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    LOC4340018 granule-bound starch synthase 1, chloroplastic/amyloplastic-like [ Oryza sativa Japonica Group (Japanese rice) ]

    Gene ID: 4340018, updated on 17-Sep-2024

    Summary

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    Gene symbol
    LOC4340018
    Gene description
    granule-bound starch synthase 1, chloroplastic/amyloplastic-like
    Locus tag
    OSNPB_060133000
    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
    Wx; WX1; Wx-b; waxy; GBSS1; GBSSI; WX-mq; WX1-1; Wx-oz; GBSS-I; OsGBSS1; 134P10.7
    Expression
    Biased expression in milk grains (RPKM 421.2) and mature seeds (RPKM 34.0) See more
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    Genomic context

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    Location:
    chromosome: 6
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2024_06 current ASM3414082v1 (GCF_034140825.1) 6 NC_089040.1 (1922743..1927858)
    102 previous assembly IRGSP-1.0 (GCF_001433935.1) 6 NC_029261.1 (1765524..1770644)

    Chromosome 6 - NC_089040.1Genomic Context describing neighboring genes Neighboring gene probable lysophospholipase BODYGUARD 3 Neighboring gene uncharacterized LOC4340017 Neighboring gene uncharacterized LOC4340022 Neighboring gene protein EXORDIUM-like 3

    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. Improving rice eating and cooking quality by coordinated expression of the major starch synthesis-related genes, SSII and Wx, in endosperm. Huang L, et al. Plant Mol Biol, 2021 Jul. PMID 34129189
    2. Genetic relatedness among indigenous rice varieties in the Eastern Himalayan region based on nucleotide sequences of the Waxy gene. Choudhury BI, et al. BMC Res Notes, 2014 Dec 29. PMID 25547027, Free PMC Article
    3. Starch biosynthesis in rice endosperm requires the presence of either starch synthase I or IIIa. Fujita N, et al. J Exp Bot, 2011 Oct. PMID 21730357, Free PMC Article
    4. 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

    What's a GeneRIF?
    1. The elite eating quality alleles Wx[b] and ALK[b] are regulated by OsDOF18 and coordinately improve head rice yield.
      Title: The elite eating quality alleles Wx(b) and ALK(b) are regulated by OsDOF18 and coordinately improve head rice yield.
    2. Improving rice eating and cooking quality by coordinated expression of the major starch synthesis-related genes, SSII and Wx, in endosperm.
      Title: Improving rice eating and cooking quality by coordinated expression of the major starch synthesis-related genes, SSII and Wx, in endosperm.
    3. Data show that the genetic relatedness among indigenous rice varieties in Northeast India was assessed with Wx locus, Wx(hp), encoding a granule-bound starch synthase (GBSSI).
      Title: Genetic relatedness among indigenous rice varieties in the Eastern Himalayan region based on nucleotide sequences of the Waxy gene.
    4. Starch biosynthesis in rice endosperm requires the presence of either starch synthase I or IIIa.
      Title: Starch biosynthesis in rice endosperm requires the presence of either starch synthase I or IIIa.
    Submit: New GeneRIF Correction

    Pathways from PubChem

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    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RefSeq

    Function Evidence Code Pubs
    enables glycogen (starch) synthase activity IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    granule-bound starch synthase 1, chloroplastic/amyloplastic
    Names
    ADP(UDP)-glucose starch glycosyl transferase
    LOC_Os06g04200
    P0679C08.19
    P0679C08.25
    glutinous endosperm 1
    granule bound starch synthase
    granule-bound starch synthase I
    starch granule-bond starch syntase
    starch granule-bond starch synthase
    starch granule-bound starch synthase
    starch synthase
    waxy locus
    NP_001389652.1
    NP_001389653.1
    XP_015644486.1
    XP_015644488.1
    XP_015644489.1
    XP_015644490.1
    XP_066167225.1
    XP_066167226.1
    XP_066167227.1

    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_001402723.1 → NP_001389652.1  granule-bound starch synthase 1, chloroplastic/amyloplastic

      Status: VALIDATED

      Source sequence(s)
      AB066094, CI154405, CI592084
      UniProtKB/Swiss-Prot
      A2Y8X2, Q0DEV5
      UniProtKB/TrEMBL
      A0A076FRI5, A0A0D6DQE1, A0A0D6DQH2, A0A3Q9T378, A0A3Q9T3Z7, A0A8J8YHT8, B1B5Z0, B1B5Z1, B7EHV0, B8XEI6, B8XEJ3, B8XEJ8, B8XEK5, B8XEK7, B9FRC3, C6ZGE5, C8CBK6, C8CBL5, D0TZY6, D3U2H9, R4JL77

    2. NM_001402724.1 → NP_001389653.1  granule-bound starch synthase 1, chloroplastic/amyloplastic

      Status: VALIDATED

      Source sequence(s)
      AB066094, C19483, CI154405, CI592084
      UniProtKB/Swiss-Prot
      A2Y8X2, Q0DEV5
      UniProtKB/TrEMBL
      A0A076FRI5, A0A0D6DQE1, A0A0D6DQH2, A0A3Q9T378, A0A3Q9T3Z7, A0A8J8YHT8, B1B5Z0, B1B5Z1, B7EHV0, B8XEI6, B8XEJ3, B8XEJ8, B8XEK5, B8XEK7, B9FRC3, C6ZGE5, C8CBK6, C8CBL5, D0TZY6, D3U2H9, R4JL77

    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_089040.1 Reference ASM3414082v1 Primary Assembly

      Range
      1922743..1927858
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_015789003.3 → XP_015644489.1  granule-bound starch synthase 1, chloroplastic/amyloplastic isoform X1

      UniProtKB/TrEMBL
      A0A076FRI5, A0A0D6DQE1, A0A0D6DQH2, A0A3Q9T378, A0A3Q9T3Z7, B1B5Z1, B8XEI6, B8XEJ3, B8XEJ8, B8XEK5, B8XEK7, C6ZGE5, C8CBK6, C8CBL5, D0TZY6, R4JL77
      Conserved Domains (1) summary
      cd03791
      Location:84 → 583
      GT1_Glycogen_synthase_DULL1_like; This family is most closely related to the GT1 family of glycosyltransferases. Glycogen synthase catalyzes the formation and elongation of the alpha-1,4-glucose backbone using ADP-glucose, the second and key step of glycogen biosynthesis. This family ...

    2. XM_066311128.1 → XP_066167225.1  granule-bound starch synthase 1, chloroplastic/amyloplastic isoform X1

      UniProtKB/TrEMBL
      A0A076FRI5, A0A0D6DQE1, A0A0D6DQH2, A0A3Q9T378, A0A3Q9T3Z7, B1B5Z1, B8XEI6, B8XEJ3, B8XEJ8, B8XEK5, B8XEK7, C6ZGE5, C8CBK6, C8CBL5, D0TZY6, R4JL77

    3. XM_066311129.1 → XP_066167226.1  granule-bound starch synthase 1, chloroplastic/amyloplastic isoform X2

      UniProtKB/Swiss-Prot
      A2Y8X2, Q0DEV5
      UniProtKB/TrEMBL
      A0A076FRI5, A0A0D6DQE1, A0A0D6DQH2, A0A3Q9T378, A0A3Q9T3Z7, A0A8J8YHT8, B1B5Z0, B1B5Z1, B7EHV0, B8XEI6, B8XEJ3, B8XEJ8, B8XEK5, B8XEK7, B9FRC3, C6ZGE5, C8CBK6, C8CBL5, D0TZY6, D3U2H9, R4JL77

    4. XM_015789002.3 → XP_015644488.1  granule-bound starch synthase 1, chloroplastic/amyloplastic isoform X1

      UniProtKB/TrEMBL
      A0A076FRI5, A0A0D6DQE1, A0A0D6DQH2, A0A3Q9T378, A0A3Q9T3Z7, B1B5Z1, B8XEI6, B8XEJ3, B8XEJ8, B8XEK5, B8XEK7, C6ZGE5, C8CBK6, C8CBL5, D0TZY6, R4JL77
      Conserved Domains (1) summary
      cd03791
      Location:84 → 583
      GT1_Glycogen_synthase_DULL1_like; This family is most closely related to the GT1 family of glycosyltransferases. Glycogen synthase catalyzes the formation and elongation of the alpha-1,4-glucose backbone using ADP-glucose, the second and key step of glycogen biosynthesis. This family ...

    5. XM_015789004.3 → XP_015644490.1  granule-bound starch synthase 1, chloroplastic/amyloplastic isoform X2

      UniProtKB/Swiss-Prot
      A2Y8X2, Q0DEV5
      UniProtKB/TrEMBL
      A0A076FRI5, A0A0D6DQE1, A0A0D6DQH2, A0A3Q9T378, A0A3Q9T3Z7, A0A8J8YHT8, B1B5Z0, B1B5Z1, B7EHV0, B8XEI6, B8XEJ3, B8XEJ8, B8XEK5, B8XEK7, B9FRC3, C6ZGE5, C8CBK6, C8CBL5, D0TZY6, D3U2H9, R4JL77
      Conserved Domains (1) summary
      cd03791
      Location:84 → 580
      GT5_Glycogen_synthase_DULL1-like; Glycogen synthase GlgA and similar proteins

    6. XM_066311130.1 → XP_066167227.1  granule-bound starch synthase 1, chloroplastic/amyloplastic isoform X2

      UniProtKB/Swiss-Prot
      A2Y8X2, Q0DEV5
      UniProtKB/TrEMBL
      A0A076FRI5, A0A0D6DQE1, A0A0D6DQH2, A0A3Q9T378, A0A3Q9T3Z7, A0A8J8YHT8, B1B5Z0, B1B5Z1, B7EHV0, B8XEI6, B8XEJ3, B8XEJ8, B8XEK5, B8XEK7, B9FRC3, C6ZGE5, C8CBK6, C8CBL5, D0TZY6, D3U2H9, R4JL77

    7. XM_015789000.3 → XP_015644486.1  granule-bound starch synthase 1, chloroplastic/amyloplastic isoform X1

      UniProtKB/TrEMBL
      A0A076FRI5, A0A0D6DQE1, A0A0D6DQH2, A0A3Q9T378, A0A3Q9T3Z7, B1B5Z1, B8XEI6, B8XEJ3, B8XEJ8, B8XEK5, B8XEK7, C6ZGE5, C8CBK6, C8CBL5, D0TZY6, R4JL77
      Conserved Domains (1) summary
      cd03791
      Location:84 → 583
      GT1_Glycogen_synthase_DULL1_like; This family is most closely related to the GT1 family of glycosyltransferases. Glycogen synthase catalyzes the formation and elongation of the alpha-1,4-glucose backbone using ADP-glucose, the second and key step of glycogen biosynthesis. This family ...
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q0DEV5.1 GenPept UniProtKB/Swiss-Prot:Q0DEV5

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