U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    Chd1l chromodomain helicase DNA binding protein 1-like [ Rattus norvegicus (Norway rat) ]

    Gene ID: 310707, updated on 28-Oct-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    Chd1lprovided by RGD
    Official Full Name
    chromodomain helicase DNA binding protein 1-likeprovided by RGD
    Primary source
    RGD:1311935
    See related
    EnsemblRapid:ENSRNOG00000017669 AllianceGenome:RGD:1311935
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    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; histone reader activity; and poly-ADP-D-ribose modification-dependent protein binding activity. Predicted to be involved in DNA repair and chromatin remodeling. Predicted to be located in cytosol; nucleoplasm; and plasma membrane. Predicted to be active in nucleus and site of double-strand break. Orthologous to human CHD1L (chromodomain helicase DNA binding protein 1 like). [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Biased expression in Kidney (RPKM 229.0), Liver (RPKM 57.8) and 9 other tissues See more
    Orthologs
    human mouse all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See Chd1l in Genome Data Viewer
    Location:
    2q34
    Exon count:
    28
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 2 NC_086020.1 (187819869..187906359, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 2 NC_051337.1 (185138526..185217498, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 2 NC_005101.4 (199714044..199792270, complement)

    Chromosome 2 - NC_086020.1Genomic Context describing neighboring genes Neighboring gene olfactory receptor family 13 subfamily L member 2 Neighboring gene olfactory receptor pseudogene 391 Neighboring gene flavin containing dimethylaniline monoxygenase 5 Neighboring gene uncharacterized LOC102550575 Neighboring gene protein kinase AMP-activated non-catalytic subunit beta 2 Neighboring gene transfer RNA glutamine (anticodon CUG) 4

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages 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

    Go to the top of the pageHelp

    Related articles in PubMed

    1. Poly(ADP-ribose)-dependent regulation of DNA repair by the chromatin remodeling enzyme ALC1. Ahel D, et al. Science, 2009 Sep 4. PMID 19661379, Free PMC Article
    2. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

    Go to the top of the page Help

    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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables ATP-dependent chromatin remodeler activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables DNA helicase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables catalytic activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone reader activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables nucleosome binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables nucleotide binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables nucleotide binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables poly-ADP-D-ribose modification-dependent protein binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in DNA damage response IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in DNA damage response ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in DNA duplex unwinding IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in DNA repair IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in DNA repair ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in chromatin remodeling IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in chromatin remodeling ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm 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
    		  
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in plasma membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in site of DNA damage ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in site of double-strand break ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

    Go to the top of the page Help
    Preferred Names
    chromodomain-helicase-DNA-binding protein 1-like
    NP_001101174.2
    XP_008759572.1
    XP_008759575.1
    XP_008759576.1
    XP_038959729.1
    XP_038959732.1
    XP_063137972.1
    XP_063137974.1

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    NEW Try the new Transcript table

    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_001107704.2 → NP_001101174.2  chromodomain-helicase-DNA-binding protein 1-like

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000002
      Related
      ENSRNOP00000084164.2, ENSRNOT00000099918.2

    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_086020.1 Reference GRCr8

      Range
      187819869..187906359 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063281902.1 → XP_063137972.1  chromodomain-helicase-DNA-binding protein 1-like isoform X1

    2. XM_063281904.1 → XP_063137974.1  chromodomain-helicase-DNA-binding protein 1-like isoform X3

      UniProtKB/TrEMBL
      D4ACG6
      Related
      ENSRNOP00000048925.6, ENSRNOT00000043937.7

    3. XM_008761354.4 → XP_008759576.1  chromodomain-helicase-DNA-binding protein 1-like isoform X5

      See identical proteins and their annotated locations for XP_008759576.1

      UniProtKB/TrEMBL
      A0A8I5ZYW5
      Conserved Domains (4) summary
      cd00046
      Location:1 → 133
      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:1 → 256
      SNF2_N; SNF2 family N-terminal domain
      pfam00271
      Location:274 → 387
      Helicase_C; Helicase conserved C-terminal domain
      cl00019
      Location:648 → 798
      Macro; Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ...

    4. XM_008761353.4 → XP_008759575.1  chromodomain-helicase-DNA-binding protein 1-like isoform X4

      See identical proteins and their annotated locations for XP_008759575.1

      UniProtKB/TrEMBL
      A0A8I5ZYW5, A0A8I6A8B4
      Related
      ENSRNOP00000086360.1, ENSRNOT00000115624.2
      Conserved Domains (4) summary
      cd00046
      Location:90 → 230
      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:74 → 353
      SNF2_N; SNF2 family N-terminal domain
      pfam00271
      Location:371 → 484
      Helicase_C; Helicase conserved C-terminal domain
      cl00019
      Location:745 → 852
      Macro; Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ...

    5. XM_008761350.4 → XP_008759572.1  chromodomain-helicase-DNA-binding protein 1-like isoform X2

      See identical proteins and their annotated locations for XP_008759572.1

      UniProtKB/TrEMBL
      A0A8I5ZYW5
      Conserved Domains (4) summary
      cd00046
      Location:90 → 230
      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:74 → 353
      SNF2_N; SNF2 family N-terminal domain
      pfam00271
      Location:371 → 484
      Helicase_C; Helicase conserved C-terminal domain
      cl00019
      Location:745 → 895
      Macro; Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ...

    6. XM_039103801.2 → XP_038959729.1  chromodomain-helicase-DNA-binding protein 1-like isoform X6

      UniProtKB/TrEMBL
      A0A8I5ZYW5
      Conserved Domains (2) summary
      PLN03142
      Location:19 → 494
      PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
      cd03331
      Location:623 → 773
      Macro_Poa1p-like_SNF2; macrodomain, Poa1p-like family, SNF2 subfamily

    7. XM_039103804.2 → XP_038959732.1  chromodomain-helicase-DNA-binding protein 1-like isoform X7

      UniProtKB/TrEMBL
      A6K3B4
      Conserved Domains (2) summary
      PLN03142
      Location:1 → 164
      PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
      cd03331
      Location:293 → 443
      Macro_Poa1p-like_SNF2; macrodomain, Poa1p-like family, SNF2 subfamily

    RNA

    1. XR_010063611.1 RNA Sequence

    2. XR_005501136.2 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools