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Aliases for ARCN1 Gene

Aliases for ARCN1 Gene

  • Archain 1 2 3 5
  • Coatomer Protein Complex, Subunit Delta 2 3
  • 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
  • Coatomer Subunit Delta 3
  • Archain 4
  • SRMMD 3

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 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).

Additional gene information for ARCN1 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for ARCN1 Gene

Genomics for ARCN1 Gene

GeneHancer (GH) Regulatory Elements for ARCN1 Gene

Promoters and enhancers for ARCN1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH11I118571 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 550.8 +0.4 378 2.9 PKNOX1 SMAD1 ARNT ARID4B SIN3A DMAP1 YY1 POLR2B ZNF766 SP3 IFT46 ARCN1 RPL5P30 KMT2A CCDC84 VPS11 ENSG00000255121 HINFP HMBS
GH11I119090 Promoter/Enhancer 2.5 EPDnew Ensembl ENCODE dbSUPER 52.1 +521.3 521285 5.9 HDGF PKNOX1 SMAD1 ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 GC11M119097 H2AFX KMT2A HINFP UBE4A ARCN1 BCL9L RPL5P30 ENSG00000254909 CCDC84
GH11I118906 Promoter/Enhancer 2.9 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 25 +346.4 346406 24.6 CLOCK MLX ZFP64 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF143 BCL9L DPAGT1 UBE4A ENSG00000254909 RPL23AP64 ARCN1 ENSG00000254428 RNF26 CCDC84 KMT2A
GH11I117809 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 34.4 -762.8 -762759 0.9 HDGF SMAD1 ARNT YBX1 ZNF2 ZBTB7B ZNF48 ZNF280A ZNF207 NCOA1 UBE4A ARCN1 DSCAML1 KMT2A SIDT2 FXYD2 MPZL2 RNF214 RPS27P19 DDX6
GH11I118433 Promoter/Enhancer 2.7 VISTA EPDnew Ensembl ENCODE dbSUPER 19.2 -134.3 -134299 8.2 CLOCK ZFP64 DMAP1 YY1 ZNF213 E2F8 ZNF143 SP3 NFYC ZNF610 KMT2A VPS11 TMEM25 IFT46 ARCN1 HINFP THY1 CCDC84 LOC101929089 ATP5MG
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around ARCN1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the ARCN1 gene promoter:

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)

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, posLast=142142, Lys233, posLast=256256, Lys263, posLast=336336, Lys363, and Lys485

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

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

Suggested Antigen Peptide Sequences for ARCN1 Gene

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

GENATLAS Biochemistry:
archain,homologous to DNA sequences from Drosophila and mice
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).

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,IDA 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

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
endoplasmic reticulum 5
cytosol 5
golgi apparatus 5
mitochondrion 2
extracellular 1
peroxisome 1
nucleus 1

Subcellular locations from the

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

Gene Ontology (GO) - Cellular Components for ARCN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000139 Golgi membrane 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

Gene Ontology (GO) - Biological Process for ARCN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006810 transport IEA --
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 TAS,IEA --
GO:0008344 adult locomotory behavior 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

Unigene Clusters for ARCN1 Gene

Archain 1:
Representative Sequences:

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

No ASD Table

Relevant External Links for ARCN1 Gene

GeneLoc Exon Structure for
ARCN1
ECgene alternative splicing isoforms for
ARCN1

Expression for ARCN1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP 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, PaxDb, MaxQB, and MOPED for ARCN1 Gene



Protein tissue co-expression partners for ARCN1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of ARCN1 Gene:

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(4.4)
  • Lung(2.6)
  • Skin(2.4)
  • Heart(2.3)
  • Spleen(2.2)
  • Kidney(2.1)
  • 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 33 34
  • 99.93 (n)
oppossum
(Monodelphis domestica)
Mammalia ARCN1 34
  • 97 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia ARCN1 34
  • 96 (a)
OneToOne
dog
(Canis familiaris)
Mammalia ARCN1 33 34
  • 94.13 (n)
cow
(Bos Taurus)
Mammalia ARCN1 33 34
  • 93.35 (n)
mouse
(Mus musculus)
Mammalia Arcn1 33 16 34
  • 92.5 (n)
rat
(Rattus norvegicus)
Mammalia Arcn1 33
  • 92.43 (n)
chicken
(Gallus gallus)
Aves ARCN1 33 34
  • 81.44 (n)
lizard
(Anolis carolinensis)
Reptilia ARCN1 34
  • 85 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia arcn1 33
  • 76.13 (n)
Str.824 33
African clawed frog
(Xenopus laevis)
Amphibia arcn1-prov 33
zebrafish
(Danio rerio)
Actinopterygii arcn1b 34
  • 81 (a)
OneToMany
arcn1a 33 34
  • 73.54 (n)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.2657 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP010719 33
  • 59.96 (n)
fruit fly
(Drosophila melanogaster)
Insecta deltaCOP 33 34
  • 58.3 (n)
dgrCOP 35
  • 56 (a)
worm
(Caenorhabditis elegans)
Secernentea C13B9.3 35 33
  • 54.48 (n)
copd-1 34
  • 50 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes RET2 34 36
  • 31 (a)
OneToOne
thale cress
(Arabidopsis thaliana)
eudicotyledons AT5G05010 33
  • 54.43 (n)
soybean
(Glycine max)
eudicotyledons Gma.2422 33
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.561 33
rice
(Oryza sativa)
Liliopsida Os05g0311000 33
  • 53.99 (n)
wheat
(Triticum aestivum)
Liliopsida Ta.23804 33
corn
(Zea mays)
Liliopsida Zm.17239 33
sea squirt
(Ciona savignyi)
Ascidiacea CSA.9714 34
  • 65 (a)
OneToOne
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.7899 33
Species where no ortholog for ARCN1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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)

Paralogs for ARCN1 Gene

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

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 from dbSNP and Humsavar for ARCN1 Gene

SNP ID Clin Chr 11 pos Variation AA Info Type
rs886040858 pathogenic, Short stature, rhizomelic, with microcephaly, micrognathia, and developmental delay 118,581,395(+) AGAGAG/AGAG coding_sequence_variant, frameshift, intron_variant
rs886040859 pathogenic, Short stature, rhizomelic, with microcephaly, micrognathia, and developmental delay 118,581,502(+) C/A coding_sequence_variant, intron_variant, stop_gained
rs886040860 pathogenic, Short stature, rhizomelic, with microcephaly, micrognathia, and developmental delay 118,583,991(+) AAAA/AAA coding_sequence_variant, frameshift
rs1000368786 -- 118,599,281(+) C/T intron_variant
rs1000375857 -- 118,570,493(+) C/A upstream_transcript_variant

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

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

Disorders for ARCN1 Gene

MalaCards: The human disease database

(2) MalaCards diseases for ARCN1 Gene - From: HGMD, OMIM, ClinVar, 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}.

Additional Disease Information for ARCN1

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 22 58
  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 22 58
  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 58
  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 58
  5. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58

Products for ARCN1 Gene

Sources for ARCN1 Gene

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