U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC4325003 gibberellin 20 oxidase 2-like [ Oryza sativa Japonica Group (Japanese rice) ]

Gene ID: 4325003, updated on 12-Jul-2024

Summary

Go to the top of the page Help
Gene symbol
LOC4325003
Gene description
gibberellin 20 oxidase 2-like
Locus tag
OSNPB_010883800
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
sd1; GA20; Sd-1; 20ox2; C20ox2; SD1-2E; GA20OX2; Os20ox2; osGA20ox2
Expression
Broad expression in roots before flowering (RPKM 5.8), leaves before flowering (RPKM 3.1) and 5 other tissues See more
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See LOC4325003 in Genome Data Viewer
Location:
chromosome: 1
Exon count:
3
Annotation release Status Assembly Chr Location
RS_2024_06 current ASM3414082v1 (GCF_034140825.1) 1 NC_089035.1 (39012696..39015818)
102 previous assembly IRGSP-1.0 (GCF_001433935.1) 1 NC_029256.1 (38382358..38385504)

Chromosome 1 - NC_089035.1Genomic Context describing neighboring genes Neighboring gene ubinuclein-1 Neighboring gene uncharacterized LOC136354780 Neighboring gene probable methyltransferase PMT24 Neighboring gene uncharacterized LOC136354785 Neighboring gene NAC domain-containing protein 48-like

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help
  • 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

Go to the top of the pageHelp

Related articles in PubMed

  1. Year-round flowering gene e1, a mutation at the E1 locus on rice chromosome 7 and its combination with green revolution gene sd1 in an isogenic cell line. Tomita M, et al. Gene, 2022 Mar 20. PMID 34995737
  2. Genetic Performance of the Semidwarfing Allele sd1 Derived from a Japonica Rice Cultivar and Minimum Requirements to Detect Its Single-Nucleotide Polymorphism by MiSeq Whole-Genome Sequencing. Tomita M, et al. Biomed Res Int, 2018. PMID 29850513, Free PMC Article
  3. Control of grain protein contents through SEMIDWARF1 mutant alleles: sd1 increases the grain protein content in Dee-geo-woo-gen but not in Reimei. Terao T, et al. Mol Genet Genomics, 2015 Jun. PMID 25492221
  4. Green revolution: a mutant gibberellin-synthesis gene in rice. Sasaki A, et al. Nature, 2002 Apr 18. PMID 11961544

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Year-round flowering gene e1, a mutation at the E1 locus on rice chromosome 7 and its combination with green revolution gene sd1 in an isogenic cell line.
    Title: Year-round flowering gene e1, a mutation at the E1 locus on rice chromosome 7 and its combination with green revolution gene sd1 in an isogenic cell line.
  2. a G to T single nucleotide polymorphism at position 38,382,746 in the sd1 locus on chromosome 1 of Koshihikari, causing a loss-of-function mutation of GA20-oxidase.
    Title: Genetic Performance of the Semidwarfing Allele sd1 Derived from a Japonica Rice Cultivar and Minimum Requirements to Detect Its Single-Nucleotide Polymorphism by MiSeq Whole-Genome Sequencing.
  3. Mutation of the SD1 gene is considered to be a key factor in controlling the protein content in rice grains.
    Title: Control of grain protein contents through SEMIDWARF1 mutant alleles: sd1 increases the grain protein content in Dee-geo-woo-gen but not in Reimei.
Submit: New GeneRIF Correction

Pathways from PubChem

Go to the top of the page

General gene information

Go to the top of the page Help

Homology

Gene Ontology Provided by RefSeq

Function Evidence Code Pubs
enables gibberellin 20-oxidase activity IEA
Inferred from Electronic Annotation
more info
 PubMed 
Process Evidence Code Pubs
involved_in flower development IEA
Inferred from Electronic Annotation
more info
 PubMed 
involved_in gibberellin biosynthetic process IEA
Inferred from Electronic Annotation
more info
 PubMed 
involved_in response to light stimulus IEA
Inferred from Electronic Annotation
more info
 PubMed 
involved_in unidimensional cell growth IEA
Inferred from Electronic Annotation
more info
 PubMed 

General protein information

Go to the top of the page Help
Preferred Names
gibberellin 20 oxidase 2
Names
B1065E10.46
GA 20-oxidase 2
GA C20oxidase2
Gibberellin C-20 oxidase 2
LOC_Os01g66100
Protein semidwarf-1
SD1-2-protein
gibberellin-20 oxidase
putative gibberellin 20-oxidase
NP_001415098.1

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_001428169.1 → NP_001415098.1  gibberellin 20 oxidase 2

    Status: VALIDATED

    Source sequence(s)
    AB077025, AP014957, CB649398, CI285773
    UniProtKB/Swiss-Prot
    P0C5H5, Q0JH50, Q6YLX3, Q7EC22, Q7GBH4, Q8RVF5, Q8S492
    UniProtKB/TrEMBL
    B6F2D9, F7J3E1, G8HA06, G8HA97

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_089035.1 Reference ASM3414082v1 Primary Assembly

    Range
    39012696..39015818
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q0JH50.1 GenPept UniProtKB/Swiss-Prot:Q0JH50

Gene LinkOut

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

Molecular Biology Databases
Research Materials