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    LOC103637982 CHD3-type chromatin-remodeling factor PICKLE [ Zea mays ]

    Gene ID: 103637982, updated on 14-Dec-2023

    Summary

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    Gene symbol
    LOC103637982
    Gene description
    CHD3-type chromatin-remodeling factor PICKLE
    Locus tag
    ZEAMMB73_Zm00001d045109
    Gene type
    protein coding
    RefSeq status
    MODEL
    Organism
    Zea mays
    Lineage
    Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; PACMAD clade; Panicoideae; Andropogonodae; Andropogoneae; Tripsacinae; Zea
    Also known as
    chd3a; rmr12; GRMZM2G409865
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    Genomic context

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    See LOC103637982 in Genome Data Viewer
    Location:
    chromosome: 9
    Exon count:
    31
    Annotation release Status Assembly Chr Location
    103 current Zm-B73-REFERENCE-NAM-5.0 (GCF_902167145.1) 9 NC_050104.1 (14967159..14988063)
    102.20200423 previous assembly B73 RefGen_v4 (GCF_000005005.2) 9 NC_024467.2 (13084718..13105585)

    Chromosome 9 - NC_050104.1Genomic Context describing neighboring genes Neighboring gene transcription factor LRL3 Neighboring gene replication termination factor 2 Neighboring gene uncharacterized LOC100278723 Neighboring gene Putative two-component response regulator family protein

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. Locus-specific paramutation in Zea mays is maintained by a PICKLE-like chromodomain helicase DNA-binding 3 protein controlling development and male gametophyte function. Deans NC, et al. PLoS Genet, 2020 Dec. PMID 33320854, Free PMC Article
    2. Anchoring 9,371 maize expressed sequence tagged unigenes to the bacterial artificial chromosome contig map by two-dimensional overgo hybridization. Gardiner J, et al. Plant Physiol, 2004 Apr. PMID 15020742, Free PMC Article
    3. Insights into corn genes derived from large-scale cDNA sequencing. Alexandrov NN, et al. Plant Mol Biol, 2009 Jan. PMID 18937034, Free PMC Article

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Locus-specific paramutation in Zea mays is maintained by a PICKLE-like chromodomain helicase DNA-binding 3 protein controlling development and male gametophyte function.
      Title: Locus-specific paramutation in Zea mays is maintained by a PICKLE-like chromodomain helicase DNA-binding 3 protein controlling development and male gametophyte function.
    Submit: New GeneRIF Correction

    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 chromatin remodeling IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    involved_in negative 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
    CHD3-type chromatin-remodeling factor PICKLE
    Names
    putative homeodomain-like transcription factor superfamily protein
    required to maintain repression 12

    NCBI Reference Sequences (RefSeq)

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    RefSeqs of Annotated Genomes: Zea mays Annotation Release 103 details...Open this link in a new tab

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference Zm-B73-REFERENCE-NAM-5.0 Primary Assembly

    Genomic

    1. NC_050104.1 Reference Zm-B73-REFERENCE-NAM-5.0 Primary Assembly

      Range
      14967159..14988063
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_008660979.3 → XP_008659201.1  CHD3-type chromatin-remodeling factor PICKLE isoform X1

      UniProtKB/TrEMBL
      A0A1D6NTP1, A0A1D6NTP5, A0A1D6NTR2, A0A3L6D9K6, A0A7U3W5F2, A0A8J8YN73
      Conserved Domains (7) summary
      smart00249
      Location:58 → 98
      PHD; PHD zinc finger
      smart00298
      Location:199 → 247
      CHROMO; Chromatin organization modifier domain
      cd00024
      Location:104 → 153
      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 ...
      pfam06461
      Location:920 → 1040
      DUF1086; Domain of Unknown Function (DUF1086)
      pfam06465
      Location:852 → 894
      DUF1087; Domain of Unknown Function (DUF1087)
      pfam08074
      Location:1069 → 1170
      CHDCT2; CHDCT2 (NUC038) domain
      cl26465
      Location:278 → 778
      SNF2_N; SNF2 family N-terminal domain

    2. XM_008660980.3 → XP_008659202.1  CHD3-type chromatin-remodeling factor PICKLE isoform X2

      UniProtKB/TrEMBL
      A0A1D6NTP5, A0A1D6NTP7, A0A1D6NTR2, A0A7U3W5F2
      Conserved Domains (7) summary
      smart00249
      Location:58 → 98
      PHD; PHD zinc finger
      smart00298
      Location:199 → 247
      CHROMO; Chromatin organization modifier domain
      cd00024
      Location:104 → 153
      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 ...
      pfam06461
      Location:920 → 1040
      DUF1086; Domain of Unknown Function (DUF1086)
      pfam06465
      Location:852 → 894
      DUF1087; Domain of Unknown Function (DUF1087)
      pfam08074
      Location:1069 → 1168
      CHDCT2; CHDCT2 (NUC038) domain
      cl26465
      Location:278 → 778
      SNF2_N; SNF2 family N-terminal domain

    RNA

    1. XR_004852554.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version

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