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0CHD4_HUMAN*   SwissProt (?) | Description Local Annotation Link Reference
General Information
NameCHD4
DescriptionChromodomain helicase-dna-binding protein 4 (chd-4) (mi-2 autoantigen 218 kda protein) (mi2-beta).
SpeciesHomo sapiens (NCBI taxonomy ID: 9606)
GO0004003 ATP-dependent DNA helicase activity (TAS)
0003677 DNA binding (TAS)
0005515 protein binding (IPI)
0008270 zinc ion binding (TAS)
0007001 chromosome organization and biogenesis (sen... (TAS)
0006357 regulation of transcription from RNA polyme... (TAS)

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schematic display of those terms with internal associations, click the node and browse the corresponding GO term
Domain Architecture (Details)
InterPro domains unassigned to SynO:
The CHDCT2 C-terminal domain is found in PHD/RING fingers and chromo domain-associated CHD-like helicases .
  IPR012957:CHD, C-terminal 2
This domain is found in proteins involved in a variety of processes including transcription regulation (e.g..NF2.TH1.rahma.OT1).NA repair (e.g..RCC6.AD16.AD5).NA recombination (e.g..AD54).nd chromatin unwinding (e.g..SWI) as well as a variety of other proteins with little functional information (e.g..odestar.TL1) . SNF2 functions as the ATPase component of the SNF2/SWI multisubunit complex.hich utilises energy derived from ATP hydrolysis to disrupt histone-DNA interactions.esulting in the increased accessibility of DNA to transcription factors.Proteins that contain this domain appear to be distantly related to theDEAX box helicases .oweverno helicase activity has ever been demonstrated for these proteins.
  IPR000330:SNF2-related
This entry represents several eukaryotic domains of unknown function.hich are present in chromodomain helicase DNA binding proteins. This domain is often found in conjunction with .nd .
  IPR009462:Protein of unknown function DUF1086
The CHD N-terminal domain is found in PHD/RING fingers and chromo domain-associated helicases .
  IPR012958:CHD, N-terminal
This entry is found in DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism.ncluding nuclear transcription.re mRNA splicing.ibosome biogenesis.ucleocytoplasmic transport.ranslation.NA decay and organellar gene expression.
  IPR014001:DEAD-like helicases, N-terminal
This is a group of proteins of unknown function.
  IPR009463:Protein of unknown function DUF1087
The domain.hich defines this group of proteins is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit.ut an integral part of the helicase.The eukaryotic translation initiation factor 4A (eIF4A) is a member of the DEA(D/H)-box RNA helicase family This is a diverse group of proteins that couples an ATPase activity to RNA binding and unwinding. The structure of the carboxyl-terminal domain of eIF4A has been determined to 1.75 A resolution; it has a parallel alpha-beta topology that superimposes.ith minor variations.n the structures and conserved motifs of the equivalent domain in other.istantly related helicases .
  IPR001650:Helicase, C-terminal
The homeodomain (PHD) finger .s a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of.ut distinct from the C3HC4 type RING finger.The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively.he interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain.he PHD finger is thought to bind two zinc ions.
  IPR001965:Zinc finger, PHD-type
The CHROMO (CHRromatin Organization MOdifier) domain .s a conserved region of around 60 amino acids.riginally identified in Drosophila modifiers of variegation.These are proteins that alter the structure of chromatin to the condensed morphology of heterochromatin. cytologically visible condition where gene expression is repressed. In one of these proteins.olycomb.he chromo domain has been shown to be important for chromatin targeting. Proteins that contain a chromo domain appear to fall into 3 classes. The first class includes proteins having an N-terminal chromo domain followed by a region termed the chromo shadow domain .g. Drosophila and human heterochromatin protein Su(var)205 (HP1). The second class includes proteins with a single chromo domain.g. Drosophila protein Polycomb (Pc); mammalian modifier 3; human Mi-2 autoantigenand and several yeast and Caenorhabditis elegans hypothetical proteins. In the third class paired tandem chromo domains are found.g. in mammalian DNA-binding/helicase proteins CHD-1 to CHD-4 and yeast protein CHD1.
  IPR000953:Chromo
Quality control of intracellular proteins is essential for cellular homeostasis. Molecular chaperones recognise and contribute to the refolding of misfolded or unfolded proteins.hereas the ubiquitin-proteasome system mediates the degradation of such abnormal proteins. Ubiquitin-protein ligases (E3s) determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently.owever.-box proteins.hich contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans.ave been identified as a new type of E3 .The RING-finger is a specialised type of Zn-finger of 40 to 60 residues that binds two atoms of zinc.nd is probably involved in mediating protein-protein interactions. . There are two different variants.he C3HC4-type and a C3H2C3-type.hich is clearly related despite the different cysteine/histidine pattern. The latter type is sometimes referred to as RING-H2 finger. The RING domain is a protein interaction domain which has been implicated in a range of diverse biological processes.E3 ubiquitin-protein ligase activity is intrinsic to the RING domain ofc-Cbl and is likely to be a general function of this domain; Various RINGfingers exhibit binding to E2 ubiquitin-conjugating enzymes (Ubcs) .Several 3D-structures for RING-fingers are known . The 3D structure of the zinc ligation system is unique to the RING domain and is referred to as the cross-brace motif. The spacing of the cysteines in such a domain is C-x(2)-C-x(9 to 39)-C-x(1 to 3)-H-x(2 to 3)-C-x(2)-C-x(4 to 48)-C-x(2)-C. Metal ligand pairs one and three co-ordinate to bind one zinc ion.hilst pairs two and four bind the second.s illustrated in the following schematic representation:Note that in the older literature.ome RING-fingers are denoted as LIM-domains. The LIM-domain Zn-finger is a fundamentally different family.lbeit with similar Cys-spacing (see ).
  IPR001841:Zinc finger, RING-type
High mobility group (HMG) box domains are involved in binding DNA.nd may be involved in protein-protein interactions as well. The structure of the HMG-box domain consists of three helices in an irregular array. HMG-box domains are found in one or more copies in HMG-box proteins.hich form a large.iverse family involved in the regulation of DNA-dependent processes such as transcription.eplication.nd strand repair.ll of which require the bending and unwinding of chromatin. Many of these proteins are regulators of gene expression. HMG-box proteins are found in a variety of eukaryotic organisms.nd can be broadly divided into two groups.ased on sequence-dependent and sequence-independent DNA recognition; the former usually contain one HMG-box motif.hile the latter can contain multiple HMG-box motifs. HMG-box domains can be found in single or multiple copies in the following protein classes: HMG1 and HMG2 non-histone components of chromatin; SRY (sex determining region Y protein) involved in differential gonadogenesis; the SOX family of transcription factors ; sequence-specific LEF1 (lymphoid enhancer binding factor 1) and TCF-1 (T-cell factor 1) involved in regulation of organogenesis and thymocyte differentiation ; structure-specific recognition protein SSRP involved in transcription and replication; MTF1 mitochondrial transcription factor; nucleolar transcription factors UBF 1/2 (upstream binding factor) involved in transcription by RNA polymerase I; Abf2 yeast ARS-binding factor ; yeast transcription factors lxr1.ox1.hp6b and Spp41; mating type proteins (MAT) involved in the sexual reproduction of fungi ; and the YABBY plant-specific transcription factors. The SSF signature in this entry is currently under review. Please be aware that some of the protein hits may be false positives.
  IPR009071:High mobility group box
This family includes the beta (or middle) subunit of the oligomeric (alpha2beta2gamma2) diol dehydratases (DDH) and glycerol dehydratases (GDH).hich are enzymes produced by some enterobacteria.s well as the beta subunit of the tetrameric (alpha2beta2) glycerol dehydratase reactivase.hich removes damaged coenzyme B12 from GDH that has suffered mechanism-based inactivation . The beta subunit of GDH reactivase resembles that of GDH and DDH.isplaying a three-layer alpha/beta/alpha fold.xcept that the reactivase subunit lacks some B12-binding elements.The SSF signature in this entry is currently under review. Please be aware that some of the protein hits may be false positives.
  IPR010254:B12-dependent dehydratases, beta subunit
Zinc finger domains (ZnFs) are common.elatively small protein motifs that fold around one or more zinc ions. In addition to their role as a DNA-binding module.nFs have recently been shown to mediate protein:protein and protein:lipid interactions. There are at least 14 different classes of Zn fingers.hich differ in the nature and arrangement of their zinc-binding residues .The FYVE zinc finger domain is conserved from yeast to man.nd is named after four proteins that it has been found in: Fab1.OTB/ZK632.12.ac1.nd EEA1. It functions in the membrane recruitment of cytosolic proteins by binding to phosphatidylinositol 3-phosphate (PI3P).hich is found mainly on endosomes .The plant homeodomain (PHD) zinc finger domain has a C4HC3-type motif.nd is widely distributed in eukaryotes.eing found in many chromatin regulatory factors .Both the FYVE and the PHD zinc finger motifs display strikingly similar dimetal(zinc)-bound alpha+beta folds.The SSF signature in this entry is currently under review. Please be aware that some of the protein hits may be false positives.
  IPR011011:Zinc finger, FYVE/PHD-type
IPR012957:CHDCT2 
Evalue:-129.10237121582 
Location:1724-1896IPR000330:SNF2_N 
Evalue:-101.769554138184 
Location:729-1025IPR009462:DUF1086 
Evalue:-99.5686340332031 
Location:1366-1523IPR012958:CHDNT 
Evalue:-37.0969085693359 
Location:163-217IPR009463:DUF1087 
Evalue:-31.2006587982178 
Location:1288-1353IPR001650:Helicase_C 
Evalue:-28.0087738037109 
Location:1085-1164IPR001965:PHD 
Evalue:-18.7447280883789 
Location:451-496IPR001965:PHD 
Evalue:-18.6382713317871 
Location:372-417IPR000953:CHROMO 
Evalue:-16.1023729087096 
Location:499-579IPR000953:Chromo 
Evalue:-13.4559316635132 
Location:622-674IPR000005:HTH_ARAC_FAMILY_1 
Evalue:0 
Location:0-0
SequencesProtein: CHD4_HUMAN (1912 aa)
mRNA: BC038596 NM_001273
Local Annotation
Synapse Ontology
A process that increases long-term neuronal synaptic plasticity, the ability of neuronal synapses to change long-term as circumstances require. Long-term neuronal synaptic plasticity generally involves increase or decrease in actual synapse numbers.
sdb:0039 positive regulation of long-term neuronal synaptic plasticity  (Evidence:keywords)
A process that increases short-term neuronal synaptic plasticity, the ability of neuronal synapses to change in the short-term as circumstances require. Short-term neuronal synaptic plasticity generally involves increasing or decreasing synaptic sensitivity.
sdb:0043 positive regulation of short-term neuronal synaptic plasticity  (Evidence:keywords)
KO assignmentNot mapped to KEGG
Loci Structure (Details)Loci index, Chromosomal location, Length, Possible relational loci clusterExon1: 204 residues, 6549509-6550120Exon2: 56 residues, 6550295-6550459Exon3: 67 residues, 6552500-6552696Exon4: 46 residues, 6557211-6557344Exon5: 38 residues, 6557455-6557564Exon6: 48 residues, 6557835-6557973Exon7: 26 residues, 6558272-6558344Exon8: 45 residues, 6560470-6560600Exon9: 34 residues, 6560717-6560815Exon10: 57 residues, 6561075-6561241Exon11: 50 residues, 6561563-6561708Exon12: 46 residues, 6562041-6562175Exon13: 31 residues, 6562274-6562363Exon14: 31 residues, 6562453-6562540Exon15: 62 residues, 6562624-6562805Exon16: 60 residues, 6566810-6566986Exon17: 81 residues, 6567138-6567376Exon18: 43 residues, 6567724-6567849Exon19: 41 residues, 6570892-6571010Exon20: 46 residues, 6571120-6571252Exon21: 49 residues, 6571342-6571484Exon22: 60 residues, 6571819-6571993Exon23: 42 residues, 6572122-6572244Exon24: 48 residues, 6572517-6572655Exon25: 69 residues, 6572842-6573043Exon26: 66 residues, 6573885-6574077Exon27: 34 residues, 6574760-6574857Exon28: 46 residues, 6575432-6575564Exon29: 70 residues, 6577320-6577526Exon30: 70 residues, 6577648-6577852Exon31: 82 residues, 6579199-6579439Exon32: 61 residues, 6579643-6579822Exon33: 47 residues, 6579960-6580096Exon34: 44 residues, 6580352-6580480Exon35: 82 residues, 6580715-6580957Exon36: 41 residues, 6581074-6581193Exon37: 74 residues, 6581386-6581602Exon38: 42 residues, 6581802-6581924Exon39: 61 residues, 6585700-6585878Exon40: 30 residues, 6586726-6586812Exon41: 2 residues, -Jump to CHD4_HUMANExon1: 204 residues, 6549509-6550120Exon2: 56 residues, 6550295-6550459Exon3: 67 residues, 6552500-6552696Exon4: 46 residues, 6557211-6557344Exon5: 38 residues, 6557455-6557564Exon6: 48 residues, 6557835-6557973Exon7: 26 residues, 6558272-6558344Exon8: 45 residues, 6560470-6560600Exon9: 34 residues, 6560717-6560815Exon10: 57 residues, 6561075-6561241Exon11: 50 residues, 6561563-6561708Exon12: 46 residues, 6562041-6562175Exon13: 31 residues, 6562274-6562363Exon14: 119 residues, 6562453-6562805Exon15: 60 residues, 6566810-6566986Exon16: 81 residues, 6567138-6567376Exon17: 43 residues, 6567724-6567849Exon18: 41 residues, 6570892-6571010Exon19: 46 residues, 6571120-6571252Exon20: 49 residues, 6571342-6571484Exon21: 60 residues, 6571819-6571993Exon22: 42 residues, 6572122-6572244Exon23: 48 residues, 6572517-6572655Exon24: 69 residues, 6572842-6573043Exon25: 66 residues, 6573885-6574077Exon26: 34 residues, 6574760-6574857Exon27: 46 residues, 6575432-6575564Exon28: 70 residues, 6577320-6577526Exon29: 70 residues, 6577648-6577852Exon30: 82 residues, 6579199-6579439Exon31: 61 residues, 6579643-6579822Exon32: 47 residues, 6579960-6580096Exon33: 44 residues, 6580352-6580480Exon34: 82 residues, 6580715-6580957Exon35: 41 residues, 6581074-6581193Exon36: 74 residues, 6581386-6581602Exon37: 39 residues, 6581802-6581915Exon38: 61 residues, 6585700-6585878Exon39: 22 residues, 6586726-6586787Exon40: 2 residues, -Jump to CHD4_HUMAN  
Tune and view alternative isoforms
Loci Cluster (Details)Loci: 4009 6326275-6354976 ~-29K 8222(SCNN1A)(-)Loci: 2731 6424326-6431144 ~-7K 8225(TNFRSF7)(+)Loci: 4010 6441666-6450104 ~-8K 8228(VAMP1)(-)Loci: 4011 6518966-6535498 ~-17K 8239(-)Loci: 4012 6549509-6586812 ~-37K 8245(CHD4)(-)Loci: 4013 6598261-6615548 ~-17K 8247(GPR92)(-)Loci: 2732 6703481-6711289 ~-8K 8256(COPS7A)(+)Loci: 2733 6846966-6850253 ~-3K 8271(TPI1)(+)Loci: 2734 7174236-7201985 ~-28K 8292(CLSTN3)(+)Loci: 4008 5928407-6103946 ~-176K 8213(VWF)(-)Link out to UCSC