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LOC4340099 pectate lyase [ Oryza sativa Japonica Group (Japanese rice) ]

Gene ID: 4340099, updated on 12-Jul-2024

Summary

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Gene symbol
LOC4340099
Gene description
pectate lyase
Locus tag
OSNPB_060144200
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
Restricted expression toward flower buds (RPKM 105.6) See more
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Genomic context

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See LOC4340099 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 (2494043..2495840, complement)
102 previous assembly IRGSP-1.0 (GCF_001433935.1) 6 NC_029261.1 (2336431..2338207, complement)

Chromosome 6 - NC_089040.1Genomic Context describing neighboring genes Neighboring gene DNA-repair protein XRCC1 Neighboring gene E3 ubiquitin-protein ligase Os03g0188200-like Neighboring gene uncharacterized LOC136356888 Neighboring gene carboxypeptidase SOL1

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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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
OSJNBa0007O20.11
Os06g0144200
putative pectate lyase homolog

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_089040.1 Reference ASM3414082v1 Primary Assembly

    Range
    2494043..2495840 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_015787090.3 → XP_015642576.1  pectate lyase

    UniProtKB/TrEMBL
    A0A0P0WSR5, Q0DEM8, Q5VQ73
    Conserved Domains (2) summary
    smart00656
    Location:180 → 371
    Amb_all; Amb_all domain
    pfam04431
    Location:54 → 95
    Pec_lyase_N; Pectate lyase, N-terminus
Nucleotide Protein
Heading Accession and Version

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