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    kdm5c lysine demethylase 5C [ Danio rerio (zebrafish) ]

    Gene ID: 553406, updated on 9-Dec-2024

    Summary

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    Official Symbol
    kdm5cprovided by ZNC
    Official Full Name
    lysine demethylase 5Cprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-060810-94
    See related
    Ensembl:ENSDARG00000006124 AllianceGenome:ZFIN:ZDB-GENE-060810-94
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    jarid1c; im:7158173; wu:fa28h03; wu:fi31b07; si:ch211-218o21.2
    Summary
    Predicted to enable histone H3K4me/H3K4me2/H3K4me3 demethylase activity. Acts upstream of or within negative regulation of neuron apoptotic process. Predicted to be located in chromatin. Predicted to be active in nucleus. Is expressed in brain; head; muscle; spinal cord; and telencephalon. Human ortholog(s) of this gene implicated in descending colon cancer and syndromic X-linked intellectual disability Claes-Jensen type. Orthologous to several human genes including KDM5C (lysine demethylase 5C). [provided by Alliance of Genome Resources, Dec 2024]
    Orthologs
    all
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    Genomic context

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    See kdm5c in Genome Data Viewer
    Location:
    chromosome: 8
    Exon count:
    29
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 8 NC_007119.7 (36983529..37026607)
    105 previous assembly GRCz10 (GCF_000002035.5) 8 NC_007119.6 (36951081..36994173)

    Chromosome 8 - NC_007119.7Genomic Context describing neighboring genes Neighboring gene novel protein similar to vertebrate membrane associated guanylate kinase, WW and PDZ domain containing 1 (MAGI1) Neighboring gene IQ motif and Sec7 domain ArfGEF 2b Neighboring gene si:ch211-218o21.4 Neighboring gene renin binding protein

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • BioProject: PRJEB1986
    • Analysis date: Fri Dec 8 19:48:10 2017

    Bibliography

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    Related articles in PubMed

    1. KDM7 is a dual demethylase for histone H3 Lys 9 and Lys 27 and functions in brain development. Tsukada Y, et al. Genes Dev, 2010 Mar 1. PMID 20194436, Free PMC Article
    2. The X-linked mental retardation gene SMCX/JARID1C defines a family of histone H3 lysine 4 demethylases. Iwase S, et al. Cell, 2007 Mar 23. PMID 17320160
    3. Genomic responses of DNA methylation and transcript profiles in zebrafish cells upon nutrient deprivation stress. Fan X, et al. Sci Total Environ, 2020 Jun 20. PMID 32208287
    4. The histone demethylase Jmjd3 regulates zebrafish myeloid development by promoting spi1 expression. Yu SH, et al. Biochim Biophys Acta Gene Regul Mech, 2018 Feb. PMID 29378332, Free PMC Article
    5. The Kdm/Kmt gene families in the self-fertilizing mangrove rivulus fish, Kryptolebias marmoratus, suggest involvement of histone methylation machinery in development and reproduction. Fellous A, et al. Gene, 2019 Mar 1. PMID 30458291

    See all (11) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables dioxygenase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone H3K4me/H3K4me2/H3K4me3 demethylase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables histone H3K4me/H3K4me2/H3K4me3 demethylase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables oxidoreductase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within chromatin organization IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in chromatin remodeling IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within negative regulation of neuron apoptotic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of DNA-templated transcription IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in chromatin IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    lysine-specific demethylase 5C
    Names
    lysine (K)-specific demethylase 5C
    smcx
    NP_001116706.1
    XP_017212821.1
    XP_068079057.1
    XP_068079058.1

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001123234.1 → NP_001116706.1  lysine-specific demethylase 5C

      Status: PROVISIONAL

      Source sequence(s)
      BX537348
      UniProtKB/TrEMBL
      A0A8M1NGK0, B0S6L0
      Related
      ENSDARP00000110667.2, ENSDART00000127053.3
      Conserved Domains (7) summary
      smart00501
      Location:80 → 170
      BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
      smart00545
      Location:13 → 54
      JmjN; Small domain found in the jumonji family of transcription factors
      pfam02373
      Location:535 → 651
      JmjC; JmjC domain, hydroxylase
      cd15604
      Location:360 → 405
      PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      cd15608
      Location:1254 → 1311
      PHD2_KDM5C_5D; PHD finger 2 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      pfam02928
      Location:741 → 793
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:806 → 1134
      PLU-1; PLU-1-like protein

    RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

    Reference GRCz11 Primary Assembly

    Genomic

    1. NC_007119.7 Reference GRCz11 Primary Assembly

      Range
      36983529..37026607
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017357332.3 → XP_017212821.1  lysine-specific demethylase 5C isoform X2

      UniProtKB/TrEMBL
      A0A8M6Z830
      Conserved Domains (7) summary
      smart00501
      Location:80 → 170
      BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
      smart00545
      Location:13 → 54
      JmjN; Small domain found in the jumonji family of transcription factors
      pfam02373
      Location:516 → 632
      JmjC; JmjC domain, hydroxylase
      cd15604
      Location:341 → 386
      PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      cd15608
      Location:1235 → 1292
      PHD2_KDM5C_5D; PHD finger 2 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      pfam02928
      Location:722 → 774
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:787 → 1115
      PLU-1; PLU-1-like protein

    2. XM_068222957.1 → XP_068079058.1  lysine-specific demethylase 5C isoform X1

      UniProtKB/TrEMBL
      A0A8M1NGK0, B0S6L0

    3. XM_068222956.1 → XP_068079057.1  lysine-specific demethylase 5C isoform X1

      UniProtKB/TrEMBL
      A0A8M1NGK0, B0S6L0
    Nucleotide Protein Strain
    Heading Accession and Version

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