EuRBPDB

Description

RBDs

RBPome

Expression

Transcripts

Gene Model

Phenotypes

GWAS

PPI

Paralogs

Orthologs

Gene Ontology

Description

Ensembl ID: ENSG00000170004 (Gene tree)
Gene ID: 1107
Gene Symbol: CHD3
Alias: Mi-2a|ZFH|Mi2-ALPHA
Full Name: chromodomain helicase DNA binding protein 3
Gene Type: protein_coding
Species: Homo_sapiens
Status: confidence
Strand: Plus strand
Length: 27,985 bases
Position: chr17:7,884,776-7,912,760
Accession: 1918
RBP type: canonical RBP
Summary: This gene encodes a member of the CHD family of proteins which are characterized by the presence of chromo (chromatin organization modifier) domains and SNF2-related helicase/ATPase domains. This protein is one of the components of a histone deacetylase complex referred to as the Mi-2/NuRD complex which participates in the remodeling of chromatin by deacetylating histones. Chromatin remodeling is essential for many processes including transcription. Autoantibodies against this protein are found in a subset of patients with dermatomyositis. Three alternatively spliced transcripts encoding different isoforms have been described. [provided by RefSeq, Jul 2008]

RNA binding domains(RBDs)

Protein ID	Domain	Pfam ID	E-value	Domain number	Total number
ENSP00000350907	ResIII	PF04851.15	7e-08	1	1
ENSP00000332628	ResIII	PF04851.15	7.3e-08	1	1
ENSP00000369716	ResIII	PF04851.15	7.4e-08	1	1

RNA binding proteome (RBPome)

PID	Title	Method	Time	Author	Doi
29431736	Capturing the interactome of newly transcribed RNA	PolyT-RICK & Hela	2018 Feb 12	Bao X	DOI: 10.1038/nmeth.4595
29431736	Capturing the interactome of newly transcribed RNA	RICK & Hela	2018 Feb 12	Bao X	DOI: 10.1038/nmeth.4595
22658674	Insights into RNA biology from an atlas of mammalian mRNA-binding proteins	RIC & Hela	2012 May 31	Castello A	DOI: 10.1016/j.cell.2012.04.031

Expression

Transcripts

Transcript ID	Name	Length	RefSeq ID	Protein ID	Length	RefSeq ID	UniportKB ID
ENST00000481999	CHD3-211	2515	-	-	- (aa)	-	-
ENST00000574022	CHD3-217	103	-	-	- (aa)	-	-
ENST00000358181	CHD3-202	7286	-	ENSP00000350907	1966 (aa)	-	Q12873
ENST00000572579	CHD3-214	931	-	-	- (aa)	-	-
ENST00000466233	CHD3-207	648	-	-	- (aa)	-	-
ENST00000449744	CHD3-205	880	-	ENSP00000411959	277 (aa)	-	H7C3H7
ENST00000380358	CHD3-203	7356	XM_005256427	ENSP00000369716	2059 (aa)	XP_005256484	Q12873
ENST00000570758	CHD3-212	174	-	-	- (aa)	-	-
ENST00000573936	CHD3-216	749	-	ENSP00000459321	249 (aa)	-	I3L229
ENST00000473376	CHD3-209	562	-	-	- (aa)	-	-
ENST00000330494	CHD3-201	7328	XM_017024063	ENSP00000332628	2000 (aa)	XP_016879552	Q12873
ENST00000571249	CHD3-213	330	-	ENSP00000458861	110 (aa)	-	I3L1I4
ENST00000470531	CHD3-208	3744	-	ENSP00000467547	63 (aa)	-	K7EPV1
ENST00000479080	CHD3-210	519	-	-	- (aa)	-	-
ENST00000439235	CHD3-204	1263	-	ENSP00000395252	383 (aa)	-	H7C0J3
ENST00000572750	CHD3-215	750	-	-	- (aa)	-	-
ENST00000452447	CHD3-206	1573	-	ENSP00000405861	525 (aa)	-	H7C2H0

Gene Model

Click here to download ENSG00000170004's gene model file

Phenotypes

ensgID	Trait	pValue	Pubmed ID
ENSG00000170004	Blood Pressure	9.7649203E-005	-
ENSG00000170004	Stroke	1E-8	26089329
ENSG00000170004	Stroke	5E-9	26089329

GWAS

ensgID	SNP	Chromosome	Position	SNP-risk	Trait	PubmedID	95% CI	Or or BEAT	EFO ID
ENSG00000170004	rs7503751	17	7886224	A	Systolic blood pressure	28739976	[0.42-0.98] unit decrease	0.701	EFO_0006335
ENSG00000170004	rs7503751	17	7886224	A	Systolic blood pressure	28739976	[0.27-0.59] unit decrease	0.431	EFO_0006335
ENSG00000170004	rs9899375	17	7908297	T	Stroke	26089329	[1.86-3.55]	2.57	EFO_0000712
ENSG00000170004	rs9899375	17	7908297	T	Ischemic stroke	26089329	[2.21-4.93]	3.3	HP_0002140
ENSG00000170004	rs7222046	17	7903211	?	Macular thickness	30535121	[0.27-0.55] unit decrease	0.411	EFO_0008375
ENSG00000170004	rs7503751	17	7886224	?	Systolic blood pressure	30595370			EFO_0006335
ENSG00000170004	rs11078713	17	7892654	?	Smoking status	30595370			EFO_0006527
ENSG00000170004	rs28441558	17	7899800	C	Prostate cancer	29892016	[1.12-1.20]	1.16	EFO_0001663
ENSG00000170004	rs11078713	17	7892654	G	Smoking initiation (ever regular vs never regular) (MTAG)	30643251	[0.0063-0.0106] unit decrease	0.00849662	EFO_0006527
ENSG00000170004	rs11078713	17	7892654	G	Smoking initiation (ever regular vs never regular)	30643251	[0.0095-0.0196] unit decrease	0.014582893	EFO_0006527
ENSG00000170004	rs28441558	17	7899800	C	Smoking initiation (ever regular vs never regular)	30643251	[0.025-0.046] unit decrease	0.03556498	EFO_0006527

Protein-Protein Interaction (PPI)

Clik here to download ENSG00000170004's network

* RBP PPI network refers to all genes directly bind to RBP

Paralogs

Ensembl ID	Gene Symbol	Coverage	Identiy	Paralog	Gene Symbol	Coverage	Identiy
ENSG00000170004	CHD3	99	64.038	ENSG00000111642	CHD4	99	75.184

Orthologs

Ensembl ID	Gene Symbol	Coverage	Identiy	Ortholog	Gene Symbol	Coverage	Identiy	Species
ENSG00000170004	CHD3	84	76.418	ENSAPOG00000005614	chd3	94	80.208	Acanthochromis_polyacanthus
ENSG00000170004	CHD3	68	100.000	ENSAMEG00000003025	-	100	97.434	Ailuropoda_melanoleuca
ENSG00000170004	CHD3	81	83.516	ENSACIG00000019671	chd3	99	83.516	Amphilophus_citrinellus
ENSG00000170004	CHD3	91	81.100	ENSAOCG00000023784	chd3	97	81.675	Amphiprion_ocellaris
ENSG00000170004	CHD3	91	80.756	ENSAPEG00000006341	chd3	95	77.728	Amphiprion_percula
ENSG00000170004	CHD3	91	81.315	ENSATEG00000000848	chd3	95	82.105	Anabas_testudineus
ENSG00000170004	CHD3	96	85.355	ENSACAG00000004276	CHD3	96	84.829	Anolis_carolinensis
ENSG00000170004	CHD3	99	99.053	ENSANAG00000034323	CHD3	99	99.520	Aotus_nancymaae
ENSG00000170004	CHD3	91	78.816	ENSACLG00000009222	chd3	99	74.804	Astatotilapia_calliptera
ENSG00000170004	CHD3	100	98.350	ENSBTAG00000014377	CHD3	100	98.350	Bos_taurus
ENSG00000170004	CHD3	100	99.466	ENSCJAG00000014766	CHD3	100	99.466	Callithrix_jacchus
ENSG00000170004	CHD3	100	98.001	ENSCAFG00000016859	CHD3	100	98.001	Canis_familiaris
ENSG00000170004	CHD3	99	97.154	ENSCAFG00020007422	CHD3	100	98.582	Canis_lupus_dingo
ENSG00000170004	CHD3	99	98.686	ENSCHIG00000016737	CHD3	100	98.686	Capra_hircus
ENSG00000170004	CHD3	100	99.034	ENSTSYG00000035658	CHD3	100	99.034	Carlito_syrichta
ENSG00000170004	CHD3	99	97.538	ENSCAPG00000014864	CHD3	99	94.932	Cavia_aperea
ENSG00000170004	CHD3	99	97.538	ENSCPOG00000022653	CHD3	99	97.441	Cavia_porcellus
ENSG00000170004	CHD3	100	99.466	ENSCCAG00000034792	CHD3	100	99.466	Cebus_capucinus
ENSG00000170004	CHD3	100	99.695	ENSCATG00000041717	CHD3	100	99.695	Cercocebus_atys
ENSG00000170004	CHD3	99	97.917	ENSCLAG00000010523	CHD3	100	98.603	Chinchilla_lanigera
ENSG00000170004	CHD3	99	99.618	ENSCSAG00000011122	CHD3	100	99.441	Chlorocebus_sabaeus
ENSG00000170004	CHD3	99	82.027	ENSCPBG00000011966	CHD3	99	87.687	Chrysemys_picta_bellii
ENSG00000170004	CHD3	100	99.593	ENSCANG00000037641	CHD3	100	99.593	Colobus_angolensis_palliatus
ENSG00000170004	CHD3	98	97.673	ENSCGRG00001011306	Chd3	100	97.673	Cricetulus_griseus_chok1gshd
ENSG00000170004	CHD3	93	97.794	ENSCGRG00000007878	Chd3	99	97.794	Cricetulus_griseus_crigri
ENSG00000170004	CHD3	91	79.605	ENSCSEG00000004489	chd3	99	76.156	Cynoglossus_semilaevis
ENSG00000170004	CHD3	86	82.400	ENSCVAG00000007293	chd3	95	82.996	Cyprinodon_variegatus
ENSG00000170004	CHD3	99	72.658	ENSDARG00000021405	chd3	99	76.587	Danio_rerio
ENSG00000170004	CHD3	98	83.864	ENSDNOG00000047846	CHD3	98	83.864	Dasypus_novemcinctus
ENSG00000170004	CHD3	99	97.917	ENSDORG00000010713	Chd3	100	98.085	Dipodomys_ordii
ENSG00000170004	CHD3	99	91.304	ENSETEG00000017733	CHD3	100	92.164	Echinops_telfairi
ENSG00000170004	CHD3	89	67.857	ENSEBUG00000008310	chd3	99	70.404	Eptatretus_burgeri
ENSG00000170004	CHD3	99	93.913	ENSEASG00005019360	CHD3	100	98.854	Equus_asinus_asinus
ENSG00000170004	CHD3	99	93.913	ENSECAG00000010051	CHD3	100	98.909	Equus_caballus
ENSG00000170004	CHD3	99	97.338	ENSEEUG00000015205	CHD3	92	100.000	Erinaceus_europaeus
ENSG00000170004	CHD3	78	90.476	ENSELUG00000019499	chd3	99	90.476	Esox_lucius
ENSG00000170004	CHD3	100	98.205	ENSFCAG00000009629	CHD3	100	98.205	Felis_catus
ENSG00000170004	CHD3	99	97.154	ENSFDAG00000008220	CHD3	99	96.189	Fukomys_damarensis
ENSG00000170004	CHD3	89	80.305	ENSGMOG00000013599	chd3	91	80.914	Gadus_morhua
ENSG00000170004	CHD3	98	69.157	ENSGAFG00000004055	chd3	99	76.581	Gambusia_affinis
ENSG00000170004	CHD3	97	70.892	ENSGACG00000019275	chd3	100	70.997	Gasterosteus_aculeatus
ENSG00000170004	CHD3	76	95.833	ENSGAGG00000013164	CHD3	98	87.101	Gopherus_agassizii
ENSG00000170004	CHD3	100	99.700	ENSGGOG00000013496	CHD3	100	99.700	Gorilla_gorilla
ENSG00000170004	CHD3	99	98.344	ENSHGLG00000012017	CHD3	100	98.344	Heterocephalus_glaber_female
ENSG00000170004	CHD3	99	94.697	ENSHGLG00100013902	CHD3	99	91.594	Heterocephalus_glaber_male
ENSG00000170004	CHD3	99	66.850	ENSHCOG00000010170	chd3	96	73.357	Hippocampus_comes
ENSG00000170004	CHD3	86	78.807	ENSIPUG00000003271	chd3	96	80.919	Ictalurus_punctatus
ENSG00000170004	CHD3	99	98.864	ENSSTOG00000025907	CHD3	100	99.068	Ictidomys_tridecemlineatus
ENSG00000170004	CHD3	100	96.802	ENSJJAG00000017633	Chd3	100	97.827	Jaculus_jaculus
ENSG00000170004	CHD3	86	89.573	ENSKMAG00000019292	chd3	97	75.903	Kryptolebias_marmoratus
ENSG00000170004	CHD3	87	81.008	ENSLBEG00000028485	chd3	92	81.008	Labrus_bergylta
ENSG00000170004	CHD3	99	76.749	ENSLACG00000008031	CHD3	99	74.374	Latimeria_chalumnae
ENSG00000170004	CHD3	96	77.225	ENSLOCG00000013965	chd3	97	77.174	Lepisosteus_oculatus
ENSG00000170004	CHD3	94	94.542	ENSLAFG00000000572	CHD3	100	94.542	Loxodonta_africana
ENSG00000170004	CHD3	100	99.644	ENSMFAG00000020113	CHD3	100	99.644	Macaca_fascicularis
ENSG00000170004	CHD3	99	98.864	ENSMMUG00000022221	CHD3	100	97.200	Macaca_mulatta
ENSG00000170004	CHD3	100	99.644	ENSMNEG00000001728	CHD3	100	99.644	Macaca_nemestrina
ENSG00000170004	CHD3	100	99.695	ENSMLEG00000032249	CHD3	100	99.695	Mandrillus_leucophaeus
ENSG00000170004	CHD3	91	70.041	ENSMAMG00000000564	chd3	99	77.466	Mastacembelus_armatus
ENSG00000170004	CHD3	99	97.122	ENSMAUG00000013873	Chd3	100	95.973	Mesocricetus_auratus
ENSG00000170004	CHD3	100	98.981	ENSMICG00000008741	CHD3	100	98.981	Microcebus_murinus
ENSG00000170004	CHD3	98	97.823	ENSMOCG00000004848	Chd3	100	97.823	Microtus_ochrogaster
ENSG00000170004	CHD3	94	74.599	ENSMMOG00000012699	chd3	99	74.041	Mola_mola
ENSG00000170004	CHD3	99	87.826	ENSMODG00000007509	CHD3	100	94.667	Monodelphis_domestica
ENSG00000170004	CHD3	99	96.975	MGP_CAROLIEiJ_G0016564	Chd3	100	97.561	Mus_caroli
ENSG00000170004	CHD3	100	96.946	ENSMUSG00000018474	Chd3	100	96.946	Mus_musculus
ENSG00000170004	CHD3	99	97.132	MGP_PahariEiJ_G0017695	Chd3	100	97.772	Mus_pahari
ENSG00000170004	CHD3	100	96.898	MGP_SPRETEiJ_G0017400	Chd3	100	97.667	Mus_spretus
ENSG00000170004	CHD3	86	98.308	ENSMPUG00000008861	CHD3	100	98.308	Mustela_putorius_furo
ENSG00000170004	CHD3	100	97.203	ENSMLUG00000014643	-	100	97.203	Myotis_lucifugus
ENSG00000170004	CHD3	99	97.917	ENSNGAG00000000773	Chd3	99	97.380	Nannospalax_galili
ENSG00000170004	CHD3	85	75.396	ENSNBRG00000000636	chd3	98	76.016	Neolamprologus_brichardi
ENSG00000170004	CHD3	99	100.000	ENSNLEG00000009770	CHD3	100	96.885	Nomascus_leucogenys
ENSG00000170004	CHD3	99	92.235	ENSMEUG00000005852	CHD3	87	91.209	Notamacropus_eugenii
ENSG00000170004	CHD3	99	98.099	ENSOPRG00000011069	CHD3	100	96.955	Ochotona_princeps
ENSG00000170004	CHD3	99	97.688	ENSODEG00000017785	CHD3	100	97.688	Octodon_degus
ENSG00000170004	CHD3	94	75.026	ENSONIG00000009292	chd3	100	75.000	Oreochromis_niloticus
ENSG00000170004	CHD3	99	94.783	ENSOCUG00000029299	CHD3	100	93.845	Oryctolagus_cuniculus
ENSG00000170004	CHD3	99	65.121	ENSORLG00000007107	chd3	93	71.911	Oryzias_latipes
ENSG00000170004	CHD3	99	63.258	ENSORLG00020008387	chd3	95	73.786	Oryzias_latipes_hni
ENSG00000170004	CHD3	91	68.724	ENSOMEG00000013691	chd3	99	78.308	Oryzias_melastigma
ENSG00000170004	CHD3	98	98.528	ENSOGAG00000003216	CHD3	100	98.528	Otolemur_garnettii
ENSG00000170004	CHD3	99	95.856	ENSOARG00000017855	CHD3	99	96.347	Ovis_aries
ENSG00000170004	CHD3	100	97.536	ENSPPAG00000032886	CHD3	100	97.536	Pan_paniscus
ENSG00000170004	CHD3	99	97.850	ENSPPRG00000000626	CHD3	100	98.172	Panthera_pardus
ENSG00000170004	CHD3	100	99.903	ENSPTRG00000008714	CHD3	100	99.903	Pan_troglodytes
ENSG00000170004	CHD3	100	99.600	ENSPANG00000023938	CHD3	100	99.600	Papio_anubis
ENSG00000170004	CHD3	93	80.474	ENSPKIG00000006305	chd3	99	79.332	Paramormyrops_kingsleyae
ENSG00000170004	CHD3	68	95.349	ENSPSIG00000010177	CHD3	98	90.876	Pelodiscus_sinensis
ENSG00000170004	CHD3	99	97.075	ENSPEMG00000014262	Chd3	100	97.075	Peromyscus_maniculatus_bairdii
ENSG00000170004	CHD3	97	100.000	ENSPCIG00000005442	CHD3	98	95.582	Phascolarctos_cinereus
ENSG00000170004	CHD3	91	80.272	ENSPFOG00000012464	chd3	87	80.135	Poecilia_formosa
ENSG00000170004	CHD3	86	83.133	ENSPLAG00000002887	chd3	96	83.133	Poecilia_latipinna
ENSG00000170004	CHD3	85	73.734	ENSPMEG00000016725	chd3	94	73.247	Poecilia_mexicana
ENSG00000170004	CHD3	89	84.502	ENSPREG00000011044	chd3	99	77.942	Poecilia_reticulata
ENSG00000170004	CHD3	100	94.900	ENSPPYG00000007940	CHD3	100	94.900	Pongo_abelii
ENSG00000170004	CHD3	95	97.761	ENSPCAG00000004350	CHD3	96	97.761	Procavia_capensis
ENSG00000170004	CHD3	100	98.302	ENSPCOG00000020952	CHD3	100	98.979	Propithecus_coquereli
ENSG00000170004	CHD3	99	97.727	ENSPVAG00000016344	CHD3	87	98.021	Pteropus_vampyrus
ENSG00000170004	CHD3	94	78.585	ENSPNAG00000020393	chd3	98	81.611	Pygocentrus_nattereri
ENSG00000170004	CHD3	92	96.950	ENSRNOG00000009722	Chd3	100	96.950	Rattus_norvegicus
ENSG00000170004	CHD3	100	96.444	ENSRBIG00000033562	CHD3	100	96.444	Rhinopithecus_bieti
ENSG00000170004	CHD3	100	99.695	ENSRROG00000029554	CHD3	100	99.695	Rhinopithecus_roxellana
ENSG00000170004	CHD3	100	99.350	ENSSBOG00000020719	CHD3	100	99.350	Saimiri_boliviensis_boliviensis
ENSG00000170004	CHD3	98	94.912	ENSSHAG00000014412	CHD3	100	94.912	Sarcophilus_harrisii
ENSG00000170004	CHD3	86	80.727	ENSSFOG00015023123	chd3	98	75.444	Scleropages_formosus
ENSG00000170004	CHD3	79	91.304	ENSSMAG00000006451	chd3	99	77.237	Scophthalmus_maximus
ENSG00000170004	CHD3	98	64.436	ENSSDUG00000005792	chd3	95	73.535	Seriola_dumerili
ENSG00000170004	CHD3	91	80.756	ENSSPAG00000013694	chd3	98	81.053	Stegastes_partitus
ENSG00000170004	CHD3	99	99.237	ENSSSCG00000021363	CHD3	100	98.473	Sus_scrofa
ENSG00000170004	CHD3	99	67.225	ENSTRUG00000014990	chd3	89	76.335	Takifugu_rubripes
ENSG00000170004	CHD3	96	73.771	ENSTNIG00000012998	chd3	99	73.202	Tetraodon_nigroviridis
ENSG00000170004	CHD3	77	98.824	ENSTBEG00000011454	-	71	97.619	Tupaia_belangeri
ENSG00000170004	CHD3	97	99.383	ENSTTRG00000010295	CHD3	97	99.383	Tursiops_truncatus
ENSG00000170004	CHD3	92	97.387	ENSUAMG00000005475	CHD3	99	97.387	Ursus_americanus
ENSG00000170004	CHD3	89	88.273	ENSVPAG00000010794	-	62	100.000	Vicugna_pacos
ENSG00000170004	CHD3	99	97.348	ENSVVUG00000028011	CHD3	99	98.455	Vulpes_vulpes
ENSG00000170004	CHD3	97	72.589	ENSXETG00000012991	chd3	92	73.806	Xenopus_tropicalis
ENSG00000170004	CHD3	69	80.556	ENSXCOG00000000809	chd3	96	83.089	Xiphophorus_couchianus
ENSG00000170004	CHD3	80	82.967	ENSXMAG00000016035	chd3	99	82.967	Xiphophorus_maculatus

Gene Ontology

Go ID	Go_term	PubmedID	Evidence	Category
GO:0003677	DNA binding	-	IEA	Function
GO:0003723	RNA binding	22658674.	HDA	Function
GO:0004003	ATP-dependent DNA helicase activity	9326634.	TAS	Function
GO:0004386	helicase activity	9688266.	NAS	Function
GO:0005515	protein binding	9804427.12505151.15383276.16169070.19703393.20676135.21642969.21900206.22720776.26816381.	IPI	Function
GO:0005524	ATP binding	-	IEA	Function
GO:0005634	nucleus	22720776.	IDA	Component
GO:0005634	nucleus	9688266.	NAS	Component
GO:0005654	nucleoplasm	-	TAS	Component
GO:0005730	nucleolus	-	IDA	Component
GO:0005737	cytoplasm	17626165.	IDA	Component
GO:0005813	centrosome	17626165.	IDA	Component
GO:0005815	microtubule organizing center	-	IDA	Component
GO:0006333	chromatin assembly or disassembly	-	IEA	Process
GO:0006355	regulation of transcription, DNA-templated	9688266.	NAS	Process
GO:0006357	regulation of transcription by RNA polymerase II	9326634.	TAS	Process
GO:0007051	spindle organization	17626165.	IDA	Process
GO:0007098	centrosome cycle	17626165.	IDA	Process
GO:0008270	zinc ion binding	9688266.	NAS	Function
GO:0016581	NuRD complex	17827154.	IDA	Component
GO:0032508	DNA duplex unwinding	-	IEA	Process
GO:1901796	regulation of signal transduction by p53 class mediator	-	TAS	Process