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kdm4b lysine (K)-specific demethylase 4B [ Danio rerio (zebrafish) ]

Gene ID: 556504, updated on 4-Jan-2025

Summary

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Official Symbol
kdm4bprovided by ZNC
Official Full Name
lysine (K)-specific demethylase 4Bprovided by ZNC
Primary source
ZFIN:ZDB-GENE-060503-664
See related
Ensembl:ENSDARG00000099675 AllianceGenome:ZFIN:ZDB-GENE-060503-664
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
jmjd2b; si:ch211-124a3.4
Summary
Predicted to enable histone H3K9 demethylase activity. Predicted to be involved in chromatin remodeling and regulation of gene expression. Predicted to act upstream of or within chromatin organization. Predicted to be located in chromatin. Predicted to be active in nucleus. Is expressed in caudal hematopoietic tissue. Human ortholog(s) of this gene implicated in autosomal dominant intellectual developmental disorder; breast cancer; colorectal cancer; malignant peripheral nerve sheath tumor; and stomach cancer. Orthologous to human KDM4B (lysine demethylase 4B). [provided by Alliance of Genome Resources, Jan 2025]
Orthologs
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Genomic context

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See kdm4b in Genome Data Viewer
Location:
chromosome: 22
Exon count:
22
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCz11 (GCF_000002035.6) 22 NC_007133.7 (4315256..4407871, complement)
105 previous assembly GRCz10 (GCF_000002035.5) 22 NC_007133.6 (3862408..3955023, complement)

Chromosome 22 - NC_007133.7Genomic Context describing neighboring genes Neighboring gene major histocompatibility complex class I ULA Neighboring gene uncharacterized LOC101883897 Neighboring gene uncharacterized LOC110438264 Neighboring gene ubiquitin-like with PHD and ring finger domains 1 Neighboring gene TIR domain containing adaptor molecule 1

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. 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
  2. Zbtb46 Controls Dendritic Cell Activation by Reprogramming Epigenetic Regulation of cd80/86 and cd40 Costimulatory Signals in a Zebrafish Model. Shao T, et al. J Immunol, 2022 Jun 15. PMID 35675955
  3. 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
  4. A network of epigenetic regulators guides developmental haematopoiesis in vivo. Huang HT, et al. Nat Cell Biol, 2013 Dec. PMID 24240475, Free PMC Article
  5. 15000 unique zebrafish EST clusters and their future use in microarray for profiling gene expression patterns during embryogenesis. Lo J, et al. Genome Res, 2003 Mar. PMID 12618376, Free PMC Article

See all (7) 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 dioxygenase activity IEA
Inferred from Electronic Annotation
more info
  
enables histone H3K9 demethylase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables histone H3K9me2/H3K9me3 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
  
involved_in regulation of gene expression 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 4B
Names
jumonji domain containing 2B
NP_001076274.1

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_001082805.1 → NP_001076274.1  lysine-specific demethylase 4B

    See identical proteins and their annotated locations for NP_001076274.1

    Status: PROVISIONAL

    Source sequence(s)
    BX927276, CU074310
    UniProtKB/TrEMBL
    A0A8M9P494, B7ZVT3, Q1LUQ0
    Related
    ENSDARP00000133766.1, ENSDART00000162523.2
    Conserved Domains (7) summary
    smart00545
    Location:95 → 136
    JmjN; Small domain found in the jumonji family of transcription factors
    PRK00404
    Location:978 → 1099
    tatB; sec-independent translocase; Provisional
    smart00333
    Location:905 → 953
    TUDOR; Tudor domain
    pfam02373
    Location:256 → 372
    JmjC; JmjC domain, hydroxylase
    cd15576
    Location:676 → 774
    PHD_JMJD2B; PHD finger found in Jumonji domain-containing protein 2B (JMJD2B)
    pfam07321
    Location:408 → 512
    YscO; Type III secretion protein YscO
    cl22851
    Location:783 → 892
    PHD_SF; PHD finger superfamily

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_007133.7 Reference GRCz11 Primary Assembly

    Range
    4315256..4407871 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein Strain
Heading Accession and Version

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