Human Gene SEC16A (ENST00000684901.1_4) from GENCODE V47lift37
  Description: SEC16 homolog A, endoplasmic reticulum export factor, transcript variant 1 (from RefSeq NM_014866.2)
Gencode Transcript: ENST00000684901.1_4
Gencode Gene: ENSG00000148396.19_17
Transcript (Including UTRs)
   Position: hg19 chr9:139,334,557-139,377,492 Size: 42,936 Total Exon Count: 32 Strand: -
Coding Region
   Position: hg19 chr9:139,336,207-139,372,067 Size: 35,861 Coding Exon Count: 30 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr9:139,334,557-139,377,492)mRNA (may differ from genome)Protein (2357 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedReactomeUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SC16A_HUMAN
DESCRIPTION: RecName: Full=Protein transport protein Sec16A; AltName: Full=SEC16 homolog A;
FUNCTION: Defines endoplasmic reticulum exit sites (ERES) and is required for secretory cargo traffic from the endoplasmic reticulum to the Golgi apparatus. SAR1A-GTP-dependent assembly of SEC16A on the ER membrane forms an organized scaffold defining an ERES. Required for normal transitional endoplasmic reticulum (tER) organization.
SUBUNIT: SEC16A and SEC16B are each present in multiple copies in a heteromeric complex. Interacts with SEC23A.
SUBCELLULAR LOCATION: Endoplasmic reticulum membrane; Peripheral membrane protein. Golgi apparatus membrane; Peripheral membrane protein (Potential). Note=SAR1A activity is required to maintain SEC16A localization at discrete locations on the ER membrane perhaps by preventing its dissociation.
TISSUE SPECIFICITY: Ubiquitous. Expressed at higher levels in the pancreas.
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR.
SIMILARITY: Belongs to the SEC16 family.
SEQUENCE CAUTION: Sequence=BAA20769.4; Type=Erroneous initiation; Sequence=CAI13949.1; Type=Erroneous gene model prediction; Sequence=CAI13951.1; Type=Erroneous gene model prediction;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -112.40294-0.382 Picture PostScript Text
3' UTR -556.201650-0.337 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR024880 - Sec16
IPR024340 - Sec16_CCD

Pfam Domains:
PF12931 - Sec23-binding domain of Sec16
PF12932 - Vesicle coat trafficking protein Sec16 mid-region

ModBase Predicted Comparative 3D Structure on O15027
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details Gene Details  
Gene SorterGene Sorter Gene Sorter  
 RGDEnsembl   
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding

Biological Process:
GO:0007029 endoplasmic reticulum organization
GO:0015031 protein transport
GO:0016192 vesicle-mediated transport
GO:0021762 substantia nigra development
GO:0048208 COPII vesicle coating

Cellular Component:
GO:0000139 Golgi membrane
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0005794 Golgi apparatus
GO:0005829 cytosol
GO:0016020 membrane


-  Descriptions from all associated GenBank mRNAs
  LF205598 - JP 2014500723-A/13101: Polycomb-Associated Non-Coding RNAs.
MA441175 - JP 2018138019-A/13101: Polycomb-Associated Non-Coding RNAs.
AK094041 - Homo sapiens cDNA FLJ36722 fis, clone UTERU2011621.
AK124843 - Homo sapiens cDNA FLJ42853 fis, clone BRHIP2008269.
BC070488 - Homo sapiens KIAA0310, mRNA (cDNA clone IMAGE:6044493), partial cds.
BC098454 - Homo sapiens SEC16 homolog A (S. cerevisiae), mRNA (cDNA clone IMAGE:6429542), partial cds.
AK094756 - Homo sapiens cDNA FLJ37437 fis, clone BRAWH2003025.
BC040710 - Homo sapiens KIAA0310, mRNA (cDNA clone IMAGE:6019850), partial cds.
BC016873 - Homo sapiens SEC16 homolog A (S. cerevisiae), mRNA (cDNA clone IMAGE:3884106), partial cds.
BC008332 - Homo sapiens SEC16 homolog A (S. cerevisiae), mRNA (cDNA clone IMAGE:3505732), partial cds.
BC001404 - Homo sapiens SEC16 homolog A (S. cerevisiae), mRNA (cDNA clone IMAGE:3139772), partial cds.
BC028183 - Homo sapiens SEC16 homolog A (S. cerevisiae), mRNA (cDNA clone IMAGE:4508322), partial cds.
AK126215 - Homo sapiens cDNA FLJ44227 fis, clone THYMU3006367.
AK074565 - Homo sapiens cDNA FLJ90084 fis, clone HEMBA1005070, similar to SKIN SECRETORY PROTEIN XP2 PRECURSOR.
AK129634 - Homo sapiens cDNA FLJ26123 fis, clone SYN00752.
AB002308 - Homo sapiens KIAA0310 mRNA for KIAA0310 protein.
AB593115 - Homo sapiens SEC16A mRNA for protein transport protein Sec16A, complete cds, clone: HP07225-RBd18G07.
JD388528 - Sequence 369552 from Patent EP1572962.
JD439010 - Sequence 420034 from Patent EP1572962.
BC051290 - Homo sapiens KIAA0310, mRNA (cDNA clone IMAGE:3505814), partial cds.
LF346409 - JP 2014500723-A/153912: Polycomb-Associated Non-Coding RNAs.
LF346410 - JP 2014500723-A/153913: Polycomb-Associated Non-Coding RNAs.
DQ570798 - Homo sapiens piRNA piR-30910, complete sequence.
JD290747 - Sequence 271771 from Patent EP1572962.
JD528294 - Sequence 509318 from Patent EP1572962.
JD489350 - Sequence 470374 from Patent EP1572962.
JD381896 - Sequence 362920 from Patent EP1572962.
JD052591 - Sequence 33615 from Patent EP1572962.
AK310722 - Homo sapiens cDNA, FLJ17764.
AK316194 - Homo sapiens cDNA, FLJ79093 complete cds.
DQ597601 - Homo sapiens piRNA piR-35667, complete sequence.
DQ593401 - Homo sapiens piRNA piR-33513, complete sequence.
JD268596 - Sequence 249620 from Patent EP1572962.
DQ582957 - Homo sapiens piRNA piR-50069, complete sequence.
JD449850 - Sequence 430874 from Patent EP1572962.
JD088751 - Sequence 69775 from Patent EP1572962.
JD268037 - Sequence 249061 from Patent EP1572962.
AK302210 - Homo sapiens cDNA FLJ61186 complete cds.
AK301371 - Homo sapiens cDNA FLJ52782 complete cds.
LF346411 - JP 2014500723-A/153914: Polycomb-Associated Non-Coding RNAs.
JD214630 - Sequence 195654 from Patent EP1572962.
JD210088 - Sequence 191112 from Patent EP1572962.
DQ580830 - Homo sapiens piRNA piR-48942, complete sequence.
JD380183 - Sequence 361207 from Patent EP1572962.
JD176629 - Sequence 157653 from Patent EP1572962.
JD237447 - Sequence 218471 from Patent EP1572962.
JD545964 - Sequence 526988 from Patent EP1572962.
JD467156 - Sequence 448180 from Patent EP1572962.
DQ584788 - Homo sapiens piRNA piR-51900, complete sequence.
JD333696 - Sequence 314720 from Patent EP1572962.
BC125018 - Homo sapiens SEC16 homolog A (S. cerevisiae), mRNA (cDNA clone IMAGE:40072120), partial cds.
BC125019 - Homo sapiens SEC16 homolog A (S. cerevisiae), mRNA (cDNA clone IMAGE:40072123), partial cds.
DQ593152 - Homo sapiens piRNA piR-33264, complete sequence.
JD201604 - Sequence 182628 from Patent EP1572962.
JD241401 - Sequence 222425 from Patent EP1572962.
DQ903855 - Homo sapiens SEC16L (SEC16L) mRNA, complete cds.
AB384458 - Synthetic construct DNA, clone: pF1KA0310, Homo sapiens SEC16A gene for KIAA0310 protein, complete cds, without stop codon, in Flexi system.
LF346413 - JP 2014500723-A/153916: Polycomb-Associated Non-Coding RNAs.
AK130247 - Homo sapiens cDNA FLJ26737 fis, clone PRS00528.
DQ582852 - Homo sapiens piRNA piR-32964, complete sequence.
LF346415 - JP 2014500723-A/153918: Polycomb-Associated Non-Coding RNAs.
LF346416 - JP 2014500723-A/153919: Polycomb-Associated Non-Coding RNAs.
DQ593261 - Homo sapiens piRNA piR-33373, complete sequence.
DQ582591 - Homo sapiens piRNA piR-32703, complete sequence.
DQ577953 - Homo sapiens piRNA piR-46065, complete sequence.
DQ595727 - Homo sapiens piRNA piR-61839, complete sequence.
LF346417 - JP 2014500723-A/153920: Polycomb-Associated Non-Coding RNAs.
LF346418 - JP 2014500723-A/153921: Polycomb-Associated Non-Coding RNAs.
DQ593080 - Homo sapiens piRNA piR-33192, complete sequence.
LF346422 - JP 2014500723-A/153925: Polycomb-Associated Non-Coding RNAs.
LF346423 - JP 2014500723-A/153926: Polycomb-Associated Non-Coding RNAs.
LF346424 - JP 2014500723-A/153927: Polycomb-Associated Non-Coding RNAs.
LF346425 - JP 2014500723-A/153928: Polycomb-Associated Non-Coding RNAs.
DQ587756 - Homo sapiens piRNA piR-54868, complete sequence.
JD355146 - Sequence 336170 from Patent EP1572962.
JD052835 - Sequence 33859 from Patent EP1572962.
JD371059 - Sequence 352083 from Patent EP1572962.
DQ584720 - Homo sapiens piRNA piR-51832, complete sequence.
JD329232 - Sequence 310256 from Patent EP1572962.
JD103204 - Sequence 84228 from Patent EP1572962.
JD229496 - Sequence 210520 from Patent EP1572962.
DQ580913 - Homo sapiens piRNA piR-49025, complete sequence.
JD348672 - Sequence 329696 from Patent EP1572962.
LF346426 - JP 2014500723-A/153929: Polycomb-Associated Non-Coding RNAs.
JD078864 - Sequence 59888 from Patent EP1572962.
LF346427 - JP 2014500723-A/153930: Polycomb-Associated Non-Coding RNAs.
LF346428 - JP 2014500723-A/153931: Polycomb-Associated Non-Coding RNAs.
LF346429 - JP 2014500723-A/153932: Polycomb-Associated Non-Coding RNAs.
LF346430 - JP 2014500723-A/153933: Polycomb-Associated Non-Coding RNAs.
AB621812 - Homo sapiens SEC16A mRNA for protein transport protein Sec16A, partial cds, clone: HP07225-RBd93C08.
LF346431 - JP 2014500723-A/153934: Polycomb-Associated Non-Coding RNAs.
MA581986 - JP 2018138019-A/153912: Polycomb-Associated Non-Coding RNAs.
MA581987 - JP 2018138019-A/153913: Polycomb-Associated Non-Coding RNAs.
MA581988 - JP 2018138019-A/153914: Polycomb-Associated Non-Coding RNAs.
MA581990 - JP 2018138019-A/153916: Polycomb-Associated Non-Coding RNAs.
MA581992 - JP 2018138019-A/153918: Polycomb-Associated Non-Coding RNAs.
MA581993 - JP 2018138019-A/153919: Polycomb-Associated Non-Coding RNAs.
MA581994 - JP 2018138019-A/153920: Polycomb-Associated Non-Coding RNAs.
MA581995 - JP 2018138019-A/153921: Polycomb-Associated Non-Coding RNAs.
MA581999 - JP 2018138019-A/153925: Polycomb-Associated Non-Coding RNAs.
MA582000 - JP 2018138019-A/153926: Polycomb-Associated Non-Coding RNAs.
MA582001 - JP 2018138019-A/153927: Polycomb-Associated Non-Coding RNAs.
MA582002 - JP 2018138019-A/153928: Polycomb-Associated Non-Coding RNAs.
MA582003 - JP 2018138019-A/153929: Polycomb-Associated Non-Coding RNAs.
MA582004 - JP 2018138019-A/153930: Polycomb-Associated Non-Coding RNAs.
MA582005 - JP 2018138019-A/153931: Polycomb-Associated Non-Coding RNAs.
MA582006 - JP 2018138019-A/153932: Polycomb-Associated Non-Coding RNAs.
MA582007 - JP 2018138019-A/153933: Polycomb-Associated Non-Coding RNAs.
MA582008 - JP 2018138019-A/153934: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein O15027 (Reactome details) participates in the following event(s):

R-HSA-5694417 SEC16 complex binds SAR1B:GTP:SEC23:SEC24
R-HSA-203973 Vesicle budding
R-HSA-204008 SEC31:SEC13 and v-SNARE recruitment
R-HSA-204005 COPII-mediated vesicle transport
R-HSA-199977 ER to Golgi Anterograde Transport
R-HSA-199991 Membrane Trafficking
R-HSA-948021 Transport to the Golgi and subsequent modification
R-HSA-5653656 Vesicle-mediated transport
R-HSA-446203 Asparagine N-linked glycosylation
R-HSA-597592 Post-translational protein modification
R-HSA-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: A1YCA4, J3KNL6, KIAA0310, NM_014866, O15027, Q4G0D7, Q5SXP0, Q5SXP1, Q8N347, Q96HP1, SC16A_HUMAN, SEC16, SEC16L, uc330nnm.1, uc330nnm.2
UCSC ID: ENST00000684901.1_4
RefSeq Accession: NM_014866.2
Protein: O15027 (aka SC16A_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.