Human Gene COPA (ENST00000241704.8_8) from GENCODE V47lift37
  Description: COPI coat complex subunit alpha, transcript variant 2 (from RefSeq NM_004371.4)
Gencode Transcript: ENST00000241704.8_8
Gencode Gene: ENSG00000122218.17_18
Transcript (Including UTRs)
   Position: hg19 chr1:160,258,384-160,313,040 Size: 54,657 Total Exon Count: 33 Strand: -
Coding Region
   Position: hg19 chr1:160,259,947-160,312,960 Size: 53,014 Coding Exon Count: 33 

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 (chr1:160,258,384-160,313,040)mRNA (may differ from genome)Protein (1224 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: COPA_HUMAN
DESCRIPTION: RecName: Full=Coatomer subunit alpha; AltName: Full=Alpha-coat protein; Short=Alpha-COP; AltName: Full=HEP-COP; Short=HEPCOP; Contains: RecName: Full=Xenin; AltName: Full=Xenopsin-related peptide; Contains: RecName: Full=Proxenin;
FUNCTION: The coatomer is a cytosolic protein complex that binds to dilysine motifs and reversibly associates with Golgi non- clathrin-coated vesicles, which further mediate biosynthetic protein transport from the ER, via the Golgi up to the trans Golgi network. Coatomer complex is required for budding from Golgi membranes, and is essential for the retrograde Golgi-to-ER transport of dilysine-tagged proteins. In mammals, the coatomer can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins; the complex also influences the Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors (By similarity).
FUNCTION: Xenin stimulates exocrine pancreatic secretion. It inhibits pentagastrin-stimulated secretion of acid, to induce exocrine pancreatic secretion and to affect small and large intestinal motility. In the gut, xenin interacts with the neurotensin receptor.
SUBUNIT: Oligomeric complex that consists of at least the alpha, beta, beta', gamma, delta, epsilon and zeta subunits. Probably interacts with PEX11A. Interacts with SCYL1 (By similarity).
SUBCELLULAR LOCATION: Cytoplasm (By similarity). Golgi apparatus membrane; Peripheral membrane protein; Cytoplasmic side (By similarity). Cytoplasmic vesicle, COPI-coated vesicle membrane; Peripheral membrane protein; Cytoplasmic side (By similarity). Note=The coatomer is cytoplasmic or polymerized on the cytoplasmic side of the Golgi, as well as on the vesicles/buds originating from it (By similarity).
SUBCELLULAR LOCATION: Xenin: Secreted (By similarity).
TISSUE SPECIFICITY: Uniformly expressed in a wide range of adult and fetal tissues. Xenin is found in gastric, duodenal and jejunal mucosa. Circulates in the blood. Seems to be confined to specific endocrine cells.
DEVELOPMENTAL STAGE: Xenin is released into the circulation after a meal.
RNA EDITING: Modified_positions=164; Note=Edited at about 31%.
SIMILARITY: Contains 6 WD repeats.
WEB RESOURCE: Name=Wikipedia; Note=Xenin entry; URL="http://en.wikipedia.org/wiki/Xenin";

-  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: COPA
Diseases sorted by gene-association score: autoimmune interstitial lung, joint, and kidney disease* (1731), parainfluenza virus type 3 (11), lung disease (7), lymphocytic choriomeningitis (7)
* = Manually curated disease association

-  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.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 77.21 RPKM in Cells - Cultured fibroblasts
Total median expression: 1972.68 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 -24.9080-0.311 Picture PostScript Text
3' UTR -400.201563-0.256 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
IPR016391 - Coatomer_asu
IPR010714 - Coatomer_asu_C
IPR006692 - Coatomer_WD-assoc_reg
IPR020472 - G-protein_beta_WD-40_rep
IPR015943 - WD40/YVTN_repeat-like_dom
IPR001680 - WD40_repeat
IPR019775 - WD40_repeat_CS
IPR017986 - WD40_repeat_dom

Pfam Domains:
PF00400 - WD domain, G-beta repeat
PF04053 - Coatomer WD associated region
PF06957 - Coatomer (COPI) alpha subunit C-terminus
PF12894 - Anaphase-promoting complex subunit 4 WD40 domain

SCOP Domains:
48452 - TPR-like
50952 - Soluble quinoprotein glucose dehydrogenase
50956 - Thermostable phytase (3-phytase)
50960 - TolB, C-terminal domain
63825 - YWTD domain
63829 - Calcium-dependent phosphotriesterase
69304 - Tricorn protease N-terminal domain
101898 - NHL repeat
50965 - Galactose oxidase, central domain
75011 - 3-carboxy-cis,cis-mucoante lactonizing enzyme
101908 - Putative isomerase YbhE
117289 - Nucleoporin domain
50969 - YVTN repeat-like/Quinoprotein amine dehydrogenase
50974 - Nitrous oxide reductase, N-terminal domain
50978 - WD40 repeat-like
50993 - Peptidase/esterase 'gauge' domain
69322 - Tricorn protease domain 2
50998 - Quinoprotein alcohol dehydrogenase-like
51004 - C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase
82171 - DPP6 N-terminal domain-like
52317 - Class I glutamine amidotransferase-like

ModBase Predicted Comparative 3D Structure on P53621
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 orthologGenome Browser
Gene DetailsGene Details   Gene Details
Gene SorterGene Sorter   Gene Sorter
 RGDEnsembl  SGD
     Protein Sequence
     Alignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005179 hormone activity
GO:0005198 structural molecule activity

Biological Process:
GO:0006886 intracellular protein transport
GO:0006888 ER to Golgi vesicle-mediated transport
GO:0006890 retrograde vesicle-mediated transport, Golgi to ER
GO:0006891 intra-Golgi vesicle-mediated transport
GO:0010469 regulation of receptor activity
GO:0015031 protein transport
GO:0016192 vesicle-mediated transport
GO:0030157 pancreatic juice secretion

Cellular Component:
GO:0000139 Golgi membrane
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005737 cytoplasm
GO:0005789 endoplasmic reticulum membrane
GO:0005794 Golgi apparatus
GO:0005829 cytosol
GO:0016020 membrane
GO:0030117 membrane coat
GO:0030126 COPI vesicle coat
GO:0030133 transport vesicle
GO:0030663 COPI-coated vesicle membrane
GO:0031410 cytoplasmic vesicle
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  LF205465 - JP 2014500723-A/12968: Polycomb-Associated Non-Coding RNAs.
BC038447 - Homo sapiens coatomer protein complex, subunit alpha, mRNA (cDNA clone MGC:45155 IMAGE:5533230), complete cds.
U24105 - Homo sapiens coatomer protein (COPA) mRNA, complete cds.
KJ896625 - Synthetic construct Homo sapiens clone ccsbBroadEn_06019 COPA gene, encodes complete protein.
AB385218 - Synthetic construct DNA, clone: pF1KB9459, Homo sapiens COPA gene for coatomer subunit alpha, complete cds, without stop codon, in Flexi system.
AK307953 - Homo sapiens cDNA, FLJ97901.
MA441042 - JP 2018138019-A/12968: Polycomb-Associated Non-Coding RNAs.
JD529583 - Sequence 510607 from Patent EP1572962.
AK129830 - Homo sapiens cDNA FLJ26320 fis, clone HRT00273, highly similar to Coatomer alpha subunit.
JD285199 - Sequence 266223 from Patent EP1572962.
JD232871 - Sequence 213895 from Patent EP1572962.
LF320779 - JP 2014500723-A/128282: Polycomb-Associated Non-Coding RNAs.
JD313050 - Sequence 294074 from Patent EP1572962.
JD182930 - Sequence 163954 from Patent EP1572962.
JD393928 - Sequence 374952 from Patent EP1572962.
JD318957 - Sequence 299981 from Patent EP1572962.
JD239516 - Sequence 220540 from Patent EP1572962.
JD083669 - Sequence 64693 from Patent EP1572962.
JD110207 - Sequence 91231 from Patent EP1572962.
JD516193 - Sequence 497217 from Patent EP1572962.
JD084885 - Sequence 65909 from Patent EP1572962.
JD447604 - Sequence 428628 from Patent EP1572962.
JD331971 - Sequence 312995 from Patent EP1572962.
JD175701 - Sequence 156725 from Patent EP1572962.
JD308544 - Sequence 289568 from Patent EP1572962.
JD205996 - Sequence 187020 from Patent EP1572962.
JD321357 - Sequence 302381 from Patent EP1572962.
JD529584 - Sequence 510608 from Patent EP1572962.
JD430404 - Sequence 411428 from Patent EP1572962.
JD523779 - Sequence 504803 from Patent EP1572962.
JD243294 - Sequence 224318 from Patent EP1572962.
JD243293 - Sequence 224317 from Patent EP1572962.
JD131048 - Sequence 112072 from Patent EP1572962.
JD354427 - Sequence 335451 from Patent EP1572962.
JD275673 - Sequence 256697 from Patent EP1572962.
JD158817 - Sequence 139841 from Patent EP1572962.
JD158816 - Sequence 139840 from Patent EP1572962.
JD289000 - Sequence 270024 from Patent EP1572962.
JD474500 - Sequence 455524 from Patent EP1572962.
JD186536 - Sequence 167560 from Patent EP1572962.
JD432454 - Sequence 413478 from Patent EP1572962.
JD102035 - Sequence 83059 from Patent EP1572962.
JD426627 - Sequence 407651 from Patent EP1572962.
JD545023 - Sequence 526047 from Patent EP1572962.
JD253341 - Sequence 234365 from Patent EP1572962.
JD554785 - Sequence 535809 from Patent EP1572962.
JD163632 - Sequence 144656 from Patent EP1572962.
JD391485 - Sequence 372509 from Patent EP1572962.
LF320778 - JP 2014500723-A/128281: Polycomb-Associated Non-Coding RNAs.
LF320776 - JP 2014500723-A/128279: Polycomb-Associated Non-Coding RNAs.
LF320775 - JP 2014500723-A/128278: Polycomb-Associated Non-Coding RNAs.
LF320774 - JP 2014500723-A/128277: Polycomb-Associated Non-Coding RNAs.
LF320773 - JP 2014500723-A/128276: Polycomb-Associated Non-Coding RNAs.
LF320772 - JP 2014500723-A/128275: Polycomb-Associated Non-Coding RNAs.
LF320771 - JP 2014500723-A/128274: Polycomb-Associated Non-Coding RNAs.
LF320770 - JP 2014500723-A/128273: Polycomb-Associated Non-Coding RNAs.
LF320769 - JP 2014500723-A/128272: Polycomb-Associated Non-Coding RNAs.
LF320768 - JP 2014500723-A/128271: Polycomb-Associated Non-Coding RNAs.
LF320767 - JP 2014500723-A/128270: Polycomb-Associated Non-Coding RNAs.
LF320764 - JP 2014500723-A/128267: Polycomb-Associated Non-Coding RNAs.
LF320763 - JP 2014500723-A/128266: Polycomb-Associated Non-Coding RNAs.
LF320762 - JP 2014500723-A/128265: Polycomb-Associated Non-Coding RNAs.
LF320761 - JP 2014500723-A/128264: Polycomb-Associated Non-Coding RNAs.
LF320760 - JP 2014500723-A/128263: Polycomb-Associated Non-Coding RNAs.
LF320759 - JP 2014500723-A/128262: Polycomb-Associated Non-Coding RNAs.
LF320758 - JP 2014500723-A/128261: Polycomb-Associated Non-Coding RNAs.
MA556356 - JP 2018138019-A/128282: Polycomb-Associated Non-Coding RNAs.
MA556355 - JP 2018138019-A/128281: Polycomb-Associated Non-Coding RNAs.
MA556353 - JP 2018138019-A/128279: Polycomb-Associated Non-Coding RNAs.
MA556352 - JP 2018138019-A/128278: Polycomb-Associated Non-Coding RNAs.
MA556351 - JP 2018138019-A/128277: Polycomb-Associated Non-Coding RNAs.
MA556350 - JP 2018138019-A/128276: Polycomb-Associated Non-Coding RNAs.
MA556349 - JP 2018138019-A/128275: Polycomb-Associated Non-Coding RNAs.
MA556348 - JP 2018138019-A/128274: Polycomb-Associated Non-Coding RNAs.
MA556347 - JP 2018138019-A/128273: Polycomb-Associated Non-Coding RNAs.
MA556346 - JP 2018138019-A/128272: Polycomb-Associated Non-Coding RNAs.
MA556345 - JP 2018138019-A/128271: Polycomb-Associated Non-Coding RNAs.
MA556344 - JP 2018138019-A/128270: Polycomb-Associated Non-Coding RNAs.
MA556341 - JP 2018138019-A/128267: Polycomb-Associated Non-Coding RNAs.
MA556340 - JP 2018138019-A/128266: Polycomb-Associated Non-Coding RNAs.
MA556339 - JP 2018138019-A/128265: Polycomb-Associated Non-Coding RNAs.
MA556338 - JP 2018138019-A/128264: Polycomb-Associated Non-Coding RNAs.
MA556337 - JP 2018138019-A/128263: Polycomb-Associated Non-Coding RNAs.
MA556336 - JP 2018138019-A/128262: Polycomb-Associated Non-Coding RNAs.
MA556335 - JP 2018138019-A/128261: Polycomb-Associated Non-Coding RNAs.
LF320750 - JP 2014500723-A/128253: Polycomb-Associated Non-Coding RNAs.
MA556327 - JP 2018138019-A/128253: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_arapPathway - ADP-Ribosylation Factor

Reactome (by CSHL, EBI, and GO)

Protein P53621 (Reactome details) participates in the following event(s):

R-HSA-6807872 Active ARF recruits coatomer
R-HSA-6811412 Active ARF recruits coatomer to the Golgi
R-HSA-6807875 ARFGAP, cargo, v-SNAREs and p24 proteins bind nascent COPI complex
R-HSA-6811417 ARFGAP, cargo, vSNARES and p24 proteins bind COPI vesicles at Golgi
R-HSA-6811426 Retrograde COPI vesicles bind kinesin and microtubules
R-HSA-6811418 ARFGAPs stimulate ARF GTPase activity at the Golgi membrane
R-HSA-6811423 Retrograde vesicle is tethered at the ER by the NRZ complex and t-SNAREs
R-HSA-6807877 ARFGAPs stimulate ARF GTPase activity
R-HSA-6809003 ERGIC-to-Golgi vesicles bind dynein:dynactin
R-HSA-6809011 cis-Golgi t-SNAREs bind YKT6 on tethered vesicle
R-HSA-6809006 Vesicle is tethered through binding GOLGA2:GORASP1, GOLGB1 and the COG complex
R-HSA-6807878 COPI-mediated anterograde transport
R-HSA-6811434 COPI-dependent Golgi-to-ER retrograde traffic
R-HSA-199977 ER to Golgi Anterograde Transport
R-HSA-8856688 Golgi-to-ER retrograde transport
R-HSA-199991 Membrane Trafficking
R-HSA-948021 Transport to the Golgi and subsequent modification
R-HSA-6811442 Intra-Golgi and retrograde Golgi-to-ER traffic
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: COPA_HUMAN, ENST00000241704.1, ENST00000241704.2, ENST00000241704.3, ENST00000241704.4, ENST00000241704.5, ENST00000241704.6, ENST00000241704.7, NM_004371, P53621, Q5T201, Q8IXZ9, uc317eje.1, uc317eje.2
UCSC ID: ENST00000241704.8_8
RefSeq Accession: NM_004371.4
Protein: P53621 (aka COPA_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.