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CHD9 Gene

protein-coding   GIFtS: 55
GCID: GC16P053041

Chromodomain Helicase DNA Binding Protein 9

  Search for CHD9
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Chromodomain Helicase DNA Binding Protein 91 2     PPAR-Alpha-Interacting Complex Protein 320 KDa2 3
Chromatin-Related Mesenchymal Modulator2 3     AD0132
Chromatin-Remodeling Factor CHROM12 3     Chromatin Remodeling Factor CHROM12
Kismet Homolog 22 3     Chromodomain-Helicase-DNA-Binding Protein 92
Peroxisomal Proliferator-Activated Receptor A-Interacting Complex 320 KDa
Protein2 3
     Ciprofibrate Bound Protein P2402
CHD-92 3     PPAR{Gamma}-Interacting Cofactor 320 KDa2
CReMM2 3     proteinx00082
KISH22 3     EC 3.6.4.123
PRIC3202 3     KIAA03083
ATP-Dependent Helicase CHD92 3     EC 3.6.18

External Ids:    HGNC: 257011   Entrez Gene: 802052   Ensembl: ENSG000001772007   UniProtKB: Q3L8U13   

Export aliases for CHD9 gene to outside databases

Previous GC identifers: GC16P051646 GC16P051747 GC16P038976


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for CHD9 Gene:
CHD9 (chromodomain helicase DNA binding protein 9) is a protein-coding gene. GO annotations related to this gene include helicase activity. An important paralog of this gene is CHD6.

UniProtKB/Swiss-Prot: CHD9_HUMAN, Q3L8U1
Function: Acts as a transcriptional coactivator for PPARA and possibly other nuclear receptors. Proposed to be a
ATP-dependent chromatin remodeling protein. Has DNA-dependent ATPase activity and binds to A/T-rich DNA.
Associates with A/T-rich regulatory regions in promoters of genes that participate in the differentiation of
progenitors during osteogenesis (By similarity)

Gene Wiki entry for CHD9 Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000016.9  NT_010498.16  NC_018927.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the CHD9 gene promoter:
         STAT1   p53   Pax-5   AML1a   STAT5A   C/EBPalpha   GATA-1   FAC1   STAT3   Pax-4a   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 2): CHD9 promoter sequence
   Search Chromatin IP Primers for CHD9

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat CHD9


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 16q12.2   Ensembl cytogenetic band:  16q12.2   HGNC cytogenetic band: 16q12.2

CHD9 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CHD9 gene location

GeneLoc information about chromosome 16         GeneLoc Exon Structure

GeneLoc location for GC16P053041:  view genomic region     (about GC identifiers)

Start:
53,088,945 bp from pter      End:
53,363,062 bp from pter
Size:
274,118 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: CHD9_HUMAN, Q3L8U1 (See protein sequence)
Recommended Name: Chromodomain-helicase-DNA-binding protein 9  
Size: 2897 amino acids; 326022 Da
Subunit: Interacts with PPARA. Probably interacts with ESR1 and NR1I3
Sequence caution: Sequence=AAF24170.1; Type=Erroneous translation; Note=Wrong choice of frame;
Sequence=BAB14112.1; Type=Erroneous initiation;
Secondary accessions: B2RTU2 B9ZVQ0 O15025 Q1WF12 Q6DTK9 Q9H9V7 Q9UHM2
Alternative splicing: 3 isoforms:  Q3L8U1-1   Q3L8U1-2   Q3L8U1-3   

Explore the universe of human proteins at neXtProt for CHD9: NX_Q3L8U1

Explore proteomics data for CHD9 at MOPED

Post-translational modifications: 

  • Phosphorylated on serine and tyrosine residues1
  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus
  • Selected DME Specific Peptides for CHD9 (Q3L8U1) (see all 43)
     GAEEKIL  DSDWNPQ  KASFVAS  MCRRVCR 


    See CHD9 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_079410.4  
    ENSEMBL proteins: 
     ENSP00000457466   ENSP00000456793   ENSP00000455307   ENSP00000457929   ENSP00000381522  
     ENSP00000460155   ENSP00000457355   ENSP00000456415   ENSP00000462685   ENSP00000462008  
     ENSP00000396345  
    Reactome Protein details: Q3L8U1

    CHD9 Human Recombinant Protein Products:

    Browse Purified and Recombinant Proteins at EMD Millipore
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    Browse OriGene full length recombinant human proteins expressed in human HEK293 cells
    Browse OriGene Protein Over-expression Lysates
    OriGene Custom MassSpec
    OriGene Custom Protein Services for CHD9
    GenScript Custom Purified and Recombinant Proteins Services for CHD9
    Novus Biologicals CHD9 Protein
    Browse Sino Biological Recombinant Proteins
    Browse Sino Biological Cell Lysates
    Browse ProSpec Recombinant Proteins
    Cloud-Clone Corp. Proteins for CHD9

     
    Search eBioscience for Proteins for CHD9 

    CHD9 Antibody Products:

    EMD Millipore Mono- and Polyclonal Antibodies for the study of CHD9
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    Browse OriGene Antibodies
    OriGene Custom Antibody Services for CHD9
    Novus Biologicals CHD9 Antibody
    Abcam antibodies for CHD9
    Cloud-Clone Corp. Antibodies for CHD9
    Search ThermoFisher Antibodies for CHD9
    LSBio Antibodies in human, mouse, rat for CHD9

    CHD9 Assay Products:

    Browse Kits and Assays available from EMD Millipore
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    GenScript Custom Assay Services for CHD9
    Browse Enzo Life Sciences for kits & assays
    Cloud-Clone Corp. ELISAs for CHD9
    Cloud-Clone Corp. CLIAs for CHD9
    Search eBioscience for ELISAs for CHD9 


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    Selected InterPro protein domains (see all 8):
     IPR000953 Chromo_domain/shadow
     IPR000330 SNF2_N
     IPR023780 Chromo_domain
     IPR016197 Chromodomain-like
     IPR006576 BRK_domain

    Graphical View of Domain Structure for InterPro Entry Q3L8U1

    ProtoNet protein and cluster: Q3L8U1

    3 Blocks protein domains:
    IPB000330 SNF2 related domain
    IPB000953 Chromo domain
    IPB006576 Domain in transcription and CHROMO domain helicase


    UniProtKB/Swiss-Prot: CHD9_HUMAN, Q3L8U1
    Similarity: Belongs to the SNF2/RAD54 helicase family
    Similarity: Contains 2 chromo domains
    Similarity: Contains 1 helicase ATP-binding domain
    Similarity: Contains 1 helicase C-terminal domain


    Find genes that share domains with CHD9           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: CHD9_HUMAN, Q3L8U1
    Function: Acts as a transcriptional coactivator for PPARA and possibly other nuclear receptors. Proposed to be a
    ATP-dependent chromatin remodeling protein. Has DNA-dependent ATPase activity and binds to A/T-rich DNA.
    Associates with A/T-rich regulatory regions in promoters of genes that participate in the differentiation of
    progenitors during osteogenesis (By similarity)
    Catalytic activity: ATP + H(2)O = ADP + phosphate

         Enzyme Numbers (IUBMB): EC 3.6.12 EC 3.6.4.121

         Gene Ontology (GO): Selected molecular function terms (see all 8):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003676nucleic acid binding ----
    GO:0003677DNA binding IEA--
    GO:0004386helicase activity IEA--
    GO:0005515protein binding IPI16554032
    GO:0005524ATP binding IEA--
         
    Find genes that share ontologies with CHD9           About GenesLikeMe


    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for CHD9
       inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for CHD9

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for CHD9
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for CHD9

    miRNA
    Products:
        
    miRTarBase miRNAs that target CHD9:
    hsa-mir-7-5p (MIRT025670), hsa-mir-210-3p (MIRT003181), hsa-let-7e-5p (MIRT051555), hsa-mir-26b-5p (MIRT028901), hsa-mir-155-5p (MIRT020560)

    Block miRNA regulation of human, mouse, rat CHD9 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate CHD9 (see all 140):
    hsa-miR-124* hsa-miR-376b hsa-miR-106a hsa-miR-519a hsa-miR-208b hsa-miR-376a* hsa-miR-92b hsa-miR-520b
    SwitchGear 3'UTR luciferase reporter plasmidCHD9 3' UTR sequence
    Inhib. RNA
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    OriGene RNAi products in human, mouse, rat for CHD9
    Predesigned siRNA for gene silencing in human, mouse, rat CHD9

    Gene Editing
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    DNA2.0 Custom Protein Engineering Service for CHD9

    Clone
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    OriGene clones in human, mouse for CHD9 (see all 5)
    OriGene ORF clones in mouse, rat for CHD9
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector: CHD9 (NM_025134)
    Browse Sino Biological Human cDNA Clones
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for CHD9
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat CHD9

    Cell Line
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    Browse ESI BIO Cell Lines and PureStem Progenitors for CHD9 
    In Situ Assay
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CHD9


    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    CHD9_HUMAN, Q3L8U1: Cytoplasm. Nucleus
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5
    cytosol3
    plasma membrane3
    peroxisome1

    Gene Ontology (GO): 3 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus ----
    GO:0005654nucleoplasm TAS--
    GO:0005737cytoplasm IEA--

    Find genes that share ontologies with CHD9           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    SuperPaths for CHD9 About   (see all 7)  
    See pathways by source

    SuperPathContained pathways About
    1Fatty acid, triacylglycerol, and ketone body metabolism
    Fatty acid, triacylglycerol, and ketone body metabolism0.65
    PPARA Activates Gene Expression0.63
    Regulation of Lipid Metabolism by Peroxisome proliferator-activated receptor alpha (PPARalpha)0.65
    Transcriptional Regulation of White Adipocyte Differentiation0.38
    2Circadian Repression of Expression by REV-ERBA
    Circadian Repression of Expression by REV-ERBA0.88
    YAP1- and WWTR1 (TAZ)-stimulated gene expression0.40
    RORA Activates Circadian Expression0.88
    3Regulation of Cholesterol Biosynthesis by SREBP (SREBF)
    Regulation of Cholesterol Biosynthesis by SREBP (SREBF)0.75
    Activation of Gene Expression by SREBP (SREBF)0.75
    4Circadian Clock
    Circadian Clock0.66
    BMAL1-CLOCK/NPAS2 Activates Circadian Expression0.66
    5Gene Expression
    Generic Transcription Pathway0.40
    Gene Expression0.40


    Find genes that share SuperPaths with CHD9           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways


    Selected Reactome Pathways for CHD9 (see all 10)
        Transcriptional regulation of white adipocyte differentiation
    Circadian Clock
    Transcriptional activation of mitochondrial biogenesis
    YAP1- and WWTR1 (TAZ)-stimulated gene expression
    Regulation of lipid metabolism by Peroxisome proliferator-activated receptor alpha (PPARalpha)


        Pathway & Disease-focused RT2 Profiler PCR Arrays including CHD9: 
              Epigenetic Chromatin Remodeling Factors in human mouse rat
              PPAR Targets in human mouse rat

    Interactions:

        Search GeneGlobe Interaction Network for CHD9

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for CHD9 (Q3L8U11, 3 ENSP000003815224) via UniProtKB, MINT, STRING, and/or I2D (see all 161)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    PPARAQ078691, 3, ENSP000002627354EBI-960730,EBI-78615 I2D: score=1 STRING: ENSP00000262735
    MED19A0JLT23, ENSP000003373404STRING: ENSP00000337340 I2D: score=1 
    NR3C1P041503, ENSP000002315094I2D: score=1 STRING: ENSP00000231509
    ESR1P033723, ENSP000002062494I2D: score=2 STRING: ENSP00000206249
    RXRAP197933, ENSP000004196924I2D: score=1 STRING: ENSP00000419692
    About this table

    Gene Ontology (GO): 5 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006351transcription, DNA-templated IEA--
    GO:0006355regulation of transcription, DNA-templated IEA--
    GO:0016568chromatin modification IEA--
    GO:0044255cellular lipid metabolic process TAS--
    GO:0044281small molecule metabolic process TAS--

    Find genes that share ontologies with CHD9           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for CHD9



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for CHD9 gene: 
    NM_025134.4  

    Unigene Clusters for CHD9:

    Chromodomain helicase DNA binding protein 9
    Hs.59159  [show with all ESTs], Hs.622347
    Unigene Representative Sequences: DQ333316, AY243504
    Selected Ensembl transcripts including schematic representations, and UCSC links where relevant (see all 20):
    ENST00000566029(uc002egy.3 uc002ehb.3 uc002ehf.3 uc010cbw.3)
    ENST00000561869 ENST00000565832 ENST00000564582 ENST00000564845 ENST00000563410
    ENST00000398510 ENST00000562785 ENST00000564255 ENST00000565803(uc002ehd.2)
    ENST00000569794 ENST00000565442 ENST00000562791 ENST00000569225(uc002ehe.1)
    ENST00000219084 ENST00000565119 ENST00000562806 ENST00000564600
    miRNA
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    Block miRNA regulation of human, mouse, rat CHD9 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate CHD9 (see all 140):
    hsa-miR-124* hsa-miR-376b hsa-miR-106a hsa-miR-519a hsa-miR-208b hsa-miR-376a* hsa-miR-92b hsa-miR-520b
    SwitchGear 3'UTR luciferase reporter plasmidCHD9 3' UTR sequence
    Inhib. RNA
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    OriGene RNAi products in human, mouse, rat for CHD9
    Predesigned siRNA for gene silencing in human, mouse, rat CHD9
    Clone
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    OriGene clones in human, mouse for CHD9 (see all 5)
    OriGene ORF clones in mouse, rat for CHD9
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector: CHD9 (NM_025134)
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for CHD9
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat CHD9
    Primer
    Products:
        
    OriGene qSTAR qPCR primer pairs in human, mouse for CHD9
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat CHD9
      QuantiTect SYBR Green Assays in human, mouse, rat CHD9
      QuantiFast Probe-based Assays in human, mouse, rat CHD9

    Additional mRNA sequence: AY243504.1 

    Selected DOTS entries (see all 25):

    DT.40234597  DT.451990  DT.100744035  DT.120682003  DT.100018802  DT.97763956  DT.95268432  DT.40296262 
    DT.100698940  DT.40237799  DT.304267  DT.91702075  DT.100684135  DT.100697831  DT.75136672  DT.86839773 
    DT.120682027  DT.40280710  DT.95268431  DT.97788608  DT.120681981  DT.120682081  DT.307234  DT.407404 

    Selected AceView cDNA sequences (see all 240):

    AA451902 AI086081 AL600124 BX115889 NM_025134 AA328576 AA427584 AB002306 
    AW467652 BQ082952 BC022889 AI913162 CB164376 BC033770 AI962541 AL712926 
    BC027491 AA858328 BF794256 R24637 AI478531 AL693511 AX747409 BM477038 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for CHD9 (see all 10)    About this scheme

    ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5a · 5b · 5c ^ 6 ^ 7a · 7b ^ 8 ^ 9a · 9b ^ 10 ^ 11 ^ 12a · 12b ^ 13 ^ 14 ^ 15 ^ 16 ^ 17a · 17b ^ 18 ^ 19a · 19b ^
    SP1:                                                                                                                                                            
    SP2:                                                                                                  -                                                         
    SP3:                                                                                                                                                            
    SP4:                                                                                                                                                            
    SP5:                                                  -                                                                                                         

    ExUns: 20 ^ 21 ^ 22 ^ 23a · 23b ^ 24 ^ 25 ^ 26 ^ 27 ^ 28 ^ 29 ^ 30a · 30b ^ 31 ^ 32 ^ 33 ^ 34 ^ 35 ^ 36a · 36b ^ 37
    SP1:                                                  -     -                                               -                     
    SP2:                                                                                                                              
    SP3:                                                                                                                              
    SP4:                                                                                                                              
    SP5:                                                                                                                              


    ECgene alternative splicing isoforms for CHD9

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    CHD9 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: CAAATATGGT
    CHD9 Expression
    About this image

    CHD9 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    CHD9 Protein Expression

    SOURCE GeneReport for Unigene clusters: Hs.59159 Hs.622347

    UniProtKB/Swiss-Prot: CHD9_HUMAN, Q3L8U1
    Tissue specificity: Widely expressed at low levels. In bone marrow, expression is restricted to osteoprogenitor
    cells adjacent to mature osteoblasts

        Pathway & Disease-focused RT2 Profiler PCR Arrays including CHD9: 
              Epigenetic Chromatin Remodeling Factors in human mouse rat
              PPAR Targets in human mouse rat

    Primer
    Products:
    OriGene qSTAR qPCR primer pairs in human, mouse for CHD9
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat CHD9
    QuantiTect SYBR Green Assays in human, mouse, rat CHD9
    QuantiFast Probe-based Assays in human, mouse, rat CHD9
    In Situ
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CHD9

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of animals.

    Orthologs for CHD9 gene from Selected species (see all 12)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Chd91 , 5 chromodomain helicase DNA binding protein 91, 5 87.14(n)1
    91.07(a)1
      8 (44.25 cM)5
    1091511  NM_177224.21  NP_796198.11 
     908288355 
    chicken
    (Gallus gallus)
    Aves CHD91 chromodomain helicase DNA binding protein 9 80.84(n)
    85.94(a)
      415722  XM_414088.4  XP_414088.3 
    lizard
    (Anolis carolinensis)
    Reptilia CHD96
    chromodomain helicase DNA binding protein 9
    81(a)
    1 ↔ 1
    LGc(363118-428314)
    zebrafish
    (Danio rerio)
    Actinopterygii chd91 chromodomain helicase DNA binding protein 9 62.22(n)
    66.59(a)
      572355  XM_005169014.1  XP_005169071.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta kis6
    kismet
    19(a)
    1 → many
    2L(210735-250823)
    worm
    (Caenorhabditis elegans)
    Secernentea chd-76
    Protein CHD-7 (chd-7) mRNA, complete cds
    27(a)
    1 → many
    I(4685868-4698575) WBGene00007053


    ENSEMBL Gene Tree for CHD9 (if available)
    TreeFam Gene Tree for CHD9 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for CHD9 gene
    CHD62  CHD52  CHD42  CHD12  CHD72  CHD82  CHD32  CHD22  
    11 SIMAP similar genes for CHD9 using alignment to 10 protein entries:     CHD9_HUMAN (see all proteins):
    CHD2    CHD8    CHD7    CHD6    SMARCA5    CHD5
    DKFZp434K213    DKFZp434P202    CHD1L    SMARCA1    HELLS

    Find genes that share paralogs with CHD9           About GenesLikeMe



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for CHD9 (see all 4954)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 16 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs129257431,2
    A--53086961(+) ctgctC/Tctcct 1 -- us2k10--------
    rs129212741,2
    A--53086967(+) ctcctC/Gctctt 1 -- us2k10--------
    rs129257561,2
    A--53086974(+) tcttcC/Ttcctc 1 -- us2k10--------
    rs287519231,2
    --53087168(+) CTCCTC/GCTGCT 1 -- us2k10--------
    rs106813841,2
    C--53087173(+) CTCCTCCT/-GCTCC 1 -- cds11Minor allele frequency- -:0.00NA 2
    rs3688439171,2
    C--53087183(+) CTCCTC/GCTCCT 1 -- us2k10--------
    rs133318311,2
    C,F--53087196(+) tcctcC/Tttctc 1 -- us2k14Minor allele frequency- T:0.06WA NA EA 360
    rs1904198471,2
    --53087215(+) CCTCCC/TTGTCC 1 -- us2k10--------
    rs1912385721,2
    --53087244(+) CACTTC/TGACCA 1 -- us2k10--------
    rs80550631,2
    A,H--53087294(+) CACACT/ACACAC 1 -- us2k14Minor allele frequency- A:0.00NS EA 418

    HapMap Linkage Disequilibrium report for CHD9 (53088945 - 53338945 bp, first 250kb of CHD9)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for CHD9 (see all 11):    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2671644CNV Deletion23128226
    esv1370771CNV Insertion17803354
    nsv510419CNV Loss20534489
    nsv833232CNV Loss17160897
    nsv9443CNV Loss18304495
    nsv827652CNV Loss20364138
    nsv906665CNV Loss21882294
    esv21460CNV Loss19812545
    nsv906666CNV Loss21882294
    nsv483048CNV Gain15286789

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing CHD9
    DNA2.0 Custom Variant and Variant Library Synthesis for CHD9

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    Find genes that share disorders with CHD9           About GenesLikeMe

    Genetic Association Database (GAD): CHD9
    Human Genome Epidemiology (HuGE) Navigator: CHD9 (1 document)

    Export disorders for CHD9 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for CHD9 gene, integrated from 10 sources (see all 24):
    (articles sorted by number of sources associating them with CHD9)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Prediction of the coding sequences of unidentified human genes. VII. The complete sequences of 100 new cDNA clones from brain which can code for large proteins in vitro. (PubMed id 9205841)1, 2, 3 Nagase T.... Ohara O. (DNA Res. 1997)
    2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)1, 4 Rose J.E....Uhl G.R. (Mol. Med. 2010)
    3. PRIC320, a transcription coactivator, isolated from peroxisome proliferator-binding protein complex. (PubMed id 16554032)1, 2 Surapureddi S.... Reddy J.K. (Biochem. Biophys. Res. Commun. 2006)
    4. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PubMed id 17081983)1, 2 Olsen J.V....Mann M. (Cell 2006)
    5. Characterization and functional analysis of CReMM, a novel chromodomain helicase DNA-binding protein. (PubMed id 16095617)1, 2 Shur I. and Benayahu D. (J. Mol. Biol. 2005)
    6. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    7. Gene expression profiling in the human hypothalamus-pituitary-adrenal axis and full-length cDNA cloning. (PubMed id 10931946)1, 2 Hu R.-M.... Chen J.-L. (Proc. Natl. Acad. Sci. U.S.A. 2000)
    8. The SOX2-interactome in brain cancer cells identifies the requirement of MSI2 and USP9X for the growth of brain tumor cells. (PubMed id 23667531)1 Cox J.L....Rizzino A. (PLoS ONE 2013)
    9. Multiethnic meta-analysis of genome-wide association studies in &gt;100 000 subjects identifies 23 fibrinogen-associated Loci but no strong evidence of a causal association between circulating fibrinogen and cardiovascular disease. (PubMed id 23969696)1 Sabater-Lleal M....O'Donnell C.J. (Circulation 2013)
    10. Mass spectrometric analysis of lysine ubiquitylation reveals promiscuity at site level. (PubMed id 21139048)1 Danielsen J.M....Nielsen M.L. (amp 2011)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 80205 HGNC: 25701 AceView: CHD9 Ensembl:ENSG00000177200 euGenes: HUgn80205
    ECgene: CHD9 H-InvDB: CHD9

    (According to HUGE)
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    HUGE: KIAA0308

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for CHD9 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for CHD9 gene:
    Search GeneIP for patents involving CHD9

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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