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Aliases for SEC13 Gene

Aliases for SEC13 Gene

  • SEC13 Homolog, Nuclear Pore And COPII Coat Complex Component 2 3 5
  • 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 Innate Immune System and Class I MHC mediated antigen processing and presentation.

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 GATSL3 (PubMed:25457612, PubMed:27487210).

Gene Wiki entry 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
GH03G010201 2 FANTOM5 Ensembl ENCODE dbSUPER 9.8 +116.7 116667 6.7 HDGF FOXA2 PKNOX1 CREB3L1 MLX ARNT AGO1 ZFP64 ARID4B SIN3A IRAK2 TATDN2 VHL GHRLOS ARPC4 FANCD2OS GHRL SEC13 CAMK1 ARPC4-TTLL3
GH03G010436 1.7 FANTOM5 Ensembl ENCODE dbSUPER 10.5 -116.7 -116734 2.8 PKNOX1 KLF17 RAD21 TCF12 EGR1 ZSCAN5C SCRT2 FOS ETV6 EGR2 MIR885 SEC13 TATDN2 GC03P010530 GC03M010552
GH03G010247 1.4 ENCODE dbSUPER 10.7 +72.0 71962 3.0 HDGF PKNOX1 FOXA2 CREB3L1 ARNT WRNIP1 ARID4B SIN3A DMAP1 ZNF2 GHRLOS GHRL IRAK2 FANCD2OS VHL SEC13 IL17RE JAGN1 ARPC4 ARPC4-TTLL3
GH03G010251 1.3 ENCODE dbSUPER 10.7 +70.1 70057 0.2 HDGF PKNOX1 FOXA2 MLX ARID4B ZNF48 TCF12 ZNF766 GATA2 ELK1 GHRL VHL IRAK2 SEC13 FANCD2OS IL17RE PRRT3 ARPC4 TADA3 ARPC4-TTLL3
GH03G010344 0.9 ENCODE dbSUPER 11.9 -23.3 -23254 0.0 CTCF TRIM22 REST ZNF501 ZNF2 RAD21 KLF16 PATZ1 SMC3 ZNF143 SEC13 MIR885 MIR378B GC03M010355
- 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 MLX CREB3L1 AGO1 FEZF1 DMAP1 SLC30A9 ZNF143 SP3 NFYC SSRP1

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 GATSL2 and GATSL3; 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).
    SequenceCaution:
    • Sequence=AAH02634.2; Type=Erroneous initiation; Evidence={ECO:0000305};

    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

No data available for DME Specific Peptides for SEC13 Gene

Domains & 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 GATSL3 (PubMed:25457612, PubMed:27487210).

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

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. Note=In interphase, localizes at both sides of the NPC.

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

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:0006888 ER to Golgi vesicle-mediated transport IEA --
GO:0007062 sister chromatid cohesion TAS --
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

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 34 35
  • 99.48 (n)
oppossum
(Monodelphis domestica)
Mammalia SEC13 35
  • 94 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SEC13 35
  • 92 (a)
OneToOne
dog
(Canis familiaris)
Mammalia SEC13 34 35
  • 91.93 (n)
cow
(Bos Taurus)
Mammalia SEC13 34 35
  • 90.27 (n)
mouse
(Mus musculus)
Mammalia Sec13 34 16 35
  • 89.44 (n)
rat
(Rattus norvegicus)
Mammalia Sec13 34
  • 89.03 (n)
chicken
(Gallus gallus)
Aves SEC13 34 35
  • 80.94 (n)
lizard
(Anolis carolinensis)
Reptilia SEC13 35
  • 82 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia sec13 34
  • 78.75 (n)
MGC76017 34
zebrafish
(Danio rerio)
Actinopterygii sec13 34 35
  • 80.1 (n)
wufa08f09 34
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.5202 34
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP003183 34
  • 65.81 (n)
fruit fly
(Drosophila melanogaster)
Insecta sec13 34 35
  • 61.63 (n)
worm
(Caenorhabditis elegans)
Secernentea npp-20 34 35
  • 50.06 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_ACR199C 34
  • 56.67 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SEC13 34 35 37
  • 55.22 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0C16643g 34
  • 52.66 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT2G30050 34
  • 58.42 (n)
soybean
(Glycine max)
eudicotyledons Gma.3967 34
rice
(Oryza sativa)
Liliopsida Os02g0135800 34
  • 56.31 (n)
Os.8830 34
barley
(Hordeum vulgare)
Liliopsida Hv.1426 34
wheat
(Triticum aestivum)
Liliopsida Ta.2942 34
corn
(Zea mays)
Liliopsida Zm.12162 34
sea squirt
(Ciona savignyi)
Ascidiacea CSA.2429 35
  • 68 (a)
OneToOne
bread mold
(Neurospora crassa)
Ascomycetes NCU04063 34
  • 56.2 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes sec13 34
  • 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 D.I. (Hum. Mol. Genet. 1994) 2 3 4 22 64
  2. A Tumor suppressor complex with GAP activity for the Rag GTPases that signal amino acid sufficiency to mTORC1. (PMID: 23723238) Bar-Peled L. … Sabatini D.M. (Science 2013) 3 4 64
  3. Structural basis for cargo regulation of COPII coat assembly. (PMID: 18692470) Stagg S.M. … Balch W.E. (Cell 2008) 2 3 64
  4. Architecture of a coat for the nuclear pore membrane. (PMID: 18160040) Hsia K.C. … Hoelz A. (Cell 2007) 3 4 64
  5. The Ca2+-binding protein ALG-2 is recruited to endoplasmic reticulum exit sites by Sec31A and stabilizes the localization of Sec31A. (PMID: 16957052) Yamasaki A. … Komada M. (Mol. Biol. Cell 2006) 3 4 64

Products for SEC13 Gene

  • Addgene plasmids for SEC13

Sources for SEC13 Gene

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