U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

COPZ1 COPI coat complex subunit zeta 1 [ Homo sapiens (human) ]

Gene ID: 22818, updated on 7-Apr-2024

Summary

Go to the top of the page Help
Official Symbol
COPZ1provided by HGNC
Official Full Name
COPI coat complex subunit zeta 1provided by HGNC
Primary source
HGNC:HGNC:2243
See related
Ensembl:ENSG00000111481 MIM:615472; AllianceGenome:HGNC:2243
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
COPZ; CGI-120; HSPC181; zeta-COP; zeta1-COP
Summary
This gene encodes a subunit of the cytoplasmic coatamer protein complex, which is involved in autophagy and intracellular protein trafficking. The coatomer protein complex is comprised of seven subunits and functions as the coat protein of coat protein complex (COP)I-vesicles. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2012]
Expression
Ubiquitous expression in thyroid (RPKM 49.0), colon (RPKM 30.9) and 25 other tissues See more
Orthologs
mouse all
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
Location:
12q13.13
Exon count:
9
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (54325131..54351846)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (54291719..54318429)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (54718915..54745630)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene CRISPRi-FlowFISH-validated HNRNPA1 regulatory element Neighboring gene CRISPRi-FlowFISH-validated COPZ1 and HNRNPA1 regulatory element Neighboring gene CRISPRi-FlowFISH-validated HNRNPA1 and NFE2 regulatory element 1 Neighboring gene CRISPRi-FlowFISH-validated COPZ1, HNRNPA1 and NFE2 regulatory element Neighboring gene CRISPRi-FlowFISH-validated HNRNPA1 and NFE2 regulatory element 2 Neighboring gene nuclear factor, erythroid 2 Neighboring gene RNA, U6 small nuclear 950, pseudogene Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:54722975-54723665 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr12:54723666-54724355 Neighboring gene microRNA 148b Neighboring gene RNA, 7SL, cytoplasmic 744, pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:54750728-54751553 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:54751554-54752378 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:54752379-54753203 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4527 Neighboring gene GPR84, ZNF385A, ITGA5 and GTSF1 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6441 Neighboring gene G protein-coupled receptor 84 Neighboring gene zinc finger protein 385A Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr12:54781074-54781708 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:54781709-54782342 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4528 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4529 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:54805235-54806017 Neighboring gene integrin subunit alpha 5 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:54806018-54806799

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help
  • 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

Go to the top of the pageHelp

Related articles in PubMed

  1. Targeting COPZ1 non-oncogene addiction counteracts the viability of thyroid tumor cells. Anania MC, et al. Cancer Lett, 2017 Dec 1. PMID 28951131
  2. COPI coatomer complex proteins facilitate the translocation of anthrax lethal factor across vesicular membranes in vitro. Tamayo AG, et al. Proc Natl Acad Sci U S A, 2008 Apr 1. PMID 18356299, Free PMC Article
  3. ER-to-Golgi transport: COP I and COP II function (Review). Duden R. Mol Membr Biol, 2003 Jul-Sep. PMID 12893528
  4. Tumor-specific silencing of COPZ2 gene encoding coatomer protein complex subunit ζ 2 renders tumor cells dependent on its paralogous gene COPZ1. Shtutman M, et al. Proc Natl Acad Sci U S A, 2011 Jul 26. PMID 21746916, Free PMC Article
  5. Solution structure of human zeta-COP: direct evidences for structural similarity between COP I and clathrin-adaptor coats. Yu W, et al. J Mol Biol, 2009 Mar 6. PMID 19167404

See all (81) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Loss of COPZ1 induces NCOA4 mediated autophagy and ferroptosis in glioblastoma cell lines.
    Title: Loss of COPZ1 induces NCOA4 mediated autophagy and ferroptosis in glioblastoma cell lines.
  2. siRNA-mediated COPZ1 depletion causes abortive autophagy, endoplasmic reticulum stress, unfolded protein response and apoptosis in thyroid tumor cells.
    Title: Targeting COPZ1 non-oncogene addiction counteracts the viability of thyroid tumor cells.
  3. The knockdown of COPZ1, but not of COPZ2 encoding isoform coatomer protein complex zeta2, caused Golgi apparatus collapse, blocked autophagy, and induced apoptosis in both proliferating and nondividing tumor cells.
    Title: Tumor-specific silencing of COPZ2 gene encoding coatomer protein complex subunit ζ 2 renders tumor cells dependent on its paralogous gene COPZ1.
Submit: New GeneRIF Correction

Phenotypes

Go to the top of the page Help

Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
A genome- and phenome-wide association study to identify genetic variants influencing platelet count and volume and their pleiotropic effects.
EBI GWAS Catalog
GWAS of blood cell traits identifies novel associated loci and epistatic interactions in Caucasian and African-American children.
EBI GWAS Catalog
New gene functions in megakaryopoiesis and platelet formation.
EBI GWAS Catalog

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

Go to the top of the page Help

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env Tandem affinity purification and mass spectrometry analysis identify subunit zeta 1 of coatomer protein complex (COPZ1), 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 zeta 1 of coatomer protein complex (COPZ1), 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 zeta 1 of coatomer protein complex (COPZ1), 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 zeta 1 of coatomer protein complex (COPZ1), 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

Go to the top of the page Help
Products Interactant Other Gene Complex Source Pubs Description

General gene information

Go to the top of the page Help

Markers

Homology

Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in intra-Golgi vesicle-mediated transport IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in intra-Golgi vesicle-mediated transport IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in intra-Golgi vesicle-mediated transport ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in intracellular protein transport IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum TAS
Traceable Author Statement
more info
 PubMed 
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 cytosol TAS
Traceable Author Statement
more info
  
located_in endoplasmic reticulum membrane TAS
Traceable Author Statement
more info
  
located_in transport vesicle TAS
Traceable Author Statement
more info
  

General protein information

Go to the top of the page Help
Preferred Names
coatomer subunit zeta-1
Names
coatomer protein complex subunit zeta 1
coatomer protein complex, subunit zeta
zeta-1 COP
zeta-1-coat protein

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

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.

mRNA and Protein(s)

  1. NM_001271734.2 → NP_001258663.1  coatomer subunit zeta-1 isoform 2

    See identical proteins and their annotated locations for NP_001258663.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an internal in-frame exon in the coding region, compared to variant 1. The encoded isoform (2) is shorter, compared to isoform 1.
    Source sequence(s)
    AF151878, AK293377, CB127540
    Consensus CDS
    CCDS61138.1
    UniProtKB/TrEMBL
    Q53FU3
    Related
    ENSP00000410620.2, ENST00000455864.6
    Conserved Domains (1) summary
    cd14829
    Location:7 → 122
    Zeta-COP; zeta subunit of the F-COPI complex

  2. NM_001271735.2 → NP_001258664.1  coatomer subunit zeta-1 isoform 3

    See identical proteins and their annotated locations for NP_001258664.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate in-frame splice site and lacks an internal in-frame exon in the coding region, compared to variant 1. The encoded isoform (3) is shorter, compared to isoform 1.
    Source sequence(s)
    AF151878, CB127540, DA562746
    Consensus CDS
    CCDS61137.1
    UniProtKB/TrEMBL
    Q53FU3
    Related
    ENSP00000448444.1, ENST00000552362.5
    Conserved Domains (1) summary
    cd14829
    Location:14 → 145
    Zeta-COP; zeta subunit of the F-COPI complex

  3. NM_001271736.2 → NP_001258665.1  coatomer subunit zeta-1 isoform 4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) uses an alternate in-frame splice site in the 5' coding region and uses a downstream start codon compared to variant 1. The encoded isoform (4) has a distinct and longer N-terminus, compared to isoform 1.
    Source sequence(s)
    AF151878, AK311027
    Consensus CDS
    CCDS61139.1
    UniProtKB/TrEMBL
    Q53FU3
    Related
    ENSP00000449270.1, ENST00000549043.5
    Conserved Domains (1) summary
    pfam01217
    Location:20 → 161
    Clat_adaptor_s; Clathrin adaptor complex small chain

  4. NM_016057.3 → NP_057141.1  coatomer subunit zeta-1 isoform 1

    See identical proteins and their annotated locations for NP_057141.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes isoform 1.
    Source sequence(s)
    AF151878
    Consensus CDS
    CCDS8877.1
    UniProtKB/Swiss-Prot
    B4DDX8, B4DHZ0, F8VS17, F8VWL5, P61923, Q549N6, Q9Y3C3
    UniProtKB/TrEMBL
    Q53FU3
    Related
    ENSP00000262061.2, ENST00000262061.7
    Conserved Domains (1) summary
    cd14829
    Location:14 → 145
    Zeta-COP; zeta subunit of the F-COPI complex

RNA

  1. NR_073424.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) lacks an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AF151878, AK295325, CB127540

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    54325131..54351846
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    54291719..54318429
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P61923.1 GenPept UniProtKB/Swiss-Prot:P61923

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Chemical Information
Molecular Biology Databases
Research Materials
Tools
Miscellaneous