COPA COPI coat complex subunit alpha [Homo sapiens (human)] - Gene

Summary

Official Symbol: COPAprovided by HGNC
Official Full Name: COPI coat complex subunit alphaprovided by HGNC
Primary source: HGNC:HGNC:2230
See related: Ensembl:ENSG00000122218 MIM:601924; AllianceGenome:HGNC:2230
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: AILJK; HEP-COP; alpha-COP
Summary: In eukaryotic cells, protein transport between the endoplasmic reticulum and Golgi compartments is mediated in part by non-clathrin-coated vesicular coat proteins (COPs). Seven coat proteins have been identified, and they represent subunits of a complex known as coatomer. The subunits are designated alpha-COP, beta-COP, beta-prime-COP, gamma-COP, delta-COP, epsilon-COP, and zeta-COP. The alpha-COP, encoded by COPA, shares high sequence similarity with RET1P, the alpha subunit of the coatomer complex in yeast. Also, the N-terminal 25 amino acids of alpha-COP encode the bioactive peptide, xenin, which stimulates exocrine pancreatic secretion and may act as a gastrointestinal hormone. Alternative splicing results in multiple splice forms encoding distinct isoforms. [provided by RefSeq, Jul 2008]
Expression: Ubiquitous expression in thyroid (RPKM 39.8), colon (RPKM 29.3) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 1q23.2

Exon count:: 33

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (160288594..160343250, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (159425670..159480322, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (160258384..160313040, complement)

Chromosome 1 - NC_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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 Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Heterozygous mutations in the C-terminal domain of COPA underlie a complex autoin fl ammatory syndrome.
Title: Heterozygous mutations in the C-terminal domain of COPA underlie a complex autoinﬂammatory syndrome.
An extended motif in the SARS-CoV-2 spike modulates binding and release of host coatomer in retrograde trafficking.
Title: An extended motif in the SARS-CoV-2 spike modulates binding and release of host coatomer in retrograde trafficking.
A Zebra at the Rodeo: Dyspnea, Hematuria, and a Family History of Arthritis.
Title: A Zebra at the Rodeo: Dyspnea, Hematuria, and a Family History of Arthritis.
Mutations in COPA lead to abnormal trafficking of STING to the Golgi and interferon signaling.
Title: Mutations in COPA lead to abnormal trafficking of STING to the Golgi and interferon signaling.
Hazara Nairovirus Requires COPI Components in both Arf1-Dependent and Arf1-Independent Stages of Its Replication Cycle.
Title: Hazara Nairovirus Requires COPI Components in both Arf1-Dependent and Arf1-Independent Stages of Its Replication Cycle.
median serum levels elevated in polycystic ovary syndrome
Title: The relationship between elevated serum xenin and insulin resistance in women with polycystic ovary syndrome: a case-control study.
COPI facilitated dengue virus (DENV) production in an endothelial cell line and in all DENV serotypes, indicating the importance of coat protein complex in facilitating DENV infection.
Title: Coat protein complex I facilitates dengue virus production.
Loss of RAB6-interacting golgin (GORAB) causes impairment of coat protein complex I (COPI)-mediated retrieval of trans-Golgi enzymes, resulting in a deficit in glycosylation of secretory cargo proteins.
Title: GORAB scaffolds COPI at the trans-Golgi for efficient enzyme recycling and correct protein glycosylation.
knockdown of COPA caused increased expression of viral late genes despite substantial inhibition of viral DNA replication.
Title: Identification of Host Factors Involved in Human Cytomegalovirus Replication, Assembly, and Egress Using a Two-Step Small Interfering RNA Screen.
Reduced RNA editing of COPA gene is associated with psoriasis.
Title: Decreased A-to-I RNA editing as a source of keratinocytes' dsRNA in psoriasis.

Submit: New GeneRIF Correction See all GeneRIFs (20)

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

Associated conditions

Description	Tests
Autoimmune interstitial lung disease-arthritis syndrome MedGen: C5243948 OMIM: 616414 GeneReviews: Not available	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Envelope surface glycoprotein gp120	env	Tandem affinity purification and mass spectrometry analysis identify subunit alpha of coatomer protein complex (COPA), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into Staufen1 RNP complexes isolated from HIV-1-expressing cells	PubMed
Gag-Pol	gag-pol	Tandem affinity purification and mass spectrometry analysis identify subunit alpha of coatomer protein complex (COPA), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into Staufen1 RNP complexes isolated from HIV-1-expressing cells	PubMed
Nef	nef	Tandem affinity purification and mass spectrometry analysis identify subunit alpha of coatomer protein complex (COPA), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into Staufen1 RNP complexes isolated from HIV-1-expressing cells	PubMed
Pr55(Gag)	gag	Tandem affinity purification and mass spectrometry analysis identify subunit alpha of coatomer protein complex (COPA), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into Staufen1 RNP complexes isolated from HIV-1-expressing cells	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH36199 (e-PCR)
- UniSTS:38410

D1S2004E (e-PCR)
- UniSTS:151313

RH36433 (e-PCR)
- UniSTS:58694

STS-T81091 (e-PCR)
- UniSTS:82264

SHGC-31631 (e-PCR)
- UniSTS:26978

D1S2032E (e-PCR)
- UniSTS:151432

RH47886 (e-PCR)
- UniSTS:53897

D4S3307 (e-PCR)
- UniSTS:67010

A002P23 (e-PCR)
- UniSTS:15843

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables hormone activity	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables structural molecule activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in endoplasmic reticulum to Golgi vesicle-mediated transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in intra-Golgi vesicle-mediated transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in intracellular protein transport	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within pancreatic juice secretion	IDA Inferred from Direct Assay more info	PubMed
involved_in retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum	IBA Inferred from Biological aspect of Ancestor more info
involved_in signal transduction	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
part_of COPI vesicle coat	IBA Inferred from Biological aspect of Ancestor more info
part_of COPI vesicle coat	IDA Inferred from Direct Assay more info	PubMed
part_of COPI vesicle coat	ISS Inferred from Sequence or Structural Similarity more info
located_in Golgi membrane	TAS Traceable Author Statement more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	TAS Traceable Author Statement more info
located_in endoplasmic reticulum membrane	TAS Traceable Author Statement more info
located_in extracellular exosome	HDA more info	PubMed
located_in extracellular space	IDA Inferred from Direct Assay more info	PubMed
located_in growth cone	IDA Inferred from Direct Assay more info	PubMed
located_in membrane	HDA more info	PubMed
located_in transport vesicle	TAS Traceable Author Statement more info

General protein information

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Preferred Names: coatomer subunit alpha

Names: alpha coat protein; coatomer protein complex subunit alpha; proxenin; xenin

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.

Genomic

NG_050927.1 RefSeqGene

Range

5315..59971

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_1336

mRNA and Protein(s)

NM_001098398.2 → NP_001091868.1 coatomer subunit alpha isoform 1

See identical proteins and their annotated locations for NP_001091868.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AL513282, BC038447, DC308331

Consensus CDS

CCDS41424.1

UniProtKB/TrEMBL

A0A3B3IS84, A0A3B3IT15

Related

ENSP00000357048.3, ENST00000368069.7

Conserved Domains (5) summary

COG2319
Location:2 → 317

WD40; WD40 repeat [General function prediction only]

cd00200
Location:9 → 318

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

pfam04053
Location:339 → 776

Coatomer_WDAD; Coatomer WD associated region

pfam06957
Location:825 → 1227

COPI_C; Coatomer (COPI) alpha subunit C-terminus

sd00039
Location:15 → 49

7WD40; WD40 repeat [structural motif]
NM_004371.4 → NP_004362.2 coatomer subunit alpha isoform 2

See identical proteins and their annotated locations for NP_004362.2

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1, resulting in a shorter protein (isoform 2).

Source sequence(s)

AL513282, DC308331, U24105

Consensus CDS

CCDS1202.1

UniProtKB/Swiss-Prot

P53621, Q5T201, Q8IXZ9

UniProtKB/TrEMBL

A0A3B3IS84, A0A3B3IT15

Related

ENSP00000241704.7, ENST00000241704.8

Conserved Domains (5) summary

COG2319
Location:2 → 317

WD40; WD40 repeat [General function prediction only]

cd00200
Location:9 → 318

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

pfam04053
Location:339 → 767

Coatomer_WDAD; Coatomer WD associated region

pfam06957
Location:816 → 1218

COPI_C; Coatomer (COPI) alpha subunit C-terminus

sd00039
Location:15 → 49

7WD40; WD40 repeat [structural motif]