Human Gene CHD9 (ENST00000566029.5) Description and Page Index
  Description: Homo sapiens chromodomain helicase DNA binding protein 9 (CHD9), transcript variant 2, mRNA. (from RefSeq NM_025134)
Gencode Transcript: ENST00000566029.5
Gencode Gene: ENSG00000177200.17
Transcript (Including UTRs)
   Position: hg38 chr16:53,055,033-53,329,150 Size: 274,118 Total Exon Count: 39 Strand: +
Coding Region
   Position: hg38 chr16:53,156,090-53,324,895 Size: 168,806 Coding Exon Count: 38 

Page IndexSequence and LinksUniProtKB CommentsCTDRNA-Seq ExpressionMicroarray Expression
RNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA DescriptionsPathways
Other NamesMethods
Data last updated: 2019-09-04

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr16:53,055,033-53,329,150)mRNA (may differ from genome)Protein (2881 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsHGNC
ReactomeStanford SOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Chromodomain-helicase-DNA-binding protein 9; Short=CHD-9; EC=; AltName: Full=ATP-dependent helicase CHD9; AltName: Full=Chromatin-related mesenchymal modulator; Short=CReMM; AltName: Full=Chromatin-remodeling factor CHROM1; AltName: Full=Kismet homolog 2; AltName: Full=PPAR-alpha-interacting complex protein 320 kDa; AltName: Full=Peroxisomal proliferator-activated receptor A-interacting complex 320 kDa protein;
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.
SUBUNIT: Interacts with PPARA. Probably interacts with ESR1 and NR1I3.
INTERACTION: Q07869:PPARA; NbExp=2; IntAct=EBI-960730, EBI-78615;
TISSUE SPECIFICITY: Widely expressed at low levels. In bone marrow, expression is restricted to osteoprogenitor cells adjacent to mature osteoblasts.
PTM: Phosphorylated on serine and tyrosine residues.
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.
SEQUENCE CAUTION: Sequence=AAF24170.1; Type=Erroneous translation; Note=Wrong choice of frame; Sequence=BAB14112.1; Type=Erroneous initiation;

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 6.68 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 211.63 RPKM

View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -56.90209-0.272 Picture PostScript Text
3' UTR -988.504255-0.232 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR006576 - BRK_domain
IPR023780 - Chromo_domain
IPR000953 - Chromo_domain/shadow
IPR016197 - Chromodomain-like
IPR014001 - Helicase_ATP-bd
IPR001650 - Helicase_C
IPR000330 - SNF2_N

Pfam Domains:
PF07533 - BRK domain
PF00385 - Chromo (CHRromatin Organisation MOdifier) domain
PF00271 - Helicase conserved C-terminal domain
PF00176 - SNF2 family N-terminal domain

ModBase Predicted Comparative 3D Structure on Q3L8U1
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
Protein SequenceProtein Sequence    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0003677 DNA binding
GO:0004386 helicase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016787 hydrolase activity
GO:0016817 hydrolase activity, acting on acid anhydrides

Biological Process:
GO:0006325 chromatin organization
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0019216 regulation of lipid metabolic process

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm

-  Descriptions from all associated GenBank mRNAs
  BC022889 - Homo sapiens chromodomain helicase DNA binding protein 9, mRNA (cDNA clone IMAGE:4615992), partial cds.
AY647157 - Homo sapiens KISH2 (KISH2) mRNA, complete cds.
AK092208 - Homo sapiens cDNA FLJ34889 fis, clone NT2NE2017397, weakly similar to Rattus norvegicus beta-catenin binding protein mRNA.
AX747409 - Sequence 934 from Patent EP1308459.
BC033770 - Homo sapiens chromodomain helicase DNA binding protein 9, mRNA (cDNA clone IMAGE:4338949), partial cds.
DQ333316 - Homo sapiens PRIC320 isoform 1 mRNA, complete cds.
AY243500 - Homo sapiens chromatin remodeling factor CHROM1 mRNA, complete cds; alternatively spliced.
BC140815 - Homo sapiens chromodomain helicase DNA binding protein 9, mRNA (cDNA clone MGC:176492 IMAGE:9021683), complete cds.
BC144622 - Homo sapiens chromodomain helicase DNA binding protein 9, mRNA (cDNA clone MGC:178170 IMAGE:9053153), complete cds.
AB002306 - Homo sapiens KIAA0308 mRNA, partial cds.
AY243501 - Homo sapiens chromatin remodeling factor CHROM2 mRNA, complete cds; alternatively spliced.
AK299045 - Homo sapiens cDNA FLJ57565 partial cds, highly similar to Chromodomain-helicase-DNA-binding protein 9 (EC 3.6.1.-).
BC027491 - Homo sapiens chromodomain helicase DNA binding protein 9, mRNA (cDNA clone IMAGE:3911222), partial cds.
JD394786 - Sequence 375810 from Patent EP1572962.
JD451250 - Sequence 432274 from Patent EP1572962.
CU689732 - Synthetic construct Homo sapiens gateway clone IMAGE:100017919 5' read CHD9 mRNA.
KJ903287 - Synthetic construct Homo sapiens clone ccsbBroadEn_12681 CHD9 gene, encodes complete protein.
JD314444 - Sequence 295468 from Patent EP1572962.
JD357514 - Sequence 338538 from Patent EP1572962.
JD521971 - Sequence 502995 from Patent EP1572962.
JD308553 - Sequence 289577 from Patent EP1572962.
JD138705 - Sequence 119729 from Patent EP1572962.
JD304001 - Sequence 285025 from Patent EP1572962.
JD248292 - Sequence 229316 from Patent EP1572962.
JD066999 - Sequence 48023 from Patent EP1572962.
JD301973 - Sequence 282997 from Patent EP1572962.
JD036508 - Sequence 17532 from Patent EP1572962.
AK022240 - Homo sapiens cDNA FLJ12178 fis, clone MAMMA1000731.
DQ059482 - Homo sapiens ciprofibrate bound protein p240 isoform PRIC320-2 mRNA, complete cds.
JD328148 - Sequence 309172 from Patent EP1572962.
AK022582 - Homo sapiens cDNA FLJ12520 fis, clone NT2RM2001823, weakly similar to CHD1 PROTEIN.
AB528593 - Synthetic construct DNA, clone: pF1KA0308, Homo sapiens CHD9 gene for chromodomain helicase DNA binding protein 9, without stop codon, in Flexi system.
AY243502 - Homo sapiens chromatin remodeling factor CHROM4 mRNA, partial sequence; alternatively spliced.
AY243504 - Homo sapiens chromatin remodeling factor CHROM3 mRNA, complete cds; alternatively spliced.
JD255732 - Sequence 236756 from Patent EP1572962.
JD425873 - Sequence 406897 from Patent EP1572962.
JD212185 - Sequence 193209 from Patent EP1572962.
JD295477 - Sequence 276501 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q3L8U1 (Reactome details) participates in the following event(s):

R-HSA-400143 Fatty acid ligands activate PPARA
R-HSA-400206 Regulation of lipid metabolism by Peroxisome proliferator-activated receptor alpha (PPARalpha)
R-HSA-556833 Metabolism of lipids
R-HSA-1430728 Metabolism

-  Other Names for This Gene
  Alternate Gene Symbols: AD-013, B2RTU2, B9ZVQ0, CHD9_HUMAN, KIAA0308, KISH2, NM_025134, O15025, PRIC320, Q1WF12, Q3L8U1, Q6DTK9, Q9H9V7, Q9UHM2, uc002egy.1, uc002egy.2, uc002egy.3, uc002egy.4, x0008
UCSC ID: uc002egy.4
RefSeq Accession: NM_025134
Protein: Q3L8U1 (aka CHD9_HUMAN)
CCDS: CCDS45485.1, CCDS76865.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.