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    LOC4334048 serine hydroxymethyltransferase, mitochondrial [ Oryza sativa Japonica Group (Japanese rice) ]

    Gene ID: 4334048, updated on 12-Jul-2024

    Summary

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    Gene symbol
    LOC4334048
    Gene description
    serine hydroxymethyltransferase, mitochondrial
    Locus tag
    OSNPB_030738400
    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
    Expression
    Broad expression in roots after flowering (RPKM 423.1), leaves before flowering (RPKM 395.7) and 5 other tissues See more
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    Genomic context

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    See LOC4334048 in Genome Data Viewer
    Location:
    chromosome: 3
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2024_06 current ASM3414082v1 (GCF_034140825.1) 3 NC_089037.1 (31182110..31186751)
    102 previous assembly IRGSP-1.0 (GCF_001433935.1) 3 NC_029258.1 (30299556..30304239)

    Chromosome 3 - NC_089037.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC4334044 Neighboring gene uncharacterized LOC4334045 Neighboring gene linoleate 9S-lipoxygenase 2-like Neighboring gene protein JINGUBANG

    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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    Markers

    Homology

    Gene Ontology Provided by RefSeq

    Function Evidence Code Pubs
    enables cobalt ion binding IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables glycine hydroxymethyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables pyridoxal phosphate binding IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables serine binding IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in L-serine catabolic process IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    involved_in folic acid metabolic process IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    involved_in glycine biosynthetic process from serine IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    involved_in tetrahydrofolate interconversion IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    serine hydroxymethyltransferase, mitochondrial
    Names
    Os03g0738400

    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_089037.1 Reference ASM3414082v1 Primary Assembly

      Range
      31182110..31186751
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_015774325.2 → XP_015629811.1  serine hydroxymethyltransferase, mitochondrial

      UniProtKB/TrEMBL
      B8AJX7, B9FBQ3, Q0DNR3, Q10D68
      Conserved Domains (1) summary
      PLN03226
      Location:37 → 513
      PLN03226; serine hydroxymethyltransferase; Provisional
    Nucleotide Protein
    Heading Accession and Version

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