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    kdm5bb lysine demethylase 5Bb [ Danio rerio (zebrafish) ]

    Gene ID: 415256, updated on 9-Dec-2024

    Summary

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    Official Symbol
    kdm5bbprovided by ZNC
    Official Full Name
    lysine demethylase 5Bbprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-030424-1
    See related
    Ensembl:ENSDARG00000003098 AllianceGenome:ZFIN:ZDB-GENE-030424-1
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    plu1; cb264; jarid1bb; zgc:85741; wu:fc44h11
    Summary
    Predicted to enable histone H3K4me/H3K4me2/H3K4me3 demethylase activity. Predicted to be involved in chromatin remodeling and regulation of DNA-templated transcription. Predicted to act upstream of or within chromatin organization. Predicted to be located in chromatin. Predicted to be active in nucleus. Is expressed in several structures, including hindbrain neural plate; musculature system; nervous system; neural tube; and solid lens vesicle. Human ortholog(s) of this gene implicated in autosomal recessive intellectual developmental disorder 65; breast cancer; and high grade glioma. Orthologous to human KDM5B (lysine demethylase 5B). [provided by Alliance of Genome Resources, Dec 2024]
    Orthologs
    all
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    Genomic context

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    See kdm5bb in Genome Data Viewer
    Location:
    chromosome: 8
    Exon count:
    28
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 8 NC_007119.7 (28306539..28342487, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 8 NC_007119.6 (28287400..28323384, complement)

    Chromosome 8 - NC_007119.7Genomic Context describing neighboring genes Neighboring gene RAP1A, member of RAS oncogene family a Neighboring gene leiomodin 1a (smooth muscle) Neighboring gene kelch-like protein 12 Neighboring gene tubulin alpha 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. Enhancer activity-based identification of functional enhancers using zebrafish embryos. Taminato T, et al. Genomics, 2016 Aug. PMID 27256877
    2. High-throughput functional analysis of autism genes in zebrafish identifies convergence in dopaminergic and neuroimmune pathways. Weinschutz Mendes H, et al. Cell Rep, 2023 Mar 28. PMID 36933215, Free PMC Article
    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. An intestinal cell type in zebrafish is the nexus for the SARS-CoV-2 receptor and the Renin-Angiotensin-Aldosterone System that contributes to COVID-19 comorbidities. Postlethwait JH, et al. bioRxiv, 2020 Sep 2. PMID 32908984, Free PMC Article
    5. A network of epigenetic regulators guides developmental haematopoiesis in vivo. Huang HT, et al. Nat Cell Biol, 2013 Dec. PMID 24240475, Free PMC Article

    See all (8) 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 histone H3K4me/H3K4me2/H3K4me3 demethylase activity ISS
    Inferred from Sequence or Structural Similarity
    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 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 5B-B
    Names
    [histone H3]-trimethyl-L-lysine(4) demethylase 5B-B
    histone demethylase JARID1B-B
    jumonji/ARID domain-containing protein 1B-B
    lysine (K)-specific demethylase 5Bb
    putative DNA/chromatin binding motif
    NP_001002166.2
    XP_005167081.1
    XP_009302264.1

    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_001002166.2 → NP_001002166.2  lysine-specific demethylase 5B-B

      Status: VALIDATED

      Source sequence(s)
      BX664742, EH449360
      UniProtKB/Swiss-Prot
      B0S5X8, B0S5X9, Q6IQX0
      UniProtKB/TrEMBL
      A0A8M1N012, F1QXN4
      Related
      ENSDARP00000102232.2, ENSDART00000108508.4

    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
      28306539..28342487 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_009303989.4 → XP_009302264.1  lysine-specific demethylase 5B-B isoform X2

      UniProtKB/Swiss-Prot
      B0S5X8, B0S5X9, Q6IQX0
      UniProtKB/TrEMBL
      A0A8M3BBT1
      Conserved Domains (9) summary
      smart00501
      Location:81 → 171
      BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
      smart00545
      Location:14 → 55
      JmjN; Small domain found in the jumonji family of transcription factors
      pfam02373
      Location:491 → 607
      JmjC; JmjC domain, hydroxylase
      cd15603
      Location:316 → 361
      PHD1_KDM5B; PHD finger 1 found in lysine-specific demethylase 5B (KDM5B)
      cd15607
      Location:1189 → 1232
      PHD2_KDM5B; PHD finger 2 found in lysine-specific demethylase 5B (KDM5B)
      cd15687
      Location:1464 → 1512
      PHD3_KDM5B; PHD finger 3 found in lysine-specific demethylase 5B (KDM5B)
      pfam02928
      Location:697 → 749
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:762 → 1096
      PLU-1; PLU-1-like protein
      pfam15315
      Location:1268 → 1317
      FRG2; Facioscapulohumeral muscular dystrophy candidate 2

    2. XM_005167024.5 → XP_005167081.1  lysine-specific demethylase 5B-B isoform X1

      UniProtKB/Swiss-Prot
      B0S5X8, B0S5X9, Q6IQX0
      UniProtKB/TrEMBL
      A0A8M2BEG9, G1K2I1
      Related
      ENSDARP00000023794.9, ENSDART00000005583.9
      Conserved Domains (8) summary
      smart00501
      Location:81 → 171
      BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
      smart00545
      Location:14 → 55
      JmjN; Small domain found in the jumonji family of transcription factors
      pfam02373
      Location:491 → 607
      JmjC; JmjC domain, hydroxylase
      cd15603
      Location:316 → 361
      PHD1_KDM5B; PHD finger 1 found in lysine-specific demethylase 5B (KDM5B)
      cd15607
      Location:1189 → 1232
      PHD2_KDM5B; PHD finger 2 found in lysine-specific demethylase 5B (KDM5B)
      cd15687
      Location:1465 → 1513
      PHD3_KDM5B; PHD finger 3 found in lysine-specific demethylase 5B (KDM5B)
      pfam02928
      Location:697 → 749
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:762 → 1096
      PLU-1; PLU-1-like protein
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6IQX0.2 GenPept UniProtKB/Swiss-Prot:Q6IQX0

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