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

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

Summary

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

Genomic context

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

Expression

  • 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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

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

Pathways from BioSystems

  • 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

Products Interactant Other Gene Complex Source Pubs Description

General gene information

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

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)

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_001276418.1NP_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:14971859
    ACE1-Sec16-like; Ancestral coatomer element 1 (ACE1) of COPII coat complex assembly protein Sec16
  2. NM_014866.1NP_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:14971859
    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_011519260.2XP_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:14971859
    ACE1-Sec16-like; Ancestral coatomer element 1 (ACE1) of COPII coat complex assembly protein Sec16
  2. XM_011519248.2XP_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:14971859
    ACE1-Sec16-like; Ancestral coatomer element 1 (ACE1) of COPII coat complex assembly protein Sec16
  3. XM_011519247.2XP_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:14971859
    ACE1-Sec16-like; Ancestral coatomer element 1 (ACE1) of COPII coat complex assembly protein Sec16
  4. XM_011519246.2XP_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:14971859
    ACE1-Sec16-like; Ancestral coatomer element 1 (ACE1) of COPII coat complex assembly protein Sec16
  5. XM_011519262.1XP_011517564.1  protein transport protein Sec16A isoform X15

    Conserved Domains (1) summary
    cd09233
    Location:12601622
    ACE1-Sec16-like; Ancestral coatomer element 1 (ACE1) of COPII coat complex assembly protein Sec16
  6. XM_011519261.1XP_011517563.1  protein transport protein Sec16A isoform X14

    Conserved Domains (1) summary
    cd09233
    Location:14821710
    ACE1-Sec16-like; Ancestral coatomer element 1 (ACE1) of COPII coat complex assembly protein Sec16
  7. XM_011519258.1XP_011517560.1  protein transport protein Sec16A isoform X12

    Conserved Domains (1) summary
    cd09233
    Location:14971803
    ACE1-Sec16-like; Ancestral coatomer element 1 (ACE1) of COPII coat complex assembly protein Sec16
  8. XM_011519257.1XP_011517559.1  protein transport protein Sec16A isoform X11

    Related
    ENSP00000387583.2, ENST00000431893.3
    Conserved Domains (1) summary
    cd09233
    Location:14971859
    ACE1-Sec16-like; Ancestral coatomer element 1 (ACE1) of COPII coat complex assembly protein Sec16
  9. XM_017015363.1XP_016870852.1  protein transport protein Sec16A isoform X8

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

    Conserved Domains (1) summary
    cd09233
    Location:14971859
    ACE1-Sec16-like; Ancestral coatomer element 1 (ACE1) of COPII coat complex assembly protein Sec16
  11. XM_011519249.1XP_011517551.1  protein transport protein Sec16A isoform X2

    Conserved Domains (1) summary
    cd09233
    Location:14971859
    ACE1-Sec16-like; Ancestral coatomer element 1 (ACE1) of COPII coat complex assembly protein Sec16
  12. XM_011519256.1XP_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:14971859
    ACE1-Sec16-like; Ancestral coatomer element 1 (ACE1) of COPII coat complex assembly protein Sec16
  13. XM_011519254.1XP_011517556.1  protein transport protein Sec16A isoform X7

    Conserved Domains (1) summary
    cd09233
    Location:14971859
    ACE1-Sec16-like; Ancestral coatomer element 1 (ACE1) of COPII coat complex assembly protein Sec16
  14. XM_011519251.1XP_011517553.1  protein transport protein Sec16A isoform X4

    Conserved Domains (1) summary
    cd09233
    Location:14971859
    ACE1-Sec16-like; Ancestral coatomer element 1 (ACE1) of COPII coat complex assembly protein Sec16
  15. XM_005266134.2XP_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:14971859
    ACE1-Sec16-like; Ancestral coatomer element 1 (ACE1) of COPII coat complex assembly protein Sec16
  16. XM_011519263.2XP_011517565.1  protein transport protein Sec16A isoform X16

    Conserved Domains (1) summary
    cd09233
    Location:12601622
    ACE1-Sec16-like; Ancestral coatomer element 1 (ACE1) of COPII coat complex assembly protein Sec16
  17. XM_011519255.2XP_011517557.1  protein transport protein Sec16A isoform X9

    Conserved Domains (1) summary
    cd09233
    Location:14971859
    ACE1-Sec16-like; Ancestral coatomer element 1 (ACE1) of COPII coat complex assembly protein Sec16
  18. XM_011519252.2XP_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:14971859
    ACE1-Sec16-like; Ancestral coatomer element 1 (ACE1) of COPII coat complex assembly protein Sec16
  19. XM_011519259.2XP_011517561.1  protein transport protein Sec16A isoform X13

    Related
    ENSP00000360771.3, OTTHUMP00000022589, ENST00000371706.7
    Conserved Domains (1) summary
    cd09233
    Location:14971859
    ACE1-Sec16-like; Ancestral coatomer element 1 (ACE1) of COPII coat complex assembly protein Sec16
  20. XM_011519250.2XP_011517552.1  protein transport protein Sec16A isoform X3

    Conserved Domains (1) summary
    cd09233
    Location:14971859
    ACE1-Sec16-like; Ancestral coatomer element 1 (ACE1) of COPII coat complex assembly protein Sec16
  21. XM_011519264.2XP_011517566.1  protein transport protein Sec16A isoform X17

    Conserved Domains (1) summary
    cd09233
    Location:14971859
    ACE1-Sec16-like; Ancestral coatomer element 1 (ACE1) of COPII coat complex assembly protein Sec16
  22. XM_017015364.1XP_016870853.1  protein transport protein Sec16A isoform X18

RNA

  1. XR_929881.2 RNA Sequence

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