Human Gene ARCN1 (ENST00000264028.5_4) from GENCODE V47lift37
  Description: archain 1, transcript variant 1 (from RefSeq NM_001655.5)
Gencode Transcript: ENST00000264028.5_4
Gencode Gene: ENSG00000095139.15_8
Transcript (Including UTRs)
   Position: hg19 chr11:118,443,124-118,473,748 Size: 30,625 Total Exon Count: 10 Strand: +
Coding Region
   Position: hg19 chr11:118,443,263-118,471,429 Size: 28,167 Coding Exon Count: 10 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr11:118,443,124-118,473,748)mRNA (may differ from genome)Protein (511 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: COPD_HUMAN
DESCRIPTION: RecName: Full=Coatomer subunit delta; AltName: Full=Archain; AltName: Full=Delta-coat protein; Short=Delta-COP;
FUNCTION: The coatomer is 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. 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).
SUBUNIT: Oligomeric complex that consists of at least the alpha, beta, beta', gamma, delta, epsilon and zeta subunits.
SUBCELLULAR LOCATION: Cytoplasm (By similarity). Golgi apparatus membrane; Peripheral membrane protein; Cytoplasmic side (By similarity). Cytoplasmic vesicle, COPI-coated vesicle membrane; Peripheral membrane protein; Cytoplasmic side (By similarity). Note=The coatomer is cytoplasmic or polymerized on the cytoplasmic side of the Golgi, as well as on the vesicles/buds originating from it (By similarity).
TISSUE SPECIFICITY: Ubiquitously expressed.
SIMILARITY: Belongs to the adaptor complexes medium subunit family. Delta-COP subfamily.
SIMILARITY: Contains 1 MHD (mu homology) domain.
SEQUENCE CAUTION: Sequence=CAA57072.1; Type=Erroneous initiation;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: ARCN1
Diseases sorted by gene-association score: short stature, rhizomelic, with microcephaly, micrognathia, and developmental delay* (920), parainfluenza virus type 3 (7)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 62.49 RPKM in Cells - Cultured fibroblasts
Total median expression: 1620.94 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -50.80139-0.365 Picture PostScript Text
3' UTR -608.792319-0.263 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR022775 - AP_mu_sigma_su
IPR008968 - Clathrin_mu_C
IPR011012 - Longin-like_dom

Pfam Domains:
PF00928 - Adaptor complexes medium subunit family
PF01217 - Clathrin adaptor complex small chain

SCOP Domains:
49447 - Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor
64356 - SNARE-like

ModBase Predicted Comparative 3D Structure on P48444
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologGenome BrowserGenome Browser
Gene DetailsGene Details Gene DetailsGene DetailsGene Details
Gene SorterGene Sorter Gene SorterGene SorterGene Sorter
 RGDEnsembl WormBaseSGD
    Protein SequenceProtein Sequence
    AlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003723 RNA binding

Biological Process:
GO:0006886 intracellular protein transport
GO:0006888 ER to Golgi vesicle-mediated transport
GO:0006890 retrograde vesicle-mediated transport, Golgi to ER
GO:0008344 adult locomotory behavior
GO:0015031 protein transport
GO:0016192 vesicle-mediated transport
GO:0021691 cerebellar Purkinje cell layer maturation
GO:0043473 pigmentation
GO:0048193 Golgi vesicle transport

Cellular Component:
GO:0000139 Golgi membrane
GO:0005737 cytoplasm
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0005794 Golgi apparatus
GO:0005829 cytosol
GO:0016020 membrane
GO:0030126 COPI vesicle coat
GO:0030133 transport vesicle
GO:0030137 COPI-coated vesicle
GO:0030663 COPI-coated vesicle membrane
GO:0031410 cytoplasmic vesicle


-  Descriptions from all associated GenBank mRNAs
  AF272381 - Homo sapiens clone 1370-7 MLL protein mRNA, partial cds.
AK304019 - Homo sapiens cDNA FLJ51620 complete cds, highly similar to Coatomer subunit delta.
LP895224 - Sequence 88 from Patent EP3253886.
AK312298 - Homo sapiens cDNA, FLJ92603, Homo sapiens archain 1 (ARCN1), mRNA.
BC064936 - Homo sapiens archain 1, mRNA (cDNA clone IMAGE:6157700), complete cds.
BX640860 - Homo sapiens mRNA; cDNA DKFZp686M09245 (from clone DKFZp686M09245).
JD106505 - Sequence 87529 from Patent EP1572962.
X81197 - H.sapiens mRNA (clone pPH2) for archain.
BC080638 - Homo sapiens cDNA clone IMAGE:6584541, containing frame-shift errors.
BC093636 - Homo sapiens archain 1, mRNA (cDNA clone MGC:120671 IMAGE:7939481), complete cds.
BC093638 - Homo sapiens archain 1, mRNA (cDNA clone MGC:120673 IMAGE:7939483), complete cds.
JD273116 - Sequence 254140 from Patent EP1572962.
KJ896450 - Synthetic construct Homo sapiens clone ccsbBroadEn_05844 ARCN1 gene, encodes complete protein.
X81198 - H.sapiens mRNA (clone p5) for archain.
JD083647 - Sequence 64671 from Patent EP1572962.
JD181905 - Sequence 162929 from Patent EP1572962.
JD122387 - Sequence 103411 from Patent EP1572962.
JD206169 - Sequence 187193 from Patent EP1572962.
JD413964 - Sequence 394988 from Patent EP1572962.
JD102147 - Sequence 83171 from Patent EP1572962.
JD327743 - Sequence 308767 from Patent EP1572962.
JD432739 - Sequence 413763 from Patent EP1572962.
JD295248 - Sequence 276272 from Patent EP1572962.
JD280010 - Sequence 261034 from Patent EP1572962.
JD490846 - Sequence 471870 from Patent EP1572962.
JD426715 - Sequence 407739 from Patent EP1572962.
JD220893 - Sequence 201917 from Patent EP1572962.
JD489025 - Sequence 470049 from Patent EP1572962.
JD362630 - Sequence 343654 from Patent EP1572962.
JD460290 - Sequence 441314 from Patent EP1572962.
JD072025 - Sequence 53049 from Patent EP1572962.
JD072026 - Sequence 53050 from Patent EP1572962.
JD506186 - Sequence 487210 from Patent EP1572962.
JD099311 - Sequence 80335 from Patent EP1572962.
JD293455 - Sequence 274479 from Patent EP1572962.
JD342087 - Sequence 323111 from Patent EP1572962.
JD480382 - Sequence 461406 from Patent EP1572962.
JD421247 - Sequence 402271 from Patent EP1572962.
JD509016 - Sequence 490040 from Patent EP1572962.
JD245318 - Sequence 226342 from Patent EP1572962.
JD044106 - Sequence 25130 from Patent EP1572962.
JD424359 - Sequence 405383 from Patent EP1572962.
JD196979 - Sequence 178003 from Patent EP1572962.
JD238858 - Sequence 219882 from Patent EP1572962.
JD358050 - Sequence 339074 from Patent EP1572962.
JD147949 - Sequence 128973 from Patent EP1572962.
JD516082 - Sequence 497106 from Patent EP1572962.
JD398081 - Sequence 379105 from Patent EP1572962.
JD226534 - Sequence 207558 from Patent EP1572962.
JD240730 - Sequence 221754 from Patent EP1572962.
JD100985 - Sequence 82009 from Patent EP1572962.
JD163404 - Sequence 144428 from Patent EP1572962.
JD079176 - Sequence 60200 from Patent EP1572962.
JD320087 - Sequence 301111 from Patent EP1572962.
JD527639 - Sequence 508663 from Patent EP1572962.
JD353277 - Sequence 334301 from Patent EP1572962.
JD298403 - Sequence 279427 from Patent EP1572962.
JD024264 - Sequence 5288 from Patent EP1572962.
JD034447 - Sequence 15471 from Patent EP1572962.
JD304245 - Sequence 285269 from Patent EP1572962.
JD155562 - Sequence 136586 from Patent EP1572962.
JD045140 - Sequence 26164 from Patent EP1572962.
JD045141 - Sequence 26165 from Patent EP1572962.
JD452901 - Sequence 433925 from Patent EP1572962.
JD373713 - Sequence 354737 from Patent EP1572962.
JD355753 - Sequence 336777 from Patent EP1572962.
JD467476 - Sequence 448500 from Patent EP1572962.
JD172350 - Sequence 153374 from Patent EP1572962.
JD063451 - Sequence 44475 from Patent EP1572962.
JD237008 - Sequence 218032 from Patent EP1572962.
JD074389 - Sequence 55413 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein P48444 (Reactome details) participates in the following event(s):

R-HSA-6807872 Active ARF recruits coatomer
R-HSA-6811412 Active ARF recruits coatomer to the Golgi
R-HSA-6807875 ARFGAP, cargo, v-SNAREs and p24 proteins bind nascent COPI complex
R-HSA-6811417 ARFGAP, cargo, vSNARES and p24 proteins bind COPI vesicles at Golgi
R-HSA-6811426 Retrograde COPI vesicles bind kinesin and microtubules
R-HSA-6811418 ARFGAPs stimulate ARF GTPase activity at the Golgi membrane
R-HSA-6811423 Retrograde vesicle is tethered at the ER by the NRZ complex and t-SNAREs
R-HSA-6807877 ARFGAPs stimulate ARF GTPase activity
R-HSA-6809003 ERGIC-to-Golgi vesicles bind dynein:dynactin
R-HSA-6809011 cis-Golgi t-SNAREs bind YKT6 on tethered vesicle
R-HSA-6809006 Vesicle is tethered through binding GOLGA2:GORASP1, GOLGB1 and the COG complex
R-HSA-6807878 COPI-mediated anterograde transport
R-HSA-6811434 COPI-dependent Golgi-to-ER retrograde traffic
R-HSA-199977 ER to Golgi Anterograde Transport
R-HSA-8856688 Golgi-to-ER retrograde transport
R-HSA-199991 Membrane Trafficking
R-HSA-948021 Transport to the Golgi and subsequent modification
R-HSA-6811442 Intra-Golgi and retrograde Golgi-to-ER traffic
R-HSA-5653656 Vesicle-mediated transport
R-HSA-446203 Asparagine N-linked glycosylation
R-HSA-597592 Post-translational protein modification
R-HSA-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: B4E1X2, COPD, COPD_HUMAN, E9PEU4, ENST00000264028.1, ENST00000264028.2, ENST00000264028.3, ENST00000264028.4, NM_001655, P48444, Q52M80, uc317hol.1, uc317hol.2
UCSC ID: ENST00000264028.5_4
RefSeq Accession: NM_001655.5
Protein: P48444 (aka COPD_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.