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    LOC4334071 probable histone H2A variant 3 [ Oryza sativa Japonica Group (Japanese rice) ]

    Gene ID: 4334071, updated on 17-Jul-2024

    Summary

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    Gene symbol
    LOC4334071
    Gene description
    probable histone H2A variant 3
    Locus tag
    OSNPB_030743400
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    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
    OsJ_12526; OJ1365_D05.1
    Expression
    Ubiquitous expression in leaves after flowering (RPKM 208.3), roots after flowering (RPKM 173.6) and 6 other tissues See more
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    Genomic context

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    See LOC4334071 in Genome Data Viewer
    Location:
    chromosome: 3
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    RS_2024_06 current ASM3414082v1 (GCF_034140825.1) 3 NC_089037.1 (31396489..31399296)
    102 previous assembly IRGSP-1.0 (GCF_001433935.1) 3 NC_029258.1 (30513818..30516487)

    Chromosome 3 - NC_089037.1Genomic Context describing neighboring genes Neighboring gene pentatricopeptide repeat-containing protein At3g04750, mitochondrial Neighboring gene uncharacterized LOC136355593 Neighboring gene uncharacterized LOC136355594 Neighboring gene calmodulin-like protein 4

    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
    2. Manual GO annotation of predictive protein signatures: the InterPro approach to GO curation. Burge S, et al. Database (Oxford), 2012. PMID 22301074, Free PMC Article
    3. TreeGrafter: phylogenetic tree-based annotation of proteins with Gene Ontology terms and other annotations. Tang H, et al. Bioinformatics, 2019 Feb 1. PMID 30032202, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Homology

    Gene Ontology Provided by RefSeq

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables protein heterodimerization activity IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables structural constituent of chromatin IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in heterochromatin formation IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of chromatin IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    part_of nucleosome IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    probable histone H2A variant 3
    Names
    LOC_Os03g53190
    OSJNBb0036F07.3

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001418714.1 → NP_001405643.1  probable histone H2A variant 3

      Status: VALIDATED

      Source sequence(s)
      AU091930, CF299346, CI319920, CI609251
      UniProtKB/Swiss-Prot
      Q10D30, Q84MP7

    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_089037.1 Reference ASM3414082v1 Primary Assembly

      Range
      31396489..31399296
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q84MP7.1 GenPept UniProtKB/Swiss-Prot:Q84MP7

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Molecular Biology Databases
    Research Materials