EuRBPDB

Description

Ensembl ID: ENSG00000101596 (Gene tree)
Gene ID: 23347
Gene Symbol: SMCHD1
Alias: KIAA0650|FSHD2
Full Name: structural maintenance of chromosomes flexible hinge domain containing 1
Gene Type: protein_coding
Species: Homo_sapiens
Status: putative
Strand: Plus strand
Length: 149,280 bases
Position: chr18:2,655,738-2,805,017
Accession: 29090
RBP type: non-canonical RBP
Summary: This gene encodes a protein which contains a hinge region domain found in members of the SMC (structural maintenance of chromosomes) protein family. [provided by RefSeq, Dec 2011]

RNA binding proteome (RBPome)

PID	Title	Method	Time	Author	Doi
30607034	Comprehensive identification of RNA protein interactions in any organism using orthogonal organic phase separation (OOPS)	OOPS & HEK293	2019 Jan 3	Queiroz RML	DOI: 10.1038/s41587-018-0001-2
29431736	Capturing the interactome of newly transcribed RNA	PolyT-RICK & Hela	2018 Feb 12	Bao X	DOI: 10.1038/nmeth.4595
30607034	Comprehensive identification of RNA protein interactions in any organism using orthogonal organic phase separation (OOPS)	OOPS & U2OS	2019 Jan 3	Queiroz RML	DOI: 10.1038/s41587-018-0001-2

Expression

Transcripts

Transcript ID	Name	Length	RefSeq ID	Protein ID	Length	RefSeq ID	UniportKB ID
ENST00000583800	SMCHD1-210	865	-	ENSP00000463036	48 (aa)	-	J3KTK7
ENST00000581711	SMCHD1-207	546	-	-	- (aa)	-	-
ENST00000581631	SMCHD1-206	729	-	-	- (aa)	-	-
ENST00000609587	SMCHD1-213	460	-	-	- (aa)	-	-
ENST00000577880	SMCHD1-203	4951	-	ENSP00000463049	1388 (aa)	-	J3KTL8
ENST00000645355	SMCHD1-215	2315	-	ENSP00000495392	212 (aa)	-	A0A2R8YE92
ENST00000584897	SMCHD1-211	4143	-	ENSP00000464684	150 (aa)	-	J3QSH1
ENST00000577300	SMCHD1-202	506	-	-	- (aa)	-	-
ENST00000585229	SMCHD1-212	555	-	ENSP00000462050	49 (aa)	-	J3KRK8
ENST00000320876	SMCHD1-201	8821	XM_011525642	ENSP00000326603	2005 (aa)	XP_011523944	A6NHR9
ENST00000642953	SMCHD1-214	1263	-	ENSP00000493989	308 (aa)	-	A0A2R8YCU7
ENST00000581226	SMCHD1-204	459	-	-	- (aa)	-	-
ENST00000583441	SMCHD1-209	657	-	-	- (aa)	-	-
ENST00000583344	SMCHD1-208	738	-	-	- (aa)	-	-
ENST00000581383	SMCHD1-205	806	-	-	- (aa)	-	-

Gene Model

Phenotypes

ensgID	Trait	pValue	Pubmed ID
ENSG00000101596	Body Mass Index	5.69753154810362E-5	17903300
ENSG00000101596	Body Mass Index	4.060674613382E-5	17903300
ENSG00000101596	Body Mass Index	1.5532367385506E-5	17903300
ENSG00000101596	Iron	8.7370000E-004	19880490
ENSG00000101596	Conotruncal cardiac defects	4E-6	24800985
ENSG00000101596	Prostatic Neoplasms	4E-6	27515689
ENSG00000101596	Electromagnetic Radiation	4E-6	27515689

GWAS

ensgID	SNP	Chromosome	Position	SNP-risk	Trait	PubmedID	95% CI	Or or BEAT	EFO ID
ENSG00000101596	rs201024040	18	2710383	AT	Nicotine withdrawal symptom count	29532581	[0.69-1.59] unit increase	1.14	EFO_0009263
ENSG00000101596	rs11872184	18	2739735	?	Conotruncal heart defects	24800985	[2.15-7.74]	4.08	Orphanet_2445
ENSG00000101596	rs685958	18	2735461	A	Highest math class taken (MTAG)	30038396	[0.0058-0.0124] unit increase	0.0091	EFO_0004875

Protein-Protein Interaction (PPI)

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

Orthologs identified by RBPome

Ensembl ID	Gene Symbol	Coverage	Identiy	Ortholog	Gene Symbol	Coverage	Identiy	Species
ENSG00000101596	SMCHD1	96	97.872	ENSMUSG00000024054	Smchd1	99	87.066	Mus_musculus

Gene Ontology

Go ID	Go_term	PubmedID	Evidence	Category
GO:0000784	nuclear chromosome, telomeric region	24270157.	IDA	Component
GO:0001740	Barr body	23542155.	IDA	Component
GO:0003677	DNA binding	-	IEA	Function
GO:0005515	protein binding	23542155.	IPI	Function
GO:0005524	ATP binding	-	IEA	Function
GO:0006302	double-strand break repair	-	IEA	Process
GO:0009048	dosage compensation by inactivation of X chromosome	23542155.	IDA	Process
GO:0016887	ATPase activity	-	ISS	Function
GO:0035861	site of double-strand break	24790221.25294876.	IDA	Component
GO:0042803	protein homodimerization activity	-	ISS	Function
GO:0043584	nose development	28067909.28067911.	IMP	Process
GO:0045739	positive regulation of DNA repair	24790221.	IMP	Process
GO:0060820	inactivation of X chromosome by heterochromatin assembly	-	ISS	Process
GO:0060821	inactivation of X chromosome by DNA methylation	-	IEA	Process
GO:0070868	heterochromatin organization involved in chromatin silencing	-	ISS	Process
GO:2000042	negative regulation of double-strand break repair via homologous recombination	25294876.	IMP	Process
GO:2001034	positive regulation of double-strand break repair via nonhomologous end joining	25294876.	IMP	Process