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

    Gene ID: 1314, updated on 9-Dec-2024

    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; AIAISD; 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
    NEW
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    Try the new Transcript table

    Genomic context

    See COPA in Genome Data Viewer
    Location:
    1q23.2
    Exon count:
    33
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (160288594..160343250, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (159425670..159480322, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (160258384..160313040, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ribosomal protein SA pseudogene 18 Neighboring gene uncharacterized LOC107985219 Neighboring gene peroxisomal biogenesis factor 19 Neighboring gene SUMO1 pseudogene 3 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:160312973-160313920 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1920 Neighboring gene nicastrin Neighboring gene nescient helix-loop-helix 1

    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 Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    HIV-1 interactions

    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

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ26320

    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 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 PubMed 
    located_in transport vesicle TAS
    Traceable Author Statement
    more info
     

    General protein information

    Preferred Names
    coatomer subunit alpha
    Names
    alpha coat protein
    coatomer protein complex subunit alpha
    proxenin
    xenin

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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

    1. NG_050927.1 RefSeqGene

      Range
      5315..59971
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_1336

    mRNA and Protein(s)

    1. NM_001098398.2NP_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:2317
      WD40; WD40 repeat [General function prediction only]
      cd00200
      Location:9318
      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:339776
      Coatomer_WDAD; Coatomer WD associated region
      pfam06957
      Location:8251227
      COPI_C; Coatomer (COPI) alpha subunit C-terminus
      sd00039
      Location:1549
      7WD40; WD40 repeat [structural motif]
    2. NM_004371.4NP_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:2317
      WD40; WD40 repeat [General function prediction only]
      cd00200
      Location:9318
      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:339767
      Coatomer_WDAD; Coatomer WD associated region
      pfam06957
      Location:8161218
      COPI_C; Coatomer (COPI) alpha subunit C-terminus
      sd00039
      Location:1549
      7WD40; WD40 repeat [structural motif]

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      160288594..160343250 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      159425670..159480322 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)