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LOC4344175 protein CHROMATIN REMODELING 5 [ Oryza sativa Japonica Group (Japanese rice) ]

Gene ID: 4344175, updated on 10-Oct-2024

Summary

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Gene symbol
LOC4344175
Gene description
protein CHROMATIN REMODELING 5
Locus tag
OSNPB_070660200
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
OJ1477_F01.130-1
Expression
Ubiquitous expression in roots after flowering (RPKM 36.3), leaves before flowering (RPKM 32.8) and 6 other tissues See more
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Genomic context

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See LOC4344175 in Genome Data Viewer
Location:
chromosome: 7
Exon count:
32
Annotation release Status Assembly Chr Location
RS_2024_06 current ASM3414082v1 (GCF_034140825.1) 7 NC_089041.1 (28053382..28067678, complement)
102 previous assembly IRGSP-1.0 (GCF_001433935.1) 7 NC_029262.1 (27825780..27840054, complement)

Chromosome 7 - NC_089041.1Genomic Context describing neighboring genes Neighboring gene uncharacterized protein At5g39865 Neighboring gene DEAD-box ATP-dependent RNA helicase 10-like Neighboring gene uncharacterized LOC9272302 Neighboring gene RNA pseudouridine synthase 6, chloroplastic Neighboring gene putative cis-zeatin O-glucosyltransferase

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
  2. Manual GO annotation of predictive protein signatures: the InterPro approach to GO curation. Burge S, et al. Database (Oxford), 2012. PMID 22301074, Free PMC Article
  3. TreeGrafter: phylogenetic tree-based annotation of proteins with Gene Ontology terms and other annotations. Tang H, et al. Bioinformatics, 2019 Feb 1. PMID 30032202, Free PMC Article

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 hydrolysis activity IEA
Inferred from Electronic Annotation
more info
 PubMed 
enables ATP-dependent chromatin remodeler activity IEA
Inferred from Electronic Annotation
more info
 PubMed 
enables DNA binding IEA
Inferred from Electronic Annotation
more info
 PubMed 
enables chromatin binding IEA
Inferred from Electronic Annotation
more info
 PubMed 
enables histone binding IEA
Inferred from Electronic Annotation
more info
 PubMed 
Process Evidence Code Pubs
involved_in nucleosome organization IEA
Inferred from Electronic Annotation
more info
 PubMed 
involved_in regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 PubMed 
Component Evidence Code Pubs
part_of chromatin IEA
Inferred from Electronic Annotation
more info
 PubMed 
located_in nucleus IEA
Inferred from Electronic Annotation
more info
 PubMed 

General protein information

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Preferred Names
protein CHROMATIN REMODELING 5
Names
Os07g0660200
P0496C02.115-1
chromodomain-helicase-DNA-binding protein-like 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
    28053382..28067678 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_015791202.3 → XP_015646688.1  protein CHROMATIN REMODELING 5

    UniProtKB/TrEMBL
    B9FUP1
    Conserved Domains (6) summary
    cd00024
    Location:507 → 560
    CHROMO; Chromatin organization modifier (chromo) domain is a conserved region of around 50 amino acids found in a variety of chromosomal proteins, which appear to play a role in the functional organization of the eukaryotic nucleus. Experimental evidence ...
    cd00046
    Location:617 → 763
    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.
    pfam00176
    Location:600 → 886
    SNF2_N; SNF2 family N-terminal domain
    pfam00271
    Location:928 → 1026
    Helicase_C; Helicase conserved C-terminal domain
    pfam13907
    Location:1500 → 1594
    DUF4208; Domain of unknown function (DUF4208)
    cl21498
    Location:1320 → 1384
    SANT; 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is ...

  2. XM_066312196.1 → XP_066168293.1  protein CHROMATIN REMODELING 5

  3. XM_066312197.1 → XP_066168294.1  protein CHROMATIN REMODELING 5

Nucleotide Protein
Heading Accession and Version

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