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Aliases for SEC13 Gene

Aliases for SEC13 Gene

  • SEC13 Homolog, Nuclear Pore And COPII Coat Complex Component 2 3 5
  • GATOR Complex Protein SEC13 3 4
  • SEC13-Related Protein 3 4
  • SEC13-Like Protein 1 3 4
  • D3S1231E 3 4
  • SEC13L1 3 4
  • SEC13R 3 4
  • 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
  • Protein SEC13 Homolog 3
  • SEC13-Like 1 Isoform 3
  • Npp-20 3

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. Among its related pathways are Cell Cycle, Mitotic and Protein processing in endoplasmic reticulum.

UniProtKB/Swiss-Prot 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.

  • 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

Additional gene information for SEC13 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SEC13 Gene

Genomics for SEC13 Gene

Regulatory Elements for SEC13 Gene

Enhancers for SEC13 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH03H010188 2.1 FANTOM5 Ensembl ENCODE dbSUPER 18.5 +126.3 126344 12 HDGF PKNOX1 FOXA2 ARNT ARID4B SIN3A ZNF2 ZBTB7B YY1 ZNF143 BRPF1 SETD5 IRAK2 GHRLOS LINC00852 TATDN2 FANCD2 BRK1 GHRL TTLL3
GH03H009889 1.4 ENCODE dbSUPER 19.9 +430.4 430371 2 HDGF PKNOX1 ARNT ARID4B SIN3A DMAP1 ZNF2 ZBTB7B YY1 ZNF207 BRPF1 RAD18 SETD5 JAGN1 FANCD2 GHRLOS TTLL3 SEC13 LINC00852 BRK1
GH03H009883 1.8 FANTOM5 Ensembl ENCODE dbSUPER 11.4 +436.8 436797 2 PKNOX1 ARNT TCF12 GTF3C2 ZNF766 GATA2 ATF7 FOS ZNF592 SMARCA4 CIDEC IL17RC JAGN1 BRPF1 RAD18 SETD5 GHRLOS SEC13 FANCD2 LINC00852
GH03H010201 1.9 FANTOM5 Ensembl ENCODE dbSUPER 9.8 +116.7 116667 6 FOXA2 ATF1 MLX ZFP64 ARID4B DMAP1 YY1 FOS REST PPARG IRAK2 TATDN2 VHL GHRLOS ARPC4 FANCD2OS GHRL SEC13 CAMK1 ARPC4-TTLL3
GH03H010436 1.7 FANTOM5 Ensembl ENCODE dbSUPER 10.5 -116.7 -116734 2 PKNOX1 KLF17 RAD21 TCF12 EGR1 ZSCAN5C SCRT2 FOS ATF7 ETV6 MIR885 SEC13 TATDN2 GC03P010558 GC03M010552
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SEC13 on UCSC Golden Path with GeneCards custom track

Promoters for SEC13 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000148388 588 2000 PKNOX1 MLX ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 SLC30A9 ZNF207

Genomic Location for SEC13 Gene

Chromosome:
3
Start:
10,293,131 bp from pter
End:
10,321,188 bp from pter
Size:
28,058 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).

    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 isoforms=2, 338
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for SEC13 Gene

Domains & Families for SEC13 Gene

Gene Families for SEC13 Gene

Suggested Antigen Peptide Sequences for SEC13 Gene

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.
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:0005515 protein binding 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 Model Products

  • Taconic Biosciences Mouse Models for SEC13

CRISPR Products

miRNA for SEC13 Gene

miRTarBase miRNAs that target SEC13

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for SEC13
  • Applied Biological Materials Clones for SEC13
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

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
extracellular 5
nucleus 5
endoplasmic reticulum 5
cytosol 5
lysosome 5
golgi apparatus 4
cytoskeleton 2
plasma membrane 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

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:0006810 transport IEA --
GO:0006886 intracellular protein transport NAS 7987303
GO:0007062 sister chromatid cohesion TAS --
GO:0015031 protein transport IEA --
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

Unigene Clusters for SEC13 Gene

SEC13 homolog (S. cerevisiae):
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for SEC13
  • Applied Biological Materials Clones for SEC13
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

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
ECgene alternative splicing isoforms for
SEC13

Expression for SEC13 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP 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, PaxDb, MaxQB, and MOPED for SEC13 Gene



Protein tissue co-expression partners for SEC13 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SEC13 Gene:

SEC13

SOURCE GeneReport for Unigene cluster for SEC13 Gene:

Hs.166924

Evidence on tissue expression from TISSUES for SEC13 Gene

  • Nervous system(4.8)
  • Liver(4.4)
  • Blood(4.2)
  • Lung(2.2)
  • Kidney(2.1)
  • Intestine(2)
  • Pancreas(2)
genes like me logo Genes that share expression patterns with SEC13: view

Primer Products

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 33 34
  • 99.48 (n)
oppossum
(Monodelphis domestica)
Mammalia SEC13 34
  • 94 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SEC13 34
  • 92 (a)
OneToOne
dog
(Canis familiaris)
Mammalia SEC13 33 34
  • 91.93 (n)
cow
(Bos Taurus)
Mammalia SEC13 33 34
  • 90.27 (n)
mouse
(Mus musculus)
Mammalia Sec13 33 16 34
  • 89.44 (n)
rat
(Rattus norvegicus)
Mammalia Sec13 33
  • 89.03 (n)
chicken
(Gallus gallus)
Aves SEC13 33 34
  • 80.94 (n)
lizard
(Anolis carolinensis)
Reptilia SEC13 34
  • 82 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia sec13 33
  • 78.75 (n)
MGC76017 33
zebrafish
(Danio rerio)
Actinopterygii sec13 33 34
  • 80.1 (n)
wufa08f09 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.5202 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP003183 33
  • 65.81 (n)
fruit fly
(Drosophila melanogaster)
Insecta sec13 33 34
  • 61.63 (n)
worm
(Caenorhabditis elegans)
Secernentea npp-20 33 34
  • 50.06 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_ACR199C 33
  • 56.67 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SEC13 33 34 36
  • 55.22 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0C16643g 33
  • 52.66 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT2G30050 33
  • 58.42 (n)
soybean
(Glycine max)
eudicotyledons Gma.3967 33
rice
(Oryza sativa)
Liliopsida Os02g0135800 33
  • 56.31 (n)
Os.8830 33
barley
(Hordeum vulgare)
Liliopsida Hv.1426 33
wheat
(Triticum aestivum)
Liliopsida Ta.2942 33
corn
(Zea mays)
Liliopsida Zm.12162 33
sea squirt
(Ciona savignyi)
Ascidiacea CSA.2429 34
  • 68 (a)
OneToOne
bread mold
(Neurospora crassa)
Ascomycetes NCU04063 33
  • 56.2 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes sec13 33
  • 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 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)

Paralogs for SEC13 Gene

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

Pseudogenes.org Pseudogenes for SEC13 Gene

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

No data available for Paralogs for SEC13 Gene

Variants for SEC13 Gene

Sequence variations from dbSNP and Humsavar for SEC13 Gene

SNP ID Clin Chr 03 pos Sequence Context AA Info Type
rs1000000526 -- 10,304,477(+) TACCT(G/T)CTCAA intron-variant
rs1000272185 -- 10,303,902(+) TCAAA(A/G)CGCAG intron-variant
rs1000296017 -- 10,302,881(+) ACACA(C/T)GCTAC intron-variant
rs1000513850 -- 10,308,173(+) CCTCA(A/G)TCAAG intron-variant
rs1000580618 -- 10,309,516(+) GTCTT(C/T)CTTTA intron-variant

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)

Relevant External Links for SEC13 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SEC13

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

Disorders for SEC13 Gene

Relevant External Links for SEC13

Genetic Association Database (GAD)
SEC13
Human Genome Epidemiology (HuGE) Navigator
SEC13
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SEC13

No disorders were found for SEC13 Gene.

No data available for MalaCards , 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 60
  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 60
  3. 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 60
  4. Structural basis for cargo regulation of COPII coat assembly. (PMID: 18692470) Stagg SM … Balch WE (Cell 2008) 2 3 60
  5. Architecture of a coat for the nuclear pore membrane. (PMID: 18160040) Hsia KC … Hoelz A (Cell 2007) 3 4 60

Products for SEC13 Gene

  • Addgene plasmids for SEC13

Sources for SEC13 Gene

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