EuRBPDB

Basic Information
Cancer Related Information

Description

RBPome

Expression

Transcripts

Gene Model

Pathways

Phenotypes

GWAS

PPI

Orthologs

Gene Ontology

Description

Ensembl ID: ENSG00000008952 (Gene tree)
Gene ID: 7095
Gene Symbol: SEC62
Alias: Dtrp1|HTP1|TLOC1
Full Name: SEC62 homolog, preprotein translocation factor
Gene Type: protein_coding
Species: Homo_sapiens
Status: putative
Strand: Plus strand
Length: 31,739 bases
Position: chr3:169,966,635-169,998,373
Accession: 11846
RBP type: non-canonical RBP
Summary: The Sec61 complex is the central component of the protein translocation apparatus of the endoplasmic reticulum (ER) membrane. The protein encoded by this gene and SEC63 protein are found to be associated with ribosome-free SEC61 complex. It is speculated that Sec61-Sec62-Sec63 may perform post-translational protein translocation into the ER. The Sec61-Sec62-Sec63 complex might also perform the backward transport of ER proteins that are subject to the ubiquitin-proteasome-dependent degradation pathway. The encoded protein is an integral membrane protein located in the rough ER. [provided by RefSeq, Jul 2008]

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
30607034	Comprehensive identification of RNA protein interactions in any organism using orthogonal organic phase separation (OOPS)	OOPS & MCF10A	2019 Jan 3	Queiroz RML	DOI: 10.1038/s41587-018-0001-2
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
27453046	Comprehensive Identification of RNA-Binding Domains in Human Cells	RIC & Hela	2016 Aug 18	Castello A	DOI: 10.1016/j.molcel.2016.06.029

Expression

Transcripts

Transcript ID	Name	Length	RefSeq ID	Protein ID	Length	RefSeq ID	UniportKB ID
ENST00000481435	SEC62-208	627	-	-	- (aa)	-	-
ENST00000461933	SEC62-203	363	-	-	- (aa)	-	-
ENST00000470355	SEC62-206	370	-	-	- (aa)	-	-
ENST00000469515	SEC62-204	785	-	ENSP00000418342	101 (aa)	-	F8WCJ7
ENST00000480708	SEC62-207	1430	-	ENSP00000420331	399 (aa)	-	Q99442
ENST00000460513	SEC62-202	641	-	ENSP00000419319	85 (aa)	-	F8WF48
ENST00000497277	SEC62-210	525	-	-	- (aa)	-	-
ENST00000469890	SEC62-205	822	-	-	- (aa)	-	-
ENST00000337002	SEC62-201	6568	XM_011513114	ENSP00000337688	399 (aa)	XP_011511416	Q99442
ENST00000487736	SEC62-209	508	-	ENSP00000420304	47 (aa)	-	F8WDG8

Gene Model

Click here to download ENSG00000008952's gene model file

Pathways

Pathway ID	Pathway Name	Source
hsa03060	Protein export	KEGG
hsa04141	Protein processing in endoplasmic reticulum	KEGG

Phenotypes

ensgID	Trait	pValue	Pubmed ID
ENSG00000008952	Blood Pressure	1.1010000E-005	-
ENSG00000008952	Emotions	2E-6	27089181

GWAS

ensgID	SNP	Chromosome	Position	SNP-risk	Trait	PubmedID	95% CI	Or or BEAT	EFO ID
ENSG00000008952	rs17217370	3	169990503	A	Subjective well-being	27089181	[0.18-0.43] unit increase	0.30127034	EFO_0007869

Protein-Protein Interaction (PPI)

Clik here to download ENSG00000008952's network

* 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
ENSG00000008952	SEC62	99	97.619	ENSMUSG00000027706	Sec62	100	92.481	Mus_musculus

Gene Ontology

Go ID	Go_term	PubmedID	Evidence	Category
GO:0005783	endoplasmic reticulum	21873635.	IBA	Component
GO:0005789	endoplasmic reticulum membrane	-	TAS	Component
GO:0005791	rough endoplasmic reticulum	-	ISS	Component
GO:0005829	cytosol	-	TAS	Component
GO:0006613	cotranslational protein targeting to membrane	9020021.	TAS	Process
GO:0006620	posttranslational protein targeting to endoplasmic reticulum membrane	22375059.	IMP	Process
GO:0008565	protein transporter activity	21873635.	IBA	Function
GO:0016020	membrane	21873635.	IBA	Component
GO:0016020	membrane	22375059.	IDA	Component
GO:0016021	integral component of membrane	9020021.	TAS	Component
GO:0030176	integral component of endoplasmic reticulum membrane	-	IEA	Component
GO:0031204	posttranslational protein targeting to membrane, translocation	21873635.	IBA	Process
GO:0031204	posttranslational protein targeting to membrane, translocation	29719251.	IMP	Process
GO:0038023	signaling receptor activity	9020021.	TAS	Function

Cancer associated literatures

PID	Title	Article	Time	Author	Doi
28002801	Effect of 3q oncogenes SEC62 and SOX2 on lymphatic metastasis and clinical outcome of head and neck squamous cell carcinomas.	Oncotarget	2017 Jan 17	Bochen F	doi: 10.18632/oncotarget.13986.
16547154	Genomic and expression analysis of the 3q25-q26 amplification unit reveals TLOC1/SEC62 as a probable target gene in prostate cancer.	Mol Cancer Res	2006 Mar	Jung V	-
24304694	Targeting cell migration and the endoplasmic reticulum stress response with calmodulin antagonists: a clinically tested small molecule phenocopy of SEC62 gene silencing in human tumor cells.	BMC Cancer	2013 Dec 5	Linxweiler M	doi: 10.1186/1471-2407-13-574.
22197383	Sec62 bridges the gap from 3q amplification to molecular cell biology in non-small cell lung cancer.	Am J Pathol	2012 Feb	Linxweiler M	doi: 10.1016/j.ajpath.2011.10.039

Expression in 33 cancers

Mutations

Cancer	Chr	Position	Mutation Type	dbSNP	Protein-change	Allele Freq
BLCA	chr3	169988310	Silent	NA	L227L	0.2
BLCA	chr3	169992914	Missense_Mutation	novel	D351N	0.27
BLCA	chr3	169992613	Silent	novel	L250L	0.11
BLCA	chr3	169976949	Missense_Mutation	novel	S50L	0.39
BLCA	chr3	169976976	Nonsense_Mutation	novel	S59*	0.21
BRCA	chr3	169966829	Missense_Mutation	NA	E3K	0.26
BRCA	chr3	169975644	Missense_Mutation	novel	A25T	0.24
BRCA	chr3	169982857	Missense_Mutation	novel	K134N	0.16
CESC	chr3	169992999	Missense_Mutation	rs748038777	C379Y	0.06
CESC	chr3	169966688	5'Flank	NA		0.45
CESC	chr3	169966829	Missense_Mutation	NA	E3K	0.41
CESC	chr3	169993326	3'UTR	novel		0.47
COAD	chr3	169982876	Frame_Shift_Del	rs754536169	*D144Mfs58**	0.33
COAD	chr3	169983200	Frame_Shift_Del	NA	*K167Nfs35**	0.06
COAD	chr3	169985860	Missense_Mutation	NA	I202N	0.18
COAD	chr3	169988357	Missense_Mutation	NA	V243A	0.37
COAD	chr3	169992833	Frame_Shift_Ins	novel	*K324Rfs23**	0.08
COAD	chr3	169992834	Nonsense_Mutation	novel	*V325Kfs4**	0.08
ESCA	chr3	169993170	3'UTR	novel		0.11
ESCA	chr3	169993835	3'UTR	novel		0.16
ESCA	chr3	169993299	3'UTR	novel		0.08
GBM	chr3	169977021	Missense_Mutation	NA	T74N	0.45
HNSC	chr3	169982812	In_Frame_Ins	novel	K119_E120insTGM	0.13
HNSC	chr3	169985821	Missense_Mutation	novel	Y189C	0.18
KIRC	chr3	169976964	Missense_Mutation	novel	C55F	0.3
KIRC	chr3	169993020	Missense_Mutation	novel	E386A	0.07
KIRP	chr3	169988337	Silent	NA	A236A	0.27
KIRP	chr3	169983212	Missense_Mutation	novel	L170V	0.31
LAML	chr3	169994445	3'UTR	novel		1
LAML	chr3	169992867	Frame_Shift_Ins	novel	*E338Rfs9**	0.15
LIHC	chr3	169966497	5'Flank	novel		0.17
LIHC	chr3	169966666	5'Flank	novel		0.42
LUAD	chr3	169992806	Missense_Mutation	NA	S315R	0.27
LUAD	chr3	169975649	Missense_Mutation	NA	K26N	0.33
LUAD	chr3	169992878	Missense_Mutation	rs762601555	R339W	0.13
LUAD	chr3	169976985	Missense_Mutation	novel	A62V	0.25
LUSC	chr3	169982778	Missense_Mutation	novel	K108T	0.27
OV	chr3	169975641	Missense_Mutation	NA	V24L	0.12
OV	chr3	169975709	Nonsense_Mutation	novel	Y46*	0.05
OV	chr3	169992883	Missense_Mutation	novel	H340Q	0.1
OV	chr3	169975619	Missense_Mutation	novel	E16D	0.06
PAAD	chr3	169992985	Silent	novel	Q374Q	0.06
PRAD	chr3	169993061	Frame_Shift_Ins	novel	*400F	0.25
PRAD	chr3	169993063	Nonstop_Mutation	novel	400Yext3	0.25
SARC	chr3	169996569	3'UTR	novel		0.56
SKCM	chr3	169992698	Missense_Mutation	NA	R279G	0.33
SKCM	chr3	169982736	Missense_Mutation	NA	A94V	0.09
SKCM	chr3	169982746	Silent	NA	V97V	0.36
STAD	chr3	169992962	Missense_Mutation	NA	T367A	0.14
THCA	chr3	169992835	Frame_Shift_Ins	novel	*V325Nfs24**	0.07
THCA	chr3	169992836	Missense_Mutation	novel	V325L	0.02
THCA	chr3	169976976	Missense_Mutation	novel	S59L	0.31
THYM	chr3	169966616	5'Flank	novel		0.19
UCEC	chr3	169982833	Missense_Mutation	NA	K126N	0.15
UCEC	chr3	169992918	Missense_Mutation	rs146483233	R352Q	0.09
UCEC	chr3	169966839	Missense_Mutation	NA	R6K	0.55
UCEC	chr3	169983208	Missense_Mutation	NA	F168L	0.49
UCEC	chr3	169992611	Missense_Mutation	NA	L250I	0.39
UCEC	chr3	169993120	3'UTR	novel		0.4
UCEC	chr3	169993121	3'UTR	novel		0.4
UCEC	chr3	169976995	Silent	NA	K65K	0.28
UCEC	chr3	169982880	Missense_Mutation	novel	K142R	0.17
UCEC	chr3	169993316	3'UTR	novel		0.46
UCEC	chr3	169993158	3'UTR	novel		0.15
UCEC	chr3	169993810	3'UTR	novel		0.51
UCEC	chr3	169993206	3'UTR	rs574096149		0.32
UCEC	chr3	169996253	3'UTR	novel		0.46
UCEC	chr3	169992655	Missense_Mutation	novel	F264L	0.11
UCEC	chr3	169988359	Missense_Mutation	novel	A244S	0.35
UCEC	chr3	169966689	5'Flank	novel		0.29
UCEC	chr3	169994445	3'UTR	novel		0.32
UCEC	chr3	169993207	3'UTR	rs114020608		0.25
UCEC	chr3	169992698	Missense_Mutation	NA	R279G	0.1
UCEC	chr3	169993742	3'UTR	novel		0.14

Copy Number Variations (CNVs)

Cancer	Type	Freq	Q-value
BLCA	AMP	0.4485	0.0018563
CESC	AMP	0.7424	2.3522e-34
ESCA	AMP	0.6467	2.8915e-20
KIRC	AMP	0.1212	2.0306e-05
KIRP	AMP	0.3229	0.15981
LUAD	AMP	0.2422	1.027e-07
PAAD	AMP	0.1304	0.16151
PRAD	AMP	0.124	2.4906e-06
SARC	DEL	0.1712	0.0086757
TGCT	AMP	0.2467	7.0307e-05

Survival Analysis

Cancer	P-value	Q-value
KIRC	0.00011	Kaplan-Meier Survival Analysis
STAD	0.033	Kaplan-Meier Survival Analysis
HNSC	0.00082	Kaplan-Meier Survival Analysis
SKCM	0.0001	Kaplan-Meier Survival Analysis
PAAD	0.033	Kaplan-Meier Survival Analysis
UCEC	0.046	Kaplan-Meier Survival Analysis
LGG	0.0042	Kaplan-Meier Survival Analysis
OV	0.031	Kaplan-Meier Survival Analysis

Drugs

EuRBPDB

Description

RBPome

Expression

Transcripts

Gene Model

Pathways

Phenotypes

GWAS

PPI

Orthologs

Gene Ontology

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Cell lines and drugs in GSE70138 or GSE92742