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    LOC4326436 helicase-like transcription factor CHR28 [ Oryza sativa Japonica Group (Japanese rice) ]

    Gene ID: 4326436, updated on 1-Aug-2024

    Summary

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    Gene symbol
    LOC4326436
    Gene description
    helicase-like transcription factor CHR28
    Locus tag
    OSNPB_010779400
    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 roots before flowering (RPKM 46.8), roots after flowering (RPKM 33.6) and 6 other tissues See more
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    Genomic context

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    See LOC4326436 in Genome Data Viewer
    Location:
    chromosome: 1
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_06 current ASM3414082v1 (GCF_034140825.1) 1 NC_089035.1 (33605891..33616087, complement)
    102 previous assembly IRGSP-1.0 (GCF_001433935.1) 1 NC_029256.1 (33000058..33010270, complement)

    Chromosome 1 - NC_089035.1Genomic Context describing neighboring genes Neighboring gene insulin-degrading enzyme-like 1, peroxisomal Neighboring gene L-type lectin-domain containing receptor kinase IX.1 Neighboring gene uncharacterized LOC4326437 Neighboring gene katanin p80 WD40 repeat-containing subunit B1 homolog KTN80.4

    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 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 ATP binding IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables ATP-dependent chromatin remodeler activity IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in DNA repair 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
    helicase-like transcription factor CHR28
    Names
    Os01g0779400
    P0010B10.13-1
    P0010B10.13-2
    SNF2 family N-terminal domain-containing protein
    putative ATPase

    NCBI Reference Sequences (RefSeq)

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    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
      33605891..33616087 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_015760756.3 → XP_015616242.1  helicase-like transcription factor CHR28 isoform X6

      UniProtKB/TrEMBL
      B8AAE9, B9ETC0
      Conserved Domains (4) summary
      cd00046
      Location:498 → 672
      DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
      cd00162
      Location:844 → 885
      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 ...
      pfam00176
      Location:404 → 806
      SNF2_N; SNF2 family N-terminal domain
      pfam00271
      Location:981 → 1079
      Helicase_C; Helicase conserved C-terminal domain

    2. XM_066304423.1 → XP_066160520.1  helicase-like transcription factor CHR28 isoform X5

      UniProtKB/TrEMBL
      B8AAE9, B9ETC0

    3. XM_015760752.3 → XP_015616238.1  helicase-like transcription factor CHR28 isoform X4

      UniProtKB/TrEMBL
      A0A0P0V8X9, A0A979HL48, B8AAE9, B9ETC0, Q0JIT1, Q5ZCG5
      Conserved Domains (3) summary
      COG0553
      Location:465 → 1211
      HepA; Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination and repair]
      cd18008
      Location:477 → 804
      DEXDc_SHPRH-like; DEXH-box helicase domain of SHPRH-like proteins
      cl17238
      Location:931 → 964
      RING_Ubox; The superfamily of RING finger (Really Interesting New Gene) domain and U-box domain

    4. XM_015760746.3 → XP_015616232.1  helicase-like transcription factor CHR28 isoform X2

      UniProtKB/TrEMBL
      B8AAE9, B9ETC0
      Conserved Domains (3) summary
      COG0553
      Location:492 → 1238
      HepA; Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination and repair]
      cd18008
      Location:504 → 831
      DEXDc_SHPRH-like; DEXH-box helicase domain of SHPRH-like proteins
      cl17238
      Location:958 → 991
      RING_Ubox; The superfamily of RING finger (Really Interesting New Gene) domain and U-box domain

    5. XM_015760750.3 → XP_015616236.1  helicase-like transcription factor CHR28 isoform X3

      UniProtKB/TrEMBL
      A0A0N7KDV0, A0A979HL94, B8AAE9, B9ETC0, Q5ZCG4, X2GIR4
      Conserved Domains (3) summary
      COG0553
      Location:480 → 1226
      HepA; Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination and repair]
      cd18008
      Location:492 → 819
      DEXDc_SHPRH-like; DEXH-box helicase domain of SHPRH-like proteins
      cl17238
      Location:946 → 979
      RING_Ubox; The superfamily of RING finger (Really Interesting New Gene) domain and U-box domain

    6. XM_015760742.3 → XP_015616228.1  helicase-like transcription factor CHR28 isoform X1

      UniProtKB/TrEMBL
      B8AAE9, B9ETC0
      Conserved Domains (3) summary
      COG0553
      Location:507 → 1253
      HepA; Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination and repair]
      cd18008
      Location:519 → 846
      DEXDc_SHPRH-like; DEXH-box helicase domain of SHPRH-like proteins
      cl17238
      Location:973 → 1006
      RING_Ubox; The superfamily of RING finger (Really Interesting New Gene) domain and U-box domain
    Nucleotide Protein
    Heading Accession and Version

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