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    ARCN1 archain 1 [ Homo sapiens (human) ]

    Gene ID: 372, updated on 3-Nov-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
    mouse all
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    Genomic context

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    See ARCN1 in Genome Data Viewer
    Location:
    11q23.3
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (118572409..118603033)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (118591694..118622309)
    RS_2024_09 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 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. 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
    2. 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
    3. Expanding the phenotypic spectrum of ARCN1-related syndrome. Ritter AL, et al. Genet Med, 2022 Jun. PMID 35300924, Free PMC Article
    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. The coatomer protein delta-COP, encoded by the archain gene, is conserved across diverse eukaryotes. Tunnacliffe A, et al. Mamm Genome, 1996 Oct. PMID 8854871

    See all (174) 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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    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
    		Compare labs

    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
      Related
      ENSP00000352385.4, ENST00000359415.8

    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_2024_08

    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)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      118591694..118622309
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P48444.1 GenPept UniProtKB/Swiss-Prot:P48444

    Gene LinkOut

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

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