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    kdm6ba lysine (K)-specific demethylase 6B, a [ Danio rerio (zebrafish) ]

    Gene ID: 556678, updated on 25-Apr-2024

    Summary

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    Official Symbol
    kdm6baprovided by ZNC
    Official Full Name
    lysine (K)-specific demethylase 6B, aprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-091005-1
    See related
    Ensembl:ENSDARG00000088087 AllianceGenome:ZFIN:ZDB-GENE-091005-1
    Gene type
    protein coding
    RefSeq status
    MODEL
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    jmjd3b
    Summary
    Predicted to enable histone H3-tri/di-methyl-lysine-27 demethylase activity and metal ion binding activity. Acts upstream of or within heart development and heart trabecula morphogenesis. Predicted to be located in nucleus. Is expressed in brain; heart; and otic vesicle. Orthologous to human KDM6B (lysine demethylase 6B). [provided by Alliance of Genome Resources, Apr 2022]
    Orthologs
    human mouse all
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    Genomic context

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    See kdm6ba in Genome Data Viewer
    Location:
    chromosome: 7
    Exon count:
    28
    Annotation release Status Assembly Chr Location
    106 current GRCz11 (GCF_000002035.6) 7 NC_007118.7 (21632079..21778336)
    105 previous assembly GRCz10 (GCF_000002035.5) 7 NC_007118.6 (21365640..21511998)

    Chromosome 7 - NC_007118.7Genomic Context describing neighboring genes Neighboring gene serine (or cysteine) peptidase inhibitor, clade H, member 2 Neighboring gene dynein, axonemal, heavy chain 2 Neighboring gene uncharacterized LOC101882514 Neighboring gene transmembrane protein 88 b Neighboring gene transmembrane 4 L six family member 5

    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. Histone demethylases Kdm6ba and Kdm6bb redundantly promote cardiomyocyte proliferation during zebrafish heart ventricle maturation. Akerberg AA, et al. Dev Biol, 2017 Jun 1. PMID 28372944, Free PMC Article
    2. A histone demethylase is necessary for regeneration in zebrafish. Stewart S, et al. Proc Natl Acad Sci U S A, 2009 Nov 24. PMID 19897725, Free PMC Article
    3. Silencing of odorant receptor genes by G protein βγ signaling ensures the expression of one odorant receptor per olfactory sensory neuron. Ferreira T, et al. Neuron, 2014 Feb 19. PMID 24559675, Free PMC Article
    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 (10) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. loss of both kdm6ba and kdm6bb shows Kdm6b proteins share redundant and pleiotropic roles in organogenesis without impacting initial cell fate specification.
      Title: Histone demethylases Kdm6ba and Kdm6bb redundantly promote cardiomyocyte proliferation during zebrafish heart ventricle maturation.
    Submit: New GeneRIF Correction

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables histone H3K27me2/H3K27me3 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 heart development IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within heart trabecula morphogenesis IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    lysine-specific demethylase 6B

    NCBI Reference Sequences (RefSeq)

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    RefSeqs of Annotated Genomes: Danio rerio Annotation Release 106 details...Open this link in a new tab

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

    Reference GRCz11 Primary Assembly

    Genomic

    1. NC_007118.7 Reference GRCz11 Primary Assembly

      Range
      21632079..21778336
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_009303125.3 → XP_009301400.1  lysine-specific demethylase 6B

      See identical proteins and their annotated locations for XP_009301400.1

      UniProtKB/TrEMBL
      A0A1D5NSI1, A0A8M3AU53
      Conserved Domains (4) summary
      pfam02373
      Location:1730 → 1838
      JmjC; JmjC domain, hydroxylase
      smart00558
      Location:1696 → 1760
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      cl25496
      Location:478 → 693
      Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
      cl26464
      Location:128 → 507
      Atrophin-1; Atrophin-1 family

    2. XM_005172240.4 → XP_005172297.1  lysine-specific demethylase 6B

      See identical proteins and their annotated locations for XP_005172297.1

      UniProtKB/TrEMBL
      A0A1D5NSI1, A0A8M3AU53
      Conserved Domains (4) summary
      pfam02373
      Location:1730 → 1838
      JmjC; JmjC domain, hydroxylase
      smart00558
      Location:1696 → 1760
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      cl25496
      Location:478 → 693
      Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
      cl26464
      Location:128 → 507
      Atrophin-1; Atrophin-1 family

    3. XM_021477780.1 → XP_021333455.1  lysine-specific demethylase 6B

      UniProtKB/TrEMBL
      A0A1D5NSI1, A0A8M3AU53
      Conserved Domains (4) summary
      pfam02373
      Location:1730 → 1838
      JmjC; JmjC domain, hydroxylase
      smart00558
      Location:1696 → 1760
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      cl25496
      Location:478 → 693
      Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
      cl26464
      Location:128 → 507
      Atrophin-1; Atrophin-1 family

    4. XM_021477779.1 → XP_021333454.1  lysine-specific demethylase 6B

      UniProtKB/TrEMBL
      A0A1D5NSI1, A0A8M3AU53
      Conserved Domains (4) summary
      pfam02373
      Location:1730 → 1838
      JmjC; JmjC domain, hydroxylase
      smart00558
      Location:1696 → 1760
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      cl25496
      Location:478 → 693
      Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
      cl26464
      Location:128 → 507
      Atrophin-1; Atrophin-1 family

    5. XM_005172239.4 → XP_005172296.1  lysine-specific demethylase 6B

      See identical proteins and their annotated locations for XP_005172296.1

      UniProtKB/TrEMBL
      A0A1D5NSI1, A0A8M3AU53
      Related
      ENSDARP00000142796.1, ENSDART00000173641.2
      Conserved Domains (4) summary
      pfam02373
      Location:1730 → 1838
      JmjC; JmjC domain, hydroxylase
      smart00558
      Location:1696 → 1760
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      cl25496
      Location:478 → 693
      Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
      cl26464
      Location:128 → 507
      Atrophin-1; Atrophin-1 family
    Nucleotide Protein Strain
    Heading Accession and Version

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