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

Gene ID: 327168, updated on 2-Nov-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, Nov 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 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

Gene LinkOut

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