Aliases for CHD9 Gene

Aliases for CHD9 Gene

  • Chromodomain Helicase DNA Binding Protein 9 2 3 5
  • Peroxisomal Proliferator-Activated Receptor A-Interacting Complex 320 KDa Protein 3 4
  • PPAR-Alpha-Interacting Complex Protein 320 KDa 3 4
  • Chromodomain-Helicase-DNA-Binding Protein 9 3 4
  • Chromatin-Related Mesenchymal Modulator 3 4
  • ATP-Dependent Helicase CHD9 3 4
  • Kismet Homolog 2 3 4
  • PRIC320 3 4
  • CHD-9 3 4
  • CReMM 3 4
  • KISH2 3 4
  • PPAR{Gamma}-Interacting Cofactor 320 KDa 3
  • Chromatin Remodeling Factor CHROM1 3
  • Chromatin-Remodeling Factor CHROM1 4
  • Ciprofibrate Bound Protein P240 3
  • Proteinx0008 3
  • EC 3.6.4.12 4
  • KIAA0308 4
  • EC 3.6.1 52
  • AD013 3

External Ids for CHD9 Gene

Previous GeneCards Identifiers for CHD9 Gene

  • GC16P051646
  • GC16P051747
  • GC16P038976

Summaries for CHD9 Gene

GeneCards Summary for CHD9 Gene

CHD9 (Chromodomain Helicase DNA Binding Protein 9) is a Protein Coding gene. Diseases associated with CHD9 include Charge Syndrome and Brain Cancer. Among its related pathways are Regulation of lipid metabolism by Peroxisome proliferator-activated receptor alpha (PPARalpha) and Gene Expression. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and helicase activity. An important paralog of this gene is CHD7.

UniProtKB/Swiss-Prot Summary for CHD9 Gene

  • 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

Additional gene information for CHD9 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for CHD9 Gene

Genomics for CHD9 Gene

GeneHancer (GH) Regulatory Elements for CHD9 Gene

Promoters and enhancers for CHD9 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH16J053129 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 500.2 +76.0 76023 4 EP300 HNRNPK ZBTB40 ZNF217 CTCF NRF1 POLR2G SP1 ZFX POLR2A CHD9 ENSG00000261291 piR-38051-115 RF00017-2074
GH16J053054 Promoter/Enhancer 2.4 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 512.2 +0.8 765 3.4 CTCF NRF1 TCF12 MYC POLR2G USF1 GTF2E2 TEAD4 ZFX ZIC2 CHD9 lnc-RBL2-7 RBL2 piR-40250-007
GH16J053097 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 511.9 +44.3 44329 3.8 ZNF217 SIN3A TCF12 POLR2G USF1 NCOR1 JUND FOS ZNF10 EP300 CHD9 RF00017-2073 piR-38051-115 lnc-RBL2-7
GH16J053051 Promoter/Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 45.2 -2.2 -2194 2 ZNF300 POLR2G NCOR1 RBAK NONO JUND FOS ZNF10 ZBTB5 POLR2A ENSG00000277639 LOC105371267 CHD9 RBL2 RPGRIP1L ENSG00000261056 LOC100128523
GH16J053500 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 22.5 +448.3 448274 4.9 EP300 FOXK2 ZBTB40 SIN3A NRF1 POLR2G SP1 NCOR1 PHF8 FOS AKTIP lnc-RPGRIP1L-3 RBL2 CHD9 ENSG00000261056 piR-58834
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CHD9 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for CHD9

Top Transcription factor binding sites by QIAGEN in the CHD9 gene promoter:
  • AML1a
  • C/EBPalpha
  • FAC1
  • GATA-1
  • p53
  • Pax-4a
  • Pax-5
  • STAT1
  • STAT3
  • STAT5A

Genomic Locations for CHD9 Gene

Genomic Locations for CHD9 Gene
chr16:53,054,998-53,329,150
(GRCh38/hg38)
Size:
274,153 bases
Orientation:
Plus strand
chr16:53,088,945-53,363,062
(GRCh37/hg19)
Size:
274,118 bases
Orientation:
Plus strand

Genomic View for CHD9 Gene

Genes around CHD9 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CHD9 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CHD9 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CHD9 Gene

Proteins for CHD9 Gene

  • Protein details for CHD9 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q3L8U1-CHD9_HUMAN
    Recommended name:
    Chromodomain-helicase-DNA-binding protein 9
    Protein Accession:
    Q3L8U1
    Secondary Accessions:
    • B2RTU2
    • B9ZVQ0
    • O15025
    • Q1WF12
    • Q6DTK9
    • Q9H9V7
    • Q9UHM2

    Protein attributes for CHD9 Gene

    Size:
    2897 amino acids
    Molecular mass:
    326022 Da
    Quaternary structure:
    • Interacts with PPARA. Probably interacts with ESR1 and NR1I3.
    SequenceCaution:
    • Sequence=AAF24170.1; Type=Erroneous translation; Note=Wrong choice of frame.; Evidence={ECO:0000305}; Sequence=BAB14112.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for CHD9 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for CHD9 Gene

Selected DME Specific Peptides for CHD9 Gene

Q3L8U1:
  • VLIFSQMVR
  • PKQKRHRCRNPNKLD
  • PVPRGRKGK
  • GAEEKIL
  • ILKPMMLRRLK
  • IFDSDWNP
  • KASFVAS
  • RRGRRKNVEG
  • MCRRVCR
  • DEMGLGKT
  • SRQMIQQYEM
  • AVLQSMSG
  • FCEEDIDQIL
  • TITIESEG
  • DFYRVVSTFG
  • DEAHRLK
  • TGTPLQN
  • ETIIEVELT
  • KDKRIQQKIKRFK
  • LDILEDY
  • ECFRVEKNLL
  • MGLGKTIQ
  • DSDWNPQ
  • QKKYYRAILE
  • QNLQNLQSLQ
  • RADPALCFLE
  • ITTFEMIL
  • FNPDYVE
  • SRRGRRPKS
  • MLRRLKEDV
  • AGGLGINL
  • RCHRIGQ
  • KAVKVYRL
  • KQEKANRI
  • YLVKWCSLPYE
  • WPKDRVMINRLD
  • PITEERASRTLYR
  • CNKVLLRVRMLY
  • NWEREFRTWT
  • LLIGVFK
  • NTMMELRKCCNHPYLI
  • EDPEYKP
  • QQRWTRRE

Post-translational modifications for CHD9 Gene

Domains & Families for CHD9 Gene

Gene Families for CHD9 Gene

Human Protein Atlas (HPA):
  • Enzymes
  • Plasma proteins
  • Predicted intracellular proteins

Protein Domains for CHD9 Gene

Blocks:
  • Chromo domain
  • SNF2 related domain
  • Domain in transcription and CHROMO domain helicase
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for CHD9 Gene

GenScript: Design optimal peptide antigens:
  • CHD9 protein (B7ZML1_HUMAN)
  • Peroxisomal proliferator-activated receptor A-interacting complex 320 kDa protein (CHD9_HUMAN)
  • CHD9 protein (Q8N4Q2_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q3L8U1

UniProtKB/Swiss-Prot:

CHD9_HUMAN :
  • Belongs to the SNF2/RAD54 helicase family.
Family:
  • Belongs to the SNF2/RAD54 helicase family.
genes like me logo Genes that share domains with CHD9: view

Function for CHD9 Gene

Molecular function for CHD9 Gene

UniProtKB/Swiss-Prot 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).
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=ATP + H2O = ADP + H(+) + phosphate; Xref=Rhea:RHEA:13065, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616, ChEBI:CHEBI:43474, ChEBI:CHEBI:456216; EC=3.6.4.12;.

Enzyme Numbers (IUBMB) for CHD9 Gene

Phenotypes From GWAS Catalog for CHD9 Gene

Gene Ontology (GO) - Molecular Function for CHD9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0003678 DNA helicase activity IEA --
GO:0004386 helicase activity IEA --
GO:0005515 protein binding IEA --
GO:0005524 ATP binding IEA --
genes like me logo Genes that share ontologies with CHD9: view
genes like me logo Genes that share phenotypes with CHD9: view

Animal Models for CHD9 Gene

MGI Knock Outs for CHD9:
  • Chd9 Chd9<tm1a(EUCOMM)Wtsi>

Animal Model Products

CRISPR Products

Clone Products

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for CHD9 Gene

Localization for CHD9 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CHD9 Gene

Cytoplasm. Nucleus.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CHD9 gene
Compartment Confidence
nucleus 5
cytosol 3
plasma membrane 2
extracellular 1
cytoskeleton 1
peroxisome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Plasma membrane (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for CHD9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm TAS --
GO:0005737 cytoplasm IEA --
genes like me logo Genes that share ontologies with CHD9: view

Pathways & Interactions for CHD9 Gene

genes like me logo Genes that share pathways with CHD9: view

Gene Ontology (GO) - Biological Process for CHD9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006325 chromatin organization IEA --
GO:0019216 regulation of lipid metabolic process TAS --
GO:0032508 DNA duplex unwinding IEA --
genes like me logo Genes that share ontologies with CHD9: view

No data available for SIGNOR curated interactions for CHD9 Gene

Drugs & Compounds for CHD9 Gene

(3) Drugs for CHD9 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Phosphoric acid Approved Pharma 0
Water Approved Pharma 0
ATP Investigational Nutra Agonist, Activator, Full agonist, Antagonist, Pore Blocker, Potentiation 0

(1) Additional Compounds for CHD9 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
ADP
  • 5'-Adenylphosphoric acid
  • Adenosine 5'-diphosphate
  • ADENOSINE-5'-diphosphATE
  • H3ADP
  • 5'-Adenylphosphate
Full agonist, Agonist, Partial agonist, Antagonist, Gating inhibitor 58-64-0
genes like me logo Genes that share compounds with CHD9: view

Transcripts for CHD9 Gene

mRNA/cDNA for CHD9 Gene

7 REFSEQ mRNAs :
21 NCBI additional mRNA sequence :
21 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for CHD9 Gene

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: -
SP6:
SP7:
SP8:
SP9: - - -
SP10: - -

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:
SP6:
SP7:
SP8:
SP9:
SP10:

Relevant External Links for CHD9 Gene

GeneLoc Exon Structure for
CHD9

Expression for CHD9 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for CHD9 Gene

Protein differential expression in normal tissues from HIPED for CHD9 Gene

This gene is overexpressed in Pancreatic juice (23.9), Heart (11.9), Prostate (10.0), Retina (8.5), and Peripheral blood mononuclear cells (6.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for CHD9 Gene



Protein tissue co-expression partners for CHD9 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for CHD9

SOURCE GeneReport for Unigene cluster for CHD9 Gene:

Hs.59159

mRNA Expression by UniProt/SwissProt for CHD9 Gene:

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

Evidence on tissue expression from TISSUES for CHD9 Gene

  • Lung(4.8)
  • Nervous system(4.7)
  • Bone(4.5)
  • Adrenal gland(4.2)
  • Kidney(2)
genes like me logo Genes that share expression patterns with CHD9: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for CHD9 Gene

Orthologs for CHD9 Gene

This gene was present in the common ancestor of animals.

Orthologs for CHD9 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia CHD9 31 30
  • 99.6 (n)
OneToOne
dog
(Canis familiaris)
Mammalia CHD9 31 30
  • 93.43 (n)
OneToOne
cow
(Bos Taurus)
Mammalia CHD9 31 30
  • 93.17 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia -- 31
  • 89 (a)
OneToMany
-- 31
  • 80 (a)
OneToMany
mouse
(Mus musculus)
Mammalia Chd9 17 31 30
  • 87.14 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia CHD9 31
  • 87 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Chd9 30
  • 82.95 (n)
chicken
(Gallus gallus)
Aves CHD9 31 30
  • 80.84 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia CHD9 31
  • 81 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii chd9 31 30
  • 62.22 (n)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta kis 31
  • 19 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea chd-7 31
  • 27 (a)
OneToMany
Species where no ortholog for CHD9 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)

Evolution for CHD9 Gene

ENSEMBL:
Gene Tree for CHD9 (if available)
TreeFam:
Gene Tree for CHD9 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CHD9: view image

Paralogs for CHD9 Gene

(11) SIMAP similar genes for CHD9 Gene using alignment to 10 proteins:

  • CHD9_HUMAN
  • B7ZML1_HUMAN
  • H3BRU9_HUMAN
  • H3BSP3_HUMAN
  • H3BTW3_HUMAN
  • H3BV31_HUMAN
  • I3L340_HUMAN
  • J3KRH9_HUMAN
  • J3KSW5_HUMAN
  • Q8N4Q2_HUMAN
genes like me logo Genes that share paralogs with CHD9: view

Variants for CHD9 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for CHD9 Gene

SNP ID Clinical significance and condition Chr 16 pos Variation AA Info Type
708120 Benign: not provided 53,324,329(+) A/G MISSENSE_VARIANT
rs6499548 - p.Asp2312Glu

Additional dbSNP identifiers (rs#s) for CHD9 Gene

Structural Variations from Database of Genomic Variants (DGV) for CHD9 Gene

Variant ID Type Subtype PubMed ID
dgv2979n100 CNV loss 25217958
dgv521e214 CNV loss 21293372
esv1370771 CNV insertion 17803354
esv21460 CNV loss 19812545
esv2671644 CNV deletion 23128226
esv3582202 CNV loss 25503493
esv3582203 CNV loss 25503493
esv3638643 CNV gain 21293372
nsv1063647 CNV loss 25217958
nsv1066719 CNV loss 25217958
nsv476217 CNV novel sequence insertion 20440878
nsv510419 OTHER sequence alteration 20534489
nsv572617 CNV loss 21841781
nsv827652 CNV loss 20364138
nsv833232 CNV loss 17160897
nsv833233 CNV gain 17160897
nsv9443 CNV loss 18304495

Variation tolerance for CHD9 Gene

Residual Variation Intolerance Score: 0.566% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 7.75; 83.22% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CHD9 Gene

Human Gene Mutation Database (HGMD)
CHD9
SNPedia medical, phenotypic, and genealogical associations of SNPs for
CHD9

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CHD9 Gene

Disorders for CHD9 Gene

MalaCards: The human disease database

(3) MalaCards diseases for CHD9 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
charge syndrome
  • hhs
brain cancer
  • adult brain tumor
coloboma of macula
  • agenesis of macula
- elite association - COSMIC cancer census association via MalaCards
Search CHD9 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for CHD9

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with CHD9: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CHD9 Gene

Publications for CHD9 Gene

  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. (PMID: 9205841) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 1997) 2 3 4 54
  2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 41 54
  3. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PMID: 17081983) Olsen JV … Mann M (Cell 2006) 3 4 54
  4. PRIC320, a transcription coactivator, isolated from peroxisome proliferator-binding protein complex. (PMID: 16554032) Surapureddi S … Reddy JK (Biochemical and biophysical research communications 2006) 3 4 54
  5. Characterization and functional analysis of CReMM, a novel chromodomain helicase DNA-binding protein. (PMID: 16095617) Shur I … Benayahu D (Journal of molecular biology 2005) 3 4 54

Products for CHD9 Gene

Sources for CHD9 Gene