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ARCN1 Gene(Protein Coding)

Archain 1

GCID:
GC11P118572
GIFtS:
55
Genes Participants
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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. Among its related pathways are Vesicle-mediated transport and Transport to the Golgi and subsequent modification. GO annotations related to this gene include poly(A) RNA binding.

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).

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

Products:

  1. Regulatory Element

Regulatory Elements for ARCN1 Gene

Enhancers for ARCN1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH11G119090 1.7 Ensembl ENCODE dbSUPER 23.1 +521.3 521285 5.9 CREB3L1 AGO1 DMAP1 YY1 SLC30A9 ZNF143 ZNF263 SP3 NFYC TBX21 HINFP ARCN1 RNF26 ENSG00000254909 C2CD2L BCL9L RPL23AP64 UBE4A RPS25 IFT46
GH11G118398 1.6 Ensembl ENCODE dbSUPER 19.2 -171.6 -171589 5.1 CREB3L1 ARNT WRNIP1 ARID4B SIN3A DMAP1 ZBTB7B YY1 ZNF766 ZNF207 ARCN1 RNF26 ENSG00000254909 ENSG00000254428 RPL23AP64 UBE4A IFT46 BCL9L ENSG00000255384 KMT2A
GH11G117906 1.5 Ensembl ENCODE dbSUPER 19.1 -663.5 -663502 4.1 HDGF PKNOX1 ATF1 ARNT ZNF133 TCF12 GTF3C2 GATA2 FOS ZNF263 ARCN1 UBE4A TMPRSS13 FXYD6-FXYD2 FXYD6 ENSG00000254844 DSCAML1 RNF214 ENSG00000254528 FXYD2
GH11G119167 1.1 ENCODE 25.7 +596.5 596542 2.8 PKNOX1 ARNT WRNIP1 ZFP64 ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF302 BCL9L IFT46 ENSG00000254909 UBE4A RPL23AP64 ARCN1 HINFP DDX6 ENSG00000254428 ENSG00000272186
GH11G118603 2 FANTOM5 Ensembl ENCODE dbSUPER 10.7 +36.2 36241 9.9 HDGF PKNOX1 CREB3L1 ARNT ARID4B SIN3A FEZF1 ZNF2 ZNF143 ZNF207 IFT46 TREHP1 LOC105369519 TREH ENSG00000255176 ARCN1 TTC36 ENSG00000255384 KMT2A ATP5L
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around ARCN1 on UCSC Golden Path with GeneCards custom track

Promoters for ARCN1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000045643 613 2401 PKNOX1 CREB3L1 ARNT AGO1 WRNIP1 ARID4B SIN3A DMAP1 YY1 ZNF766

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

Genomic Location for ARCN1 Gene

Chromosome:
11
Start:
118,572,387 bp from pter
End:
118,603,033 bp from pter
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 Structure • Gene Density

RefSeq DNA sequence for ARCN1 Gene

Proteins for ARCN1 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • 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

Protein Expression for ARCN1 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for ARCN1 Gene

  • Ubiquitination at posLast=3838, posLast=142142, posLast=233233, Lys256, Lys263, posLast=336336, posLast=363363, and Lys485
  • Modification sites at PhosphoSitePlus

Other Protein References for ARCN1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for ARCN1 Gene

Domains & Families for ARCN1 Gene

Protein Domains for ARCN1 Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for ARCN1 Gene

GenScript: Design optimal peptide antigens:

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

No data available for Gene Families for ARCN1 Gene

Function for ARCN1 Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line
  7. Flow Cytometry

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).

Gene Ontology (GO) - Molecular Function for ARCN1 Gene

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

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , 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

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 IEA,TAS --
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

Products:

  1. Drug

(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

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone
  5. Flow Cytometry

mRNA/cDNA for ARCN1 Gene

(3) REFSEQ mRNAs :
(8) Additional mRNA sequences :
(755) Selected AceView cDNA sequences:
(5) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for ARCN1 Gene

Archain 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

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

Products:

  1. Primer

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

mRNA expression in normal human tissues for ARCN1 Gene
mRNA expression by BioGPS for ARCN1 GenemRNA expression by GTEx 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

Primer Products

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 34 35
  • 99.93 (n)
oppossum
(Monodelphis domestica)
 Mammalia ARCN1 35
  • 97 (a)
 OneToOne
platypus
(Ornithorhynchus anatinus)
 Mammalia ARCN1 35
  • 96 (a)
 OneToOne
dog
(Canis familiaris)
 Mammalia ARCN1 34 35
  • 94.13 (n)
cow
(Bos Taurus)
 Mammalia ARCN1 34 35
  • 93.35 (n)
mouse
(Mus musculus)
 Mammalia Arcn1 34 16 35
  • 92.5 (n)
rat
(Rattus norvegicus)
 Mammalia Arcn1 34
  • 92.43 (n)
chicken
(Gallus gallus)
 Aves ARCN1 34 35
  • 81.44 (n)
lizard
(Anolis carolinensis)
 Reptilia ARCN1 35
  • 85 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia arcn1 34
  • 76.13 (n)
Str.824 34
African clawed frog
(Xenopus laevis)
 Amphibia arcn1-prov 34
zebrafish
(Danio rerio)
 Actinopterygii arcn1b 35
  • 81 (a)
 OneToMany
arcn1a 34 35
  • 73.54 (n)
rainbow trout
(Oncorhynchus mykiss)
 Actinopterygii Omy.2657 34
African malaria mosquito
(Anopheles gambiae)
 Insecta AgaP_AGAP010719 34
  • 59.96 (n)
fruit fly
(Drosophila melanogaster)
 Insecta deltaCOP 34 35
  • 58.3 (n)
dgrCOP 36
  • 56 (a)
worm
(Caenorhabditis elegans)
 Secernentea C13B9.3 36 34
  • 54.48 (n)
copd-1 35
  • 50 (a)
 OneToOne
baker's yeast
(Saccharomyces cerevisiae)
 Saccharomycetes RET2 35 37
  • 31 (a)
 OneToOne
thale cress
(Arabidopsis thaliana)
 eudicotyledons AT5G05010 34
  • 54.43 (n)
soybean
(Glycine max)
 eudicotyledons Gma.2422 34
Alicante grape
(Vitis vinifera)
 eudicotyledons Vvi.561 34
rice
(Oryza sativa)
 Liliopsida Os05g0311000 34
  • 53.99 (n)
wheat
(Triticum aestivum)
 Liliopsida Ta.23804 34
corn
(Zea mays)
 Liliopsida Zm.17239 34
sea squirt
(Ciona savignyi)
 Ascidiacea CSA.9714 35
  • 65 (a)
 OneToOne
sea squirt
(Ciona intestinalis)
 Ascidiacea Cin.7899 34
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 Sequence Context AA Info Type
rs886040858 Pathogenic 118,581,399(+) CAGAG(-/AG)TGTAA intron-variant, reference, frameshift-variant
rs886040859 Pathogenic 118,581,502(+) CTTCT(A/C)AAGAG intron-variant, reference, stop-gained
rs886040860 Pathogenic 118,583,994(+) CCAAA(-/A)GTGGC reference, frameshift-variant
rs1000368786 -- 118,599,281(+) AAAGA(C/T)GGTAT intron-variant
rs1000375857 -- 118,570,493(+) AAGTA(A/C)CTGAC intron-variant, upstream-variant-2KB

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)

Relevant External Links 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

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}.

Relevant External Links for ARCN1

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
ARCN1

No disorders were found for ARCN1 Gene.

No data available for MalaCards and 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 64
  2. The coatomer protein delta-COP, encoded by the archain gene, is conserved across diverse eukaryotes. (PMID: 8854871) Tunnacliffe A. … Radice P. (Mamm. Genome 1996) 2 3 22 64
  3. ARCN1 mutations cause a recognizable craniofacial syndrome due to copi-mediated transport defects. (PMID: 27476655) Izumi K. … Shirahige K. (Am. J. Hum. Genet. 2016) 3 4 64
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64
  5. MicroRNA-33a disturbs influenza A virus replication by targeting ARCN1 and inhibiting viral ribonucleoprotein activity. (PMID: 26498766) Hu Y. … Ye X. (J. Gen. Virol. 2016) 3 64

Products for ARCN1 Gene

Sources for ARCN1 Gene

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