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LOC4345332 histone deacetylase 6 [ Oryza sativa Japonica Group (Japanese rice) ]

Gene ID: 4345332, updated on 17-Jul-2024

Summary

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Gene symbol
LOC4345332
Gene description
histone deacetylase 6
Locus tag
OSNPB_080344100
Gene type
protein coding
RefSeq status
MODEL
Organism
Oryza sativa Japonica Group
Lineage
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa
Also known as
OJ1119_B10.28
Expression
Ubiquitous expression in flower buds (RPKM 16.8), leaves after flowering (RPKM 16.3) and 6 other tissues See more
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Genomic context

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Location:
chromosome: 8
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2024_06 current ASM3414082v1 (GCF_034140825.1) 8 NC_089042.1 (15630941..15635954)
102 previous assembly IRGSP-1.0 (GCF_001433935.1) 8 NC_029263.1 (15554136..15559152)

Chromosome 8 - NC_089042.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC4345330 Neighboring gene berberine bridge enzyme-like D-2 Neighboring gene mitochondrial pyruvate carrier 4 Neighboring gene phosphoenolpyruvate/phosphate translocator 2, chloroplastic-like

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Transcriptome profiling of various organs at different developmental stages in rice Transcriptome profiling of various organs at different developmental stages in rice
  • Description: Transcriptom profiling in flower buds, flowers, flag leaves and roots sampled before flowering and after flowering, milk grains and mature seeds
  • BioProject: PRJNA243371
  • Publication: PMID 26387578
  • Analysis date: Fri Dec 15 20:02:59 2017

Bibliography

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Related articles in PubMed

  1. Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Rice Full-Length cDNA Consortium, et al. Science, 2003 Jul 18. PMID 12869764

GeneRIFs: Gene References Into Functions

General gene information

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Homology

Gene Ontology Provided by RefSeq

Function Evidence Code Pubs
enables histone deacetylase activity IEA
Inferred from Electronic Annotation
more info
 PubMed 
Process Evidence Code Pubs
involved_in regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 PubMed 
Component Evidence Code Pubs
located_in nucleus IEA
Inferred from Electronic Annotation
more info
 PubMed 

General protein information

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Preferred Names
histone deacetylase 6
Names
Os08g0344100
putative histone deacetylase

NCBI Reference Sequences (RefSeq)

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RefSeqs of Annotated Genomes: GCF_034140825.1-RS_2024_06

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference ASM3414082v1 Primary Assembly

Genomic

  1. NC_089042.1 Reference ASM3414082v1 Primary Assembly

    Range
    15630941..15635954
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_015792602.3 → XP_015648088.1  histone deacetylase 6

    UniProtKB/TrEMBL
    B8B9W7, B9G2J7, Q0J6A5, Q6ZB59
    Conserved Domains (1) summary
    cd09991
    Location:27 → 332
    HDAC_classI; Class I histone deacetylases
Nucleotide Protein
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