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    Chd2 chromodomain helicase DNA binding protein 2 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 308738, updated on 9-Dec-2024

    Summary

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    Symbol
    Chd2provided by RGD
    Full Name
    chromodomain helicase DNA binding protein 2provided by RGD
    Primary source
    RGD:1310056
    See related
    EnsemblRapid:ENSRNOG00000012716 AllianceGenome:RGD:1310056
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to enable several functions, including ATP hydrolysis activity; ATP-dependent chromatin remodeler activity; and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in gene expression; muscle organ development; and nucleosome organization. Predicted to act upstream of or within DNA damage response and hematopoietic stem cell differentiation. Predicted to be located in chromatin. Predicted to be active in nucleus. 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, Dec 2024]
    Expression
    Biased expression in Thymus (RPKM 238.9), Spleen (RPKM 198.4) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Chd2 in Genome Data Viewer
    Location:
    1q31
    Exon count:
    47
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 1 NC_086019.1 (136597993..136726874, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 1 NC_051336.1 (127188146..127317041, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 1 NC_005100.4 (134757934..134873053, complement)

    Chromosome 1 - NC_086019.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC134483715 Neighboring gene repulsive guidance molecule BMP co-receptor a Neighboring gene uncharacterized LOC120099853 Neighboring gene uncharacterized LOC134483728

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Role of chromodomain helicase DNA-binding protein 2 in DNA damage response signaling and tumorigenesis. Nagarajan P, et al. Oncogene, 2009 Feb 26. PMID 19137022, Free PMC Article
    2. Chd2 interacts with H3.3 to determine myogenic cell fate. Harada A, et al. EMBO J, 2012 Jun 29. PMID 22569126, Free PMC Article
    3. The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts. Baltz AG, et al. Mol Cell, 2012 Jun 8. PMID 22681889
    4. Insights into RNA biology from an atlas of mammalian mRNA-binding proteins. Castello A, et al. Cell, 2012 Jun 8. PMID 22658674
    5. Proteomic analysis of podocyte exosome-enriched fraction from normal human urine. Prunotto M, et al. J Proteomics, 2013 Apr 26. PMID 23376485

    See all (6) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    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 DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables chromatin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables double-stranded DNA helicase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables forked DNA-dependent helicase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables four-way junction helicase activity IEA
    Inferred from Electronic Annotation
    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 histone binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables single-stranded 3'-5' DNA helicase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within DNA damage response ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in DNA duplex unwinding IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in gene expression ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within hematopoietic stem cell differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in muscle organ development ISO
    Inferred from Sequence Orthology
    more info
    		  
    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
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    chromodomain-helicase-DNA-binding protein 2
    NP_001100993.1
    XP_038968765.1
    XP_038968796.1
    XP_038968803.1
    XP_063118674.1
    XP_063118678.1
    XP_063118679.1
    XP_063118691.1
    XP_063118695.1
    XP_063118696.1
    XP_063118697.1
    XP_063118699.1
    XP_063118701.1

    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_001107523.1 → NP_001100993.1  chromodomain-helicase-DNA-binding protein 2

      See identical proteins and their annotated locations for NP_001100993.1

      Status: PROVISIONAL

      Source sequence(s)
      CH473980
      UniProtKB/TrEMBL
      A0A096MJY0, A6JBX9, D4AD08
      Related
      ENSRNOP00000068303.2, ENSRNOT00000076300.4
      Conserved Domains (7) summary
      cd00024
      Location:289 → 351
      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:510 → 655
      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.
      pfam00176
      Location:494 → 775
      SNF2_N; SNF2 family N-terminal domain
      pfam00271
      Location:797 → 912
      Helicase_C; Helicase conserved C-terminal domain
      pfam00385
      Location:386 → 454
      Chromo; Chromo (CHRromatin Organization MOdifier) domain
      pfam13907
      Location:1478 → 1560
      DUF4208; Domain of unknown function (DUF4208)
      pfam17104
      Location:1049 → 1172
      DUF5102; Domain of unknown function (DUF5102)

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCr8

    Genomic

    1. NC_086019.1 Reference GRCr8

      Range
      136597993..136726874 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039112868.2 → XP_038968796.1  chromodomain-helicase-DNA-binding protein 2 isoform X6

      UniProtKB/TrEMBL
      D4AD08
      Conserved Domains (6) summary
      PLN03142
      Location:370 → 923
      PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
      cd18661
      Location:278 → 349
      CD2_tandem_CHD1-2_like; repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 1 and 2, and similar proteins
      cd18666
      Location:161 → 245
      CD1_tandem_CHD1-2_like; repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 1 and 2, and similar proteins
      cd18054
      Location:366 → 602
      DEXHc_CHD2; DEAH-box helicase domain of the chromodomain helicase DNA binding protein 2
      pfam13907
      Location:1373 → 1455
      DUF4208; Domain of unknown function (DUF4208)
      pfam18375
      Location:1032 → 1120
      CDH1_2_SANT_HL1; CDH1/2 SANT-Helical linker 1

    2. XM_063262626.1 → XP_063118696.1  chromodomain-helicase-DNA-binding protein 2 isoform X4

      UniProtKB/TrEMBL
      A0A8I6GCU8, D4AD08
      Related
      ENSRNOP00000085288.1, ENSRNOT00000098073.2

    3. XM_039112837.2 → XP_038968765.1  chromodomain-helicase-DNA-binding protein 2 isoform X2

      UniProtKB/TrEMBL
      D4AD08
      Conserved Domains (6) summary
      PLN03142
      Location:468 → 1021
      PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
      cd18661
      Location:376 → 447
      CD2_tandem_CHD1-2_like; repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 1 and 2, and similar proteins
      cd18666
      Location:259 → 343
      CD1_tandem_CHD1-2_like; repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 1 and 2, and similar proteins
      cd18054
      Location:464 → 700
      DEXHc_CHD2; DEAH-box helicase domain of the chromodomain helicase DNA binding protein 2
      pfam13907
      Location:1471 → 1553
      DUF4208; Domain of unknown function (DUF4208)
      pfam18375
      Location:1130 → 1218
      CDH1_2_SANT_HL1; CDH1/2 SANT-Helical linker 1

    4. XM_063262625.1 → XP_063118695.1  chromodomain-helicase-DNA-binding protein 2 isoform X3

      UniProtKB/TrEMBL
      D4AD08

    5. XM_063262627.1 → XP_063118697.1  chromodomain-helicase-DNA-binding protein 2 isoform X5

      UniProtKB/TrEMBL
      D4AD08

    6. XM_063262604.1 → XP_063118674.1  chromodomain-helicase-DNA-binding protein 2 isoform X1

      UniProtKB/TrEMBL
      A0A0G2KA92, D4AD08

    7. XM_063262621.1 → XP_063118691.1  chromodomain-helicase-DNA-binding protein 2 isoform X2

      UniProtKB/TrEMBL
      D4AD08

    8. XM_063262608.1 → XP_063118678.1  chromodomain-helicase-DNA-binding protein 2 isoform X1

      UniProtKB/TrEMBL
      A0A0G2KA92, D4AD08

    9. XM_063262609.1 → XP_063118679.1  chromodomain-helicase-DNA-binding protein 2 isoform X1

      UniProtKB/TrEMBL
      A0A0G2KA92, D4AD08
      Related
      ENSRNOP00000075309.1, ENSRNOT00000090149.3

    10. XM_039112875.2 → XP_038968803.1  chromodomain-helicase-DNA-binding protein 2 isoform X8

      Conserved Domains (3) summary
      PLN03142
      Location:21 → 305
      PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
      pfam13907
      Location:755 → 837
      DUF4208; Domain of unknown function (DUF4208)
      pfam18375
      Location:414 → 502
      CDH1_2_SANT_HL1; CDH1/2 SANT-Helical linker 1

    11. XM_063262629.1 → XP_063118699.1  chromodomain-helicase-DNA-binding protein 2 isoform X7

      UniProtKB/TrEMBL
      D4AD08
      Related
      ENSRNOP00000110047.1, ENSRNOT00000157492.1

    12. XM_063262631.1 → XP_063118701.1  chromodomain-helicase-DNA-binding protein 2 isoform X9

    RNA

    1. XR_010052226.1 RNA Sequence

    2. XR_010052231.1 RNA Sequence

    3. XR_010052232.1 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version

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