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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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