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    LOC4338818 KH domain-containing protein At1g09660/At1g09670 [ Oryza sativa Japonica Group (Japanese rice) ]

    Gene ID: 4338818, updated on 12-Jul-2024

    Summary

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    Gene symbol
    LOC4338818
    Gene description
    KH domain-containing protein At1g09660/At1g09670
    Locus tag
    OSNPB_050419500
    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 15.0), flowers (RPKM 13.1) and 6 other tissues See more
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    Genomic context

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    See LOC4338818 in Genome Data Viewer
    Location:
    chromosome: 5
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_06 current ASM3414082v1 (GCF_034140825.1) 5 NC_089039.1 (20672642..20677344, complement)
    102 previous assembly IRGSP-1.0 (GCF_001433935.1) 5 NC_029260.1 (20568921..20573714, complement)

    Chromosome 5 - NC_089039.1Genomic Context describing neighboring genes Neighboring gene protein root UVB sensitive 6 Neighboring gene uncharacterized LOC112939097 Neighboring gene uncharacterized LOC4338819 Neighboring gene GDSL esterase/lipase At1g71691

    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 mRNA binding IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in regulation of mRNA splicing, via spliceosome IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    KH domain-containing protein At1g09660/At1g09670
    Names
    Os05g0419500

    NCBI Reference Sequences (RefSeq)

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    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_089039.1 Reference ASM3414082v1 Primary Assembly

      Range
      20672642..20677344 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_015785332.3 → XP_015640818.1  KH domain-containing protein At1g09660/At1g09670 isoform X4

      Conserved Domains (2) summary
      pfam16544
      Location:38 → 81
      STAR_dimer; Homodimerization region of STAR domain protein
      cl00098
      Location:138 → 199
      KH-I; K homology (KH) RNA-binding domain, type I

    2. XM_015785330.3 → XP_015640816.1  KH domain-containing protein At1g09660/At1g09670 isoform X2

      UniProtKB/TrEMBL
      A0A0N7KKS9, B8AYB7, B9FPN5, Q60DW1
      Conserved Domains (2) summary
      cd02395
      Location:142 → 262
      SF1_like-KH; Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 ...
      pfam16544
      Location:38 → 81
      STAR_dimer; Homodimerization region of STAR domain protein

    3. XM_015785331.3 → XP_015640817.1  KH domain-containing protein At1g09660/At1g09670 isoform X3

      Conserved Domains (2) summary
      pfam16544
      Location:38 → 83
      STAR_dimer; Homodimerization region of STAR domain protein
      cl00098
      Location:147 → 224
      KH-I; K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that ...

    4. XM_015785329.3 → XP_015640815.1  KH domain-containing protein At1g09660/At1g09670 isoform X1

      Conserved Domains (2) summary
      pfam16544
      Location:38 → 81
      STAR_dimer; Homodimerization region of STAR domain protein
      cl00098
      Location:139 → 239
      KH-I; K homology (KH) RNA-binding domain, type I
    Nucleotide Protein
    Heading Accession and Version

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