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    chd2 chromodomain helicase DNA binding protein 2 [ Danio rerio (zebrafish) ]

    Gene ID: 569795, updated on 28-Oct-2024

    Summary

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    Official Symbol
    chd2provided by ZNC
    Official Full Name
    chromodomain helicase DNA binding protein 2provided by ZNC
    Primary source
    ZFIN:ZDB-GENE-050419-256
    See related
    Ensembl:ENSDARG00000060687 AllianceGenome:ZFIN:ZDB-GENE-050419-256
    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
    si:ch211-196l7.5
    Summary
    Predicted to enable several functions, including ATP hydrolysis activity; ATP-dependent chromatin remodeler activity; and histone binding activity. Acts upstream of or within chordate embryonic development and locomotion. Predicted to be located in chromatin. Predicted to be active in nucleus. Is expressed in bone tissue; brain; heart; hematopoietic multipotent progenitor cell; and kidney. Used to study myoclonic-atonic epilepsy. Human ortholog(s) of this gene implicated in developmental and epileptic encephalopathy 94. Orthologous to human CHD2 (chromodomain helicase DNA binding protein 2). [provided by Alliance of Genome Resources, Oct 2024]
    Orthologs
    human mouse all
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    Genomic context

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    See chd2 in Genome Data Viewer
    Location:
    chromosome: 18
    Exon count:
    38
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 18 NC_007129.7 (24933473..24989580, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 18 NC_007129.6 (24946940..25010178, complement)

    Chromosome 18 - NC_007129.7Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC137488284 Neighboring gene repulsive guidance molecule BMP co-receptor a Neighboring gene uncharacterized LOC137488285 Neighboring gene family with sequence similarity 174 member B

    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. De novo loss-of-function mutations in CHD2 cause a fever-sensitive myoclonic epileptic encephalopathy sharing features with Dravet syndrome. Suls A, et al. Am J Hum Genet, 2013 Nov 7. PMID 24207121, Free PMC Article
    2. Rescue of neural crest-derived phenotypes in a zebrafish CHARGE model by Sox10 downregulation. Asad Z, et al. Hum Mol Genet, 2016 Aug 15. PMID 27418670, Free PMC Article
    3. Smarca5-mediated epigenetic programming facilitates fetal HSPC development in vertebrates. Ding Y, et al. Blood, 2021 Jan 14. PMID 32756943, Free PMC Article
    4. Phenotypic analysis of catastrophic childhood epilepsy genes. Griffin A, et al. Commun Biol, 2021 Jun 3. PMID 34083748, Free PMC Article
    5. Consequences of lineage-specific gene loss on functional evolution of surviving paralogs: ALDH1A and retinoic acid signaling in vertebrate genomes. Cañestro C, et al. PLoS Genet, 2009 May. PMID 19478994, Free PMC Article

    See all (8) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. chd2-knockdown larvae exhibited altered locomotor activity
      Title: De novo loss-of-function mutations in CHD2 cause a fever-sensitive myoclonic epileptic encephalopathy sharing features with Dravet syndrome.
    Submit: New GeneRIF Correction

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ATP hydrolysis activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables ATP-dependent chromatin remodeler activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables ATP-dependent chromatin remodeler activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables chromatin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables helicase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables hydrolase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables nucleotide binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within chordate embryonic development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within locomotion IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in nucleosome organization 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
    		  

    General protein information

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    Preferred Names
    chromodomain-helicase-DNA-binding protein 2
    NP_001268391.1
    XP_009291898.1
    XP_021323365.1
    XP_068070918.1
    XP_068070919.1
    XP_068070920.1

    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_001281462.1 → NP_001268391.1  chromodomain-helicase-DNA-binding protein 2

      Status: VALIDATED

      Source sequence(s)
      BX649578
      UniProtKB/TrEMBL
      A0A0R4IR86, A0A8M1P5T0
      Related
      ENSDARP00000138660.1, ENSDART00000163449.2
      Conserved Domains (7) summary
      cd00024
      Location:308 → 353
      CHROMO; Chromatin organization modifier (chromo) domain is a conserved region of around 50 amino acids found in a variety of chromosomal proteins, which appear to play a role in the functional organization of the eukaryotic nucleus. Experimental evidence ...
      cd00046
      Location:494 → 639
      DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
      cd00079
      Location:781 → 904
      HELICc; Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may ...
      pfam00176
      Location:478 → 759
      SNF2_N; SNF2 family N-terminal domain
      pfam00385
      Location:388 → 438
      Chromo; Chromo (CHRromatin Organization MOdifier) domain
      pfam04592
      Location:1560 → 1635
      SelP_N; Selenoprotein P, N terminal region
      pfam13907
      Location:1440 → 1531
      DUF4208; Domain of unknown function (DUF4208)

    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_007129.7 Reference GRCz11 Primary Assembly

      Range
      24933473..24989580 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_009293623.4 → XP_009291898.1  chromodomain-helicase-DNA-binding protein 2 isoform X2

      UniProtKB/TrEMBL
      A0A8M3AUW8
      Conserved Domains (7) summary
      cd00024
      Location:308 → 353
      CHROMO; Chromatin organization modifier (chromo) domain is a conserved region of around 50 amino acids found in a variety of chromosomal proteins, which appear to play a role in the functional organization of the eukaryotic nucleus. Experimental evidence ...
      cd00046
      Location:508 → 653
      DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
      cd00079
      Location:795 → 918
      HELICc; Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may ...
      pfam00176
      Location:492 → 773
      SNF2_N; SNF2 family N-terminal domain
      pfam00385
      Location:388 → 452
      Chromo; Chromo (CHRromatin Organization MOdifier) domain
      pfam04592
      Location:1574 → 1649
      SelP_N; Selenoprotein P, N terminal region
      pfam13907
      Location:1454 → 1545
      DUF4208; Domain of unknown function (DUF4208)

    2. XM_021467690.2 → XP_021323365.1  chromodomain-helicase-DNA-binding protein 2 isoform X1

      UniProtKB/TrEMBL
      A0A8M9PQC3
      Conserved Domains (5) summary
      cd00024
      Location:312 → 357
      CHROMO; Chromatin organization modifier (chromo) domain is a conserved region of around 50 amino acids found in a variety of chromosomal proteins, which appear to play a role in the functional organization of the eukaryotic nucleus. Experimental evidence ...
      pfam00385
      Location:391 → 456
      Chromo; Chromo (CHRromatin Organisation MOdifier) domain
      pfam13907
      Location:1459 → 1549
      DUF4208; Domain of unknown function (DUF4208)
      cl25751
      Location:1503 → 1796
      DUF4045; Domain of unknown function (DUF4045)
      cl26465
      Location:479 → 1054
      SNF2_N; SNF2 family N-terminal domain

    3. XM_068214818.1 → XP_068070919.1  chromodomain-helicase-DNA-binding protein 2 isoform X2

    4. XM_068214819.1 → XP_068070920.1  chromodomain-helicase-DNA-binding protein 2 isoform X3

    5. XM_068214817.1 → XP_068070918.1  chromodomain-helicase-DNA-binding protein 2 isoform X1

    Nucleotide Protein Strain
    Heading Accession and Version

    Gene LinkOut

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