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    LOC4328584 methyl-CpG-binding domain-containing protein 9 [ Oryza sativa Japonica Group (Japanese rice) ]

    Gene ID: 4328584, updated on 16-Jul-2024

    Summary

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    Gene symbol
    LOC4328584
    Gene description
    methyl-CpG-binding domain-containing protein 9
    Locus tag
    OSNPB_020192300
    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
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    Genomic context

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    See LOC4328584 in Genome Data Viewer
    Location:
    chromosome: 2
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_06 current ASM3414082v1 (GCF_034140825.1) 2 NC_089036.1 (5141965..5161774)
    102 previous assembly IRGSP-1.0 (GCF_001433935.1) 2 NC_029257.1 (5131376..5151147)

    Chromosome 2 - NC_089036.1Genomic Context describing neighboring genes Neighboring gene protein FLX-like 2 Neighboring gene uncharacterized LOC4328583 Neighboring gene glucomannan 4-beta-mannosyltransferase 1-like Neighboring gene peroxiredoxin-2E-2, chloroplastic-like

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    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

    GeneRIFs: Gene References Into Functions

    General gene information

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    Homology

    Gene Ontology Provided by RefSeq

    Function Evidence Code Pubs
    enables protein binding 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
    methyl-CpG-binding domain-containing protein 9
    Names
    Os02g0192300
    Os02g0192400
    P0437H03.106
    P0437H03.109
    P0453H10.27
    P0453H10.30
    PHD finger-like protein

    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_089036.1 Reference ASM3414082v1 Primary Assembly

      Range
      5141965..5161774
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_015769847.3 → XP_015625333.1  methyl-CpG-binding domain-containing protein 9 isoform X1

      UniProtKB/TrEMBL
      B9F3T3
      Conserved Domains (6) summary
      smart00249
      Location:131 → 193
      PHD; PHD zinc finger
      cd15519
      Location:1263 → 1308
      PHD1_Lid2p_like; PHD finger 1 found in Schizosaccharomyces pombe Lid2 complex component Lid2p and similar proteins
      pfam15612
      Location:1346 → 1389
      WHIM1; WSTF, HB1, Itc1p, MBD9 motif 1
      cl00295
      Location:1774 → 1808
      ZZ; Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have ...
      cl02556
      Location:1147 → 1213
      Bromodomain; Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
      cl02650
      Location:385 → 425
      FYRN; F/Y-rich N-terminus

    2. XM_015769848.3 → XP_015625334.1  methyl-CpG-binding domain-containing protein 9 isoform X2

      UniProtKB/TrEMBL
      B9F3T3
      Conserved Domains (5) summary
      cd15519
      Location:993 → 1038
      PHD1_Lid2p_like; PHD finger 1 found in Schizosaccharomyces pombe Lid2 complex component Lid2p and similar proteins
      pfam15612
      Location:1076 → 1119
      WHIM1; WSTF, HB1, Itc1p, MBD9 motif 1
      cl00295
      Location:1504 → 1538
      ZZ; Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have ...
      cl02556
      Location:877 → 943
      Bromodomain; Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
      cl02650
      Location:115 → 155
      FYRN; F/Y-rich N-terminus
    Nucleotide Protein
    Heading Accession and Version

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