiotic stimulus  (ISO)

Cellular Component

References
Additional References at PubMed
PMID:22301074  


Genomics

Comparative Map Data
HDAC1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1268,901,339 - 68,936,473 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl268,901,651 - 68,936,186 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha265,482,127 - 65,517,259 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0269,467,855 - 69,503,012 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl269,467,851 - 69,502,759 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1266,304,797 - 66,339,911 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0267,300,918 - 67,335,502 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0268,299,008 - 68,334,559 (-)NCBIUU_Cfam_GSD_1.0
HDAC1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38132,292,083 - 32,333,626 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl132,292,083 - 32,333,635 (+)EnsemblGRCh38hg38GRCh38
GRCh37132,757,684 - 32,799,227 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36132,530,295 - 32,571,811 (+)NCBINCBI36Build 36hg18NCBI36
Build 34132,426,800 - 32,468,317NCBI
Celera131,028,175 - 31,069,691 (+)NCBICelera
Cytogenetic Map1p35.2-p35.1NCBI
HuRef130,873,184 - 30,914,532 (+)NCBIHuRef
CHM1_1132,873,153 - 32,914,668 (+)NCBICHM1_1
T2T-CHM13v2.0132,150,000 - 32,191,544 (+)NCBIT2T-CHM13v2.0
Hdac1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm394129,409,897 - 129,436,516 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl4129,409,897 - 129,436,506 (-)EnsemblGRCm39 Ensembl
GRCm384129,516,104 - 129,542,646 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl4129,516,104 - 129,542,713 (-)EnsemblGRCm38mm10GRCm38
MGSCv374129,193,348 - 129,219,890 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv364129,018,408 - 129,044,950 (-)NCBIMGSCv36mm8
Celera1782,795,228 - 82,797,813 (+)NCBICelera
Cytogenetic Map4D2.2NCBI
cM Map463.26NCBI
Hdac1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr85147,138,328 - 147,165,387 (-)NCBIGRCr8
mRatBN7.25141,853,992 - 141,881,057 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl5141,853,989 - 141,881,111 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx5144,555,355 - 144,582,392 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.05146,325,182 - 146,352,217 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.05146,321,706 - 146,348,843 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.05147,716,664 - 147,743,723 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5147,716,664 - 147,743,723 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05151,445,686 - 151,472,652 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45148,672,515 - 148,699,810 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.15148,682,553 - 148,709,849 (-)NCBI
Celera5140,329,254 - 140,356,320 (-)NCBICelera
Cytogenetic Map5q36NCBI
Hdac1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495545210,636,366 - 10,670,864 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495545210,636,366 - 10,668,873 (+)NCBIChiLan1.0ChiLan1.0
HDAC1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21194,493,301 - 194,535,079 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11193,614,643 - 193,656,280 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0131,578,373 - 31,619,970 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1132,585,791 - 32,626,408 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl132,585,791 - 32,626,410 (+)Ensemblpanpan1.1panPan2
Hdac1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505849,495,732 - 49,526,636 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647415,320,729 - 15,350,860 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493647415,320,635 - 15,351,418 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
HDAC1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl688,749,634 - 88,785,411 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1688,749,611 - 88,785,220 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2682,882,080 - 82,907,607 (-)NCBISscrofa10.2Sscrofa10.2susScr3
HDAC1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.120100,529,782 - 100,575,953 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl20100,530,369 - 100,558,556 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603316,112,046 - 16,155,022 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Hdac1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462476415,510,866 - 15,552,025 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462476415,510,655 - 15,552,020 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in HDAC1
361 total Variants

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 reproductive system respiratory system adipose tissue
High
Medium 5 16 6 6 6 8 10 6
Low 5 6 6 6 6 6
Below cutoff

Sequence


RefSeq Acc Id: ENSCAFT00000016879   ⟹   ENSCAFP00000015619
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl268,901,651 - 68,936,186 (-)Ensembl
RefSeq Acc Id: ENSCAFT00000044286   ⟹   ENSCAFP00000036819
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl268,901,829 - 68,929,170 (-)Ensembl
RefSeq Acc Id: ENSCAFT00000080695   ⟹   ENSCAFP00000044444
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl268,901,651 - 68,929,170 (-)Ensembl
RefSeq Acc Id: ENSCAFT00845008885   ⟹   ENSCAFP00845006998
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl269,467,851 - 69,502,759 (-)Ensembl
RefSeq Acc Id: XM_022412048   ⟹   XP_022267756
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1268,901,339 - 68,936,473 (-)NCBI
Dog10K_Boxer_Tasha265,482,127 - 65,517,259 (-)NCBI
Sequence:
RefSeq Acc Id: XM_038470392   ⟹   XP_038326320
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.1266,304,797 - 66,339,911 (-)NCBI
RefSeq Acc Id: XM_038470393   ⟹   XP_038326321
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.1266,305,246 - 66,339,837 (-)NCBI
RefSeq Acc Id: XM_038531232   ⟹   XP_038387160
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.0268,299,008 - 68,334,559 (-)NCBI
RefSeq Acc Id: XM_038531233   ⟹   XP_038387161
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.0268,299,457 - 68,334,485 (-)NCBI
RefSeq Acc Id: XM_038595455   ⟹   XP_038451383
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.0267,300,918 - 67,335,502 (-)NCBI
RefSeq Acc Id: XM_038659537   ⟹   XP_038515465
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0269,467,855 - 69,503,012 (-)NCBI
RefSeq Acc Id: XM_038659538   ⟹   XP_038515466
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0269,468,304 - 69,502,933 (-)NCBI
RefSeq Acc Id: XM_544435   ⟹   XP_544435
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1268,901,646 - 68,936,399 (-)NCBI
Dog10K_Boxer_Tasha265,482,576 - 65,517,185 (-)NCBI
Sequence:
RefSeq Acc Id: XP_544435   ⟸   XM_544435
- Peptide Label: isoform X2
- UniProtKB: A0A8C0NQ85 (UniProtKB/TrEMBL),   A0A8I3MVP1 (UniProtKB/TrEMBL),   A0A8C0LN10 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_022267756   ⟸   XM_022412048
- Peptide Label: isoform X1
- UniProtKB: A0A8C0MAX5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSCAFP00000036819   ⟸   ENSCAFT00000044286
RefSeq Acc Id: ENSCAFP00000044444   ⟸   ENSCAFT00000080695
RefSeq Acc Id: ENSCAFP00000015619   ⟸   ENSCAFT00000016879
RefSeq Acc Id: XP_038326320   ⟸   XM_038470392
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038326321   ⟸   XM_038470393
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038451383   ⟸   XM_038595455
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038515465   ⟸   XM_038659537
- Peptide Label: isoform X1
- UniProtKB: A0A8C0MAX5 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038515466   ⟸   XM_038659538
- Peptide Label: isoform X2
- UniProtKB: A0A8C0NQ85 (UniProtKB/TrEMBL),   A0A8I3MVP1 (UniProtKB/TrEMBL),   A0A8C0LN10 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038387160   ⟸   XM_038531232
- Peptide Label: isoform X1
- UniProtKB: A0A8C0MAX5 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038387161   ⟸   XM_038531233
- Peptide Label: isoform X2
- UniProtKB: A0A8C0LN10 (UniProtKB/TrEMBL),   A0A8C0NQ85 (UniProtKB/TrEMBL),   A0A8I3MVP1 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSCAFP00845006998   ⟸   ENSCAFT00845008885
Protein Domains
Histone deacetylase

Promoters
RGD ID:13682549
Promoter ID:EPDNEW_C616
Type:initiation region
Name:HDAC1_1
Description:histone deacetylase 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1268,936,232 - 68,936,292EPDNEW

Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCAFG00000010597 Ensembl, UniProtKB/TrEMBL
  ENSCAFG00030004063 UniProtKB/TrEMBL
  ENSCAFG00030016828 UniProtKB/TrEMBL
  ENSCAFG00040021181 UniProtKB/TrEMBL
  ENSCAFG00845004966 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCAFT00000016879.6 UniProtKB/TrEMBL
  ENSCAFT00030007635.1 UniProtKB/TrEMBL
  ENSCAFT00030031064.1 UniProtKB/TrEMBL
  ENSCAFT00040039305.1 UniProtKB/TrEMBL
  ENSCAFT00845008885 ENTREZGENE
  ENSCAFT00845008885.1 UniProtKB/TrEMBL
Gene3D-CATH 3.40.800.20 UniProtKB/TrEMBL
InterPro His_deacetylse UniProtKB/TrEMBL
  His_deacetylse_1 UniProtKB/TrEMBL
  His_deacetylse_dom UniProtKB/TrEMBL
  His_deacetylse_dom_sf UniProtKB/TrEMBL
  Ureohydrolase_dom_sf UniProtKB/TrEMBL
NCBI Gene HDAC1 ENTREZGENE
PANTHER HISTONE DEACETYLASE 1 UniProtKB/TrEMBL
  HISTONE DEACETYLASE 2 UniProtKB/TrEMBL
  HISTONE DEACETYLASE 2-RELATED UniProtKB/TrEMBL
Pfam Hist_deacetyl UniProtKB/TrEMBL
PIRSF His_deacetylse_1 UniProtKB/TrEMBL
PRINTS HDASUPER UniProtKB/TrEMBL
  HISDACETLASE UniProtKB/TrEMBL
Superfamily-SCOP SSF52768 UniProtKB/TrEMBL
UniProt A0A8C0LN10 ENTREZGENE
  A0A8C0MAX5 ENTREZGENE, UniProtKB/TrEMBL
  A0A8C0NQ85 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I3MVP1 ENTREZGENE, UniProtKB/TrEMBL
VGNC ID VGNC:50625 ENTREZGENE