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 endoplasmic reticulum during the transport of proteins. Multiple alternatively spliced transcript variants have been found. [... See more...

Aliases for SEC13 Gene

Aliases for SEC13 Gene

  • SEC13 Homolog, Nuclear Pore And COPII Coat Complex Component 2 3 5
  • SEC13R 2 3 4
  • GATOR Complex Protein SEC13 3 4
  • Protein SEC13 Homolog 3 4
  • SEC13-Related Protein 3 4
  • SEC13-Like Protein 1 3 4
  • D3S1231E 3 4
  • SEC13L1 3 4
  • Npp-20 2 3
  • SEC13 Homolog, Nuclear Pore And COPII Coating Complex Component 3
  • SEC13 Homolog (S. Cerevisiae) 2
  • SEC13 (S. Cerevisiae)-Like 1 2
  • SEC13-Like 1 (S. Cerevisiae) 2
  • SEC13A 4
  • SEC13 5

External Ids for SEC13 Gene

Previous HGNC Symbols for SEC13 Gene

  • D3S1231E
  • SEC13L1

Previous GeneCards Identifiers for SEC13 Gene

  • GC03M010318
  • GC03M010335
  • GC03M010337
  • GC03M010350

Summaries for SEC13 Gene

Entrez Gene Summary for SEC13 Gene

  • 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 endoplasmic reticulum during the transport of proteins. Multiple alternatively spliced transcript variants have been found. [provided by RefSeq, Oct 2008]

GeneCards Summary for SEC13 Gene

SEC13 (SEC13 Homolog, Nuclear Pore And COPII Coat Complex Component) is a Protein Coding gene. Diseases associated with SEC13 include Craniolenticulosutural Dysplasia and Anemia, Congenital Dyserythropoietic, Type Ii. Among its related pathways are Cell Cycle, Mitotic and Signaling by GPCR. An important paralog of this gene is SEH1L.

UniProtKB/Swiss-Prot Summary for SEC13 Gene

  • Functions as a component of the nuclear pore complex (NPC) and the COPII coat. At the endoplasmic reticulum, SEC13 is involved in the biogenesis of COPII-coated vesicles (PubMed:8972206). Required for the exit of adipsin (CFD/ADN), an adipocyte-secreted protein from the endoplasmic reticulum (By similarity).
  • As a component of the GATOR subcomplex GATOR2, functions within the amino acid-sensing branch of the TORC1 signaling pathway. Indirectly activates mTORC1 and the TORC1 signaling pathway through the inhibition of the GATOR1 subcomplex (PubMed:23723238). It is negatively regulated by the upstream amino acid sensors SESN2 and CASTOR1 (PubMed:25457612, PubMed:27487210).

Gene Wiki entry for SEC13 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SEC13 Gene

Genomics for SEC13 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SEC13 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SEC13 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SEC13

Top Transcription factor binding sites by QIAGEN in the SEC13 gene promoter:
  • CUTL1
  • E2F-3a
  • E2F-4
  • E2F-5
  • RP58

Genomic Locations for SEC13 Gene

Latest Assembly
chr3:10,293,131-10,321,112
(GRCh38/hg38)
Size:
27,982 bases
Orientation:
Minus strand

Previous Assembly
chr3:10,342,615-10,362,796
(GRCh37/hg19 by Entrez Gene)
Size:
20,182 bases
Orientation:
Minus strand

chr3:10,334,815-10,362,862
(GRCh37/hg19 by Ensembl)
Size:
28,048 bases
Orientation:
Minus strand

Genomic View for SEC13 Gene

Genes around SEC13 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SEC13 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SEC13 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SEC13 Gene

Proteins for SEC13 Gene

  • Protein details for SEC13 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P55735-SEC13_HUMAN
    Recommended name:
    Protein SEC13 homolog
    Protein Accession:
    P55735
    Secondary Accessions:
    • A8MV37
    • B4DXJ1
    • Q5BJF0
    • Q9BRM6
    • Q9BUG7

    Protein attributes for SEC13 Gene

    Size:
    322 amino acids
    Molecular mass:
    35541 Da
    Quaternary structure:
    • At the nuclear pore: component of the Y-shaped Nup107-160 subcomplex of the nuclear pore complex (NPC). The Nup107-160 subcomplex includes NUP160, NUP133, NUP107, NUP98, NUP85, NUP43, NUP37, SEH1 and SEC13. At the COPII coat complex: interacts with SEC31A and SEC31B. Within the GATOR complex, component of the GATOR2 subcomplex, made of MIOS, SEC13, SEH1L, WDR24 and WDR59. The GATOR complex strongly interacts with RRAGA/RRAGC and RRAGB/RRAGC heterodimers (PubMed:14517296, PubMed:16495487, PubMed:16957052, PubMed:18160040, PubMed:23723238). The GATOR2 complex interacts with CASTOR2 and CASTOR1; the interaction is negatively regulated by arginine (PubMed:26972053). The GATOR2 complex interacts with SESN1, SESN2 and SESN3; the interaction is negatively regulated by amino acids (PubMed:25263562, PubMed:25457612). Interacts with SEC16A (PubMed:17428803, PubMed:19638414, PubMed:25201882). Interacts with SEC16B (PubMed:22355596).

    Three dimensional structures from OCA and Proteopedia for SEC13 Gene

    Alternative splice isoforms for SEC13 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SEC13 Gene

Post-translational modifications for SEC13 Gene

  • Ubiquitination at Lys38
  • Modification sites at PhosphoSitePlus

Antibodies for research

  • Abcam antibodies for SEC13
  • Boster Bio Antibodies for SEC13
  • Santa Cruz Biotechnology (SCBT) Antibodies for SEC13

No data available for DME Specific Peptides for SEC13 Gene

Domains & Families for SEC13 Gene

Gene Families for SEC13 Gene

Protein Domains for SEC13 Gene

InterPro:
Blocks:
  • G-protein beta WD-40 repeat signature

Suggested Antigen Peptide Sequences for SEC13 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ59881, highly similar to SEC13-related protein (A8MWR8_HUMAN)
  • SEC13-related protein (SEC13_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P55735

UniProtKB/Swiss-Prot:

SEC13_HUMAN :
  • Belongs to the WD repeat SEC13 family.
Family:
  • Belongs to the WD repeat SEC13 family.
genes like me logo Genes that share domains with SEC13: view

Function for SEC13 Gene

Molecular function for SEC13 Gene

UniProtKB/Swiss-Prot Function:
Functions as a component of the nuclear pore complex (NPC) and the COPII coat. At the endoplasmic reticulum, SEC13 is involved in the biogenesis of COPII-coated vesicles (PubMed:8972206). Required for the exit of adipsin (CFD/ADN), an adipocyte-secreted protein from the endoplasmic reticulum (By similarity).
UniProtKB/Swiss-Prot Function:
As a component of the GATOR subcomplex GATOR2, functions within the amino acid-sensing branch of the TORC1 signaling pathway. Indirectly activates mTORC1 and the TORC1 signaling pathway through the inhibition of the GATOR1 subcomplex (PubMed:23723238). It is negatively regulated by the upstream amino acid sensors SESN2 and CASTOR1 (PubMed:25457612, PubMed:27487210).

Phenotypes From GWAS Catalog for SEC13 Gene

Gene Ontology (GO) - Molecular Function for SEC13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005198 structural molecule activity IEA --
GO:0005515 protein binding IEA,IPI 15146057
GO:0042802 identical protein binding IPI 18160040
genes like me logo Genes that share ontologies with SEC13: view
genes like me logo Genes that share phenotypes with SEC13: view

Animal Models for research

  • Taconic Biosciences Mouse Models for SEC13

miRNA for SEC13 Gene

miRTarBase miRNAs that target SEC13

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SEC13

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for SEC13 Gene

Localization for SEC13 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SEC13 Gene

Cytoplasmic vesicle, COPII-coated vesicle membrane. Peripheral membrane protein. Cytoplasmic side. Endoplasmic reticulum membrane. Peripheral membrane protein. Cytoplasmic side. Nucleus, nuclear pore complex. Lysosome membrane. Note=In interphase, localizes at both sides of the NPC. {ECO:0000269 PubMed:14517296}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SEC13 gene
Compartment Confidence
nucleus 5
lysosome 5
extracellular 4
cytosol 4
golgi apparatus 4
cytoskeleton 3
endoplasmic reticulum 3
plasma membrane 2
endosome 2
mitochondrion 1
peroxisome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (3)
  • Vesicles (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SEC13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000139 Golgi membrane IEA --
GO:0000776 colocalizes_with kinetochore IDA 15146057
GO:0005634 nucleus IEA --
GO:0005635 nuclear envelope IDA 15146057
GO:0005643 nuclear pore IEA --
genes like me logo Genes that share ontologies with SEC13: view

Pathways & Interactions for SEC13 Gene

genes like me logo Genes that share pathways with SEC13: view

Pathways by source for SEC13 Gene

4 GeneGo (Thomson Reuters) pathways for SEC13 Gene
  • Delta508-CFTR traffic / ER-to-Golgi in CF
  • Normal wtCFTR traffic / ER-to-Golgi
  • Transport Clathrin-coated vesicle cycle
  • wtCFTR and delta508-CFTR traffic / Generic schema (norm and CF)

Gene Ontology (GO) - Biological Process for SEC13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002474 antigen processing and presentation of peptide antigen via MHC class I TAS --
GO:0006110 regulation of glycolytic process TAS --
GO:0006406 mRNA export from nucleus TAS --
GO:0006409 tRNA export from nucleus TAS --
GO:0006606 protein import into nucleus IBA 21873635
genes like me logo Genes that share ontologies with SEC13: view

No data available for SIGNOR curated interactions for SEC13 Gene

Drugs & Compounds for SEC13 Gene

No Compound Related Data Available

Transcripts for SEC13 Gene

mRNA/cDNA for SEC13 Gene

5 REFSEQ mRNAs :
16 NCBI additional mRNA sequence :
19 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SEC13

Alternative Splicing Database (ASD) splice patterns (SP) for SEC13 Gene

ExUns: 1a · 1b · 1c · 1d ^ 2a · 2b · 2c ^ 3a · 3b ^ 4 ^ 5 ^ 6 ^ 7a · 7b ^ 8a · 8b ^ 9a · 9b · 9c ^ 10a · 10b ^ 11a · 11b · 11c · 11d ^ 12 ^
SP1: - - - - - - - - - - - - -
SP2: - - - - - - - - - - -
SP3: - - - - -
SP4: - - - - - - - - - - -
SP5: - - - - -
SP6: - - - - - - - - - - - - - - - - - -
SP7: -
SP8: - - - - - - - - -
SP9: - - - - - - - - - - - -
SP10: - - - - - - -
SP11:
SP12: - - - - - - - - - -
SP13: - - - - - -
SP14: - - - - - - -
SP15: - - - -
SP16: - - - - - - - -
SP17:
SP18: -

ExUns: 13a · 13b ^ 14a · 14b ^ 15 ^ 16
SP1: -
SP2: -
SP3: -
SP4:
SP5:
SP6: - -
SP7: -
SP8:
SP9:
SP10:
SP11: - -
SP12:
SP13:
SP14:
SP15:
SP16:
SP17:
SP18:

Relevant External Links for SEC13 Gene

GeneLoc Exon Structure for
SEC13

Expression for SEC13 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SEC13 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for SEC13 Gene

This gene is overexpressed in Amniocyte (8.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SEC13 Gene



Protein tissue co-expression partners for SEC13 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SEC13

SOURCE GeneReport for Unigene cluster for SEC13 Gene:

Hs.166924

Evidence on tissue expression from TISSUES for SEC13 Gene

  • Nervous system(4.9)
  • Liver(4.5)
  • Blood(4.4)
  • Kidney(3)
  • Skin(2.9)
  • Lung(2.8)
  • Pancreas(2.7)
  • Intestine(2.5)
  • Muscle(2.4)
  • Stomach(2.4)
  • Heart(2.3)
  • Thyroid gland(2.1)
  • Spleen(2.1)
  • Lymph node(2)
genes like me logo Genes that share expression patterns with SEC13: view

Primer products for research

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for SEC13 Gene

Orthologs for SEC13 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for SEC13 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia SEC13 29 30
  • 99.48 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia SEC13 30
  • 94 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia SEC13 30
  • 92 (a)
OneToOne
Dog
(Canis familiaris)
Mammalia SEC13 29 30
  • 91.93 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia SEC13 29 30
  • 90.27 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Sec13 29 16 30
  • 89.44 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Sec13 29
  • 89.03 (n)
Chicken
(Gallus gallus)
Aves SEC13 29 30
  • 80.94 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia SEC13 30
  • 82 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia sec13 29
  • 78.75 (n)
MGC76017 29
Zebrafish
(Danio rerio)
Actinopterygii sec13 29 30
  • 80.1 (n)
OneToOne
wufa08f09 29
Rainbow Trout
(Oncorhynchus mykiss)
Actinopterygii Omy.5202 29
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP003183 29
  • 65.81 (n)
Fruit Fly
(Drosophila melanogaster)
Insecta sec13 29 30
  • 61.63 (n)
OneToOne
Worm
(Caenorhabditis elegans)
Secernentea npp-20 29 30
  • 50.06 (n)
OneToOne
A. gosspyii yeast
(Eremothecium gossypii)
Saccharomycetes AGOS_ACR199C 29
  • 56.67 (n)
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SEC13 29 30 32
  • 55.22 (n)
OneToOne
K. Lactis Yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0C16643g 29
  • 52.66 (n)
Thale Cress
(Arabidopsis thaliana)
eudicotyledons AT2G30050 29
  • 58.42 (n)
Soybean
(Glycine max)
eudicotyledons Gma.3967 29
Rice
(Oryza sativa)
Liliopsida Os02g0135800 29
  • 56.31 (n)
Os.8830 29
Barley
(Hordeum vulgare)
Liliopsida Hv.1426 29
Wheat
(Triticum aestivum)
Liliopsida Ta.2942 29
Corn
(Zea mays)
Liliopsida Zm.12162 29
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.2429 30
  • 68 (a)
OneToOne
Bread mold
(Neurospora crassa)
Ascomycetes NCU04063 29
  • 56.2 (n)
Fission Yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes sec13 29
  • 53.64 (n)
Species where no ortholog for SEC13 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)

Evolution for SEC13 Gene

ENSEMBL:
Gene Tree for SEC13 (if available)
TreeFam:
Gene Tree for SEC13 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SEC13: view image
Alliance of Genome Resources:
Additional Orthologs for SEC13

Paralogs for SEC13 Gene

Paralogs for SEC13 Gene

(3) SIMAP similar genes for SEC13 Gene using alignment to 7 proteins:

  • SEC13_HUMAN
  • A8MXL6_HUMAN
  • B4DXJ1_HUMAN
  • C9J0S2_HUMAN
  • C9JBJ5_HUMAN
  • C9JIB6_HUMAN
  • E7ERC8_HUMAN

Pseudogenes.org Pseudogenes for SEC13 Gene

genes like me logo Genes that share paralogs with SEC13: view

Variants for SEC13 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SEC13 Gene

SNP ID Clinical significance and condition Chr 03 pos Variation AA Info Type
rs34078590 -- p.Ser172Leu

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for SEC13 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for SEC13 Gene

Variant ID Type Subtype PubMed ID
dgv762e201 CNV deletion 23290073
esv2556727 CNV deletion 19546169
esv3383286 CNV duplication 20981092
esv4117 OTHER complex 18987735
nsv1073204 CNV deletion 25765185
nsv1121603 CNV deletion 24896259
nsv436362 CNV deletion 17901297
nsv436869 CNV insertion 17901297
nsv508903 CNV insertion 20534489

Variation tolerance for SEC13 Gene

Residual Variation Intolerance Score: 18.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.16; 23.50% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SEC13 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SEC13
Leiden Open Variation Database (LOVD)
SEC13

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SEC13 Gene

Disorders for SEC13 Gene

MalaCards: The human disease database

(3) MalaCards diseases for SEC13 Gene - From: COP

- elite association - COSMIC cancer census association via MalaCards
Search SEC13 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for SEC13

Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with SEC13: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SEC13 Gene

Publications for SEC13 Gene

  1. Molecular characterization of a novel human gene, SEC13R, related to the yeast secretory pathway gene SEC13, and mapping to a conserved linkage group on human chromosome 3p24-p25 and mouse chromosome 6. (PMID: 7987303) Swaroop A … Smith DI (Human molecular genetics 1994) 2 3 4 22
  2. KICSTOR recruits GATOR1 to the lysosome and is necessary for nutrients to regulate mTORC1. (PMID: 28199306) Wolfson RL … Sabatini DM (Nature 2017) 3 4
  3. The Sestrins interact with GATOR2 to negatively regulate the amino-acid-sensing pathway upstream of mTORC1. (PMID: 25263562) Chantranupong L … Sabatini DM (Cell reports 2014) 3 4
  4. Leucine-rich repeat kinase 2 regulates Sec16A at ER exit sites to allow ER-Golgi export. (PMID: 25201882) Cho HJ … Cai H (The EMBO journal 2014) 3 4
  5. A Tumor suppressor complex with GAP activity for the Rag GTPases that signal amino acid sufficiency to mTORC1. (PMID: 23723238) Bar-Peled L … Sabatini DM (Science (New York, N.Y.) 2013) 3 4

Products for SEC13 Gene

Sources for SEC13 Gene