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ARCN1 archain 1 [ Homo sapiens (human) ]

Gene ID: 372, updated on 7-Apr-2024

Summary

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Official Symbol
ARCN1provided by HGNC
Official Full Name
archain 1provided by HGNC
Primary source
HGNC:HGNC:649
See related
Ensembl:ENSG00000095139 MIM:600820; AllianceGenome:HGNC:649
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
COPD; SSMG; SRMMD
Summary
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]
Expression
Ubiquitous expression in thyroid (RPKM 45.3), urinary bladder (RPKM 37.0) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
11q23.3
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (118572409..118603033)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (118591694..118622309)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (118443124..118473748)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene intraflagellar transport 46 Neighboring gene uncharacterized LOC124902764 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5593 Neighboring gene ribosomal protein L5 pseudogene 30 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5594 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5595 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:118461541-118461751 Neighboring gene RNA, U6 small nuclear 1157, pseudogene Neighboring gene uncharacterized LOC124902765 Neighboring gene CRISPRi-validated cis-regulatory element chr11.5498 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3948 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3949 Neighboring gene Sharpr-MPRA regulatory region 10010 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:118479501-118480175 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:118480176-118480849 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3950 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:118486166-118486683 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:118486684-118487200 Neighboring gene pleckstrin homology like domain family B member 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:118488753-118489268 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3951 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:118501544-118502052 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:118502053-118502560 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:118505587-118506258 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:118514693-118515192 Neighboring gene microRNA 6716 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:118529141-118529690 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:118529691-118530240 Neighboring gene trehalase Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:118549589-118550250 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:118550251-118550910

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. Expanding the phenotypic spectrum of ARCN1-related syndrome. Ritter AL, et al. Genet Med, 2022 Jun. PMID 35300924, Free PMC Article
  2. Novel de novo ARCN1 intronic variant causes rhizomelic short stature with microretrognathia and developmental delay. Tidwell T, et al. Cold Spring Harb Mol Case Stud, 2020 Dec. PMID 33154040, Free PMC Article
  3. Transient N-glycosylation abnormalities likely due to a de novo loss-of-function mutation in the delta subunit of coat protein I. Reunert J, et al. Am J Med Genet A, 2019 Jul. PMID 31075182
  4. ARCN1 Mutations Cause a Recognizable Craniofacial Syndrome Due to COPI-Mediated Transport Defects. Izumi K, et al. Am J Hum Genet, 2016 Aug 4. PMID 27476655, Free PMC Article
  5. Crystallization and preliminary X-ray analysis of the C-terminal domain of δ-COP, a medium-sized subunit of the COPI complex involved in membrane trafficking. Deng K, et al. Acta Crystallogr Sect F Struct Biol Cryst Commun, 2012 Jul 1. PMID 22750876, Free PMC Article

See all (143) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Novel de novo ARCN1 intronic variant causes rhizomelic short stature with microretrognathia and developmental delay.
    Title: Novel de novo ARCN1 intronic variant causes rhizomelic short stature with microretrognathia and developmental delay.
  2. report of a clinically recognizable craniofacial disorder characterized by facial dysmorphisms, severe micrognathia, rhizomelic shortening, microcephalic dwarfism, and mild developmental delay due to loss-of-function heterozygous mutations in ARCN1, which encodes the coatomer subunit delta of COPI
    Title: ARCN1 Mutations Cause a Recognizable Craniofacial Syndrome Due to COPI-Mediated Transport Defects.
  3. The authors demonstrated that miR-33a could impede influenza A virus replication at the stage of virus internalization by suppressing ARCN1 expression.
    Title: MicroRNA-33a disturbs influenza A virus replication by targeting ARCN1 and inhibiting viral ribonucleoprotein activity.
  4. Single nucleotide polymorphisms in the PHLDB1 and ARCN1 genes are associated with increased risk of Glioma.
    Title: Fine mapping of a region of chromosome 11q23.3 reveals independent locus associated with risk of glioma.
  5. native crystals of delta-COP had unit-cell parameters a = 100.23, b = 136.77, c = 44.39 A
    Title: Crystallization and preliminary X-ray analysis of the C-terminal domain of δ-COP, a medium-sized subunit of the COPI complex involved in membrane trafficking.
Submit: New GeneRIF Correction

Phenotypes

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

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Short stature, rhizomelic, with microcephaly, micrognathia, and developmental delay
MedGen: C4310686 OMIM: 617164 GeneReviews: Not available
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Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated 2022-05-10)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated 2022-05-10)

ClinGen Genome Curation PagePubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA binding HDA PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in Golgi localization IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in adult locomotory behavior IEA
Inferred from Electronic Annotation
more info
  
involved_in cerebellar Purkinje cell layer maturation IEA
Inferred from Electronic Annotation
more info
  
involved_in endoplasmic reticulum to Golgi vesicle-mediated transport IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in intracellular protein transport TAS
Traceable Author Statement
more info
 PubMed 
involved_in pigmentation IEA
Inferred from Electronic Annotation
more info
  
involved_in retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum IBA
Inferred from Biological aspect of Ancestor
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 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 membrane HDA PubMed 
located_in transport vesicle TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
coatomer subunit delta
Names
COPI coat complex subunit delta
archain vesicle transport protein 1
coatomer delta subunit
coatomer protein complex, subunit delta
coatomer protein delta-COP
delta-COP
delta-coat protein

NCBI Reference Sequences (RefSeq)

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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_051953.1 RefSeqGene

    Range
    5023..35647
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001142281.2 → NP_001135753.1  coatomer subunit delta isoform 2

    See identical proteins and their annotated locations for NP_001135753.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an in-frame exon in the 5' coding region, compared to variant 1, and encodes a protein (isoform 2) with a shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AA856562, AK304019, AU125652, BC080638, BC093636, CR988766
    Consensus CDS
    CCDS44749.1
    UniProtKB/Swiss-Prot
    P48444
    Related
    ENSP00000376599.3, ENST00000392859.7
    Conserved Domains (2) summary
    cd09254
    Location:184 → 420
    AP_delta-COPI_MHD; Mu homology domain (MHD) of adaptor protein (AP) coat protein I (COPI) delta subunit
    cl38905
    Location:2 → 45
    longin-like; Longin-like domains

  2. NM_001425073.1 → NP_001412002.1  coatomer subunit delta isoform 3

    Status: REVIEWED

    Source sequence(s)
    AP000941

  3. NM_001425074.1 → NP_001412003.1  coatomer subunit delta isoform 4

    Status: REVIEWED

    Source sequence(s)
    AP000941

  4. NM_001425075.1 → NP_001412004.1  coatomer subunit delta isoform 5

    Status: REVIEWED

    Source sequence(s)
    AP000941

  5. NM_001425076.1 → NP_001412005.1  coatomer subunit delta isoform 6

    Status: REVIEWED

    Source sequence(s)
    AP000941

  6. NM_001425077.1 → NP_001412006.1  coatomer subunit delta isoform 7

    Status: REVIEWED

    Source sequence(s)
    AP000941

  7. NM_001425078.1 → NP_001412007.1  coatomer subunit delta isoform 8

    Status: REVIEWED

    Source sequence(s)
    AP000941

  8. NM_001425079.1 → NP_001412008.1  coatomer subunit delta isoform 9

    Status: REVIEWED

    Source sequence(s)
    AP000941

  9. NM_001425080.1 → NP_001412009.1  coatomer subunit delta isoform 10

    Status: REVIEWED

    Source sequence(s)
    AP000941

  10. NM_001425081.1 → NP_001412010.1  coatomer subunit delta isoform 11

    Status: REVIEWED

    Source sequence(s)
    AP000941

  11. NM_001655.5 → NP_001646.2  coatomer subunit delta isoform 1

    See identical proteins and their annotated locations for NP_001646.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AA856562, AU125652, BC080638, BC093636, CR988766, DB216489
    Consensus CDS
    CCDS8400.1
    UniProtKB/Swiss-Prot
    B4E1X2, E9PEU4, P48444, Q52M80
    UniProtKB/TrEMBL
    B0YIW5, B0YIW6
    Related
    ENSP00000264028.4, ENST00000264028.5
    Conserved Domains (2) summary
    cd09254
    Location:272 → 508
    AP_delta-COPI_MHD; Mu homology domain (MHD) of adaptor protein (AP) coat protein I (COPI) delta subunit
    cd14830
    Location:4 → 133
    Delta_COP_N; delta subunit of the F-COPI complex, N-terminal domain

RNA

  1. NR_189131.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AP000941

  2. NR_189132.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AP000941

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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    118572409..118603033
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005271542.5 → XP_005271599.1  coatomer subunit delta isoform X1

    Conserved Domains (2) summary
    cd09254
    Location:272 → 414
    AP_delta-COPI_MHD; Mu homology domain (MHD) of adaptor protein (AP) coat protein I (COPI) delta subunit
    cd14830
    Location:4 → 133
    Delta_COP_N; delta subunit of the F-COPI complex, N-terminal domain

  2. XM_047426899.1 → XP_047282855.1  coatomer subunit delta isoform X2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    118591694..118622309
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054368696.1 → XP_054224671.1  coatomer subunit delta isoform X1

  2. XM_054368697.1 → XP_054224672.1  coatomer subunit delta isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P48444.1 GenPept UniProtKB/Swiss-Prot:P48444

Gene LinkOut

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