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

Gene ID: 4340097, updated on 16-Jul-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
RS_2024_06 current ASM3414082v1 (GCF_034140825.1) 6 NC_089040.1 (2478417..2487276, complement)
102 previous assembly IRGSP-1.0 (GCF_001433935.1) 6 NC_029261.1 (2320819..2329659, complement)

Chromosome 6 - NC_089040.1Genomic Context describing neighboring genes Neighboring gene pentatricopeptide repeat-containing protein At4g02750 Neighboring gene pre-mRNA splicing factor SR-like 1 Neighboring gene probable sulfate transporter 3.4 Neighboring gene DNA-repair protein XRCC1 Neighboring gene E3 ubiquitin-protein ligase Os03g0188200-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
  • 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
    UniProtKB/TrEMBL
    B9FRG1

  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
    UniProtKB/TrEMBL
    B9FRG1

  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
    UniProtKB/TrEMBL
    A2Y963

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
    2478417..2487276 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_015788278.2 → XP_015643764.1  coatomer subunit beta'-1 isoform X2

    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_015788276.2 → 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
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q5VQ78.1 GenPept UniProtKB/Swiss-Prot:Q5VQ78

Gene LinkOut

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