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    Chd5 chromodomain helicase DNA binding protein 5 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 691589, updated on 27-Nov-2024

    Summary

    Official Symbol
    Chd5provided by RGD
    Official Full Name
    chromodomain helicase DNA binding protein 5provided by RGD
    Primary source
    RGD:1582725
    See related
    EnsemblRapid:ENSRNOG00000011268 AllianceGenome:RGD:1582725
    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
    Also known as
    CHD-5
    Summary
    Enables chromatin binding activity. Involved in transcription by RNA polymerase II. Located in chromatin and nucleus. Orthologous to human CHD5 (chromodomain helicase DNA binding protein 5). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Brain (RPKM 123.5) and Testes (RPKM 57.0) See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See Chd5 in Genome Data Viewer
    Location:
    5q36
    Exon count:
    43
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 5 NC_086023.1 (168130851..168181705)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 5 NC_051340.1 (162848273..162898997)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 5 NC_005104.4 (169519212..169572059)

    Chromosome 5 - NC_086023.1Genomic Context describing neighboring genes Neighboring gene ring finger protein 207 Neighboring gene uncharacterized LOC120103139 Neighboring gene ribosomal protein L22 Neighboring gene potassium voltage-gated channel subfamily A regulatory beta subunit 2 Neighboring gene small ribosomal subunit protein eS27-like Neighboring gene nephrocystin 4

    Genomic regions, transcripts, and products

    Expression

    • 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

    General gene information

    Markers

    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 H2AZ histone chaperone activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables ATP-dependent H3-H4 histone complex chaperone activity IEA
    Inferred from Electronic Annotation
    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 DNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables DNA clamp loader activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables H3K27me3 modified histone binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables H3K27me3 modified histone binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables H3K27me3 modified histone binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables chromatin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables chromatin binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables chromatin extrusion motor activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables cohesin loader activity IEA
    Inferred from Electronic Annotation
    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 histone deacetylase binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables hydrolase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    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
     
    involved_in cerebral cortex neuron differentiation ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in cerebral cortex neuron differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in chromatin looping IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in chromatin remodeling IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in chromatin remodeling IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in chromatin remodeling ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in chromatin remodeling ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of cell population proliferation ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of transcription by RNA polymerase II ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of signal transduction by p53 class mediator ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of signal transduction by p53 class mediator ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of cell differentiation ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in sperm DNA condensation ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in sperm DNA condensation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    part_of NuRD complex IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    part_of NuRD complex ISO
    Inferred from Sequence Orthology
    more info
     
    part_of NuRD complex ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in chromatin IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in chromatin IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
     
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
     
    located_in heterochromatin ISO
    Inferred from Sequence Orthology
    more info
     
    located_in heterochromatin ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in nuclear speck IEA
    Inferred from Electronic Annotation
    more info
     
    located_in nuclear speck ISO
    Inferred from Sequence Orthology
    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 IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
     
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
     

    General protein information

    Preferred Names
    chromodomain-helicase-DNA-binding protein 5
    Names
    ATP-dependent helicase CHD5
    NP_001258155.1
    XP_017449128.1
    XP_017449129.1
    XP_017449130.1
    XP_017449131.1
    XP_017449132.1
    XP_017449133.1
    XP_017449134.1
    XP_017449135.1
    XP_017449136.1
    XP_017449137.1
    XP_017449138.1
    XP_038966741.1
    XP_038966743.1
    XP_063144525.1
    XP_063144527.1
    XP_063144528.1

    NCBI Reference Sequences (RefSeq)

    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_001271226.2NP_001258155.1  chromodomain-helicase-DNA-binding protein 5

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000005
      UniProtKB/Swiss-Prot
      D3ZD32
      Related
      ENSRNOP00000087017.1, ENSRNOT00000112715.2
      Conserved Domains (11) summary
      smart00298
      Location:590623
      CHROMO; Chromatin organization modifier domain
      cd00046
      Location:718876
      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.
      cd15531
      Location:343385
      PHD1_CHD_II; PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
      cd15532
      Location:416458
      PHD2_CHD_II; PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
      pfam00176
      Location:701997
      SNF2_N; SNF2 family N-terminal domain
      pfam00271
      Location:10211136
      Helicase_C; Helicase conserved C-terminal domain
      pfam06375
      Location:196296
      BLVR; Bovine leukaemia virus receptor (BLVR)
      pfam06461
      Location:13861527
      DUF1086; Domain of Unknown Function (DUF1086)
      pfam06465
      Location:12961356
      DUF1087; Domain of Unknown Function (DUF1087)
      pfam08073
      Location:149198
      CHDNT; CHDNT (NUC034) domain
      pfam08074
      Location:17261897
      CHDCT2; CHDCT2 (NUC038) domain

    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_086023.1 Reference GRCr8

      Range
      168130851..168181705
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017593639.3XP_017449128.1  chromodomain-helicase-DNA-binding protein 5 isoform X1

      UniProtKB/Swiss-Prot
      D3ZD32
    2. XM_017593647.3XP_017449136.1  chromodomain-helicase-DNA-binding protein 5 isoform X8

      UniProtKB/Swiss-Prot
      D3ZD32
      UniProtKB/TrEMBL
      A0A8I6A737
      Related
      ENSRNOP00000086830.1, ENSRNOT00000101697.2
    3. XM_017593648.3XP_017449137.1  chromodomain-helicase-DNA-binding protein 5 isoform X11

      UniProtKB/Swiss-Prot
      D3ZD32
    4. XM_017593649.3XP_017449138.1  chromodomain-helicase-DNA-binding protein 5 isoform X12

      UniProtKB/Swiss-Prot
      D3ZD32
      Related
      ENSRNOP00000099286.1, ENSRNOT00000170038.1
    5. XM_017593640.3XP_017449129.1  chromodomain-helicase-DNA-binding protein 5 isoform X2

      UniProtKB/Swiss-Prot
      D3ZD32
    6. XM_063288457.1XP_063144527.1  chromodomain-helicase-DNA-binding protein 5 isoform X13

    7. XM_017593642.3XP_017449131.1  chromodomain-helicase-DNA-binding protein 5 isoform X4

      UniProtKB/Swiss-Prot
      D3ZD32
    8. XM_063288455.1XP_063144525.1  chromodomain-helicase-DNA-binding protein 5 isoform X9

    9. XM_063288458.1XP_063144528.1  chromodomain-helicase-DNA-binding protein 5 isoform X14

    10. XM_017593643.3XP_017449132.1  chromodomain-helicase-DNA-binding protein 5 isoform X5

      UniProtKB/Swiss-Prot
      D3ZD32
    11. XM_039110813.2XP_038966741.1  chromodomain-helicase-DNA-binding protein 5 isoform X10

      UniProtKB/Swiss-Prot
      D3ZD32
      Conserved Domains (10) summary
      PLN03142
      Location:6961214
      PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
      PRK13108
      Location:15301680
      PRK13108; prolipoprotein diacylglyceryl transferase; Reviewed
      cd15531
      Location:343385
      PHD1_CHD_II; PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
      cd15532
      Location:416458
      PHD2_CHD_II; PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
      cd18662
      Location:587640
      CD2_tandem_CHD3-4_like; repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 3 and 4, and similar proteins
      cd18667
      Location:463542
      CD1_tandem_CHD3-4_like; repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 3 and 4, and similar proteins
      pfam06461
      Location:13861527
      DUF1086; Domain of Unknown Function (DUF1086)
      pfam06465
      Location:12961349
      DUF1087; Domain of Unknown Function (DUF1087)
      pfam08073
      Location:144199
      CHDNT; CHDNT (NUC034) domain
      pfam08074
      Location:17261852
      CHDCT2; CHDCT2 (NUC038) domain
    12. XM_017593641.3XP_017449130.1  chromodomain-helicase-DNA-binding protein 5 isoform X3

      UniProtKB/Swiss-Prot
      D3ZD32
    13. XM_017593645.3XP_017449134.1  chromodomain-helicase-DNA-binding protein 5 isoform X6

      UniProtKB/Swiss-Prot
      D3ZD32
    14. XM_017593646.3XP_017449135.1  chromodomain-helicase-DNA-binding protein 5 isoform X7

      UniProtKB/Swiss-Prot
      D3ZD32
    15. XM_039110815.2XP_038966743.1  chromodomain-helicase-DNA-binding protein 5 isoform X16

      Conserved Domains (8) summary
      PLN03142
      Location:6961214
      PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
      cd15531
      Location:343385
      PHD1_CHD_II; PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
      cd15532
      Location:416458
      PHD2_CHD_II; PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
      cd18662
      Location:587640
      CD2_tandem_CHD3-4_like; repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 3 and 4, and similar proteins
      cd18667
      Location:463542
      CD1_tandem_CHD3-4_like; repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 3 and 4, and similar proteins
      pfam06461
      Location:13891515
      DUF1086; Domain of Unknown Function (DUF1086)
      pfam06465
      Location:12961349
      DUF1087; Domain of Unknown Function (DUF1087)
      pfam08073
      Location:144199
      CHDNT; CHDNT (NUC034) domain
    16. XM_017593644.3XP_017449133.1  chromodomain-helicase-DNA-binding protein 5 isoform X15

      UniProtKB/TrEMBL
      A0A0H2UHP5
      Related
      ENSRNOP00000084279.2, ENSRNOT00000101172.2