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

Gene ID: 308215, updated on 14-Nov-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
EnsemblRapid: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 several functions, including ATP hydrolysis activity; ATP-dependent chromatin remodeler activity; and methylated histone binding activity. Predicted to be involved in nucleosome organization and positive regulation by host of viral transcription. Predicted to act upstream of or within chromatin remodeling. Predicted to be located in chromatin and cytoplasm. Predicted to be active in nuclear chromosome. 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, Nov 2024]
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 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 histone binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables methylated 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
involved_in DNA duplex unwinding IEA
Inferred from Electronic Annotation
more info
  
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
located_in 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
    ENSRNOP00000073550.3, ENSRNOT00000083968.3
    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
    Related
    ENSRNOP00000104287.1, ENSRNOT00000133383.1
    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
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