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    LOC4338140 DNA (cytosine-5)-methyltransferase CMT2-like [ Oryza sativa Japonica Group (Japanese rice) ]

    Gene ID: 4338140, updated on 17-Jul-2024

    Summary

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    Gene symbol
    LOC4338140
    Gene description
    DNA (cytosine-5)-methyltransferase CMT2-like
    Locus tag
    OSNPB_050224800
    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
    OsMET2c
    Expression
    Ubiquitous expression in roots after flowering (RPKM 27.0), leaves after flowering (RPKM 22.1) and 6 other tissues See more
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    Genomic context

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    See LOC4338140 in Genome Data Viewer
    Location:
    chromosome: 5
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2024_06 current ASM3414082v1 (GCF_034140825.1) 5 NC_089039.1 (7666318..7680306, complement)
    102 previous assembly IRGSP-1.0 (GCF_001433935.1) 5 NC_029260.1 (7634182..7648214, complement)

    Chromosome 5 - NC_089039.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC136356433 Neighboring gene DNA-directed RNA polymerase V subunit 7 Neighboring gene L-type lectin-domain containing receptor kinase SIT2-like Neighboring gene uncharacterized LOC4338142 Neighboring gene uncharacterized LOC136356445

    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 (cytosine-5-)-methyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables chromatin binding IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in negative regulation of gene expression via chromosomal CpG island methylation 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
    DNA (cytosine-5)-methyltransferase CMT2-like
    Names
    DNA (cytosine-5)-methyltransferase 1
    Os05g0224800
    Os05g0224900
    chromomethylase OsMET2c

    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_089039.1 Reference ASM3414082v1 Primary Assembly

      Range
      7666318..7680306 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_015783963.3 → XP_015639449.1  DNA (cytosine-5)-methyltransferase CMT2-like

      UniProtKB/Swiss-Prot
      A0A0P0WJF8, C0SQ91, Q0DJV2, Q5KQL9, Q5KQM0
      UniProtKB/TrEMBL
      B8AZD1
      Conserved Domains (3) summary
      COG0270
      Location:907 → 1298
      Dcm; Site-specific DNA-cytosine methylase [Replication, recombination and repair]
      cd18635
      Location:862 → 918
      CD_CMT3_like; chromodomain of chromomethylase 3, and similar proteins
      cl02608
      Location:603 → 718
      BAH; or Bromo Adjacent Homology domain (also called ELM1 and BAM for Bromo Adjacent Motif). BAH domains have first been described as domains found in the polybromo protein and Yeast Rsc1/Rsc2 (Remodeling of the Structure of Chromatin). They also occur in ...
    Nucleotide Protein
    Heading Accession and Version

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