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    Chd6 chromodomain helicase DNA binding protein 6 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 311607, updated on 28-Oct-2024

    Summary

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    Official Symbol
    Chd6provided by RGD
    Official Full Name
    chromodomain helicase DNA binding protein 6provided by RGD
    Primary source
    RGD:1310465
    See related
    EnsemblRapid:ENSRNOG00000016744 AllianceGenome:RGD:1310465
    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-6
    Summary
    Predicted to enable several functions, including ATP hydrolysis activity; ATP-dependent chromatin remodeler activity; and transcription coregulator binding activity. Predicted to be involved in cell redox homeostasis; chromatin remodeling; and positive regulation of transcription by RNA polymerase II. Predicted to be located in chromatin and nucleoplasm. Predicted to be active in nucleus. Orthologous to human CHD6 (chromodomain helicase DNA binding protein 6). [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Biased expression in Thymus (RPKM 176.4), Kidney (RPKM 121.6) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Chd6 in Genome Data Viewer
    Location:
    3q42
    Exon count:
    43
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 3 NC_086021.1 (170016204..170177480, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 3 NC_051338.1 (149596509..149757765, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 3 NC_005102.4 (156937746..157099328, complement)

    Chromosome 3 - NC_086021.1Genomic Context describing neighboring genes Neighboring gene zinc fingers and homeoboxes 3 Neighboring gene uncharacterized LOC134486198 Neighboring gene lipin 3 Neighboring gene elastin microfibril interfacer 3 Neighboring gene uncharacterized LOC134486200 Neighboring gene small nucleolar RNA SNORA17 Neighboring gene uncharacterized LOC108350515 Neighboring gene uncharacterized LOC120101777

    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 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. CHD6 is a DNA-dependent ATPase and localizes at nuclear sites of mRNA synthesis. Lutz T, et al. FEBS Lett, 2006 Oct 30. PMID 17027977
    2. The carboxy-terminal Neh3 domain of Nrf2 is required for transcriptional activation. Nioi P, et al. Mol Cell Biol, 2005 Dec. PMID 16314513, Free PMC Article
    3. The Nrf2 regulatory network provides an interface between redox and intermediary metabolism. Hayes JD, et al. Trends Biochem Sci, 2014 Apr. PMID 24647116
    4. 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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    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 activity, acting on DNA ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables ATP-dependent activity, acting on DNA ISS
    Inferred from Sequence or Structural Similarity
    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 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 hydrolase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables transcription coregulator binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables transcription coregulator binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in cell redox homeostasis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in cell redox homeostasis ISO
    Inferred from Sequence Orthology
    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 positive regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of transcription by RNA polymerase II ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of gene expression IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in chromatin IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    chromodomain-helicase-DNA-binding protein 6
    Names
    ATP-dependent helicase CHD6
    NP_001101267.1
    XP_006235546.2
    XP_008760567.1
    XP_008760568.1
    XP_017447279.2
    XP_038961032.1
    XP_038961033.1
    XP_038961034.1
    XP_038961035.1
    XP_038961036.1
    XP_038961037.1
    XP_038961039.1
    XP_038961040.1
    XP_038961041.1
    XP_038961042.1
    XP_038961043.1
    XP_038961044.1
    XP_063139932.1
    XP_063139933.1
    XP_063139934.1
    XP_063139935.1
    XP_063139936.1
    XP_063139937.1

    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_001107797.2 → NP_001101267.1  chromodomain-helicase-DNA-binding protein 6 isoform 2

      See identical proteins and their annotated locations for NP_001101267.1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000003
      UniProtKB/Swiss-Prot
      D3ZA12
      UniProtKB/TrEMBL
      A0A8I5Y6Q9
      Conserved Domains (5) summary
      cd00046
      Location:479 → 628
      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:463 → 750
      SNF2_N; SNF2 family N-terminal domain
      pfam00271
      Location:782 → 896
      Helicase_C; Helicase conserved C-terminal domain
      pfam00385
      Location:375 → 428
      Chromo; Chromo (CHRromatin Organization MOdifier) domain
      cl00146
      Location:104 → 257
      TFIIS_I; N-terminal domain (domain I) of transcription elongation factor S-II (TFIIS); similar to a domain found in elongin A and CRSP70; likely to be involved in transcription; domain I from TFIIS interacts with RNA polymerase II holoenzyme

    2. NM_001434092.1 → NP_001421021.1  chromodomain-helicase-DNA-binding protein 6 isoform 1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000003

    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_086021.1 Reference GRCr8

      Range
      170016204..170177480 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039105105.2 → XP_038961033.1  chromodomain-helicase-DNA-binding protein 6 isoform X3

      UniProtKB/TrEMBL
      A0A8I5Y6Q9
      Conserved Domains (5) summary
      PTZ00449
      Location:100 → 372
      PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional
      PLN03142
      Location:458 → 983
      PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
      cd18663
      Location:371 → 429
      CD2_tandem_CHD5-9_like; repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, and similar proteins
      cd18668
      Location:287 → 352
      CD1_tandem_CHD5-9_like; repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, and similar proteins
      cl28899
      Location:459 → 680
      DEAD-like_helicase_N; N-terminal helicase domain of the DEAD-box helicase superfamily

    2. XM_017591790.3 → XP_017447279.2  chromodomain-helicase-DNA-binding protein 6 isoform X4

      UniProtKB/TrEMBL
      A0A8I6AKM1, A0A8I6ARM3
      Conserved Domains (5) summary
      PTZ00449
      Location:100 → 372
      PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional
      PLN03142
      Location:459 → 984
      PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
      cd18663
      Location:371 → 429
      CD2_tandem_CHD5-9_like; repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, and similar proteins
      cd18668
      Location:287 → 352
      CD1_tandem_CHD5-9_like; repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, and similar proteins
      cl28899
      Location:460 → 681
      DEAD-like_helicase_N; N-terminal helicase domain of the DEAD-box helicase superfamily

    3. XM_006235484.5 → XP_006235546.2  chromodomain-helicase-DNA-binding protein 6 isoform X6

      UniProtKB/TrEMBL
      A0A8I6AKM1
      Related
      ENSRNOP00000093958.2, ENSRNOT00000106235.2
      Conserved Domains (5) summary
      PTZ00449
      Location:100 → 372
      PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional
      PLN03142
      Location:459 → 984
      PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
      cd18663
      Location:371 → 429
      CD2_tandem_CHD5-9_like; repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, and similar proteins
      cd18668
      Location:287 → 352
      CD1_tandem_CHD5-9_like; repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, and similar proteins
      cl28899
      Location:460 → 681
      DEAD-like_helicase_N; N-terminal helicase domain of the DEAD-box helicase superfamily

    4. XM_039105107.2 → XP_038961035.1  chromodomain-helicase-DNA-binding protein 6 isoform X8

      UniProtKB/TrEMBL
      A0A8I5Y6Q9
      Conserved Domains (5) summary
      PTZ00449
      Location:100 → 372
      PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional
      PLN03142
      Location:459 → 984
      PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
      cd18663
      Location:371 → 429
      CD2_tandem_CHD5-9_like; repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, and similar proteins
      cd18668
      Location:287 → 352
      CD1_tandem_CHD5-9_like; repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, and similar proteins
      cl28899
      Location:460 → 681
      DEAD-like_helicase_N; N-terminal helicase domain of the DEAD-box helicase superfamily

    5. XM_039105106.2 → XP_038961034.1  chromodomain-helicase-DNA-binding protein 6 isoform X7

      UniProtKB/TrEMBL
      A0A8I5Y6Q9
      Related
      ENSRNOP00000071893.2, ENSRNOT00000089958.3
      Conserved Domains (5) summary
      PTZ00449
      Location:100 → 372
      PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional
      PLN03142
      Location:459 → 984
      PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
      cd18663
      Location:371 → 429
      CD2_tandem_CHD5-9_like; repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, and similar proteins
      cd18668
      Location:287 → 352
      CD1_tandem_CHD5-9_like; repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, and similar proteins
      cl28899
      Location:460 → 681
      DEAD-like_helicase_N; N-terminal helicase domain of the DEAD-box helicase superfamily

    6. XM_008762345.4 → XP_008760567.1  chromodomain-helicase-DNA-binding protein 6 isoform X1

      UniProtKB/TrEMBL
      A0A8I5Y6Q9, A0A8L2QC41
      Related
      ENSRNOP00000022861.7, ENSRNOT00000022861.8
      Conserved Domains (5) summary
      PTZ00449
      Location:100 → 372
      PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional
      PLN03142
      Location:459 → 984
      PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
      cd18663
      Location:371 → 429
      CD2_tandem_CHD5-9_like; repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, and similar proteins
      cd18668
      Location:287 → 352
      CD1_tandem_CHD5-9_like; repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, and similar proteins
      cl28899
      Location:460 → 681
      DEAD-like_helicase_N; N-terminal helicase domain of the DEAD-box helicase superfamily

    7. XM_063283862.1 → XP_063139932.1  chromodomain-helicase-DNA-binding protein 6 isoform X1

      UniProtKB/TrEMBL
      A0A8L2QC41

    8. XM_063283864.1 → XP_063139934.1  chromodomain-helicase-DNA-binding protein 6 isoform X2

      UniProtKB/TrEMBL
      A0A0G2K1L7
      Related
      ENSRNOP00000094454.2, ENSRNOT00000107966.2

    9. XM_008762346.4 → XP_008760568.1  chromodomain-helicase-DNA-binding protein 6 isoform X5

      UniProtKB/TrEMBL
      A0A8I6AKM1
      Related
      ENSRNOP00000076519.1, ENSRNOT00000119650.2
      Conserved Domains (5) summary
      cd00046
      Location:457 → 606
      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:441 → 728
      SNF2_N; SNF2 family N-terminal domain
      pfam00271
      Location:760 → 874
      Helicase_C; Helicase conserved C-terminal domain
      pfam00385
      Location:353 → 406
      Chromo; Chromo (CHRromatin Organization MOdifier) domain
      cl00146
      Location:82 → 235
      TFIIS_I; N-terminal domain (domain I) of transcription elongation factor S-II (TFIIS); similar to a domain found in elongin A and CRSP70; likely to be involved in transcription; domain I from TFIIS interacts with RNA polymerase II holoenzyme

    10. XM_063283863.1 → XP_063139933.1  chromodomain-helicase-DNA-binding protein 6 isoform X1

      UniProtKB/TrEMBL
      A0A8L2QC41

    11. XM_039105104.2 → XP_038961032.1  chromodomain-helicase-DNA-binding protein 6 isoform X1

      UniProtKB/TrEMBL
      A0A8I5Y6Q9, A0A8L2QC41
      Conserved Domains (5) summary
      PTZ00449
      Location:100 → 372
      PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional
      PLN03142
      Location:459 → 984
      PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
      cd18663
      Location:371 → 429
      CD2_tandem_CHD5-9_like; repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, and similar proteins
      cd18668
      Location:287 → 352
      CD1_tandem_CHD5-9_like; repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, and similar proteins
      cl28899
      Location:460 → 681
      DEAD-like_helicase_N; N-terminal helicase domain of the DEAD-box helicase superfamily

    12. XM_063283865.1 → XP_063139935.1  chromodomain-helicase-DNA-binding protein 6 isoform X10

    13. XM_039105108.2 → XP_038961036.1  chromodomain-helicase-DNA-binding protein 6 isoform X9

      UniProtKB/TrEMBL
      A0A8I6A6R3, A0A8I6AKM1
      Related
      ENSRNOP00000086889.1, ENSRNOT00000114568.2
      Conserved Domains (4) summary
      PLN03142
      Location:211 → 736
      PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
      cd18663
      Location:123 → 181
      CD2_tandem_CHD5-9_like; repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, and similar proteins
      cd18668
      Location:39 → 104
      CD1_tandem_CHD5-9_like; repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, and similar proteins
      cl28899
      Location:212 → 433
      DEAD-like_helicase_N; N-terminal helicase domain of the DEAD-box helicase superfamily

    14. XM_039105111.2 → XP_038961039.1  chromodomain-helicase-DNA-binding protein 6 isoform X14

    15. XM_039105112.2 → XP_038961040.1  chromodomain-helicase-DNA-binding protein 6 isoform X15

    16. XM_039105113.2 → XP_038961041.1  chromodomain-helicase-DNA-binding protein 6 isoform X16

    17. XM_039105116.2 → XP_038961044.1  chromodomain-helicase-DNA-binding protein 6 isoform X19

    18. XM_039105109.2 → XP_038961037.1  chromodomain-helicase-DNA-binding protein 6 isoform X12

      Conserved Domains (5) summary
      PTZ00449
      Location:81 → 372
      PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional
      PLN03142
      Location:459 → 984
      PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
      cd18663
      Location:371 → 429
      CD2_tandem_CHD5-9_like; repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, and similar proteins
      cd18668
      Location:287 → 352
      CD1_tandem_CHD5-9_like; repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, and similar proteins
      cl28899
      Location:460 → 681
      DEAD-like_helicase_N; N-terminal helicase domain of the DEAD-box helicase superfamily

    19. XM_063283867.1 → XP_063139937.1  chromodomain-helicase-DNA-binding protein 6 isoform X13

    20. XM_063283866.1 → XP_063139936.1  chromodomain-helicase-DNA-binding protein 6 isoform X11

    21. XM_039105115.2 → XP_038961043.1  chromodomain-helicase-DNA-binding protein 6 isoform X17

      Conserved Domains (5) summary
      PTZ00449
      Location:100 → 372
      PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional
      PLN03142
      Location:459 → 984
      PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
      cd18663
      Location:371 → 429
      CD2_tandem_CHD5-9_like; repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, and similar proteins
      cd18668
      Location:287 → 352
      CD1_tandem_CHD5-9_like; repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, and similar proteins
      cl28899
      Location:460 → 681
      DEAD-like_helicase_N; N-terminal helicase domain of the DEAD-box helicase superfamily

    22. XM_039105114.2 → XP_038961042.1  chromodomain-helicase-DNA-binding protein 6 isoform X18

      Conserved Domains (5) summary
      PTZ00449
      Location:100 → 372
      PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional
      PLN03142
      Location:459 → 984
      PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
      cd18663
      Location:371 → 429
      CD2_tandem_CHD5-9_like; repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, and similar proteins
      cd18668
      Location:287 → 352
      CD1_tandem_CHD5-9_like; repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, and similar proteins
      cl28899
      Location:460 → 681
      DEAD-like_helicase_N; N-terminal helicase domain of the DEAD-box helicase superfamily

    RNA

    1. XR_005501897.2 RNA Sequence

    2. XR_005501896.2 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    D3ZA12.2 GenPept UniProtKB/Swiss-Prot:D3ZA12

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