Hdac1l (histone deacetylase 1-like) - Rat Genome Database

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Gene: Hdac1l (histone deacetylase 1-like) Rattus norvegicus
Analyze
No known orthologs.
Symbol: Hdac1l
Name: histone deacetylase 1-like
RGD ID: 619975
Description: Predicted to enable histone deacetylase activity. Predicted to be involved in heterochromatin formation. Predicted to be located in chromatin; cytoplasm; and nucleus. Predicted to be part of NuRD complex. Orthologous to human HDAC1 (histone deacetylase 1); PARTICIPATES IN cell cycle pathway, mitotic; chronic myeloid leukemia pathway; Huntington's disease pathway; INTERACTS WITH ammonium chloride; trichloroethene; Triptolide.
Type: protein-coding
RefSeq Status: VALIDATED
RGD Orthologs
Alliance Orthologs
More Info homologs ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8987,901,045 - 87,903,045 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl987,896,472 - 87,903,613 (-)EnsemblGRCr8
mRatBN7.2980,452,615 - 80,454,615 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl980,453,139 - 80,454,593 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx988,882,912 - 88,884,366 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0994,010,533 - 94,011,987 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0992,394,312 - 92,395,766 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0984,893,145 - 84,894,599 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl984,893,145 - 84,894,599 (-)Ensemblrn6Rnor6.0
Rnor_5.0984,647,474 - 84,648,928 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4978,410,666 - 78,412,120 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera977,956,741 - 77,958,195 (-)NCBICelera
RGSC_v3.1978,594,094 - 78,594,861 (-)NCBI
Cytogenetic Map9q34NCBI
JBrowse:




Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. 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.
2. Essential function of histone deacetylase 1 in proliferation control and CDK inhibitor repression. Lagger G, etal., EMBO J 2002 Jun 3;21(11):2672-81.
3. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
4. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
5. GOA pipeline RGD automated data pipeline
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
7. Comprehensive gene review and curation RGD comprehensive gene curation
8. DeltaNp73 modulates nerve growth factor-mediated neuronal differentiation through repression of TrkA. Zhang J and Chen X, Mol Cell Biol. 2007 May;27(10):3868-80. Epub 2007 Mar 12.
Additional References at PubMed
PMID:15489334   PMID:22082260  


Genomics

Variants

.
Variants in Hdac1l
3 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:41
Count of miRNA genes:41
Interacting mature miRNAs:41
Transcripts:ENSRNOT00000018423
Prediction methods: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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631656Bp108Blood pressure QTL 1085.970.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)956047863101047863Rat
1582203Gluco19Glucose level QTL 193.30.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)963376862108376862Rat
8662828Vetf6Vascular elastic tissue fragility QTL 63.9artery integrity trait (VT:0010639)patent ductus arteriosus score (CMO:0002566)94445825699506504Rat
724515Uae16Urinary albumin excretion QTL 168urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)965657365108376720Rat
724547Cm21Cardiac mass QTL 212.7heart mass (VT:0007028)calculated heart weight (CMO:0000073)986720043110356905Rat
2303178Bp334Blood pressure QTL 3343.70.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)986720043121768150Rat
724544Uae9Urinary albumin excretion QTL 94.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)964220169109220169Rat
6903941Pur31Proteinuria QTL 310.036urine total protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)98672213292642305Rat
2290450Scl57Serum cholesterol level QTL 574.15blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)944458256121768150Rat
1578760Cm53Cardiac mass QTL 533.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)964220169109220169Rat
1581580Uae34Urinary albumin excretion QTL 34urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)964220169109220169Rat
1300134Bp185Blood pressure QTL 1853.73arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)968875497121768150Rat
1354626Bvd1Brain ventricular dilatation QTL 13.730.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)983161999118999486Rat
4889852Pur26Proteinuria QTL 26150.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)985262459109044727Rat
7794784Mcs31Mammary carcinoma susceptibility QTL 312.98mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)985262459118999486Rat
731164Uae25Urinary albumin excretion QTL 253.50.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)948718864108376862Rat
4889943Bss90Bone structure and strength QTL 904.1tibia area (VT:1000281)tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)95450650499506504Rat
1578757Pur6Proteinuria QTL 63.30.005urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)964220169109220169Rat


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 4 42 114 69 68 37 76 37 6 264 149 9 93 60 87 31 12 12

Sequence


Ensembl Acc Id: ENSRNOT00000018423   ⟹   ENSRNOP00000018423
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl987,896,472 - 87,903,613 (-)Ensembl
mRatBN7.2 Ensembl980,453,139 - 80,454,593 (-)Ensembl
Rnor_6.0 Ensembl984,893,145 - 84,894,599 (-)Ensembl
RefSeq Acc Id: NM_053446   ⟹   NP_445898
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8987,901,045 - 87,903,045 (-)NCBI
mRatBN7.2980,452,615 - 80,454,615 (-)NCBI
Rnor_6.0984,893,145 - 84,894,599 (-)NCBI
Rnor_5.0984,647,474 - 84,648,928 (-)NCBI
Celera977,956,741 - 77,958,195 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_445898 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAK11182 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000018423
  ENSRNOP00000018423.5
RefSeq Acc Id: NP_445898   ⟸   NM_053446
- UniProtKB: D3ZVU7 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000018423   ⟸   ENSRNOT00000018423
Protein Domains
Histone deacetylase

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZVU7-F1-model_v2 AlphaFold D3ZVU7 1-484 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:619975 AgrOrtholog
BioCyc Gene G2FUF-27018 BioCyc
Ensembl Genes ENSRNOG00000013695 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000018423 ENTREZGENE
  ENSRNOT00000018423.7 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_domain UniProtKB/TrEMBL
KEGG Report rno:84576 UniProtKB/TrEMBL
NCBI Gene 84576 ENTREZGENE
PANTHER HISTONE DEACETYLASE 1 UniProtKB/TrEMBL
  HISTONE DEACETYLASE HDAC1-RELATED UniProtKB/TrEMBL
Pfam Hist_deacetyl UniProtKB/TrEMBL
PhenoGen Hdac1l PhenoGen
PIRSF His_deacetylse_1 UniProtKB/TrEMBL
PRINTS HDASUPER UniProtKB/TrEMBL
  HISDACETLASE UniProtKB/TrEMBL
RatGTEx ENSRNOG00000013695 RatGTEx
Superfamily-SCOP SSF52768 UniProtKB/TrEMBL
UniProt D3ZVU7 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-05-16 Hdac1l  histone deacetylase 1-like  Hdac1  histone deacetylase 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-08-07 Hdac1  histone deacetylase 1      Symbol and Name status set to provisional 70820 PROVISIONAL