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

Gene ID: 308738, updated on 11-Apr-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
Ensembl: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 RNA polymerase II cis-regulatory region sequence-specific DNA binding activity and histone binding activity. Predicted to be involved in muscle organ development. Predicted to act upstream of or within cellular response to DNA damage stimulus and hematopoietic stem cell differentiation. Predicted to be located in nucleus. Human ortholog(s) of this gene implicated in developmental and epileptic encephalopathy. Orthologous to human CHD2 (chromodomain helicase DNA binding protein 2). [provided by Alliance of Genome Resources, Apr 2022]
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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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 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
  
Process Evidence Code Pubs
acts_upstream_of_or_within DNA damage response ISO
Inferred from Sequence Orthology
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
part_of 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, ENSRNOT00000076300.3
    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

  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

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

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

    UniProtKB/TrEMBL
    A0A0G2KA92

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

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

    UniProtKB/TrEMBL
    A0A0G2KA92

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

    UniProtKB/TrEMBL
    A0A0G2KA92

  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

  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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