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    LOC4338298 crooked neck-like protein 1 [ Oryza sativa Japonica Group (Japanese rice) ]

    Gene ID: 4338298, updated on 21-Dec-2023

    Summary

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    Gene symbol
    LOC4338298
    Gene description
    crooked neck-like protein 1
    Locus tag
    OSNPB_050289400
    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 after flowering (RPKM 24.5), roots after flowering (RPKM 23.6) and 6 other tissues See more
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    Genomic context

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    See LOC4338298 in Genome Data Viewer
    Location:
    chromosome: 5
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    102 current IRGSP-1.0 (GCF_001433935.1) 5 NC_029260.1 (12601141..12606127, complement)

    Chromosome 5 - NC_029260.1Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA R71 Neighboring gene small nucleolar RNA R71 Neighboring gene benzyl alcohol O-benzoyltransferase Neighboring gene N-acetylglucosaminyl-phosphatidylinositol biosynthetic protein gpi1

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_029260.1 Chromosome 5 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 
    Process Evidence Code Pubs
    involved_in mRNA splicing, via spliceosome IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    involved_in spliceosomal complex assembly IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of Prp19 complex IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    part_of U2-type catalytic step 2 spliceosome IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    part_of post-mRNA release spliceosomal complex IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    part_of precatalytic spliceosome IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    crooked neck-like protein 1
    Names
    Os05g0289400
    P0587F01.11
    putative crn

    NCBI Reference Sequences (RefSeq)

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    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_029260.1 Reference IRGSP-1.0 Primary Assembly

      Range
      12601141..12606127 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_015784665.2 → XP_015640151.1  crooked neck-like protein 1 isoform X1

      UniProtKB/TrEMBL
      B8AW38, B9FNN9, Q0DJG2, Q75HS3
      Conserved Domains (5) summary
      pfam02184
      Location:223 → 251
      HAT; HAT (Half-A-TPR) repeat
      smart00386
      Location:121 → 153
      HAT; HAT (Half-A-TPR) repeats
      COG5107
      Location:344 → 627
      RNA14; Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification]
      sd00006
      Location:107 → 135
      TPR; TPR repeat [structural motif]
      cl26712
      Location:31 → 185
      U3_assoc_6; U3 small nucleolar RNA-associated protein 6

    2. XM_015784666.2 → XP_015640152.1  crooked neck-like protein 1 isoform X2

      Conserved Domains (6) summary
      pfam02184
      Location:223 → 251
      HAT; HAT (Half-A-TPR) repeat
      smart00386
      Location:121 → 153
      HAT; HAT (Half-A-TPR) repeats
      sd00006
      Location:107 → 135
      TPR; TPR repeat [structural motif]
      pfam05843
      Location:260 → 348
      Suf; Suppressor of forked protein (Suf)
      pfam14559
      Location:219 → 280
      TPR_19; Tetratricopeptide repeat
      cl07066
      Location:340 → 406
      Mad3_BUB1_I; Mad3/BUB1 homology region 1
    Nucleotide Protein
    Heading Accession and Version

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