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    kdm5ba lysine demethylase 5Ba [ Danio rerio (zebrafish) ]

    Gene ID: 327168, updated on 9-Dec-2024

    Summary

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    Official Symbol
    kdm5baprovided by ZNC
    Official Full Name
    lysine demethylase 5Baprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-030131-5379
    See related
    Ensembl:ENSDARG00000057093 AllianceGenome:ZFIN:ZDB-GENE-030131-5379
    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
    jarid1b; jarid1ba; id:ibd5050; wu:fd15c05
    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 neural rod; paraxial mesoderm; pronephric duct; tail bud; and telencephalon. 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
    human mouse all
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    Genomic context

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    See kdm5ba in Genome Data Viewer
    Location:
    chromosome: 11
    Exon count:
    28
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 11 NC_007122.7 (24819324..24851464)
    105 previous assembly GRCz10 (GCF_000002035.5) 11 NC_007122.6 (24581492..24613840)

    Chromosome 11 - NC_007122.7Genomic Context describing neighboring genes Neighboring gene adiponectin receptor 1a Neighboring gene RAB interacting factor Neighboring gene importin 9 Neighboring gene shisa family member 4

    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. Environmental chemicals differentially affect epigenetic-related mechanisms in the zebrafish liver (ZF-L) cell line and in zebrafish embryos. Blanc M, et al. Aquat Toxicol, 2019 Oct. PMID 31442592
    2. Adiponectin and adiponectin receptor genes are coexpressed during zebrafish embryogenesis and regulated by food deprivation. Nishio S, et al. Dev Dyn, 2008 Jun. PMID 18489000
    3. 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
    4. 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
    5. A gene expression screen in zebrafish embryogenesis. Kudoh T, et al. Genome Res, 2001 Dec. PMID 11731487

    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
    		  
    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 (K)-specific demethylase 5Ba
    Names
    jumonji, AT rich interactive domain 1B (Rbp2 like)
    jumonji, AT rich interactive domain 1Ba (Rbp2 like)
    NP_001334536.1
    XP_005169321.1
    XP_021335228.1

    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_001347607.1 → NP_001334536.1  lysine (K)-specific demethylase 5Ba

      Status: VALIDATED

      Source sequence(s)
      CR628365
      UniProtKB/TrEMBL
      A0A2R8QQ41, A0A8M9Q713
      Related
      ENSDARP00000156841.1, ENSDART00000184549.1
      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:455 → 571
      JmjC; JmjC domain, hydroxylase
      cd15603
      Location:280 → 325
      PHD1_KDM5B; PHD finger 1 found in lysine-specific demethylase 5B (KDM5B)
      cd15687
      Location:1422 → 1471
      PHD3_KDM5B; PHD finger 3 found in lysine-specific demethylase 5B (KDM5B)
      pfam02928
      Location:661 → 712
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:726 → 1046
      PLU-1; PLU-1-like protein
      cl22851
      Location:1145 → 1188
      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_007122.7 Reference GRCz11 Primary Assembly

      Range
      24819324..24851464
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005169264.4 → XP_005169321.1  lysine (K)-specific demethylase 5Ba isoform X2

      See identical proteins and their annotated locations for XP_005169321.1

      UniProtKB/TrEMBL
      A0A8M2BGK4, A5WUR6
      Related
      ENSDARP00000122212.1, ENSDART00000135443.3
      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:454 → 570
      JmjC; JmjC domain, hydroxylase
      cd15603
      Location:279 → 324
      PHD1_KDM5B; PHD finger 1 found in lysine-specific demethylase 5B (KDM5B)
      cd15687
      Location:1421 → 1470
      PHD3_KDM5B; PHD finger 3 found in lysine-specific demethylase 5B (KDM5B)
      pfam02928
      Location:660 → 711
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:725 → 1045
      PLU-1; PLU-1-like protein
      cl22851
      Location:1144 → 1187
      PHD_SF; PHD finger superfamily

    2. XM_021479553.2 → XP_021335228.1  lysine (K)-specific demethylase 5Ba isoform X1

      UniProtKB/TrEMBL
      A0A2R8QQ41, A0A8M9Q713
      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:455 → 571
      JmjC; JmjC domain, hydroxylase
      cd15603
      Location:280 → 325
      PHD1_KDM5B; PHD finger 1 found in lysine-specific demethylase 5B (KDM5B)
      cd15687
      Location:1422 → 1471
      PHD3_KDM5B; PHD finger 3 found in lysine-specific demethylase 5B (KDM5B)
      pfam02928
      Location:661 → 712
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:726 → 1046
      PLU-1; PLU-1-like protein
      cl22851
      Location:1145 → 1188
      PHD_SF; PHD finger superfamily

    Reference GRCz11 ALT_DRER_TU_1

    Genomic

    1. NW_018394821.1 Reference GRCz11 ALT_DRER_TU_1

      Range
      5298..33074
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001128327.1: Suppressed sequence

      Description
      NM_001128327.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein Strain
    Heading Accession and Version

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