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    LOC4342227 sister chromatid cohesion protein SCC2 [ Oryza sativa Japonica Group (Japanese rice) ]

    Gene ID: 4342227, updated on 12-Jul-2024

    Summary

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    Gene symbol
    LOC4342227
    Gene description
    sister chromatid cohesion protein SCC2
    Locus tag
    OSNPB_070110400
    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
    Also known as
    OJ1123_C12.101
    Expression
    Ubiquitous expression in roots after flowering (RPKM 14.0), leaves before flowering (RPKM 12.7) and 6 other tissues See more
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    Genomic context

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    See LOC4342227 in Genome Data Viewer
    Location:
    chromosome: 7
    Exon count:
    28
    Annotation release Status Assembly Chr Location
    RS_2024_06 current ASM3414082v1 (GCF_034140825.1) 7 NC_089041.1 (577833..592405)
    102 previous assembly IRGSP-1.0 (GCF_001433935.1) 7 NC_029262.1 (567623..582193)

    Chromosome 7 - NC_089041.1Genomic Context describing neighboring genes Neighboring gene nucleolar GTP-binding protein 1 Neighboring gene adrenodoxin-like protein 2, mitochondrial Neighboring gene uncharacterized LOC4342228 Neighboring gene uncharacterized LOC9266639

    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 chromatin binding IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in establishment of mitotic sister chromatid cohesion IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    involved_in establishment of protein localization to chromatin IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    involved_in mitotic cohesin loading IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    involved_in regulation of gene expression IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    involved_in replication-born double-strand break repair via sister chromatid exchange IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of Scc2-Scc4 cohesin loading complex IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    sister chromatid cohesion protein SCC2
    Names
    Os07g0110400
    nipped-B-like protein
    putative IDN3 protein

    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_089041.1 Reference ASM3414082v1 Primary Assembly

      Range
      577833..592405
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_015791698.3 → XP_015647184.1  sister chromatid cohesion protein SCC2 isoform X1

      UniProtKB/TrEMBL
      B8B6V3
      Conserved Domains (6) summary
      cd15489
      Location:662 → 704
      PHD_SF; PHD finger superfamily
      sd00044
      Location:835 → 863
      HEAT; HEAT repeat [structural motif]
      pfam12765
      Location:856 → 897
      Cohesin_HEAT; HEAT repeat associated with sister chromatid cohesion
      pfam12830
      Location:1351 → 1531
      Nipped-B_C; Sister chromatid cohesion C-terminus
      cd19953
      Location:909 → 938
      PDS5; HEAT repeat [structural motif]
      cl15079
      Location:880 → 1016
      PDS5; Sister chromatid cohesion protein PDS5

    2. XM_015791699.3 → XP_015647185.1  sister chromatid cohesion protein SCC2 isoform X2

      UniProtKB/TrEMBL
      B8B6V3
      Conserved Domains (4) summary
      cd15489
      Location:517 → 559
      PHD_SF; PHD finger superfamily
      pfam12765
      Location:711 → 752
      Cohesin_HEAT; HEAT repeat associated with sister chromatid cohesion
      pfam12830
      Location:1205 → 1387
      Nipped-B_C; Sister chromatid cohesion C-terminus
      sd00044
      Location:690 → 718
      HEAT; HEAT repeat [structural motif]
    Nucleotide Protein
    Heading Accession and Version

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