Human Gene SEC24C (ENST00000345254.9_4) from GENCODE V47lift37
  Description: SEC24 homolog C, COPII coat complex component, transcript variant 2 (from RefSeq NM_198597.3)
Gencode Transcript: ENST00000345254.9_4
Gencode Gene: ENSG00000176986.16_8
Transcript (Including UTRs)
   Position: hg19 chr10:75,504,130-75,531,919 Size: 27,790 Total Exon Count: 23 Strand: +
Coding Region
   Position: hg19 chr10:75,506,591-75,530,853 Size: 24,263 Coding Exon Count: 22 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr10:75,504,130-75,531,919)mRNA (may differ from genome)Protein (1094 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SC24C_HUMAN
DESCRIPTION: RecName: Full=Protein transport protein Sec24C; AltName: Full=SEC24-related protein C;
FUNCTION: Component of the COPII coat, that covers ER-derived vesicles involved in transport from the endoplasmic reticulum to the Golgi apparatus. COPII acts in the cytoplasm to promote the transport of secretory, plasma membrane, and vacuolar proteins from the endoplasmic reticulum to the Golgi complex.
SUBUNIT: Interacts with SLC6A4 (By similarity). COPII is composed of at least five proteins: the Sec23/24 complex, the Sec13/31 complex and Sar1. SEC24C is capable of forming heterodimers with SEC24A. Interacts with TMED2 and TMED10.
INTERACTION: Q15436:SEC23A; NbExp=5; IntAct=EBI-81134, EBI-81088;
SUBCELLULAR LOCATION: Cytoplasm. Cytoplasm, perinuclear region. Endoplasmic reticulum membrane (Potential). Golgi apparatus membrane (Potential).
TISSUE SPECIFICITY: Ubiquitous.
SIMILARITY: Belongs to the SEC23/SEC24 family. SEC24 subfamily.
SEQUENCE CAUTION: Sequence=BAA07558.2; Type=Frameshift; Positions=1041;

-  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


-  MalaCards Disease Associations
  MalaCards Gene Search: SEC24C
Diseases sorted by gene-association score: velocardiofacial syndrome* (7)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

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

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 51.98 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 1371.39 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  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 -23.1094-0.246 Picture PostScript Text
3' UTR -395.901066-0.371 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
IPR007123 - Gelsolin_dom
IPR006900 - Sec23/24_helical_dom
IPR006896 - Sec23/24_trunk_dom
IPR012990 - Sec23_24_beta_S
IPR006895 - Znf_Sec23_Sec24

Pfam Domains:
PF00626 - Gelsolin repeat
PF04810 - Sec23/Sec24 zinc finger
PF04811 - Sec23/Sec24 trunk domain
PF04815 - Sec23/Sec24 helical domain
PF08033 - Sec23/Sec24 beta-sandwich domain

SCOP Domains:
81811 - Helical domain of Sec23/24
81995 - beta-sandwich domain of Sec23/24
53300 - vWA-like
55753 - Actin depolymerizing proteins
82754 - C-terminal, gelsolin-like domain of Sec23/24
82919 - Zn-finger domain of Sec23/24

Protein Data Bank (PDB) 3-D Structure
MuPIT help
3EH2 - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P53992
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 SorterGene Sorter    
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000149 SNARE binding
GO:0005515 protein binding
GO:0008270 zinc ion binding
GO:0046872 metal ion binding

Biological Process:
GO:0001701 in utero embryonic development
GO:0002474 antigen processing and presentation of peptide antigen via MHC class I
GO:0006886 intracellular protein transport
GO:0006888 ER to Golgi vesicle-mediated transport
GO:0015031 protein transport
GO:0016192 vesicle-mediated transport
GO:0019886 antigen processing and presentation of exogenous peptide antigen via MHC class II
GO:0048208 COPII vesicle coating
GO:0090110 cargo loading into COPII-coated vesicle

Cellular Component:
GO:0000139 Golgi membrane
GO:0005737 cytoplasm
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0005829 cytosol
GO:0012507 ER to Golgi transport vesicle membrane
GO:0016020 membrane
GO:0030127 COPII vesicle coat
GO:0031410 cytoplasmic vesicle


-  Descriptions from all associated GenBank mRNAs
  AK303085 - Homo sapiens cDNA FLJ60379 complete cds, highly similar to Protein transport protein Sec24C.
AK298598 - Homo sapiens cDNA FLJ60783 complete cds, highly similar to Protein transport protein Sec24C.
AK316451 - Homo sapiens cDNA, FLJ79350 complete cds, highly similar to Protein transport protein Sec24C.
BC018928 - Homo sapiens SEC24 family, member C (S. cerevisiae), mRNA (cDNA clone MGC:14092 IMAGE:4123623), complete cds.
AL832110 - Homo sapiens mRNA; cDNA DKFZp313H168 (from clone DKFZp313H168).
AK309918 - Homo sapiens cDNA, FLJ99959.
AK299826 - Homo sapiens cDNA FLJ60345 complete cds, highly similar to Protein transport protein Sec24C.
D38555 - Homo sapiens KIAA0079 mRNA, partial cds.
CU676338 - Synthetic construct Homo sapiens gateway clone IMAGE:100020506 5' read SEC24C mRNA.
JF432326 - Synthetic construct Homo sapiens clone IMAGE:100073512 SEC24 family, member C (S. cerevisiae) (SEC24C) gene, encodes complete protein.
JD020767 - Sequence 1791 from Patent EP1572962.
DQ581887 - Homo sapiens piRNA piR-49999, complete sequence.
AK098512 - Homo sapiens cDNA FLJ25646 fis, clone SYN00179, highly similar to SEC24 (S. cerevisiae) related gene family, member C.
DQ574455 - Homo sapiens piRNA piR-42567, complete sequence.
DQ578547 - Homo sapiens piRNA piR-46659, complete sequence.
DQ590313 - Homo sapiens piRNA piR-57425, complete sequence.
JD110691 - Sequence 91715 from Patent EP1572962.
JD437802 - Sequence 418826 from Patent EP1572962.
JD127333 - Sequence 108357 from Patent EP1572962.
JD525297 - Sequence 506321 from Patent EP1572962.
JD175308 - Sequence 156332 from Patent EP1572962.
JD475058 - Sequence 456082 from Patent EP1572962.
JD244477 - Sequence 225501 from Patent EP1572962.
JD486000 - Sequence 467024 from Patent EP1572962.
JD556818 - Sequence 537842 from Patent EP1572962.
DQ576390 - Homo sapiens piRNA piR-44502, complete sequence.
JD074465 - Sequence 55489 from Patent EP1572962.
JD175193 - Sequence 156217 from Patent EP1572962.
JD487259 - Sequence 468283 from Patent EP1572962.
JD350736 - Sequence 331760 from Patent EP1572962.
JD235120 - Sequence 216144 from Patent EP1572962.
JD562247 - Sequence 543271 from Patent EP1572962.
JD550581 - Sequence 531605 from Patent EP1572962.
JD278740 - Sequence 259764 from Patent EP1572962.
JD215648 - Sequence 196672 from Patent EP1572962.
JD242017 - Sequence 223041 from Patent EP1572962.
JD295176 - Sequence 276200 from Patent EP1572962.

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

Protein P53992 (Reactome details) participates in the following event(s):

R-HSA-5694435 CTAGE5 and MIA3 load procollagen VII into COPII vesicles
R-HSA-5694436 CTAGE5 and MIA3 dissociate from procollagen VII vesicle
R-HSA-983422 Disassembly of COPII coated vesicle
R-HSA-5694421 PP6 dephosphorylates SEC24
R-HSA-5694413 SEC4C,D bind GOSR2 and STX5
R-HSA-5694441 CSNK1D phosphorylates SEC23
R-HSA-5694522 Inner coat assembly and cargo binding
R-HSA-5694527 Loss of SAR1B GTPase
R-HSA-5694446 BET1:GOSR2:STX5 bind v-SNARES on tethered vesicle
R-HSA-203979 Coat Assembly
R-HSA-5694417 SEC16 complex binds SAR1B:GTP:SEC23:SEC24
R-HSA-983426 Capturing cargo and formation of prebudding complex
R-HSA-983425 Recruitment of Sec31p:Sec13p to prebudding complex and formation of COPII vesicle
R-HSA-5694439 COPII coat binds TRAPPCII and RAB1:GDP
R-HSA-203973 Vesicle budding
R-HSA-983424 Budding of COPII coated vesicle
R-HSA-204008 SEC31:SEC13 and v-SNARE recruitment
R-HSA-2130731 Formation of COPII vesicle
R-HSA-2213243 Fusion of COPII vesicle with Golgi complex
R-HSA-5694418 RAB1:GTP binds USO1 and GORASP1:GOLGA2
R-HSA-5694409 Nucleotide exchange on RAB1
R-HSA-5694530 Cargo concentration in the ER
R-HSA-983170 Antigen Presentation: Folding, assembly and peptide loading of class I MHC
R-HSA-204005 COPII-mediated vesicle transport
R-HSA-199977 ER to Golgi Anterograde Transport
R-HSA-983169 Class I MHC mediated antigen processing & presentation
R-HSA-199991 Membrane Trafficking
R-HSA-948021 Transport to the Golgi and subsequent modification
R-HSA-1655829 Regulation of cholesterol biosynthesis by SREBP (SREBF)
R-HSA-1280218 Adaptive Immune System
R-HSA-5653656 Vesicle-mediated transport
R-HSA-446203 Asparagine N-linked glycosylation
R-HSA-2132295 MHC class II antigen presentation
R-HSA-8957322 Metabolism of steroids
R-HSA-168256 Immune System
R-HSA-597592 Post-translational protein modification
R-HSA-556833 Metabolism of lipids
R-HSA-392499 Metabolism of proteins
R-HSA-1430728 Metabolism

-  Other Names for This Gene
  Alternate Gene Symbols: B4DZT4, ENST00000345254.1, ENST00000345254.2, ENST00000345254.3, ENST00000345254.4, ENST00000345254.5, ENST00000345254.6, ENST00000345254.7, ENST00000345254.8, KIAA0079 , NM_198597, P53992, Q8WV25, SC24C_HUMAN, SEC24C , uc317xex.1, uc317xex.2
UCSC ID: ENST00000345254.9_4
RefSeq Accession: NM_198597.3
Protein: P53992 (aka SC24C_HUMAN or S24C_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.