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SEC16A SEC16 homolog A, endoplasmic reticulum export factor [ Homo sapiens (human) ]

Gene ID: 9919, updated on 18-Nov-2018

Summary

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Official Symbol
SEC16Aprovided by HGNC
Official Full Name
SEC16 homolog A, endoplasmic reticulum export factorprovided by HGNC
Primary source
HGNC:HGNC:29006
See related
Ensembl:ENSG00000148396 MIM:612854; Vega:OTTHUMG00000020932
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
p250; SEC16L; KIAA0310
Summary
This gene encodes a protein that forms part of the Sec16 complex. This protein has a role in protein transport from the endoplasmic reticulum (ER) to the Golgi and mediates COPII vesicle formation at the transitional ER. Alternative splicing results in multiple transcript variants that encode different protein isoforms. [provided by RefSeq, Feb 2013]
Expression
Ubiquitous expression in stomach (RPKM 11.7), bone marrow (RPKM 11.4) and 25 other tissues See more
Orthologs
mouse all

Genomic context

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See SEC16A in Genome Data Viewer
Location:
9q34.3
Exon count:
37
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 9 NC_000009.12 (136440096..136484552, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (139334548..139379297, complement)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene endosome associated trafficking regulator 1 Neighboring gene peptidase, mitochondrial processing alpha subunit Neighboring gene inositol polyphosphate-5-phosphatase E Neighboring gene chromosome 9 open reading frame 163 Neighboring gene notch 1 Neighboring gene microRNA 4673 Neighboring gene microRNA 4674

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Jun 15 11:32:44 2016

Bibliography

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Related articles in PubMed

  1. Regulation of Sec16 levels and dynamics links proliferation and secretion. Tillmann KD, et al. J Cell Sci, 2015 Feb 15. PMID 25526736
  2. Next generation exome sequencing of paediatric inflammatory bowel disease patients identifies rare and novel variants in candidate genes. Christodoulou K, et al. Gut, 2013 Jul. PMID 22543157, Free PMC Article
  3. Are breast cancers driven by fusion genes? Edwards PA, et al. Breast Cancer Res, 2012 Mar 16. PMID 22424054, Free PMC Article
  4. Sec12 binds to Sec16 at transitional ER sites. Montegna EA, et al. PLoS One, 2012. PMID 22347445, Free PMC Article
  5. Sec16A defines the site for vesicle budding from the endoplasmic reticulum on exit from mitosis. Hughes H, et al. J Cell Sci, 2010 Dec 1. PMID 21045114, Free PMC Article

See all (81) citations in PubMed

See citations in PubMed for homologs of this gene provided by HomoloGene

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

  1. these findings highlight a novel function of Sec16A as an essential mediator of endoplasmic reticulum stress-associated unconventional secretion.
    Title: Sec16A is critical for both conventional and unconventional secretion of CFTR.
  2. Sec16A also stabilized the interacting ubiquitin ligase RNF152, which localizes to the lysosome and has structural similarity with RNF183
    Title: Sec16A, a key protein in COPII vesicle formation, regulates the stability and localization of the novel ubiquitin ligase RNF183.
  3. Mammalian endoplasmic reticulum exit sites are organized by TANGO1 acting as a scaffold, in cooperation with Sec16 for efficient secretion.
    Title: TANGO1 recruits Sec16 to coordinately organize ER exit sites for efficient secretion.
  4. Results suggest that it is the presence of rare syntenic SEC16A and MAMDC4 deletions that increases susceptibility to axial spondyloarthritis in family members who carry the HLA-B*27 allele.
    Title: Private rare deletions in SEC16A and MAMDC4 may represent novel pathogenic variants in familial axial spondyloarthritis.
  5. growth factors modulate Sec16 protein levels and dynamics. Sec16 acts as part of a coherent feed-forward loop, which integrates secretion and growth factor signaling.
    Title: Regulation of Sec16 levels and dynamics links proliferation and secretion.
  6. LRRK2 regulates the anterograde endoplasmic reticulum (ER)-Golgi transport through anchoring Sec16A at the endoplasmic reticulum exit sites (ERES).
    Title: Leucine-rich repeat kinase 2 regulates Sec16A at ER exit sites to allow ER-Golgi export.
  7. Data show that knockdown of Sec16B but not Sec16A by RNAi affected the morphology of peroxisomes, inhibited the transport of Pex16 from the ER to peroxisomes, and suppressed expression of Pex3.
    Title: Sec16B is involved in the endoplasmic reticulum export of the peroxisomal membrane biogenesis factor peroxin 16 (Pex16) in mammalian cells.
  8. Sec16A remains associated with endoplasmic reticulum exit sites throughout mitosis.
    Title: Sec16A defines the site for vesicle budding from the endoplasmic reticulum on exit from mitosis.
  9. These data are consistent with a model where Sec16 acts as a platform for COPII assembly at endoplasmic reticulum exit sites.
    Title: Organisation of human ER-exit sites: requirements for the localisation of Sec16 to transitional ER.
  10. Results suggest that KIAA0310p, a mammalian homologue of yeast Sec16, builds up endoplasmic reticulum (ER) exit sites in cooperation with p125 and plays a role in membrane traffic from the ER.
    Title: Mammalian Sec16/p250 plays a role in membrane traffic from the endoplasmic reticulum.
Submit: New GeneRIF Correction See all GeneRIFs (12)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

NHGRI GWAS Catalog

Description
Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47.
NHGRI GWA Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from BioSystems

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  • Asparagine N-linked glycosylation, organism-specific biosystem (from REACTOME)
    Asparagine N-linked glycosylation, organism-specific biosystemN-linked glycosylation is the most important form of post-translational modification for proteins synthesized and folded in the Endoplasmic Reticulum (Stanley et al. 2009). An early study in 1999 rev...
  • COPII (Coat Protein 2) Mediated Vesicle Transport, organism-specific biosystem (from REACTOME)
    COPII (Coat Protein 2) Mediated Vesicle Transport, organism-specific biosystemCOPII components (known as Sec13p, Sec23p, Sec24p, Sec31p, and Sar1p in yeast) traffic cargo from the endoplasmic reticulum to the ER-Golgi intermediate compartment (ERGIC). COPII-coated vesicles wer...
  • ER to Golgi Anterograde Transport, organism-specific biosystem (from REACTOME)
    ER to Golgi Anterograde Transport, organism-specific biosystemSecretory cargo destined to be secreted or to arrive at the plasma membrane (PM) leaves the ER via distinct exit sites. This cargo is destined for the Golgi apparatus for further processing.
  • Membrane Trafficking, organism-specific biosystem (from REACTOME)
    Membrane Trafficking, organism-specific biosystemThe secretory membrane system allows a cell to regulate delivery of newly synthesized proteins, carbohydrates, and lipids to the cell surface, a necessity for growth and homeostasis. The system is ma...
  • Metabolism of proteins, organism-specific biosystem (from REACTOME)
    Metabolism of proteins, organism-specific biosystemProtein metabolism comprises the pathways of translation, post-translational modification and protein folding.
  • Post-translational protein modification, organism-specific biosystem (from REACTOME)
    Post-translational protein modification, organism-specific biosystemAfter translation, many newly formed proteins undergo further covalent modifications that alter their functional properties and that are essentially irreversible under physiological conditions in the...
  • Transport to the Golgi and subsequent modification, organism-specific biosystem (from REACTOME)
    Transport to the Golgi and subsequent modification, organism-specific biosystemAt least two mechanisms of transport of proteins from the ER to the Golgi have been described. One is a general flow requiring no export signals (Wieland et al, 1987; Martinez-Menarguez et al, 1999)....
  • Vesicle-mediated transport, organism-specific biosystem (from REACTOME)
    Vesicle-mediated transport, organism-specific biosystemThe transit of proteins and other cargo through the cell requires a cellular transport process in which transported substances are moved in membrane-bounded vesicles. Transported substances are enclo...

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ26737, KIAA0310

Gene Ontology Provided by GOA

Function Evidence Code Pubs
protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
COPII vesicle coating IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
COPII vesicle coating TAS
Traceable Author Statement
more info
  
ER to Golgi vesicle-mediated transport IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Golgi organization IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
Golgi to plasma membrane CFTR protein transport IMP
Inferred from Mutant Phenotype
more info
 PubMed 
endoplasmic reticulum organization IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
endoplasmic reticulum organization IDA
Inferred from Direct Assay
more info
 PubMed 
endoplasmic reticulum organization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
positive regulation of protein exit from endoplasmic reticulum IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
protein exit from endoplasmic reticulum ISS
Inferred from Sequence or Structural Similarity
more info
  
protein localization to endoplasmic reticulum exit site IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
protein localization to endoplasmic reticulum exit site IMP
Inferred from Mutant Phenotype
more info
 PubMed 
protein localization to plasma membrane ISS
Inferred from Sequence or Structural Similarity
more info
  
protein stabilization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
response to endoplasmic reticulum stress IDA
Inferred from Direct Assay
more info
 PubMed 
substantia nigra development HEP PubMed 
Component Evidence Code Pubs
ER to Golgi transport vesicle membrane IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
Golgi apparatus IDA
Inferred from Direct Assay
more info
  
Golgi membrane IEA
Inferred from Electronic Annotation
more info
  
cytosol IDA
Inferred from Direct Assay
more info
 PubMed 
cytosol TAS
Traceable Author Statement
more info
  
endoplasmic reticulum IDA
Inferred from Direct Assay
more info
  
endoplasmic reticulum exit site IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
endoplasmic reticulum exit site IDA
Inferred from Direct Assay
more info
 PubMed 
endoplasmic reticulum membrane IDA
Inferred from Direct Assay
more info
 PubMed 
organelle membrane IDA
Inferred from Direct Assay
more info
 PubMed 
perinuclear region of cytoplasm ISS
Inferred from Sequence or Structural Similarity
more info
  

General protein information

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Preferred Names
protein transport protein Sec16A
Names
protein SEC16 homolog A
NP_001263347.1
NP_055681.1
XP_005266191.1
XP_011517548.1
XP_011517549.1
XP_011517550.1
XP_011517551.1
XP_011517552.1
XP_011517553.1
XP_011517554.1
XP_011517555.1
XP_011517556.1
XP_011517557.1
XP_011517558.1
XP_011517559.1
XP_011517560.1
XP_011517561.1
XP_011517562.1
XP_011517563.1
XP_011517564.1
XP_011517565.1
XP_011517566.1
XP_016870852.1
XP_016870853.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001276418.1 → NP_001263347.1  protein transport protein Sec16A isoform 2

    See identical proteins and their annotated locations for NP_001263347.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and lacks two alternate in-frame exons in the coding region compared to variant 1. It encodes isoform 2 which is shorter compared to isoform 1.
    Source sequence(s)
    AB002308, AB593115, BC070488, BM975558
    Consensus CDS
    CCDS75936.1
    UniProtKB/Swiss-Prot
    O15027
    UniProtKB/TrEMBL
    F1T0I1
    Related
    ENSP00000290037.7, ENST00000290037.10
    Conserved Domains (1) summary
    cd09233
    Location:1497 → 1859
    ACE1-Sec16-like; Ancestral coatomer element 1 (ACE1) of COPII coat complex assembly protein Sec16

  2. NM_014866.1 → NP_055681.1  protein transport protein Sec16A isoform 1

    See identical proteins and their annotated locations for NP_055681.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AB002308, BM975558
    Consensus CDS
    CCDS55351.1
    UniProtKB/Swiss-Prot
    O15027
    UniProtKB/TrEMBL
    J3KNL6
    Conserved Domains (1) summary
    cd09233
    Location:1497 → 1859
    ACE1-Sec16-like; Ancestral coatomer element 1 (ACE1) of COPII coat complex assembly protein Sec16

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000009.12 Reference GRCh38.p12 Primary Assembly

    Range
    136440096..136484552 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011519260.2 → XP_011517562.1  protein transport protein Sec16A isoform X1

    See identical proteins and their annotated locations for XP_011517562.1

    Conserved Domains (1) summary
    cd09233
    Location:1497 → 1859
    ACE1-Sec16-like; Ancestral coatomer element 1 (ACE1) of COPII coat complex assembly protein Sec16

  2. XM_011519248.2 → XP_011517550.1  protein transport protein Sec16A isoform X1

    See identical proteins and their annotated locations for XP_011517550.1

    Conserved Domains (1) summary
    cd09233
    Location:1497 → 1859
    ACE1-Sec16-like; Ancestral coatomer element 1 (ACE1) of COPII coat complex assembly protein Sec16

  3. XM_011519247.2 → XP_011517549.1  protein transport protein Sec16A isoform X1

    See identical proteins and their annotated locations for XP_011517549.1

    Conserved Domains (1) summary
    cd09233
    Location:1497 → 1859
    ACE1-Sec16-like; Ancestral coatomer element 1 (ACE1) of COPII coat complex assembly protein Sec16

  4. XM_011519246.2 → XP_011517548.1  protein transport protein Sec16A isoform X1

    See identical proteins and their annotated locations for XP_011517548.1

    Conserved Domains (1) summary
    cd09233
    Location:1497 → 1859
    ACE1-Sec16-like; Ancestral coatomer element 1 (ACE1) of COPII coat complex assembly protein Sec16

  5. XM_011519262.1 → XP_011517564.1  protein transport protein Sec16A isoform X15

    Conserved Domains (1) summary
    cd09233
    Location:1260 → 1622
    ACE1-Sec16-like; Ancestral coatomer element 1 (ACE1) of COPII coat complex assembly protein Sec16

  6. XM_011519261.1 → XP_011517563.1  protein transport protein Sec16A isoform X14

    Conserved Domains (1) summary
    cd09233
    Location:1482 → 1710
    ACE1-Sec16-like; Ancestral coatomer element 1 (ACE1) of COPII coat complex assembly protein Sec16

  7. XM_011519258.1 → XP_011517560.1  protein transport protein Sec16A isoform X12

    Conserved Domains (1) summary
    cd09233
    Location:1497 → 1803
    ACE1-Sec16-like; Ancestral coatomer element 1 (ACE1) of COPII coat complex assembly protein Sec16

  8. XM_011519257.1 → XP_011517559.1  protein transport protein Sec16A isoform X11

    Related
    ENSP00000387583.2, ENST00000431893.3
    Conserved Domains (1) summary
    cd09233
    Location:1497 → 1859
    ACE1-Sec16-like; Ancestral coatomer element 1 (ACE1) of COPII coat complex assembly protein Sec16

  9. XM_017015363.1 → XP_016870852.1  protein transport protein Sec16A isoform X8

  10. XM_011519253.1 → XP_011517555.1  protein transport protein Sec16A isoform X6

    Conserved Domains (1) summary
    cd09233
    Location:1497 → 1859
    ACE1-Sec16-like; Ancestral coatomer element 1 (ACE1) of COPII coat complex assembly protein Sec16

  11. XM_011519249.1 → XP_011517551.1  protein transport protein Sec16A isoform X2

    Conserved Domains (1) summary
    cd09233
    Location:1497 → 1859
    ACE1-Sec16-like; Ancestral coatomer element 1 (ACE1) of COPII coat complex assembly protein Sec16

  12. XM_011519256.1 → XP_011517558.1  protein transport protein Sec16A isoform X10

    See identical proteins and their annotated locations for XP_011517558.1

    UniProtKB/TrEMBL
    F1T0I1
    Conserved Domains (1) summary
    cd09233
    Location:1497 → 1859
    ACE1-Sec16-like; Ancestral coatomer element 1 (ACE1) of COPII coat complex assembly protein Sec16

  13. XM_011519254.1 → XP_011517556.1  protein transport protein Sec16A isoform X7

    Conserved Domains (1) summary
    cd09233
    Location:1497 → 1859
    ACE1-Sec16-like; Ancestral coatomer element 1 (ACE1) of COPII coat complex assembly protein Sec16

  14. XM_011519251.1 → XP_011517553.1  protein transport protein Sec16A isoform X4

    Conserved Domains (1) summary
    cd09233
    Location:1497 → 1859
    ACE1-Sec16-like; Ancestral coatomer element 1 (ACE1) of COPII coat complex assembly protein Sec16

  15. XM_005266134.2 → XP_005266191.1  protein transport protein Sec16A isoform X1

    See identical proteins and their annotated locations for XP_005266191.1

    Conserved Domains (1) summary
    cd09233
    Location:1497 → 1859
    ACE1-Sec16-like; Ancestral coatomer element 1 (ACE1) of COPII coat complex assembly protein Sec16

  16. XM_011519263.2 → XP_011517565.1  protein transport protein Sec16A isoform X16

    Conserved Domains (1) summary
    cd09233
    Location:1260 → 1622
    ACE1-Sec16-like; Ancestral coatomer element 1 (ACE1) of COPII coat complex assembly protein Sec16

  17. XM_011519255.2 → XP_011517557.1  protein transport protein Sec16A isoform X9

    Conserved Domains (1) summary
    cd09233
    Location:1497 → 1859
    ACE1-Sec16-like; Ancestral coatomer element 1 (ACE1) of COPII coat complex assembly protein Sec16

  18. XM_011519252.2 → XP_011517554.1  protein transport protein Sec16A isoform X5

    See identical proteins and their annotated locations for XP_011517554.1

    UniProtKB/Swiss-Prot
    O15027
    UniProtKB/TrEMBL
    J3KNL6
    Related
    ENSP00000325827.7, ENST00000313050.11
    Conserved Domains (1) summary
    cd09233
    Location:1497 → 1859
    ACE1-Sec16-like; Ancestral coatomer element 1 (ACE1) of COPII coat complex assembly protein Sec16

  19. XM_011519259.2 → XP_011517561.1  protein transport protein Sec16A isoform X13

    Related
    ENSP00000360771.3, OTTHUMP00000022589, ENST00000371706.7
    Conserved Domains (1) summary
    cd09233
    Location:1497 → 1859
    ACE1-Sec16-like; Ancestral coatomer element 1 (ACE1) of COPII coat complex assembly protein Sec16

  20. XM_011519250.2 → XP_011517552.1  protein transport protein Sec16A isoform X3

    Conserved Domains (1) summary
    cd09233
    Location:1497 → 1859
    ACE1-Sec16-like; Ancestral coatomer element 1 (ACE1) of COPII coat complex assembly protein Sec16

  21. XM_011519264.2 → XP_011517566.1  protein transport protein Sec16A isoform X17

    Conserved Domains (1) summary
    cd09233
    Location:1497 → 1859
    ACE1-Sec16-like; Ancestral coatomer element 1 (ACE1) of COPII coat complex assembly protein Sec16

  22. XM_017015364.1 → XP_016870853.1  protein transport protein Sec16A isoform X18

RNA

  1. XR_929881.2 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O15027.4 GenPept UniProtKB/Swiss-Prot:O15027

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