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LOC4326576 peptide deformylase 1B, chloroplastic-like [ Oryza sativa Japonica Group (Japanese rice) ]

Gene ID: 4326576, updated on 3-Apr-2024

Summary

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Gene symbol
LOC4326576
Gene description
peptide deformylase 1B, chloroplastic-like
Locus tag
OSNPB_010637600
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
PDF1B; PDF1B1; OsPDF1B; OsJ_02762; OsJ_002667; P0004A09.6
Expression
Broad expression in leaves before flowering (RPKM 73.4), roots after flowering (RPKM 46.6) and 6 other tissues See more
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Genomic context

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Location:
chromosome: 1
Exon count:
7
Annotation release Status Assembly Chr Location
102 current IRGSP-1.0 (GCF_001433935.1) 1 NC_029256.1 (25585705..25589172, complement)

Chromosome 1 - NC_029256.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC112939839 Neighboring gene uncharacterized LOC107279157 Neighboring gene polygalacturonase At1g48100 Neighboring gene myb-related protein 305 Neighboring gene anthocyanin 3'-O-beta-glucosyltransferase

Genomic regions, transcripts, and products

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Genomic Sequence:
NC_029256.1 Chromosome 1 Reference IRGSP-1.0 Primary Assembly

Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: 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. Rice peptide deformylase PDF1B is crucial for development of chloroplasts. Moon S, et al. Plant Cell Physiol, 2008 Oct. PMID 18718933
  2. 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 peptide deformylase activity IEA
Inferred from Electronic Annotation
more info
 PubMed 
Process Evidence Code Pubs
involved_in peptidyl-methionine modification IEA
Inferred from Electronic Annotation
more info
 PubMed 
Component Evidence Code Pubs
located_in chloroplast IEA
Inferred from Electronic Annotation
more info
 PubMed 
located_in mitochondrion IEA
Inferred from Electronic Annotation
more info
 PubMed 

General protein information

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Preferred Names
peptide deformylase 1B, chloroplastic
Names
LOC_Os01g45070
P0696E01.27
PDF 1B
peptide deformylase 1B1
putative polygalacturonase
XP_015612309.1

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_001398036.1 → NP_001384965.1  peptide deformylase 1B, chloroplastic

    Status: VALIDATED

    Source sequence(s)
    AK106980, CI459632
    UniProtKB/Swiss-Prot
    A0A0P0V5R4, A2ZVU5, B9EY95, Q5VNN5
    Conserved Domains (1) summary
    cd00487
    Location:80 → 220
    Pep_deformylase; Polypeptide or peptide deformylase; a family of metalloenzymes that catalyzes the removal of the N-terminal formyl group in a growing polypeptide chain following translation initiation during protein synthesis in prokaryotes. These enzymes utilize Fe(II) ...

RefSeqs of Annotated Genomes: Oryza sativa Japonica Group Annotation Release 102 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference IRGSP-1.0 Primary Assembly

Genomic

  1. NC_029256.1 Reference IRGSP-1.0 Primary Assembly

    Range
    25585705..25589172 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_015756823.2 → XP_015612309.1  peptide deformylase 1B, chloroplastic

    UniProtKB/Swiss-Prot
    Q5VNN5
    Conserved Domains (1) summary
    cd00487
    Location:80 → 220
    Pep_deformylase; Polypeptide or peptide deformylase; a family of metalloenzymes that catalyzes the removal of the N-terminal formyl group in a growing polypeptide chain following translation initiation during protein synthesis in prokaryotes. These enzymes utilize Fe(II) ...
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q5VNN5.1 GenPept UniProtKB/Swiss-Prot:Q5VNN5

Gene LinkOut

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Molecular Biology Databases