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jarid2b jumonji and AT-rich interaction domain containing 2b [ Danio rerio (zebrafish) ]

Gene ID: 558456, updated on 2-Nov-2024

Summary

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Official Symbol
jarid2bprovided by ZNC
Official Full Name
jumonji and AT-rich interaction domain containing 2bprovided by ZNC
Primary source
ZFIN:ZDB-GENE-060503-246
See related
Ensembl:ENSDARG00000062268 AllianceGenome:ZFIN:ZDB-GENE-060503-246
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
si:dkey-211c3.1
Summary
Predicted to enable chromatin binding activity. Predicted to contribute to histone H3K27 methyltransferase activity. Predicted to be involved in chromatin remodeling; regulation of gene expression; and stem cell differentiation. Predicted to act upstream of or within cell differentiation and chromatin organization. Predicted to be located in chromatin. Predicted to be part of ESC/E(Z) complex. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in autistic disorder. Orthologous to human JARID2 (jumonji and AT-rich interaction domain containing 2). [provided by Alliance of Genome Resources, Nov 2024]
Orthologs
human mouse all
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Genomic context

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See jarid2b in Genome Data Viewer
Location:
chromosome: 19
Exon count:
18
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCz11 (GCF_000002035.6) 19 NC_007130.7 (25970957..26158782)
105 previous assembly GRCz10 (GCF_000002035.5) 19 NC_007130.6 (26386554..26574298)

Chromosome 19 - NC_007130.7Genomic Context describing neighboring genes Neighboring gene biogenesis of lysosomal organelles complex-1, subunit 4, cappuccino Neighboring gene par-6 family cell polarity regulator gamma b Neighboring gene dystrobrevin binding protein 1b Neighboring gene myosin regulatory light chain interacting protein a

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. The splicing factor DHX38 enables retinal development through safeguarding genome integrity. Sun K, et al. iScience, 2023 Nov 17. PMID 37867960, Free PMC Article
  2. Structure, evolution and expression of collagen XXVIII: Lessons from the zebrafish. Gebauer JM, et al. Matrix Biol, 2016 Jan. PMID 26235539
  3. A network of epigenetic regulators guides developmental haematopoiesis in vivo. Huang HT, et al. Nat Cell Biol, 2013 Dec. PMID 24240475, Free PMC Article
  4. RFX transcription factors are essential for hearing in mice. Elkon R, et al. Nat Commun, 2015 Oct 15. PMID 26469318, Free PMC Article
  5. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

GeneRIFs: Gene References Into Functions

Pathways from PubChem

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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 chromatin binding ISS
Inferred from Sequence or Structural Similarity
more info
  
contributes_to histone H3K27 methyltransferase activity ISS
Inferred from Sequence or Structural Similarity
more info
  
NOT enables histone demethylase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
NOT enables histone demethylase activity ISS
Inferred from Sequence or Structural Similarity
more info
  
Process Evidence Code Pubs
acts_upstream_of_or_within cell differentiation IEA
Inferred from Electronic Annotation
more info
  
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
  
involved_in stem cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
  
Component Evidence Code Pubs
part_of ESC/E(Z) complex ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in chromatin IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of histone methyltransferase complex ISS
Inferred from Sequence or Structural Similarity
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
protein Jumonji
Names
jumonji, AT rich interactive domain 2b
jumonji/ARID domain-containing protein 2

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_001202459.1 → NP_001189388.1  protein Jumonji

    See identical proteins and their annotated locations for NP_001189388.1

    Status: PROVISIONAL

    Source sequence(s)
    BX842609, BX842613, BX890540
    UniProtKB/Swiss-Prot
    Q1LVC2
    Related
    ENSDARP00000084269.5, ENSDART00000089836.6
    Conserved Domains (4) summary
    smart00545
    Location:607 → 647
    JmjN; Small domain found in the jumonji family of transcription factors
    smart01014
    Location:673 → 775
    ARID; ARID/BRIGHT DNA binding domain
    pfam02373
    Location:986 → 1101
    JmjC; JmjC domain, hydroxylase
    pfam02928
    Location:1209 → 1262
    zf-C5HC2; C5HC2 zinc finger

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_007130.7 Reference GRCz11 Primary Assembly

    Range
    25970957..26158782
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_009294217.4 → XP_009292492.1  protein Jumonji isoform X1

    UniProtKB/TrEMBL
    A0A8M3AKY8
    Conserved Domains (4) summary
    smart00545
    Location:607 → 647
    JmjN; Small domain found in the jumonji family of transcription factors
    smart01014
    Location:673 → 759
    ARID; ARID/BRIGHT DNA binding domain
    pfam02373
    Location:970 → 1085
    JmjC; JmjC domain, hydroxylase
    pfam02928
    Location:1193 → 1246
    zf-C5HC2; C5HC2 zinc finger
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q1LVC2.2 GenPept UniProtKB/Swiss-Prot:Q1LVC2

Gene LinkOut

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