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LOC4340103 pectate lyase [ Oryza sativa Japonica Group (Japanese rice) ]

Gene ID: 4340103, updated on 16-Jul-2024

Summary

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Gene symbol
LOC4340103
Gene description
pectate lyase
Locus tag
OSNPB_060144900
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
P0036F10.1
Expression
Restricted expression toward flower buds (RPKM 53.4) See more
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Genomic context

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See LOC4340103 in Genome Data Viewer
Location:
chromosome: 6
Exon count:
2
Annotation release Status Assembly Chr Location
RS_2024_06 current ASM3414082v1 (GCF_034140825.1) 6 NC_089040.1 (2530726..2532680)
102 previous assembly IRGSP-1.0 (GCF_001433935.1) 6 NC_029261.1 (2372992..2374785)

Chromosome 6 - NC_089040.1Genomic Context describing neighboring genes Neighboring gene transfer RNA glycine (anticodon GCC) Neighboring gene translation factor GUF1 homolog, mitochondrial-like Neighboring gene pectate lyase Neighboring gene malonyl-coenzyme:anthocyanin 5-O-glucoside-6'''-O-malonyltransferase Neighboring gene receptor homology region, transmembrane domain- and RING domain-containing protein 2-like

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

GeneRIFs: Gene References Into Functions

General gene information

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Homology

Gene Ontology Provided by RefSeq

Function Evidence Code Pubs
enables pectate lyase activity IEA
Inferred from Electronic Annotation
more info
 PubMed 

General protein information

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Preferred Names
pectate lyase
Names
OSJNBa0007O20.18
Os06g0144900
putative pectate lyase homolog
NP_001408011.1

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_001421082.1 → NP_001408011.1  pectate lyase

    Status: VALIDATED

    Source sequence(s)
    AK070509, CI277930, CI349468, CI599575
    UniProtKB/TrEMBL
    A2Y961, B7EHZ9, Q5VP63, Q5VQ68

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
    2530726..2532680
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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