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    Chd5 chromodomain helicase DNA binding protein 5 [ Mus musculus (house mouse) ]

    Gene ID: 269610, updated on 2-Nov-2024

    Summary

    Official Symbol
    Chd5provided by MGI
    Official Full Name
    chromodomain helicase DNA binding protein 5provided by MGI
    Primary source
    MGI:MGI:3036258
    See related
    Ensembl:ENSMUSG00000005045 AllianceGenome:MGI:3036258
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    CHD-5; 4930532L22Rik; B230399N07Rik
    Summary
    Enables H3K27me3 modified histone binding activity and histone deacetylase binding activity. Involved in several processes, including negative regulation of transcription by RNA polymerase II; positive regulation of signal transduction by p53 class mediator; and sperm DNA condensation. Located in heterochromatin and nucleus. Part of NuRD complex. Is expressed in central nervous system and dorsal root ganglion. Orthologous to human CHD5 (chromodomain helicase DNA binding protein 5). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in testis adult (RPKM 38.0), frontal lobe adult (RPKM 16.9) and 5 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See Chd5 in Genome Data Viewer
    Location:
    4 E2; 4 83.04 cM
    Exon count:
    43
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 4 NC_000070.7 (152423103..152474651)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 4 NC_000070.6 (152338646..152390194)

    Chromosome 4 - NC_000070.7Genomic Context describing neighboring genes Neighboring gene RIKEN cDNA 9430083M05 gene Neighboring gene STARR-positive B cell enhancer ABC_E846 Neighboring gene isoprenylcysteine carboxyl methyltransferase Neighboring gene ring finger protein 207 Neighboring gene ribosomal protein L22 Neighboring gene potassium voltage-gated channel, shaker-related subfamily, beta member 2 Neighboring gene predicted gene 16333 Neighboring gene nephronophthisis 4 (juvenile) homolog (human)

    Genomic regions, transcripts, and products

    Expression

    • Project title: Mouse ENCODE transcriptome data Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Variation

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (2) 
    • Targeted (5)  1 citation

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by MGI

    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 hydrolysis activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables ATP-dependent chromatin remodeler activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables ATP-dependent chromatin remodeler activity IEA
    Inferred from Electronic Annotation
    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 H3K27me3 modified histone binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables H3K27me3 modified histone binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables chromatin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables chromatin binding ISO
    Inferred from Sequence Orthology
    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 IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables histone deacetylase binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Component Evidence Code Pubs
    part_of NuRD complex IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    part_of NuRD complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in chromatin IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in chromatin ISO
    Inferred from Sequence Orthology
    more info
     
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
     
    located_in heterochromatin IDA
    Inferred from Direct Assay
    more info
    PubMed 
    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 ISO
    Inferred from Sequence Orthology
    more info
     

    General protein information

    Preferred Names
    chromodomain-helicase-DNA-binding protein 5
    Names
    ATP-dependent helicase CHD5
    NP_001074845.1
    NP_001356172.1
    NP_083492.2
    XP_006538992.1
    XP_006538993.1
    XP_006538994.1
    XP_006538996.1
    XP_006538998.1
    XP_017175733.1
    XP_030109449.1

    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_001081376.1NP_001074845.1  chromodomain-helicase-DNA-binding protein 5 isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AL611985
      Consensus CDS
      CCDS38984.1
      UniProtKB/TrEMBL
      E9PYL1
      Related
      ENSMUSP00000030775.6, ENSMUST00000030775.12
      Conserved Domains (10) summary
      smart00298
      Location:594648
      CHROMO; Chromatin organization modifier domain
      cd00046
      Location:722880
      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:347389
      PHD1_CHD_II; PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
      cd15532
      Location:420462
      PHD2_CHD_II; PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
      pfam00176
      Location:7051001
      SNF2_N; SNF2 family N-terminal domain
      pfam00271
      Location:10251140
      Helicase_C; Helicase conserved C-terminal domain
      pfam06461
      Location:13901531
      DUF1086; Domain of Unknown Function (DUF1086)
      pfam06465
      Location:13001360
      DUF1087; Domain of Unknown Function (DUF1087)
      pfam08073
      Location:153202
      CHDNT; CHDNT (NUC034) domain
      pfam08074
      Location:17301901
      CHDCT2; CHDCT2 (NUC038) domain
    2. NM_001369243.1NP_001356172.1  chromodomain-helicase-DNA-binding protein 5 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AL611985
      Consensus CDS
      CCDS89866.1
      UniProtKB/Swiss-Prot
      A2A8L1, Q6ZQB2
      Related
      ENSMUSP00000005175.5, ENSMUST00000005175.5
      Conserved Domains (10) summary
      PLN03142
      Location:7001218
      PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
      PRK13108
      Location:15321684
      PRK13108; prolipoprotein diacylglyceryl transferase; Reviewed
      cd15531
      Location:347389
      PHD1_CHD_II; PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
      cd15532
      Location:420462
      PHD2_CHD_II; PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
      pfam06461
      Location:13901531
      DUF1086; Domain of Unknown Function (DUF1086)
      pfam08074
      Location:17301901
      CHDCT2; CHDCT2 (NUC038) domain
      pfam06465
      Location:13001359
      DUF1087; Domain of Unknown Function (DUF1087)
      pfam08073
      Location:153203
      CHDNT; CHDNT (NUC034) domain
      cd18662
      Location:591644
      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:467546
      CD1_tandem_CHD3-4_like; repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 3 and 4, and similar proteins
    3. NM_029216.2NP_083492.2  chromodomain-helicase-DNA-binding protein 5 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an in-frame exon, compared to variant 1. It encodes isoform 2 which is shorter than isoform 1.
      Source sequence(s)
      AL611985
      Consensus CDS
      CCDS51394.1
      UniProtKB/TrEMBL
      E9PYU4
      Related
      ENSMUSP00000132600.2, ENSMUST00000164662.8
      Conserved Domains (10) summary
      smart00298
      Location:594648
      CHROMO; Chromatin organization modifier domain
      cd00046
      Location:722880
      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:347389
      PHD1_CHD_II; PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
      cd15532
      Location:420462
      PHD2_CHD_II; PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
      pfam00176
      Location:7051001
      SNF2_N; SNF2 family N-terminal domain
      pfam00271
      Location:10251140
      Helicase_C; Helicase conserved C-terminal domain
      pfam06461
      Location:13531494
      DUF1086; Domain of Unknown Function (DUF1086)
      pfam06465
      Location:12631323
      DUF1087; Domain of Unknown Function (DUF1087)
      pfam08073
      Location:153202
      CHDNT; CHDNT (NUC034) domain
      pfam08074
      Location:16931864
      CHDCT2; CHDCT2 (NUC038) domain

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000070.7 Reference GRCm39 C57BL/6J

      Range
      152423103..152474651
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006538929.2XP_006538992.1  chromodomain-helicase-DNA-binding protein 5 isoform X1

      Conserved Domains (10) summary
      PLN03142
      Location:7001218
      PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
      PRK13108
      Location:15351687
      PRK13108; prolipoprotein diacylglyceryl transferase; Reviewed
      cd15531
      Location:347389
      PHD1_CHD_II; PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
      cd15532
      Location:420462
      PHD2_CHD_II; PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
      cd18662
      Location:591644
      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:467546
      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:13931534
      DUF1086; Domain of Unknown Function (DUF1086)
      pfam06465
      Location:13001359
      DUF1087; Domain of Unknown Function (DUF1087)
      pfam08073
      Location:148203
      CHDNT; CHDNT (NUC034) domain
      pfam08074
      Location:17331904
      CHDCT2; CHDCT2 (NUC038) domain
    2. XM_006538933.2XP_006538996.1  chromodomain-helicase-DNA-binding protein 5 isoform X5

      Conserved Domains (10) summary
      PLN03142
      Location:7001240
      PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
      PRK13108
      Location:14981650
      PRK13108; prolipoprotein diacylglyceryl transferase; Reviewed
      cd15531
      Location:347389
      PHD1_CHD_II; PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
      cd15532
      Location:420462
      PHD2_CHD_II; PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
      cd18662
      Location:591644
      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:467546
      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:13561497
      DUF1086; Domain of Unknown Function (DUF1086)
      pfam06465
      Location:12631322
      DUF1087; Domain of Unknown Function (DUF1087)
      pfam08073
      Location:148203
      CHDNT; CHDNT (NUC034) domain
      pfam08074
      Location:16961867
      CHDCT2; CHDCT2 (NUC038) domain
    3. XM_006538930.2XP_006538993.1  chromodomain-helicase-DNA-binding protein 5 isoform X2

      Conserved Domains (10) summary
      PLN03142
      Location:7001217
      PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
      PRK13108
      Location:15341686
      PRK13108; prolipoprotein diacylglyceryl transferase; Reviewed
      cd15531
      Location:347389
      PHD1_CHD_II; PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
      cd15532
      Location:420462
      PHD2_CHD_II; PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
      cd18662
      Location:591644
      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:467546
      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:13921533
      DUF1086; Domain of Unknown Function (DUF1086)
      pfam06465
      Location:12991358
      DUF1087; Domain of Unknown Function (DUF1087)
      pfam08073
      Location:148203
      CHDNT; CHDNT (NUC034) domain
      pfam08074
      Location:17321903
      CHDCT2; CHDCT2 (NUC038) domain
    4. XM_017320244.2XP_017175733.1  chromodomain-helicase-DNA-binding protein 5 isoform X3

      Conserved Domains (10) summary
      PLN03142
      Location:7001217
      PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
      PRK13108
      Location:15311683
      PRK13108; prolipoprotein diacylglyceryl transferase; Reviewed
      cd15531
      Location:347389
      PHD1_CHD_II; PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
      cd15532
      Location:420462
      PHD2_CHD_II; PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
      cd18662
      Location:591644
      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:467546
      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:13891530
      DUF1086; Domain of Unknown Function (DUF1086)
      pfam06465
      Location:12991358
      DUF1087; Domain of Unknown Function (DUF1087)
      pfam08073
      Location:148203
      CHDNT; CHDNT (NUC034) domain
      pfam08074
      Location:17291900
      CHDCT2; CHDCT2 (NUC038) domain
    5. XM_006538931.2XP_006538994.1  chromodomain-helicase-DNA-binding protein 5 isoform X4

      Conserved Domains (10) summary
      PLN03142
      Location:7001218
      PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
      PRK13108
      Location:15351687
      PRK13108; prolipoprotein diacylglyceryl transferase; Reviewed
      cd15531
      Location:347389
      PHD1_CHD_II; PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
      cd15532
      Location:420462
      PHD2_CHD_II; PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
      cd18662
      Location:591644
      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:467546
      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:13931534
      DUF1086; Domain of Unknown Function (DUF1086)
      pfam06465
      Location:13001359
      DUF1087; Domain of Unknown Function (DUF1087)
      pfam08073
      Location:148203
      CHDNT; CHDNT (NUC034) domain
      pfam08074
      Location:17331904
      CHDCT2; CHDCT2 (NUC038) domain
    6. XM_006538935.2XP_006538998.1  chromodomain-helicase-DNA-binding protein 5 isoform X7

      Conserved Domains (10) summary
      PLN03142
      Location:7001218
      PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
      PRK13108
      Location:15351687
      PRK13108; prolipoprotein diacylglyceryl transferase; Reviewed
      cd15531
      Location:347389
      PHD1_CHD_II; PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
      cd15532
      Location:420462
      PHD2_CHD_II; PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
      cd18662
      Location:591644
      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:467546
      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:13931534
      DUF1086; Domain of Unknown Function (DUF1086)
      pfam06465
      Location:13001359
      DUF1087; Domain of Unknown Function (DUF1087)
      pfam08073
      Location:148203
      CHDNT; CHDNT (NUC034) domain
      pfam08074
      Location:17331860
      CHDCT2; CHDCT2 (NUC038) domain
    7. XM_030253589.1XP_030109449.1  chromodomain-helicase-DNA-binding protein 5 isoform X6

      Conserved Domains (10) summary
      PLN03142
      Location:6261144
      PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
      PRK13108
      Location:14611613
      PRK13108; prolipoprotein diacylglyceryl transferase; Reviewed
      cd15531
      Location:273315
      PHD1_CHD_II; PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
      cd15532
      Location:346388
      PHD2_CHD_II; PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
      cd18662
      Location:517570
      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:393472
      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:13191460
      DUF1086; Domain of Unknown Function (DUF1086)
      pfam06465
      Location:12261285
      DUF1087; Domain of Unknown Function (DUF1087)
      pfam08073
      Location:74129
      CHDNT; CHDNT (NUC034) domain
      pfam08074
      Location:16591830
      CHDCT2; CHDCT2 (NUC038) domain