ENSDARG00000015427


Danio rerio

Features
Gene ID: ENSDARG00000015427
  
Biological name :hdac1
  
Synonyms : hdac1 / histone deacetylase 1
  
Possible biological names infered from orthology : Gm10093 / O09106 / Q13547
  
Species: Danio rerio
  
Chr. number: 19
Strand: 1
Band:
Gene start: 29808471
Gene end: 29821601
  
Corresponding Affymetrix probe sets: Dr.25176.1.S1_at (Zebrafish Array)   NM_173236_at (Zebrafish Genome Array with custom cdf files)   
  
Cross references: Ensembl peptide - ENSDARP00000133315
Ensembl peptide - ENSDARP00000155165
Ensembl peptide - ENSDARP00000051798
NCBI entrez gene - 192302     See in Manteia.
RefSeq - NM_173236
RefSeq Peptide - NP_775343
swissprot - A0A0R4IDY9
swissprot - F1R653
ZFIN ID - ZDB-GENE-020419-32
Ensembl - ENSDARG00000015427
  
See expression report in BioGPS
See gene description in Wikigenes
See co-cited genes in PubMed


Ortholog prediction (from Ensembl)
Ortholog nameID Species
 HDAC1ENSGALG00000003297Gallus gallus
 HDAC1ENSG00000116478Homo sapiens
 Gm10093ENSMUSG00000061062Mus musculus
 Hdac1ENSMUSG00000028800Mus musculus


Paralog prediction (from Ensembl)
Paralog nameIDSimilarity(%)
hdac3 / histone deacetylase 3 / O15379*ENSDARG0000003751453
hdac8 / histone deacetylase 8 / Q8VH37* / Q9BY41*ENSDARG0000000302135
hdac11 / histone deacetylase 11 / Q96DB2*ENSDARG0000008757317
hdac12 / histone deacetylase 12ENSDARG0000010142215


Protein motifs (from Interpro)
Interpro ID Name
 IPR000286  Histone deacetylase family
 IPR003084  Histone deacetylase
 IPR023801  Histone deacetylase domain


Gene Ontology (GO)
TypeGO IDTermEv.Code
 biological_processGO:0001764 neuron migration IMP
 biological_processGO:0001889 liver development IMP
 biological_processGO:0002244 hematopoietic progenitor cell differentiation IMP
 biological_processGO:0006325 chromatin organization IEA
 biological_processGO:0006351 transcription, DNA-templated IEA
 biological_processGO:0006355 regulation of transcription, DNA-templated IEA
 biological_processGO:0008285 negative regulation of cell proliferation IMP
 biological_processGO:0009953 dorsal/ventral pattern formation IGI
 biological_processGO:0016055 Wnt signaling pathway IGI
 biological_processGO:0016575 histone deacetylation IEA
 biological_processGO:0021754 facial nucleus development IMP
 biological_processGO:0021903 rostrocaudal neural tube patterning IMP
 biological_processGO:0030318 melanocyte differentiation IMP
 biological_processGO:0031017 exocrine pancreas development IMP
 biological_processGO:0031101 fin regeneration IMP
 biological_processGO:0033687 osteoblast proliferation IMP
 biological_processGO:0048263 determination of dorsal identity IMP
 biological_processGO:0048565 digestive tract development IMP
 biological_processGO:0048706 embryonic skeletal system development IMP
 biological_processGO:0048709 oligodendrocyte differentiation IMP
 biological_processGO:0048935 peripheral nervous system neuron development IMP
 biological_processGO:0050673 epithelial cell proliferation IMP
 biological_processGO:0050769 positive regulation of neurogenesis IMP
 biological_processGO:0060028 convergent extension involved in axis elongation IMP
 biological_processGO:0060042 retina morphogenesis in camera-type eye IMP
 biological_processGO:0060218 hematopoietic stem cell differentiation IMP
 biological_processGO:0070932 histone H3 deacetylation IEA
 cellular_componentGO:0005634 nucleus IEA
 molecular_functionGO:0004407 histone deacetylase activity IEA
 molecular_functionGO:0016787 hydrolase activity IEA
 molecular_functionGO:0032041 NAD-dependent histone deacetylase activity (H3-K14 specific) IEA
 molecular_functionGO:0046872 metal ion binding IEA


Pathways (from Reactome)
Pathway description
G0 and Early G1
Formation of the beta-catenin:TCF transactivating complex
Downregulation of SMAD2/3:SMAD4 transcriptional activity
SUMOylation of chromatin organization proteins
Regulation of TP53 Activity through Acetylation
RNA Polymerase I Transcription Initiation
RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function
Regulation of PTEN gene transcription
Factors involved in megakaryocyte development and platelet production


Phenotype (from MGI, Zfin or HPO)
IDPhenotypeDefinition Genetic BG
 ZFA:0000008 brain brain decreased size , abnormal
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 ZFA:0000029 hindbrain hindbrain quality , abnormal
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 ZFA:0000035 lens lens quality , abnormal
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 ZFA:0000037 anatomical structure anatomical structure increased amount , abnormal
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 ZFA:0000054 pericardium pericardium edematous , abnormal
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 ZFA:0000076 swim bladder swim bladder aplastic , abnormal
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 ZFA:0000084 yolk yolk melanophore stripe absent , abnormal
yolk grey , abnormal
yolk swollen , abnormal
yolk shape , abnormal
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 ZFA:0000095 pharyngeal arch 3-7 skeleton pharyngeal arch 3-7 skeleton quality , abnormal
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 ZFA:0000107 eye eye decreased size , abnormal
eye quality , abnormal
eye decreased distance eye , abnormal
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 ZFA:0000112 gut gut cell increased amount , abnormal
gut increased width , abnormal
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 ZFA:0000114 heart heart quality , abnormal
heart edematous , abnormal
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 ZFA:0000123 liver liver decreased size , abnormal
liver morphology , abnormal
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 ZFA:0000135 notochord notochord quality , abnormal
notochord decreased length , abnormal
notochord increased width , abnormal
notochord anterior region increased width , abnormal
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 ZFA:0000140 pancreas pancreas morphology , abnormal
pancreas decreased size , abnormal
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 ZFA:0000152 retina retina perforate , abnormal
retina intrinsic apoptotic signaling pathway by p53 class mediator increased occurrence , abnormal
retina cell apoptotic , abnormal
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 ZFA:0000155 somite somite decreased amount , abnormal
somite U-shaped , abnormal
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 ZFA:0000200 dorsal root ganglion dorsal root ganglion mislocalised , abnormal
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 ZFA:0000206 facial nerve motor nucleus facial nerve motor nucleus morphology , abnormal
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 ZFA:0000396 nervous system nervous system quality , abnormal
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 ZFA:0000471 atrium atrium increased size , abnormal
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 ZFA:0000588 statoacoustic (VIII) ganglion statoacoustic (VIII) ganglion neuron decreased amount , abnormal
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 ZFA:0001058 caudal fin caudal fin lacks parts or has fewer parts of type dorsal root ganglion , abnormal
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 ZFA:0001077 thymus primordium thymus primordium common lymphoid progenitor absent , abnormal
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 ZFA:0001094 whole organism whole organism decreased pigmentation , abnormal
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 ZFA:0001114 head head decreased size , abnormal
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 ZFA:0001115 trunk trunk curved , abnormal
trunk decreased length , abnormal
trunk degenerate , abnormal
trunk curved ventral , abnormal
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 ZFA:0001117 post-vent region post-vent region neural crest cell present , abnormal
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 ZFA:0001161 pectoral fin pectoral fin quality , abnormal
pectoral fin aplastic , abnormal
pectoral fin decreased size , abnormal
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 ZFA:0001227 mandibular arch skeleton mandibular arch skeleton aplastic , abnormal
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 ZFA:0001249 exocrine pancreas exocrine pancreas aplastic , abnormal
exocrine pancreas decreased distribution , abnormal
exocrine pancreas growth decreased occurrence , abnormal
exocrine pancreas morphology , abnormal
exocrine pancreas cell proliferation decreased occurrence , abnormal
exocrine pancreas epithelial cell of pancreas decreased amount , abnormal
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 ZFA:0001284 optic fissure optic fissure open , abnormal
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 ZFA:0001458 cranial cartilage cranial cartilage aplastic , abnormal
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 ZFA:0001463 melanophore stripe melanophore stripe decreased amount , abnormal
melanophore stripe melanocyte decreased amount , abnormal
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 ZFA:0001501 cartilage element cartilage element morphology , abnormal
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 ZFA:0001611 pharyngeal arch 2 pharyngeal arch 2 malformed , abnormal
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 ZFA:0001612 pharyngeal arch 1 pharyngeal arch 1 malformed , abnormal
pharyngeal arch 1 has fewer parts of type chondrocyte , abnormal
pharyngeal arch 1 chondrocyte shape , abnormal
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 ZFA:0001613 pharyngeal arch 3-7 pharyngeal arch 3-7 absent , abnormal
pharyngeal arch 3-7 cell death increased process quality , abnormal
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 ZFA:0001617 otolith otolith quality , abnormal
otolith decreased distance otolith , abnormal
otolith decreased size , abnormal
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 ZFA:0005028 ventral wall of dorsal aorta ventral wall of dorsal aorta hematopoietic stem cell absent , abnormal
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 ZFA:0005741 pancreatic acinar gland pancreatic acinar gland absent , abnormal
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 ZFA:0009052 motor neuron motor neuron mislocalised , abnormal
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 ZFA:0009067 CNS neuron (sensu Vertebrata) CNS neuron (sensu Vertebrata) decreased amount , abnormal
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 ZFA:0009090 pigment cell pigment cell quality , abnormal
pigment cell irregular spatial pattern , abnormal
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 ZFA:0009091 melanocyte melanocyte mislocalised , abnormal
melanocyte position , abnormal
melanocyte cellular motility , abnormal
melanocyte decreased amount , abnormal
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 ZFA:0009096 endocrine cell endocrine cell mislocalised , abnormal
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 ZFA:0009139 endodermal cell endodermal cell decreased amount , abnormal
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Interacting proteins (from Reactome)
Interactor ID Name Interaction type
 ENSDARG00000007438 ube2ib / Q9W6H5 / ubiquitin-conjugating enzyme E2Ib / UBE2I* / P63279* / ubiquitin conjugating enzyme E2 I*  / reaction
 ENSDARG00000036096 smad3a / SMAD family member 3a / SMAD3* / Q8BUN5* / P84022* / SMAD family member 3* / Mothers against decapentaplegic homolog 3 *  / reaction / complex
 ENSDARG00000031894 lef1 / lymphoid enhancer-binding factor 1 / P27782* / Q9UJU2*  / complex
 ENSDARG00000006389 smad2 / Q9I9P9 / SMAD family member 2 / Q62432* / Q15796* / Mothers against decapentaplegic homolog 2 *  / complex / reaction
 ENSDARG00000068436 Q6PI20 / h3f3b.1 / H3 histone, family 3B.1 / H3F3B* / H3F3C* / P84243* / Q6NXT2* / H3 histone family member 3C* / H3 histone family member 3B*  / complex
 ENSDARG00000027978 yy1b / YY1 transcription factor b / YY1* / ZFP42* / Q96MM3* / P25490* / Q00899* / zinc finger protein 42* / YY1 transcription factor* / ZFP42 zinc finger protein*  / complex
 ENSDARG00000105359 Q4QRF4 / FP325123.1 / Histone H3.2   / complex
 ENSDARG00000042796 yy1a / YY1 transcription factor a / YY1* / ZFP42* / Q96MM3* / P25490* / Q00899* / zinc finger protein 42* / YY1 transcription factor* / ZFP42 zinc finger protein*  / complex
 ENSDARG00000101578 e2f4 / E2F transcription factor 4 / Q16254*  / reaction / complex
 ENSDARG00000105345 zgc:173552  / complex
 ENSDARG00000044267 sumo1 / Q7SZR5 / small ubiquitin-like modifier 1 / P63166* / P63165* / Small ubiquitin-related modifier 1 *  / complex / reaction
 ENSDARG00000014571 ctnnb1 / catenin (cadherin-associated protein), beta 1 / P35222* / catenin beta 1*  / reaction
 ENSDARG00000019293 tfdp1a / transcription factor Dp-1, a / TFDP1* / TFDP3* / Q14186* / Q5H9I0* / Q08639* / transcription factor Dp-1* / transcription factor Dp family member 3*  / reaction / complex
 ENSDARG00000045636 rbl2 / retinoblastoma-like 2 (p130) / Q64700* / Q08999* / Retinoblastoma-like protein 2 * / RB transcriptional corepressor like 2*  / reaction / complex
 ENSDARG00000059337 tgif1 / TGFB-induced factor homeobox 1 / P70284* / Q15583*  / reaction / complex
 ENSDARG00000059812 sin3ab / SIN3 transcription regulator family member Ab / SIN3A* / Q96ST3* / Q60520* / SIN3 transcription regulator family member A* / Mus musculus transcriptional regulator, SIN3A (yeast) (...  / complex / reaction
 ENSDARG00000038812 e2f5 / E2F transcription factor 5 / Q15329* / Q61502* / Transcription factor E2F5 *  / reaction / complex
 ENSDARG00000052649 Q9DDJ0 / ube2ia / ubiquitin-conjugating enzyme E2Ia / UBE2I* / P63280* / P63279* / ubiquitin conjugating enzyme E2 I*  / reaction
 ENSDARG00000079716 sin3aa / SIN3 transcription regulator family member Aa / SIN3A* / Q96ST3* / Q60520* / SIN3 transcription regulator family member A* / Mus musculus transcriptional regulator, SIN3A (yeast) (...  / reaction / complex
 ENSDARG00000069706 prmt6 / protein arginine methyltransferase 6 / Q96LA8*  / reaction / complex
 ENSDARG00000075226 smad4a / SMAD family member 4a / SMAD4* / Q13485* / SMAD family member 4*  / complex / reaction
 ENSDARG00000087646 runx1 / runt-related transcription factor 1 / Q01196*  / reaction / complex
 ENSDARG00000069006 tle3b / O13168 / transducin-like enhancer of split 3b / TLE3* / Q08122* / Q04726* / transducin like enhancer of split 3*  / complex






 

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