Human Gene CHD1 (uc003knf.3) Description and Page Index
  Description: Homo sapiens chromodomain helicase DNA binding protein 1 (CHD1), mRNA.
RefSeq Summary (NM_001270): The CHD family of proteins is characterized by the presence of chromo (chromatin organization modifier) domains and SNF2-related helicase/ATPase domains. CHD genes alter gene expression possibly by modification of chromatin structure thus altering access of the transcriptional apparatus to its chromosomal DNA template. [provided by RefSeq, Jul 2008]. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: SRR1660805.74817.1, SRR1803613.186631.1 [ECO:0000332] ##Evidence-Data-END## ##RefSeq-Attributes-START## RefSeq Select criteria :: based on conservation, expression ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr5:98,190,908-98,262,238 Size: 71,331 Total Exon Count: 35 Strand: -
Coding Region
   Position: hg19 chr5:98,192,084-98,262,090 Size: 70,007 Coding Exon Count: 35 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-15

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:98,190,908-98,262,238)mRNA (may differ from genome)Protein (1710 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeStanford SOURCETreefam
UniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: CHD1_HUMAN
DESCRIPTION: RecName: Full=Chromodomain-helicase-DNA-binding protein 1; Short=CHD-1; EC=3.6.4.12; AltName: Full=ATP-dependent helicase CHD1;
FUNCTION: ATP-dependent chromatin-remodeling factor which functions as substrate recognition component of the transcription regulatory histone acetylation (HAT) complex SAGA. Regulates polymerase II transcription. Also required for efficient transcription by RNA polymerase I, and more specifically the polymerase I transcription termination step. Regulates negatively DNA replication. Not only involved in transcription-related chromatin-remodeling, but also required to maintain a specific chromatin configuration across the genome. Is also associated with histone deacetylase (HDAC) activity (By similarity). Required for the bridging of SNF2, the FACT complex, the PAF complex as well as the U2 snRNP complex to H3K4me3. Functions to modulate the efficiency of pre-mRNA splicing in part through physical bridging of spliceosomal components to H3K4me3. Required for maintaining open chromatin and pluripotency in embryonic stem cells.
CATALYTIC ACTIVITY: ATP + H(2)O = ADP + phosphate.
SUBUNIT: Component of the SAGA complex (By similarity). Interacts with BCLAF1, NCoR, SRP20 and SAFB (By similarity). Specifically interacts with methylated H3K4me2 and H3K4me3. Interacts with the FACT complex, the PAF complex and the U2 snRNP. Interacts directly with PAF1, SFA3A1, SFA3A2, SFA3A3, SNF2 and SSRP1.
INTERACTION: B2BUF1:NS1 (xeno); NbExp=3; IntAct=EBI-1560858, EBI-4291940;
SUBCELLULAR LOCATION: Nucleus. Cytoplasm (By similarity). Note=Is released into the cytoplasm when cells enter mitosis and is reincorporated into chromatin during telophase-cytokinesis (By similarity).
DOMAIN: The 2 chromodomains are involved in the binding to the histone H3 methyllysine at position 4 (H3K4me3).
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.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): CHD1
CDC HuGE Published Literature: CHD1
Positive Disease Associations: Attention Deficit Disorder with Hyperactivity
Related Studies:
  1. Attention Deficit Disorder with Hyperactivity
    , , . [PubMed 0]

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

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 14.71 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 315.12 RPKM



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

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -35.60148-0.241 Picture PostScript Text
3' UTR -247.221176-0.210 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
IPR023780 - Chromo_domain
IPR000953 - Chromo_domain/shadow
IPR016197 - Chromodomain-like
IPR023779 - Chromodomain_CS
IPR025260 - DUF4208
IPR014001 - Helicase_ATP-bd
IPR001650 - Helicase_C
IPR000330 - SNF2_N

Pfam Domains:
PF00176 - SNF2 family N-terminal domain
PF00271 - Helicase conserved C-terminal domain
PF00385 - Chromo (CHRromatin Organisation MOdifier) domain
PF04851 - Type III restriction enzyme, res subunit
PF13907 - Domain of unknown function (DUF4208)

SCOP Domains:
46689 - Homeodomain-like
54160 - Chromo domain-like
52540 - P-loop containing nucleoside triphosphate hydrolases

Protein Data Bank (PDB) 3-D Structure
MuPIT help

2B2T
- X-ray MuPIT

2B2U
- X-ray MuPIT

2B2V
- X-ray MuPIT
To conserve bandwidth, only the images from the first 3 structures are shown.
2B2W - X-ray MuPIT 2B2Y - X-ray MuPIT 4B4C - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on O14646
FrontTopSide
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
No orthologNo orthologGenome BrowserNo orthologGenome BrowserNo ortholog
Gene Details   Gene Details 
Gene Sorter   Gene Sorter 
  Ensembl WormBase 
  Protein Sequence Protein Sequence 
  Alignment Alignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0003677 DNA binding
GO:0004003 ATP-dependent DNA helicase activity
GO:0004386 helicase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016787 hydrolase activity
GO:0035064 methylated histone binding

Biological Process:
GO:0006325 chromatin organization
GO:0006338 chromatin remodeling
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0016569 covalent chromatin modification
GO:0032508 DNA duplex unwinding
GO:0043923 positive regulation by host of viral transcription

Cellular Component:
GO:0001650 fibrillar center
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm


-  Descriptions from all associated GenBank mRNAs
  KJ901338 - Synthetic construct Homo sapiens clone ccsbBroadEn_10732 CHD1 gene, encodes complete protein.
BX648767 - Homo sapiens mRNA; cDNA DKFZp686E2337 (from clone DKFZp686E2337).
AK094871 - Homo sapiens cDNA FLJ37552 fis, clone BRCAN2028319, highly similar to Chromo domain-helicase-DNA-binding protein 1 (EC 3.6.1.-).
AF006513 - Homo sapiens CHD1 mRNA, complete cds.
JD537732 - Sequence 518756 from Patent EP1572962.
BC117134 - Homo sapiens chromodomain helicase DNA binding protein 1, mRNA (cDNA clone MGC:150743 IMAGE:40125685), complete cds.
JD082314 - Sequence 63338 from Patent EP1572962.
JD550894 - Sequence 531918 from Patent EP1572962.
JD136694 - Sequence 117718 from Patent EP1572962.
JD325680 - Sequence 306704 from Patent EP1572962.
BC054860 - Homo sapiens chromodomain helicase DNA binding protein 1, mRNA (cDNA clone IMAGE:6617223), partial cds.

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

Protein O14646 (Reactome details) participates in the following event(s):

R-HSA-9018519 Estrogen-dependent gene expression
R-HSA-8939211 ESR-mediated signaling
R-HSA-9006931 Signaling by Nuclear Receptors
R-HSA-162582 Signal Transduction

-  Other Names for This Gene
  Alternate Gene Symbols: CHD1_HUMAN, NM_001270, NP_001261, O14646, Q17RZ3
UCSC ID: uc003knf.3
RefSeq Accession: NM_001270
Protein: O14646 (aka CHD1_HUMAN)
CCDS: CCDS34204.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001270.2
exon count: 35CDS single in 3' UTR: no RNA size: 6457
ORF size: 5133CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 10466.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

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