U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    LOC4326292 protein NCA1 [ Oryza sativa Japonica Group (Japanese rice) ]

    Gene ID: 4326292, updated on 10-Oct-2024

    Summary

    Go to the top of the page Help
    Gene symbol
    LOC4326292
    Gene description
    protein NCA1
    Locus tag
    OSNPB_010104100
    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
    Ubiquitous expression in leaves before flowering (RPKM 64.6), roots after flowering (RPKM 56.8) and 6 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 LOC4326292 in Genome Data Viewer
    Location:
    chromosome: 1
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_06 current ASM3414082v1 (GCF_034140825.1) 1 NC_089035.1 (213889..218568)
    102 previous assembly IRGSP-1.0 (GCF_001433935.1) 1 NC_029256.1 (209464..214176)

    Chromosome 1 - NC_089035.1Genomic Context describing neighboring genes Neighboring gene uncharacterized protein At1g76660 Neighboring gene uncharacterized LOC4326452 Neighboring gene C-type lectin receptor-like tyrosine-protein kinase At1g52310 Neighboring gene NAC transcription factor 29 Neighboring gene ricin B-like lectin R40G3

    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. 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

    Go to the top of the page Help

    Homology

    Gene Ontology Provided by RefSeq

    Function Evidence Code Pubs
    enables protein binding IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables ubiquitin protein ligase activity IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in protein ubiquitination IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 

    General protein information

    Go to the top of the page Help
    Preferred Names
    protein NCA1
    Names
    Os01g0104100
    P0436E04.13

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    NEW Try the new Transcript table

    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
      213889..218568
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_015762080.3 → XP_015617566.1  protein NCA1 isoform X1

      Conserved Domains (4) summary
      cd00162
      Location:223 → 261
      RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...
      sd00006
      Location:363 → 400
      TPR; TPR repeat [structural motif]
      pfam13424
      Location:359 → 438
      TPR_12; Tetratricopeptide repeat
      cl00750
      Location:472 → 498
      Exonuc_VII_S; Exonuclease VII small subunit

    2. XM_015762087.3 → XP_015617573.1  protein NCA1 isoform X3

      UniProtKB/TrEMBL
      A0A5S6RAI1, A0A9K3Y7T0, B7EW19, B8ACS7, B9EYS0, Q0JRF2, Q658D5
      Conserved Domains (4) summary
      COG5222
      Location:65 → 151
      COG5222; Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
      sd00006
      Location:212 → 249
      TPR; TPR repeat [structural motif]
      pfam13424
      Location:208 → 287
      TPR_12; Tetratricopeptide repeat
      cl17238
      Location:70 → 106
      RING_Ubox; The superfamily of RING finger (Really Interesting New Gene) domain and U-box domain

    3. XM_066310967.1 → XP_066167064.1  protein NCA1 isoform X2

    Nucleotide Protein
    Heading Accession and Version

    Gene LinkOut

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

    Molecular Biology Databases
    Research Materials