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    Chd1 chromodomain helicase DNA binding protein 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 308215, updated on 11-Apr-2024

    Summary

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    Official Symbol
    Chd1provided by RGD
    Official Full Name
    chromodomain helicase DNA binding protein 1provided by RGD
    Primary source
    RGD:1306794
    See related
    Ensembl:ENSRNOG00000014434 AllianceGenome:RGD:1306794
    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 methylated histone binding activity. Predicted to be involved in positive regulation by host of viral transcription. Predicted to act upstream of or within chromatin remodeling. Predicted to be located in cytoplasm and nucleus. Human ortholog(s) of this gene implicated in castration-resistant prostate carcinoma and prostate cancer. Orthologous to human CHD1 (chromodomain helicase DNA binding protein 1). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Thymus (RPKM 339.4), Spleen (RPKM 213.7) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Chd1 in Genome Data Viewer
    Location:
    1q12
    Exon count:
    39
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 1 NC_086019.1 (65334905..65402270)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 1 NC_051336.1 (56661743..56729119)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 1 NC_005100.4 (57692828..57756762)

    Chromosome 1 - NC_086019.1Genomic Context describing neighboring genes Neighboring gene UPF0488 protein C8orf33 homolog Neighboring gene uncharacterized LOC134485094 Neighboring gene chromodomain helicase DNA binding protein 1 like 2 Neighboring gene ubiquitin-conjugating enzyme E2 L3-like Neighboring gene repulsive guidance molecule BMP co-receptor b

    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. Missense variants in the chromatin remodeler CHD1 are associated with neurodevelopmental disability. Pilarowski GO, et al. J Med Genet, 2018 Aug. PMID 28866611, Free PMC Article
    2. Recurrent deletion of CHD1 in prostate cancer with relevance to cell invasiveness. Huang S, et al. Oncogene, 2012 Sep 13. PMID 22179824, Free PMC Article
    3. CHD1 and CHD2 are positive regulators of HIV-1 gene expression. Rodgers MJ, et al. Virol J, 2014 Oct 8. PMID 25297984, Free PMC Article
    4. The tumor suppressor menin regulates hematopoiesis and myeloid transformation by influencing Hox gene expression. Chen YX, et al. Proc Natl Acad Sci U S A, 2006 Jan 24. PMID 16415155, Free PMC Article
    5. Human RNA polymerase II-association factor 1 (hPaf1/PD2) regulates histone methylation and chromatin remodeling in pancreatic cancer. Dey P, et al. PLoS One, 2011. PMID 22046413, Free PMC Article

    See all (10) 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 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 methylated histone binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    acts_upstream_of_or_within chromatin remodeling ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in chromatin remodeling ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in nucleosome organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation by host of viral transcription ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    part_of chromatin IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in nuclear chromosome ISO
    Inferred from Sequence Orthology
    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 1
    NP_001100935.1
    XP_038966704.1
    XP_038966710.1
    XP_038966713.1
    XP_038966717.1
    XP_063144628.1

    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_001107465.1 → NP_001100935.1  chromodomain-helicase-DNA-binding protein 1

      See identical proteins and their annotated locations for NP_001100935.1

      Status: PROVISIONAL

      Source sequence(s)
      CH474033
      UniProtKB/TrEMBL
      A0A0G2K5T4, A6KB55, D4AAG9
      Related
      ENSRNOP00000019358.8, ENSRNOT00000019358.8
      Conserved Domains (8) summary
      PTZ00121
      Location:1292 → 1574
      PTZ00121; MAEBL; Provisional
      PHA03420
      Location:1591 → 1691
      PHA03420; E4 protein; Provisional
      PLN03142
      Location:462 → 998
      PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
      cd18661
      Location:385 → 441
      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:268 → 352
      CD1_tandem_CHD1-2_like; repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 1 and 2, and similar proteins
      pfam13907
      Location:1408 → 1498
      DUF4208; Domain of unknown function (DUF4208)
      pfam18375
      Location:1122 → 1208
      CDH1_2_SANT_HL1; CDH1/2 SANT-Helical linker 1
      cl28899
      Location:458 → 695
      DEAD-like_helicase_N; N-terminal helicase domain of the DEAD-box helicase superfamily

    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
      65334905..65402270
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039110782.2 → XP_038966710.1  chromodomain-helicase-DNA-binding protein 1 isoform X1

      UniProtKB/TrEMBL
      A0A0G2K5T4, A6KB55, D4AAG9
      Conserved Domains (8) summary
      PTZ00121
      Location:1292 → 1574
      PTZ00121; MAEBL; Provisional
      PHA03420
      Location:1591 → 1691
      PHA03420; E4 protein; Provisional
      PLN03142
      Location:462 → 998
      PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
      cd18661
      Location:385 → 441
      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:268 → 352
      CD1_tandem_CHD1-2_like; repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 1 and 2, and similar proteins
      pfam13907
      Location:1408 → 1498
      DUF4208; Domain of unknown function (DUF4208)
      pfam18375
      Location:1122 → 1208
      CDH1_2_SANT_HL1; CDH1/2 SANT-Helical linker 1
      cl28899
      Location:458 → 695
      DEAD-like_helicase_N; N-terminal helicase domain of the DEAD-box helicase superfamily

    2. XM_039110776.2 → XP_038966704.1  chromodomain-helicase-DNA-binding protein 1 isoform X1

      UniProtKB/TrEMBL
      A0A0G2K5T4, A6KB55, D4AAG9
      Conserved Domains (8) summary
      PTZ00121
      Location:1292 → 1574
      PTZ00121; MAEBL; Provisional
      PHA03420
      Location:1591 → 1691
      PHA03420; E4 protein; Provisional
      PLN03142
      Location:462 → 998
      PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
      cd18661
      Location:385 → 441
      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:268 → 352
      CD1_tandem_CHD1-2_like; repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 1 and 2, and similar proteins
      pfam13907
      Location:1408 → 1498
      DUF4208; Domain of unknown function (DUF4208)
      pfam18375
      Location:1122 → 1208
      CDH1_2_SANT_HL1; CDH1/2 SANT-Helical linker 1
      cl28899
      Location:458 → 695
      DEAD-like_helicase_N; N-terminal helicase domain of the DEAD-box helicase superfamily

    3. XM_039110789.1 → XP_038966717.1  chromodomain-helicase-DNA-binding protein 1 isoform X2

      Conserved Domains (3) summary
      PLN03142
      Location:462 → 998
      PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
      cd18661
      Location:385 → 441
      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:268 → 352
      CD1_tandem_CHD1-2_like; repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 1 and 2, and similar proteins

    4. XM_063288558.1 → XP_063144628.1  chromodomain-helicase-DNA-binding protein 1 isoform X2

    5. XM_039110785.2 → XP_038966713.1  chromodomain-helicase-DNA-binding protein 1 isoform X1

      UniProtKB/TrEMBL
      A0A0G2K5T4, A6KB55, D4AAG9
      Conserved Domains (8) summary
      PTZ00121
      Location:1292 → 1574
      PTZ00121; MAEBL; Provisional
      PHA03420
      Location:1591 → 1691
      PHA03420; E4 protein; Provisional
      PLN03142
      Location:462 → 998
      PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
      cd18661
      Location:385 → 441
      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:268 → 352
      CD1_tandem_CHD1-2_like; repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 1 and 2, and similar proteins
      pfam13907
      Location:1408 → 1498
      DUF4208; Domain of unknown function (DUF4208)
      pfam18375
      Location:1122 → 1208
      CDH1_2_SANT_HL1; CDH1/2 SANT-Helical linker 1
      cl28899
      Location:458 → 695
      DEAD-like_helicase_N; N-terminal helicase domain of the DEAD-box helicase superfamily
    Nucleotide Protein Strain
    Heading Accession and Version

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