Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	6396
Gene name	SEC13 homolog, nuclear pore and COPII component
Gene symbol	SEC13
Synonyms (NCBI Gene)	D3S1231ESEC13L1SEC13Rnpp-20
Chromosome	3
Chromosome location	3p25.3
Summary	The protein encoded by this gene belongs to the SEC13 family of WD-repeat proteins. It is a constituent of the endoplasmic reticulum and the nuclear pore complex. It has similarity to the yeast SEC13 protein, which is required for vesicle biogenesis from

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miRTarBase ID	miRNA	Experiments	Reference
MIRT048659	hsa-miR-99a-5p	CLASH	23622248
MIRT041012	hsa-miR-505-3p	CLASH	23622248
MIRT039516	hsa-miR-652-3p	CLASH	23622248
MIRT1332174	hsa-miR-1207-3p	CLIP-seq
MIRT1332175	hsa-miR-124	CLIP-seq
MIRT1332176	hsa-miR-1245b-3p	CLIP-seq
MIRT1332177	hsa-miR-3160-5p	CLIP-seq
MIRT1332178	hsa-miR-330-3p	CLIP-seq
MIRT1332179	hsa-miR-3714	CLIP-seq
MIRT1332180	hsa-miR-3910	CLIP-seq
MIRT1332181	hsa-miR-4422	CLIP-seq
MIRT1332182	hsa-miR-4520a-3p	CLIP-seq
MIRT1332183	hsa-miR-4638-3p	CLIP-seq
MIRT1332184	hsa-miR-4645-3p	CLIP-seq
MIRT1332185	hsa-miR-506	CLIP-seq
MIRT1332186	hsa-miR-520d-5p	CLIP-seq
MIRT1332187	hsa-miR-520f	CLIP-seq
MIRT1332188	hsa-miR-524-5p	CLIP-seq
MIRT1332189	hsa-miR-936	CLIP-seq
MIRT1332174	hsa-miR-1207-3p	CLIP-seq
MIRT1332190	hsa-miR-1238	CLIP-seq
MIRT1332177	hsa-miR-3160-5p	CLIP-seq
MIRT1332178	hsa-miR-330-3p	CLIP-seq
MIRT1332181	hsa-miR-4422	CLIP-seq
MIRT1332182	hsa-miR-4520a-3p	CLIP-seq
MIRT1332183	hsa-miR-4638-3p	CLIP-seq
MIRT1332184	hsa-miR-4645-3p	CLIP-seq
MIRT1332191	hsa-miR-4659a-3p	CLIP-seq
MIRT1332192	hsa-miR-4659b-3p	CLIP-seq
MIRT1332193	hsa-miR-4703-3p	CLIP-seq
MIRT1332186	hsa-miR-520d-5p	CLIP-seq
MIRT1332187	hsa-miR-520f	CLIP-seq
MIRT1332188	hsa-miR-524-5p	CLIP-seq
MIRT1332189	hsa-miR-936	CLIP-seq
MIRT1332174	hsa-miR-1207-3p	CLIP-seq
MIRT1332190	hsa-miR-1238	CLIP-seq
MIRT2098175	hsa-miR-1910	CLIP-seq
MIRT2098176	hsa-miR-3121-5p	CLIP-seq
MIRT1332177	hsa-miR-3160-5p	CLIP-seq
MIRT2098177	hsa-miR-3179	CLIP-seq
MIRT2098178	hsa-miR-3202	CLIP-seq
MIRT2098179	hsa-miR-3614-5p	CLIP-seq
MIRT2098180	hsa-miR-3690	CLIP-seq
MIRT2098181	hsa-miR-3978	CLIP-seq
MIRT2098182	hsa-miR-4254	CLIP-seq
MIRT2098183	hsa-miR-4261	CLIP-seq
MIRT2098184	hsa-miR-4476	CLIP-seq
MIRT2098185	hsa-miR-4487	CLIP-seq
MIRT1332182	hsa-miR-4520a-3p	CLIP-seq
MIRT2098186	hsa-miR-4633-3p	CLIP-seq
MIRT1332183	hsa-miR-4638-3p	CLIP-seq
MIRT1332184	hsa-miR-4645-3p	CLIP-seq
MIRT1332191	hsa-miR-4659a-3p	CLIP-seq
MIRT1332192	hsa-miR-4659b-3p	CLIP-seq
MIRT2098187	hsa-miR-4688	CLIP-seq
MIRT1332193	hsa-miR-4703-3p	CLIP-seq
MIRT2098188	hsa-miR-486-3p	CLIP-seq
MIRT2098189	hsa-miR-499-3p	CLIP-seq
MIRT2098190	hsa-miR-499a-3p	CLIP-seq
MIRT1332187	hsa-miR-520f	CLIP-seq
MIRT1332189	hsa-miR-936	CLIP-seq
MIRT1332174	hsa-miR-1207-3p	CLIP-seq
MIRT1332190	hsa-miR-1238	CLIP-seq
MIRT1332175	hsa-miR-124	CLIP-seq
MIRT1332176	hsa-miR-1245b-3p	CLIP-seq
MIRT2618847	hsa-miR-1343	CLIP-seq
MIRT2618848	hsa-miR-3121-3p	CLIP-seq
MIRT2618849	hsa-miR-3153	CLIP-seq
MIRT1332177	hsa-miR-3160-5p	CLIP-seq
MIRT1332178	hsa-miR-330-3p	CLIP-seq
MIRT2618850	hsa-miR-3607-3p	CLIP-seq
MIRT2098179	hsa-miR-3614-5p	CLIP-seq
MIRT2618851	hsa-miR-3686	CLIP-seq
MIRT1332179	hsa-miR-3714	CLIP-seq
MIRT1332180	hsa-miR-3910	CLIP-seq
MIRT1332181	hsa-miR-4422	CLIP-seq
MIRT2618852	hsa-miR-4474-3p	CLIP-seq
MIRT1332182	hsa-miR-4520a-3p	CLIP-seq
MIRT1332183	hsa-miR-4638-3p	CLIP-seq
MIRT1332184	hsa-miR-4645-3p	CLIP-seq
MIRT2618853	hsa-miR-4646-5p	CLIP-seq
MIRT1332191	hsa-miR-4659a-3p	CLIP-seq
MIRT1332192	hsa-miR-4659b-3p	CLIP-seq
MIRT2618854	hsa-miR-4668-5p	CLIP-seq
MIRT1332193	hsa-miR-4703-3p	CLIP-seq
MIRT2618855	hsa-miR-4764-3p	CLIP-seq
MIRT2098189	hsa-miR-499-3p	CLIP-seq
MIRT2098190	hsa-miR-499a-3p	CLIP-seq
MIRT1332185	hsa-miR-506	CLIP-seq
MIRT1332186	hsa-miR-520d-5p	CLIP-seq
MIRT1332187	hsa-miR-520f	CLIP-seq
MIRT1332188	hsa-miR-524-5p	CLIP-seq
MIRT2618856	hsa-miR-604	CLIP-seq
MIRT2618857	hsa-miR-647	CLIP-seq
MIRT1332189	hsa-miR-936	CLIP-seq
MIRT1332174	hsa-miR-1207-3p	CLIP-seq
MIRT1332190	hsa-miR-1238	CLIP-seq
MIRT1332175	hsa-miR-124	CLIP-seq
MIRT1332176	hsa-miR-1245b-3p	CLIP-seq
MIRT2618847	hsa-miR-1343	CLIP-seq
MIRT2618848	hsa-miR-3121-3p	CLIP-seq
MIRT2618849	hsa-miR-3153	CLIP-seq
MIRT1332177	hsa-miR-3160-5p	CLIP-seq
MIRT1332178	hsa-miR-330-3p	CLIP-seq
MIRT2618850	hsa-miR-3607-3p	CLIP-seq
MIRT2098179	hsa-miR-3614-5p	CLIP-seq
MIRT2618851	hsa-miR-3686	CLIP-seq
MIRT1332179	hsa-miR-3714	CLIP-seq
MIRT1332180	hsa-miR-3910	CLIP-seq
MIRT1332181	hsa-miR-4422	CLIP-seq
MIRT2618852	hsa-miR-4474-3p	CLIP-seq
MIRT1332182	hsa-miR-4520a-3p	CLIP-seq
MIRT1332183	hsa-miR-4638-3p	CLIP-seq
MIRT1332184	hsa-miR-4645-3p	CLIP-seq
MIRT2618853	hsa-miR-4646-5p	CLIP-seq
MIRT1332191	hsa-miR-4659a-3p	CLIP-seq
MIRT1332192	hsa-miR-4659b-3p	CLIP-seq
MIRT2618854	hsa-miR-4668-5p	CLIP-seq
MIRT1332193	hsa-miR-4703-3p	CLIP-seq
MIRT2618855	hsa-miR-4764-3p	CLIP-seq
MIRT2098189	hsa-miR-499-3p	CLIP-seq
MIRT2098190	hsa-miR-499a-3p	CLIP-seq
MIRT1332185	hsa-miR-506	CLIP-seq
MIRT1332186	hsa-miR-520d-5p	CLIP-seq
MIRT1332187	hsa-miR-520f	CLIP-seq
MIRT1332188	hsa-miR-524-5p	CLIP-seq
MIRT2618856	hsa-miR-604	CLIP-seq
MIRT2618857	hsa-miR-647	CLIP-seq
MIRT1332189	hsa-miR-936	CLIP-seq

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GO ID	Ontology	Definition	Evidence	Reference
GO:0000776	Component	Kinetochore	IDA	15146057
GO:0005198	Function	Structural molecule activity	IBA
GO:0005198	Function	Structural molecule activity	IEA
GO:0005515	Function	Protein binding	IPI	15146057, 16189514, 16407955, 16957052, 17428803, 18160040, 18692470, 19638414, 19822759, 20696395, 24981860, 25201882, 25416956, 26496610, 27194810, 28514442, 32296183, 32814053, 33961781, 35271311
GO:0005634	Component	Nucleus	IEA
GO:0005635	Component	Nuclear envelope	IDA	15146057, 24315095
GO:0005643	Component	Nuclear pore	IEA
GO:0005643	Component	Nuclear pore	NAS	24315095
GO:0005654	Component	Nucleoplasm	IDA
GO:0005764	Component	Lysosome	IEA
GO:0005765	Component	Lysosomal membrane	IDA	28199306
GO:0005765	Component	Lysosomal membrane	IEA
GO:0005765	Component	Lysosomal membrane	TAS
GO:0005783	Component	Endoplasmic reticulum	IEA
GO:0005789	Component	Endoplasmic reticulum membrane	IEA
GO:0005789	Component	Endoplasmic reticulum membrane	TAS
GO:0005829	Component	Cytosol	TAS
GO:0006606	Process	Protein import into nucleus	IBA
GO:0006886	Process	Intracellular protein transport	NAS	7987303
GO:0006913	Process	Nucleocytoplasmic transport	NAS	27016207
GO:0012507	Component	ER to Golgi transport vesicle membrane	IEA
GO:0012507	Component	ER to Golgi transport vesicle membrane	TAS
GO:0015031	Process	Protein transport	IEA
GO:0016020	Component	Membrane	IEA
GO:0016192	Process	Vesicle-mediated transport	IEA
GO:0030127	Component	COPII vesicle coat	IBA
GO:0030127	Component	COPII vesicle coat	IDA	17499046
GO:0031080	Component	Nuclear pore outer ring	IBA
GO:0031080	Component	Nuclear pore outer ring	IDA	17360435
GO:0031080	Component	Nuclear pore outer ring	NAS	15146057
GO:0031410	Component	Cytoplasmic vesicle	IEA
GO:0031669	Process	Cellular response to nutrient levels	IDA	35831510, 36528027
GO:0032008	Process	Positive regulation of TOR signaling	IBA
GO:0032527	Process	Protein exit from endoplasmic reticulum	IBA
GO:0032527	Process	Protein exit from endoplasmic reticulum	IEA
GO:0042802	Function	Identical protein binding	IPI	18160040, 27194810
GO:0051028	Process	MRNA transport	IEA
GO:0061700	Component	GATOR2 complex	IDA	35831510, 36528027
GO:0061700	Component	GATOR2 complex	NAS	23723238
GO:0070062	Component	Extracellular exosome	HDA	19056867
GO:0090110	Process	COPII-coated vesicle cargo loading	IDA	17499046, 18843296
GO:0090114	Process	COPII-coated vesicle budding	IBA
GO:1904262	Process	Negative regulation of TORC1 signaling	NAS	23723238
GO:1904263	Process	Positive regulation of TORC1 signaling	IDA	35831510, 36528027
GO:1904263	Process	Positive regulation of TORC1 signaling	NAS	23723238

MIM	HGNC	e!Ensembl
600152	10697	ENSG00000157020

P55735

Protein name

Protein SEC13 homolog (GATOR2 complex protein SEC13) (SEC13-like protein 1) (SEC13-related protein)

Protein function

Functions as a component of the nuclear pore complex (NPC) and the COPII coat (PubMed:8972206). At the endoplasmic reticulum, SEC13 is involved in the biogenesis of COPII-coated vesicles (PubMed:8972206). Required for the exit of adipsin (CFD/AD

PDB

3BG0 , 3BG1 , 5A9Q , 7PEQ , 7R5J , 7R5K , 7UHY

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00400	WD40	4 → 41	WD domain, G-beta repeat	Repeat
PF00400	WD40	47 → 87	WD domain, G-beta repeat	Repeat
PF00400	WD40	93 → 131	WD domain, G-beta repeat	Repeat
PF00400	WD40	202 → 244	WD domain, G-beta repeat	Repeat
PF00400	WD40	254 → 290	WD domain, G-beta repeat	Repeat

Sequence

MVSVINTVDTSHEDMIHDAQMDYYGTRLATCSSDRSVKIFDVRNGGQILIADLRGHEGPV
WQVAWAHPMYGNILASCSYDRKVIIWREENGTWEKSHEHAGHDSSVNSVCWAPHDYGLIL
ACGSSDGAISLLTYTGEGQWEVKKINNAHTIGCNAVSWAPAVVPGSLIDHPSGQKPNYIK
RFASGGCDNLIKLWKEEEDGQWKEEQKLEAHSDWVRDVAWAPSIGLPTSTIASCSQDGRV
FIWTCDDASSNTWSPKLLHKFNDVVWHVSWSITANILAVSGGDNKVTLWKESVDGQWVCI
SDVNKGQGSVSASVTEGQQNEQ

Sequence length

322

Interactions

View interactions

	KEGG		Reactome
	Nucleocytoplasmic transport Protein processing in endoplasmic reticulum mTOR signaling pathway Amyotrophic lateral sclerosis		ISG15 antiviral mechanism Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal Transport of the SLBP independent Mature mRNA Transport of the SLBP Dependant Mature mRNA Transport of Mature mRNA Derived from an Intronless Transcript Transport of Mature mRNA derived from an Intron-Containing Transcript Rev-mediated nuclear export of HIV RNA Transport of Ribonucleoproteins into the Host Nucleus NS1 Mediated Effects on Host Pathways Viral Messenger RNA Synthesis NEP/NS2 Interacts with the Cellular Export Machinery Regulation of Glucokinase by Glucokinase Regulatory Protein Vpr-mediated nuclear import of PICs snRNP Assembly COPII-mediated vesicle transport MHC class II antigen presentation Separation of Sister Chromatids Resolution of Sister Chromatid Cohesion SUMOylation of DNA damage response and repair proteins SUMOylation of ubiquitinylation proteins Nuclear Pore Complex (NPC) Disassembly Regulation of HSF1-mediated heat shock response SUMOylation of SUMOylation proteins SUMOylation of chromatin organization proteins SUMOylation of RNA binding proteins Transcriptional regulation by small RNAs Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) RHO GTPases Activate Formins tRNA processing in the nucleus Mitotic Prometaphase HCMV Early Events HCMV Late Events Postmitotic nuclear pore complex (NPC) reformation Amino acids regulate mTORC1 EML4 and NUDC in mitotic spindle formation Antigen Presentation: Folding, assembly and peptide loading of class I MHC

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Show/Hide Unknown Diseases (1)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
PROGRESSIVE SUPRANUCLEAR PALSY	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (6)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Demyelinating Diseases	Demyelinating diseases	Pubtator	35143418	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus Type 2	Diabetes mellitus, type 2	Pubtator	28812028	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Heart Defects Congenital	Congenital heart defect	Pubtator	10922384	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Stomach Neoplasms	Stomach neoplasms	Pubtator	35449150	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Supranuclear Palsy Progressive	Progressive supranuclear palsy	Pubtator	33635380	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Von Hippel-Lindau Syndrome	Von Hippel-Lindau Syndrome	BEFREE	7987303		★★★★★ ★☆☆☆☆ Found in Text Mining only

SEC13 (SEC13 homolog, nuclear pore and COPII component)