This gene maps in a region, which include the mixed lineage leukemia and Friend leukemia virus integration 1 genes, where multiple disease-associated chromosome translocations occur. It is an intracellular protein. Archain sequences are well conserved among eukaryotes and this protein may play a fundamental role in eukaryotic cell biology. It has similarities to heat shock prot... See more...

Aliases for ARCN1 Gene

Aliases for ARCN1 Gene

  • Archain 1 2 3 5
  • Coatomer Protein Complex, Subunit Delta 2 3
  • COPI Coat Complex Subunit Delta 2 3
  • Coatomer Subunit Delta 3 4
  • Delta-Coat Protein 3 4
  • Delta-COP 3 4
  • COPD 3 4
  • Archain Vesicle Transport Protein 1 3
  • Coatomer Protein Delta-COP 3
  • Coatomer Delta Subunit 3
  • Archain 4
  • SRMMD 3
  • ARCN1 5

External Ids for ARCN1 Gene

Previous HGNC Symbols for ARCN1 Gene

  • COPD

Previous GeneCards Identifiers for ARCN1 Gene

  • GC11P120799
  • GC11P119954
  • GC11P118477
  • GC11P117980
  • GC11P117948
  • GC11P118444
  • GC11P114380

Summaries for ARCN1 Gene

Entrez Gene Summary for ARCN1 Gene

  • This gene maps in a region, which include the mixed lineage leukemia and Friend leukemia virus integration 1 genes, where multiple disease-associated chromosome translocations occur. It is an intracellular protein. Archain sequences are well conserved among eukaryotes and this protein may play a fundamental role in eukaryotic cell biology. It has similarities to heat shock proteins and clathrin-associated proteins, and may be involved in vesicle structure or trafficking. [provided by RefSeq, Jul 2008]

GeneCards Summary for ARCN1 Gene

ARCN1 (Archain 1) is a Protein Coding gene. Diseases associated with ARCN1 include Short Stature, Rhizomelic, With Microcephaly, Micrognathia, And Developmental Delay and Parainfluenza Virus Type 3. Among its related pathways are Transport to the Golgi and subsequent modification and Metabolism of proteins.

UniProtKB/Swiss-Prot Summary for ARCN1 Gene

  • Component of the coatomer, 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. The 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).

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for ARCN1 Gene

Genomics for ARCN1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for ARCN1 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around ARCN1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for ARCN1

Top Transcription factor binding sites by QIAGEN in the ARCN1 gene promoter:
  • AML1a
  • AP-4
  • AREB6
  • Elk-1
  • Evi-1
  • Msx-1
  • NRF-2
  • POU2F1
  • POU2F1a
  • TGIF

Genomic Locations for ARCN1 Gene

Genomic Locations for ARCN1 Gene
chr11:118,572,387-118,603,033
(GRCh38/hg38)
Size:
30,647 bases
Orientation:
Plus strand
chr11:118,443,102-118,473,748
(GRCh37/hg19)
Size:
30,647 bases
Orientation:
Plus strand

Genomic View for ARCN1 Gene

Genes around ARCN1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ARCN1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ARCN1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for ARCN1 Gene

Proteins for ARCN1 Gene

  • Protein details for ARCN1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P48444-COPD_HUMAN
    Recommended name:
    Coatomer subunit delta
    Protein Accession:
    P48444
    Secondary Accessions:
    • B4E1X2
    • E9PEU4
    • Q52M80

    Protein attributes for ARCN1 Gene

    Size:
    511 amino acids
    Molecular mass:
    57210 Da
    Quaternary structure:
    • Oligomeric complex that consists of at least the alpha, beta, beta', gamma, delta, epsilon and zeta subunits.
    SequenceCaution:
    • Sequence=CAA57072.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for ARCN1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for ARCN1 Gene

Post-translational modifications for ARCN1 Gene

  • Ubiquitination at Lys38, Lys142, Lys233, Lys241, Lys256, Lys263, Lys336, Lys351, Lys363, and Lys485
  • Modification sites at PhosphoSitePlus

Other Protein References for ARCN1 Gene

No data available for DME Specific Peptides for ARCN1 Gene

Domains & Families for ARCN1 Gene

Gene Families for ARCN1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Plasma proteins
  • Predicted intracellular proteins

Protein Domains for ARCN1 Gene

InterPro:
Blocks:
  • Clathrin adaptor complex, medium chain
ProtoNet:

Suggested Antigen Peptide Sequences for ARCN1 Gene

GenScript: Design optimal peptide antigens:
  • cDNA, FLJ92603, Homo sapiens archain 1 (ARCN1), mRNA (B0YIW5_HUMAN)
  • Delta-coat protein (COPD_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P48444

UniProtKB/Swiss-Prot:

COPD_HUMAN :
  • Belongs to the adaptor complexes medium subunit family. Delta-COP subfamily.
Family:
  • Belongs to the adaptor complexes medium subunit family. Delta-COP subfamily.
genes like me logo Genes that share domains with ARCN1: view

Function for ARCN1 Gene

Molecular function for ARCN1 Gene

UniProtKB/Swiss-Prot Function:
Component of the coatomer, 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. The 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).
GENATLAS Biochemistry:
archain,homologous to DNA sequences from Drosophila and mice

Phenotypes From GWAS Catalog for ARCN1 Gene

Gene Ontology (GO) - Molecular Function for ARCN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding HDA 22658674
genes like me logo Genes that share ontologies with ARCN1: view
genes like me logo Genes that share phenotypes with ARCN1: view

Human Phenotype Ontology for ARCN1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for ARCN1

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for ARCN1 Gene

Localization for ARCN1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for ARCN1 Gene

Cytoplasm. Golgi apparatus membrane. Peripheral membrane protein. Cytoplasmic side. Cytoplasmic vesicle, COPI-coated vesicle membrane. Peripheral membrane protein. Cytoplasmic side. Note=The coatomer is cytoplasmic or polymerized on the cytoplasmic side of the Golgi, as well as on the vesicles/buds originating from it. {ECO:0000250}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for ARCN1 gene
Compartment Confidence
golgi apparatus 5
endoplasmic reticulum 4
cytosol 4
mitochondrion 2
plasma membrane 1
extracellular 1
cytoskeleton 1
peroxisome 1
nucleus 1
endosome 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Vesicles (4)
  • Golgi apparatus (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for ARCN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000139 Golgi membrane IEA,TAS --
GO:0005737 cytoplasm IEA --
GO:0005783 endoplasmic reticulum IEA --
GO:0005789 endoplasmic reticulum membrane TAS --
GO:0005794 Golgi apparatus IEA --
genes like me logo Genes that share ontologies with ARCN1: view

Pathways & Interactions for ARCN1 Gene

genes like me logo Genes that share pathways with ARCN1: view

Pathways by source for ARCN1 Gene

5 GeneGo (Thomson Reuters) pathways for ARCN1 Gene
  • Cholesterol and Sphingolipids transport / Transport from Golgi and ER to the apical membrane (normal and CF)
  • Delta508-CFTR traffic / ER-to-Golgi in CF
  • Normal wtCFTR traffic / ER-to-Golgi
  • Transport Clathrin-coated vesicle cycle
  • wtCFTR and delta508-CFTR traffic / Generic schema (norm and CF)

Gene Ontology (GO) - Biological Process for ARCN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006886 intracellular protein transport TAS 7782067
GO:0006888 ER to Golgi vesicle-mediated transport TAS --
GO:0006890 retrograde vesicle-mediated transport, Golgi to ER IEA,TAS --
GO:0008344 adult locomotory behavior IEA --
GO:0015031 protein transport IEA --
genes like me logo Genes that share ontologies with ARCN1: view

No data available for SIGNOR curated interactions for ARCN1 Gene

Drugs & Compounds for ARCN1 Gene

(1) Drugs for ARCN1 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Guanosine triphosphate Experimental Pharma 0
genes like me logo Genes that share compounds with ARCN1: view

Transcripts for ARCN1 Gene

mRNA/cDNA for ARCN1 Gene

2 REFSEQ mRNAs :
14 NCBI additional mRNA sequence :
5 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for ARCN1

Alternative Splicing Database (ASD) splice patterns (SP) for ARCN1 Gene

No ASD Table

Relevant External Links for ARCN1 Gene

GeneLoc Exon Structure for
ARCN1

Expression for ARCN1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for ARCN1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for ARCN1 Gene

This gene is overexpressed in Salivary gland (7.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for ARCN1 Gene



Protein tissue co-expression partners for ARCN1 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for ARCN1

SOURCE GeneReport for Unigene cluster for ARCN1 Gene:

Hs.33642

mRNA Expression by UniProt/SwissProt for ARCN1 Gene:

P48444-COPD_HUMAN
Tissue specificity: Ubiquitously expressed.

Evidence on tissue expression from TISSUES for ARCN1 Gene

  • Nervous system(4.8)
  • Liver(4.5)
  • Skin(3)
  • Lung(3)
  • Kidney(2.6)
  • Muscle(2.4)
  • Blood(2.3)
  • Intestine(2.3)
  • Heart(2.3)
  • Spleen(2.2)
  • Stomach(2.1)
genes like me logo Genes that share expression patterns with ARCN1: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for ARCN1 Gene

Orthologs for ARCN1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for ARCN1 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia ARCN1 30 31
  • 99.93 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia ARCN1 31
  • 97 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia ARCN1 31
  • 96 (a)
OneToOne
Dog
(Canis familiaris)
Mammalia ARCN1 30 31
  • 94.13 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia ARCN1 30 31
  • 93.35 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Arcn1 30 17 31
  • 92.5 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Arcn1 30
  • 92.43 (n)
Chicken
(Gallus gallus)
Aves ARCN1 30 31
  • 81.44 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia ARCN1 31
  • 85 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia arcn1 30
  • 76.13 (n)
Str.824 30
African clawed frog
(Xenopus laevis)
Amphibia arcn1-prov 30
Zebrafish
(Danio rerio)
Actinopterygii arcn1b 31
  • 81 (a)
OneToMany
arcn1a 30 31
  • 73.54 (n)
OneToMany
Rainbow Trout
(Oncorhynchus mykiss)
Actinopterygii Omy.2657 30
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP010719 30
  • 59.96 (n)
Fruit Fly
(Drosophila melanogaster)
Insecta deltaCOP 30 31
  • 58.3 (n)
OneToOne
&dgr;COP 32
  • 56 (a)
Worm
(Caenorhabditis elegans)
Secernentea C13B9.3 30 32
  • 54.48 (n)
copd-1 31
  • 50 (a)
OneToOne
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes RET2 31 33
  • 31 (a)
OneToOne
Thale Cress
(Arabidopsis thaliana)
eudicotyledons AT5G05010 30
  • 54.43 (n)
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.561 30
Soybean
(Glycine max)
eudicotyledons Gma.2422 30
Rice
(Oryza sativa)
Liliopsida Os05g0311000 30
  • 53.99 (n)
Wheat
(Triticum aestivum)
Liliopsida Ta.23804 30
Corn
(Zea mays)
Liliopsida Zm.17239 30
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.9714 31
  • 65 (a)
OneToOne
Sea Vase
(Ciona intestinalis)
Ascidiacea Cin.7899 30
Species where no ortholog for ARCN1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)

Evolution for ARCN1 Gene

ENSEMBL:
Gene Tree for ARCN1 (if available)
TreeFam:
Gene Tree for ARCN1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for ARCN1: view image

Paralogs for ARCN1 Gene

(1) SIMAP similar genes for ARCN1 Gene using alignment to 5 proteins:

  • COPD_HUMAN
  • B0YIW5_HUMAN
  • B0YIW6_HUMAN
  • E9PK34_HUMAN
  • Q6P1Q5_HUMAN
genes like me logo Genes that share paralogs with ARCN1: view

No data available for Paralogs for ARCN1 Gene

Variants for ARCN1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for ARCN1 Gene

SNP ID Clinical significance and condition Chr 11 pos Variation AA Info Type
638398 Uncertain Significance: Short stature, rhizomelic, with microcephaly, micrognathia, and developmental delay 118,597,741(+) G/A MISSENSE_VARIANT
711067 Benign: not provided 118,584,612(+) C/G SYNONYMOUS_VARIANT
714500 Benign: not provided 118,583,173(+) G/A INTRON_VARIANT
718664 Benign: not provided 118,572,558(+) C/T INTRON_VARIANT
718665 Benign: not provided 118,581,258(+) G/T MISSENSE_VARIANT,INTRON_VARIANT

Additional dbSNP identifiers (rs#s) for ARCN1 Gene

Structural Variations from Database of Genomic Variants (DGV) for ARCN1 Gene

Variant ID Type Subtype PubMed ID
nsv475607 CNV novel sequence insertion 20440878
nsv832283 CNV loss 17160897

Variation tolerance for ARCN1 Gene

Residual Variation Intolerance Score: 22.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.50; 29.15% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for ARCN1 Gene

Human Gene Mutation Database (HGMD)
ARCN1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
ARCN1

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for ARCN1 Gene

Disorders for ARCN1 Gene

MalaCards: The human disease database

(7) MalaCards diseases for ARCN1 Gene - From: OMIM, ClinVar, GTR, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search ARCN1 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

COPD_HUMAN
  • Short stature, rhizomelic, with microcephaly, micrognathia, and developmental delay (SRMMD) [MIM:617164]: A disorder characterized by facial dysmorphism, severe micrognathia, microcephaly, rhizomelic short stature, and mild developmental delay. {ECO:0000269 PubMed:27476655}. Note=The disease is caused by mutations affecting the gene represented in this entry. the skeletal phenotype, that characterizes this disorder, may be due to defective type I collagen transport and reduction of collagen secretion. {ECO:0000269 PubMed:27476655}.
genes like me logo Genes that share disorders with ARCN1: view

No data available for Genatlas for ARCN1 Gene

Publications for ARCN1 Gene

  1. The human archain gene, ARCN1, has highly conserved homologs in rice and Drosophila. (PMID: 7782067) Radice P … Tunnacliffe A (Genomics 1995) 2 3 4 23
  2. The coatomer protein delta-COP, encoded by the archain gene, is conserved across diverse eukaryotes. (PMID: 8854871) Tunnacliffe A … Radice P (Mammalian genome : official journal of the International Mammalian Genome Society 1996) 2 3 23
  3. ARCN1 Mutations Cause a Recognizable Craniofacial Syndrome Due to COPI-Mediated Transport Defects. (PMID: 27476655) Izumi K … Shirahige K (American journal of human genetics 2016) 3 4
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4
  5. A reference map of the human binary protein interactome. (PMID: 32296183) Luck K … Calderwood MA (Nature 2020) 3

Products for ARCN1 Gene

Sources for ARCN1 Gene