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    LOC4340097 coatomer subunit beta'-1-like [ Oryza sativa Japonica Group (Japanese rice) ]

    Gene ID: 4340097, updated on 3-Apr-2024

    Summary

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    Gene symbol
    LOC4340097
    Gene description
    coatomer subunit beta'-1-like
    Locus tag
    OSNPB_060143900
    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
    Expression
    Ubiquitous expression in flower buds (RPKM 44.7), roots after flowering (RPKM 43.8) and 6 other tissues See more
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    Genomic context

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    See LOC4340097 in Genome Data Viewer
    Location:
    chromosome: 6
    Exon count:
    25
    Annotation release Status Assembly Chr Location
    102 current IRGSP-1.0 (GCF_001433935.1) 6 NC_029261.1 (2320819..2329659, complement)

    Chromosome 6 - NC_029261.1Genomic Context describing neighboring genes Neighboring gene probable sulfate transporter 3.4 Neighboring gene uncharacterized LOC107281412 Neighboring gene uncharacterized LOC9270660 Neighboring gene DNA-repair protein XRCC1 Neighboring gene pectate lyase

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_029261.1 Chromosome 6 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. 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 protein binding IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables structural molecule activity IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in endoplasmic reticulum to Golgi vesicle-mediated transport IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    involved_in intra-Golgi vesicle-mediated transport IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    involved_in intracellular protein transport IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    involved_in retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of COPI vesicle coat IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    coatomer subunit beta'-1
    Names
    Beta'-COP 1
    Beta'-coat protein 1
    LOC_Os06g05180
    OSJNBa0007O20.8-1
    OSJNBa0007O20.8-2
    OSJNBa0007O20.8-3
    coatomer protein complex, beta prime subunit-like
    putative coatomer protein complex, beta prime subunit

    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_001421075.1 → NP_001408004.1  coatomer subunit beta'-1 isoform 1

      Status: VALIDATED

      Source sequence(s)
      AK061962, AK103948, AK111584, AP014962, CI335340, CI432443, CI657099, CI657442

    2. NM_001421076.1 → NP_001408005.1  coatomer subunit beta'-1 isoform 1

      Status: VALIDATED

      Source sequence(s)
      AK061962, AK103948, AK111584, AP014962, CI017977, CI335340, CI432443, CI657099, CI657442

    3. NM_001421077.1 → NP_001408006.1  coatomer subunit beta'-1 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AK061962, AK103948, AK111584, AP014962, CI216417, CI335340, CI432443, CI657099, CI657442
      UniProtKB/Swiss-Prot
      A0A0P0WSR8, Q5VQ78

    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_029261.1 Reference IRGSP-1.0 Primary Assembly

      Range
      2320819..2329659 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_015788278.1 → XP_015643764.1  coatomer subunit beta'-1 isoform X3

      UniProtKB/TrEMBL
      A2Y963
      Conserved Domains (5) summary
      COG2319
      Location:24 → 474
      WD40; WD40 repeat [General function prediction only]
      cd00200
      Location:17 → 297
      WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
      sd00006
      Location:641 → 668
      TPR; TPR repeat [structural motif]
      pfam04053
      Location:320 → 764
      Coatomer_WDAD; Coatomer WD associated region
      sd00039
      Location:62 → 97
      7WD40; WD40 repeat [structural motif]

    2. XM_015788274.1 → XP_015643760.1  coatomer subunit beta'-1 isoform X1

      Conserved Domains (5) summary
      cd00200
      Location:17 → 297
      WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
      sd00006
      Location:641 → 668
      TPR; TPR repeat [structural motif]
      sd00039
      Location:62 → 97
      7WD40; WD40 repeat [structural motif]
      pfam04053
      Location:319 → 764
      Coatomer_WDAD; Coatomer WD associated region
      cl22451
      Location:819 → 902
      ASF1_hist_chap; ASF1 like histone chaperone

    3. XM_015788276.1 → XP_015643762.1  coatomer subunit beta'-1 isoform X1

      UniProtKB/TrEMBL
      B9FRG1
      Conserved Domains (5) summary
      cd00200
      Location:17 → 297
      WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
      sd00006
      Location:641 → 668
      TPR; TPR repeat [structural motif]
      sd00039
      Location:62 → 97
      7WD40; WD40 repeat [structural motif]
      pfam04053
      Location:319 → 764
      Coatomer_WDAD; Coatomer WD associated region
      cl22451
      Location:819 → 902
      ASF1_hist_chap; ASF1 like histone chaperone

    4. XM_015788275.1 → XP_015643761.1  coatomer subunit beta'-1 isoform X1

      Conserved Domains (5) summary
      cd00200
      Location:17 → 297
      WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
      sd00006
      Location:641 → 668
      TPR; TPR repeat [structural motif]
      sd00039
      Location:62 → 97
      7WD40; WD40 repeat [structural motif]
      pfam04053
      Location:319 → 764
      Coatomer_WDAD; Coatomer WD associated region
      cl22451
      Location:819 → 902
      ASF1_hist_chap; ASF1 like histone chaperone

    5. XM_015788277.2 → XP_015643763.1  coatomer subunit beta'-1 isoform X2

      UniProtKB/Swiss-Prot
      Q5VQ78
      Conserved Domains (6) summary
      COG2319
      Location:24 → 474
      WD40; WD40 repeat [General function prediction only]
      cd00200
      Location:17 → 297
      WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
      sd00006
      Location:641 → 668
      TPR; TPR repeat [structural motif]
      pfam04053
      Location:320 → 764
      Coatomer_WDAD; Coatomer WD associated region
      sd00039
      Location:62 → 97
      7WD40; WD40 repeat [structural motif]
      cl22451
      Location:819 → 900
      ASF1_hist_chap; ASF1 like histone chaperone
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5VQ78.1 GenPept UniProtKB/Swiss-Prot:Q5VQ78

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