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COPB1 Gene

protein-coding   GIFtS: 61
GCID: GC11M014436

Coatomer Protein Complex, Subunit Beta 1

(Previous names: coatomer protein complex, subunit beta)
(Previous symbol: COPB)
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(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Coatomer Protein Complex, Subunit Beta 11 2     Beta Coat Protein2
COPB1 2 3 5     beta-cop2
Beta-Coat Protein2 3     Coatomer Subunit Beta2
Coatomer Protein Complex, Subunit Beta1     Beta-COP3

External Ids:    HGNC: 22311   Entrez Gene: 13152   Ensembl: ENSG000001290837   OMIM: 6009595   UniProtKB: P536183   

Export aliases for COPB1 gene to outside databases

Previous GC identifer: GC11M014160


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for COPB1 Gene:
This gene encodes a protein subunit of the coatomer complex associated with non-clathrin coated vesicles. The
coatomer complex, also known as the coat protein complex 1, forms in the cytoplasm and is recruited to the Golgi
by activated guanosine triphosphatases. Once at the Golgi membrane, the coatomer complex may assist in the
movement of protein and lipid components back to the endoplasmic reticulum. Alternatively spliced transcript
variants have been described. (provided by RefSeq, Jan 2009)

GeneCards Summary for COPB1 Gene:
COPB1 (coatomer protein complex, subunit beta 1) is a protein-coding gene. GO annotations related to this gene include structural molecule activity.

UniProtKB/Swiss-Prot: COPB_HUMAN, P53618
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. Plays a functional role in facilitating the transport of kappa-type opioid receptor
mRNAs into axons and enhances translation of these proteins. Required for limiting lipid storage in lipid
droplets. Involved in lipid homeostasis by regulating the presence of perilipin family members PLIN2 and PLIN3 at
the lipid droplet surface and promoting the association of adipocyte surface triglyceride lipase (PNPLA2) with
the lipid droplet to mediate lipolysis (By similarity). Involved in the Golgi disassembly and reassembly
processes during cell cycle. Involved in autophagy by playing a role in early endosome function. Plays a role in
organellar compartmentalization of secretory compartments including endoplasmic reticulum (ER)-Golgi intermediate
compartment (ERGIC), Golgi, trans-Golgi network (TGN) and recycling endosomes, and in biosynthetic transport of
CAV1. Promotes degradation of Nef cellular targets CD4 and MHC class I antigens by facilitating their trafficking
to degradative compartments

Gene Wiki entry for COPB1 Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000011.9  NC_018922.2  NT_009237.19  
Regulatory elements:
   Regulatory transcription factor binding sites in the COPB1 gene promoter:
         p53   Lmo2   Msx-1   Gfi-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidCOPB1 promoter sequence
   Search Chromatin IP Primers for COPB1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat COPB1


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 11p15.2   Ensembl cytogenetic band:  11p15.2   HGNC cytogenetic band: 11p15.2

COPB1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
COPB1 gene location

GeneLoc information about chromosome 11         GeneLoc Exon Structure

GeneLoc location for GC11M014436:  view genomic region     (about GC identifiers)

Start:
14,464,986 bp from pter      End:
14,521,573 bp from pter
Size:
56,588 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: COPB_HUMAN, P53618 (See protein sequence)
Recommended Name: Coatomer subunit beta  
Size: 953 amino acids; 107142 Da
Subunit: Oligomeric complex that consists of at least the alpha, beta, beta', gamma, delta, epsilon and zeta
subunits. Interacts (via C-terminus) with HIV-1 Nef; the interaction is direct. Interacts with SCYL1. Interacts
with COPG1. Interacts (via trunk domain) with ARF1 (via switch I region); the interaction is direct. Interacts
with KCNK2/TREK (via N-terminus); this interaction increases the channel-mediated whole cell currents and
promotes plasma membrane expression of KCNK2/TREK. Interacts with anthrax lethal factor (LF); this interaction
may facilitate endosomal vesicle membrane translocation of LF and its release from the lumen of endosomal
vesicles to external milieu. Interacts with CAPN8 and PRKCE (By similarity). Interacts with ARF1 (myristoylated);
this interaction is required for binding of COPB1 to Golgi membranes (By similarity). Interacts with STX17 (By
similarity)
Miscellaneous: Brefeldin A induces dissociation from the Golgi of the beta-COP and presumably the other coatomer
subunits
Secondary accessions: D3DQX0 Q6GTT7 Q9NTK2 Q9UNW7

Explore the universe of human proteins at neXtProt for COPB1: NX_P53618

Explore proteomics data for COPB1 at MOPED

Post-translational modifications: 

  • Proteolytically cleaved between Ser-528 and Ser-529 by CAPN8 (By similarity)1
  • Ubiquitination2 at Lys107, Lys128, Lys633, Lys771, Lys786, Lys913, Lys943
  • Modification sites at PhosphoSitePlus

  • See COPB1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (3 alternative transcripts): 
    NP_001137533.1  NP_001137534.1  NP_057535.1  

    ENSEMBL proteins: 
     ENSP00000249923   ENSP00000397873   ENSP00000436383   ENSP00000431530   ENSP00000436401  
    Reactome Protein details: P53618

    COPB1 Human Recombinant Protein Products:

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    Novus Biologicals COPB1 Protein
    Novus Biologicals COPB1 Lysates
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    Browse ProSpec Recombinant Proteins
    Browse Proteins at Cloud-Clone Corp.

     
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    antibodies-online proteins for COPB1 (2 products) 

     
    antibodies-online peptides for COPB1

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    antibodies-online antibodies for COPB1 (19 products) 

    COPB1 Assay Products:

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    5 InterPro protein domains:
     IPR011710 Coatomer_bsu_C
     IPR011989 ARM-like
     IPR016460 COPB1
     IPR002553 Clathrin/coatomer_adapt-like_N
     IPR016024 ARM-type_fold

    Graphical View of Domain Structure for InterPro Entry P53618

    ProtoNet protein and cluster: P53618

    2 Blocks protein domains:
    IPB002553 Adaptin
    IPB011710 Protein of unknown function DUF1606


    UniProtKB/Swiss-Prot: COPB_HUMAN, P53618
    Similarity: Contains 6 HEAT repeats


    Find genes that share domains with COPB1           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: COPB_HUMAN, P53618
    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. Plays a functional role in facilitating the transport of kappa-type opioid receptor
    mRNAs into axons and enhances translation of these proteins. Required for limiting lipid storage in lipid
    droplets. Involved in lipid homeostasis by regulating the presence of perilipin family members PLIN2 and PLIN3 at
    the lipid droplet surface and promoting the association of adipocyte surface triglyceride lipase (PNPLA2) with
    the lipid droplet to mediate lipolysis (By similarity). Involved in the Golgi disassembly and reassembly
    processes during cell cycle. Involved in autophagy by playing a role in early endosome function. Plays a role in
    organellar compartmentalization of secretory compartments including endoplasmic reticulum (ER)-Golgi intermediate
    compartment (ERGIC), Golgi, trans-Golgi network (TGN) and recycling endosomes, and in biosynthetic transport of
    CAV1. Promotes degradation of Nef cellular targets CD4 and MHC class I antigens by facilitating their trafficking
    to degradative compartments

         Gene Ontology (GO): 3 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005198structural molecule activity IEA--
    GO:0005488binding ----
    GO:0005515protein binding IPI10199403
         
    Find genes that share ontologies with COPB1           About GenesLikeMe


    Phenotypes:
         12 GenomeRNAi human phenotypes for COPB1:
     Decreased Hepatitis C virus re  Decreased Salmonella enterica   Decreased Salmonella-containin  Decreased Wnt reporter activit 
     Decreased cell number, increas  Decreased influenza A H1N1 (A/  Decreased influenza A virus in  Decreased influenza A/WSN/33 r 
     Decreased viability of wild-ty  G0/1 arrest  Increased Salmonella enterica   Increased gamma-H2AX phosphory 

    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for COPB1

    miRNA
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    miRTarBase miRNAs that target COPB1:
    hsa-mir-195-5p (MIRT044867), hsa-mir-130b-5p (MIRT038294), hsa-mir-26a-5p (MIRT050181), hsa-mir-185-5p (MIRT045323), hsa-mir-1 (MIRT023931)

    Block miRNA regulation of human, mouse, rat COPB1 using miScript Target Protectors
    1 qRT-PCR Assays for microRNA that regulate COPB1:
    hsa-miR-3163
    SwitchGear 3'UTR luciferase reporter plasmidCOPB1 3' UTR sequence
    Inhib. RNA
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    Gene Editing
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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    COPB_HUMAN, P53618: Cytoplasm. Golgi apparatus membrane; Peripheral membrane protein; Cytoplasmic side.
    Cytoplasmic vesicle, COPI-coated vesicle membrane; Peripheral membrane protein; Cytoplasmic side. Cell membrane.
    Endoplasmic reticulum-Golgi intermediate compartment. Note=The coatomer is cytoplasmic or polymerized on the
    cytoplasmic side of the Golgi, as well as on the vesicles/buds originating from it. Proteolytic cleavage by CAPN8
    triggers translocation from Golgi to cytoplasm (By similarity). Found in perinuclear vesicular-tubular clusters
    (VTCs) and in the Golgi region where associated with vesicles, buds and rims of the Golgi stack (By similarity).
    Occasionally present at the trans-side of Golgi, but mainly present at the cis-Golgi side in transitional areas
    (TA), on so-called peripheral elements (PE) consisting of tubules and vesicles located between the cup-shaped
    transitional elements (TE) of the rough endoplasmic reticulum (RER) and the cis-most Golgi cisternae (By
    similarity). Present in cytoplasm, not associated with visible coats or membranes, with a minor fraction present
    on small clusters of tubules and vesicles (By similarity). Some association with high-density and low-density
    microsomes and mitochondria/nuclei fraction (By similarity). Very little found in plasma membrane fraction (By
    similarity)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    golgi apparatus5
    plasma membrane5
    cytosol4
    cytoskeleton2
    endoplasmic reticulum1
    nucleus1

    Gene Ontology (GO): Selected cellular component terms (see all 11):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000139Golgi membrane TAS1840503
    GO:0005737cytoplasm IDA--
    GO:0005793endoplasmic reticulum-Golgi intermediate compartment IEA--
    GO:0005794Golgi apparatus IDA--
    GO:0005798Golgi-associated vesicle TAS1840503

    Find genes that share ontologies with COPB1           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    SuperPaths for COPB1 About    
    See pathways by source

    SuperPathContained pathways About
    1Clathrin dependent protein traffic
    Clathrin dependent protein traffic0.66
    wtCFTR and delta508 CFTR traffic Generic schema norm and CF 0.37
    Transport Clathrin coated vesicle cycle0.66
    2COPI Mediated Transport
    COPI Mediated Transport0.31
    Golgi to ER Retrograde Transport0.00
    Cholesterol and Sphingolipids transport Transport from Golgi and ER to the apical membrane normal and CF 0.31
    3ER to Golgi Transport
    Delta508 CFTR traffic ER to Golgi in CF0.36
    Normal wtCFTR traffic ER to Golgi 0.36
    4Clathrin derived vesicle budding
    Membrane Trafficking0.32


    Find genes that share SuperPaths with COPB1           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways


    5 GeneGo (Thomson Reuters) Pathways for COPB1
        wtCFTR and delta508-CFTR traffic / Generic schema (norm and CF)
    Delta508-CFTR traffic / ER-to-Golgi in CF
    Cholesterol and Sphingolipids transport / Transport from Golgi and ER to the apical membrane (normal and CF)
    Normal wtCFTR traffic / ER-to-Golgi
    Transport Clathrin-coated vesicle cycle


    1 Reactome Pathway for COPB1
        COPI Mediated Transport


        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for COPB1
    Interactions:

        Search GeneGlobe Interaction Network for COPB1

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for COPB1 (P536181, 2, 3 ENSP000002499234) via UniProtKB, MINT, STRING, and/or I2D (see all 1006)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    SUN2Q9UH991, 2, 3, ENSP000002160644EBI-359063,EBI-1044964 MINT-7993501 MINT-7993475 I2D: score=1 STRING: ENSP00000216064
    COPAP536212, 3, ENSP000003570484MINT-7945693 MINT-8217717 MINT-7947479 I2D: score=7 STRING: ENSP00000357048
    COPG1Q9Y6782, 3, ENSP000003250024MINT-7945693 MINT-8217717 MINT-7947479 I2D: score=2 STRING: ENSP00000325002
    ARCN1P484442, 3, ENSP000002640284MINT-7945693 MINT-8217717 MINT-7947479 I2D: score=12 STRING: ENSP00000264028
    COPB2P356062, 3, ENSP000003294194MINT-7945693 MINT-7947479 I2D: score=1 STRING: ENSP00000329419
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 8):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006886intracellular protein transport IEA--
    GO:0006890retrograde vesicle-mediated transport, Golgi to ER TAS--
    GO:0006891intra-Golgi vesicle-mediated transport ISS--
    GO:0016032viral process IEA--
    GO:0016192vesicle-mediated transport ----

    Find genes that share ontologies with COPB1           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for COPB1 (COPB)

    1 HMDB Compound for COPB1    About this table
    CompoundSynonyms CAS #PubMed Ids
    Guanosine triphosphate5'-GTP (see all 10)86-01-1--

    3 Novoseek inferred chemical compound relationships for COPB1 gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    guanosine 5'-o-(3-thiotriphosphate) 50.8 1 1957170 (1)
    gtp 20.4 3 1957170 (1)
    caffeine 20.3 3 9352220 (1), 8449979 (1)



    Find genes that share compounds with COPB1           About GenesLikeMe



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for COPB1 gene (3 alternative transcripts): 
    NM_001144061.1  NM_001144062.1  NM_016451.4  

    Unigene Cluster for COPB1:

    Coatomer protein complex, subunit beta 1
    Hs.339278  [show with all ESTs]
    Unigene Representative Sequence: BC037280
    12 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000532088 ENST00000525214 ENST00000249923(uc001mli.2 uc001mlg.2 uc001mlh.2)
    ENST00000439561 ENST00000526527 ENST00000526191 ENST00000534234 ENST00000529866
    ENST00000534771 ENST00000533096 ENST00000533533 ENST00000529210
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      QuantiFast Probe-based Assays in human, mouse, rat COPB1

    Additional mRNA sequence: 

    AF084457.1 AF111807.1 AK001203.1 AK021446.1 AL136593.1 BC012572.1 BC037280.2 X82103.1 

    Selected DOTS entries (see all 29):

    DT.95235278  DT.100822940  DT.95108192  DT.101960558  DT.451536  DT.100663573  DT.95235280  DT.100822945 
    DT.86852836  DT.120705217  DT.97809974  DT.120705264  DT.70102283  DT.100767855  DT.100822943  DT.120705259 
    DT.120705261  DT.95235276  DT.95235281  DT.100730165  DT.100822939  DT.102832733  DT.120705250  DT.120705256 

    Selected AceView cDNA sequences (see all 506):

    BU620947 BQ937693 CA418024 AA344611 BU190069 AW305092 CA414248 BU622833 
    AA412084 AF111807 CD558135 BF970532 AA402414 CA941181 BM311300 AA554780 
    AW291132 BI793018 BP351225 CA438403 BU620120 CA419598 AA453484 BM850947 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for COPB1 (see all 15)    About this scheme

    ExUns: 1 ^ 2a · 2b · 2c · 2d ^ 3a · 3b ^ 4a · 4b ^ 5a · 5b ^ 6a · 6b · 6c · 6d ^ 7a · 7b · 7c · 7d · 7e ^ 8a · 8b ^ 9a · 9b ^ 10a · 10b ^
    SP1:                                            -           -     -                                                                                             
    SP2:                          -     -     -     -           -     -                                                                                             
    SP3:                                -     -     -           -     -                                                                                             
    SP4:                                -     -     -           -     -                                                                                             
    SP5:                                            -           -     -                                                                                             

    ExUns: 11 ^ 12 ^ 13 ^ 14 ^ 15a · 15b ^ 16 ^ 17 ^ 18 ^ 19 ^ 20 ^ 21 ^ 22 ^ 23a · 23b ^ 24 ^ 25a · 25b
    SP1:                          -                                                           -                     
    SP2:                          -                                                           -                     
    SP3:                          -                                                           -                     
    SP4:                                                                                                            
    SP5:                                                                                                            


    ECgene alternative splicing isoforms for COPB1

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

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    COPB1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TACCAAGACC
    COPB1 Expression
    About this image


    COPB1 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 17) fully expand
     
     Bone (Muscoskeletal System)    fully expand to see all 7 entries
             Zeugopod Long Bone
     
     Brain (Nervous System)    fully expand to see all 4 entries
             Cerebral Cortex
     
     Cartilage (Muscoskeletal System)
             Meckel's Cartilage
     
     Trophoblast (Extraembryonic Tissues)
             Trophoblast Cells Trophoblast
     
     Testis (Reproductive System)
             Leydig Cells Testis Interstitium
    COPB1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    COPB1 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.339278
        Custom PCR Arrays for COPB1
    Primer
    Products:
    OriGene qPCR primer pairs and template standards for COPB1
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for COPB1

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of eukaryotes.

    Orthologs for COPB1 gene from Selected species (see all 30)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Copb11 , 5 coatomer protein complex, subunit beta 11, 5 91.5(n)1
    99.27(a)1
      7 (59.31 cM)5
    703491  NM_033370.31  NP_203534.11 
     1142155595 
    chicken
    (Gallus gallus)
    Aves COPB11 coatomer protein complex, subunit beta 1 84.05(n)
    97.9(a)
      423063  NM_001006467.1  NP_001006467.1 
    lizard
    (Anolis carolinensis)
    Reptilia COPB16
    coatomer protein complex, subunit beta 1
    98(a)
    1 ↔ 1
    GL343294.1(491432-521236)
    African clawed frog
    (Xenopus laevis)
    Amphibia BX853356.12   -- 77.29(n)    BX853356.1 
    zebrafish
    (Danio rerio)
    Actinopterygii 570591482   -- 76.6(n)   325312  57059148 
    fruit fly
    (Drosophila melanogaster)
    Insecta betaCop1 beta-coatomer protein 62.06(n)
    69.7(a)
      32820  NM_078676.3  NP_523400.1 
    worm
    (Caenorhabditis elegans)
    Secernentea Y25C1A.51 Y25C1A.5 58.32(n)
    62.15(a)
      173656  NM_062040.6  NP_494441.1 
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes SEC26(YDR238C)4
    SEC261
    Essential beta-coat protein of the COPI coatomer, involved more4
    SEC261
    52.3(n)1
    44.8(a)1
      4(940816-937895)4
    8518241, 4  NP_010524.31  NP_010524.14 
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons AT4G314901 AT4G31490 55.23(n)
    51.32(a)
      829276  NM_119298.2  NP_194877.2 
    rice
    (Oryza sativa)
    Liliopsida Os.115962 Oryza sativa (japonica cultivar-group) cDNA cloneJ more 75.38(n)    AK069716.1 


    ENSEMBL Gene Tree for COPB1 (if available)
    TreeFam Gene Tree for COPB1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section

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      --

    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
    About This Section

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    Selected SNPs for COPB1 (see all 750)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 11 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1882598511,2
    --14478714(+) AACCCA/GGGAGG 3 -- ds50010--------
    rs357358531,2
    C--14478789(+) ATCTC-/AAAAAA 3 -- ds50011Minor allele frequency- A:0.00NA 2
    rs1426431731,2
    --14479054(+) CCATAC/TAACTA 3 -- ut310--------
    rs1999274141,2
    C--14479149(+) TGAAA-/ATTTTATA 3 -- cds10--------
    rs2006908761,2
    --14479354(+) TCAAGA/GACTTT 3 -- ut310--------
    rs728680071,2
    C,F--14479553(+) ACATAC/ACAAAC 3 -- int11Minor allele frequency- A:0.03NA 120
    rs1917481881,2
    --14479581(+) CTGGTA/GATTAC 3 -- int10--------
    rs30532141,2
    C--14479643(+) ttttt-/TT/TTT
            
    gagac
    6 -- int1 cds11NA 2
    rs1831783291,2
    --14479717(+) ACCTCC/TCGGGT 3 -- int10--------
    rs1460717391,2
    --14479724(+) GGGTTC/GAAGCA 3 -- int10--------

    HapMap Linkage Disequilibrium report for COPB1 (14464986 - 14521573 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 1 variation for COPB1:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv32960CNV Loss17666407

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing COPB1
    DNA2.0 Custom Variant and Variant Library Synthesis for COPB1

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 600959    OMIM disorders: --

    1 disease from the University of Copenhagen DISEASES database for COPB1:
    Otitis media

    Find genes that share disorders with COPB1           About GenesLikeMe


    Export disorders for COPB1 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for COPB1 gene, integrated from 10 sources (see all 125):
    (articles sorted by number of sources associating them with COPB1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Physical interaction of the HIV-1 Nef protein with beta-COP, a component of non-clathrin-coated vesicles essential for membrane traffic. (PubMed id 7982906)1, 2, 3 Benichou S.... Benarous R. (J. Biol. Chem. 1994)
    2. HIV-1 Nef targets MHC-I and CD4 for degradation via a final common beta-COP-dependent pathway in T cells. (PubMed id 18725938)1, 2, 9 Schaefer M.R....Collins K.L. (PLoS Pathog. 2008)
    3. Scyl1, mutated in a recessive form of spinocerebellar neurodegeneration, regulates COPI-mediated retrograde traffic. (PubMed id 18556652)1, 2 Burman J.L.... McPherson P.S. (J. Biol. Chem. 2008)
    4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    5. Towards a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs. (PubMed id 11230166)1, 2 Wiemann S.... Poustka A. (Genome Res. 2001)
    6. Identification and characterization of novel isoforms of COP I subunits. (PubMed id 11056392)1, 2 Futatsumori M.... Nakayama K. (J. Biochem. 2000)
    7. Screen and identification of proteins interacting with ADAM19 cytoplasmic tail. (PubMed id 12463424)1, 9 Huang L....Li C. (Mol. Biol. Rep. 2002)
    8. The oculocerebrorenal syndrome gene product is a 105-kD protein localized to the Golgi complex. (PubMed id 7573041)2, 9 Olivos-Glander I.M.... Nussbaum R.L. (Am. J. Hum. Genet. 1995)
    9. A Proteomics Strategy for the Identification of FAT10-Modified Sites by Mass Spectrometry. (PubMed id 23862649)1 Leng L....Wang J. (J. Proteome Res. 2014)
    10. Quantitative study of the interactome of PKCIP involved in the EGF-induced tumor cell chemotaxis. (PubMed id 23402259)1 Chen R....Zhang N. (J. Proteome Res. 2013)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 1315 HGNC: 2231 AceView: COPB Ensembl:ENSG00000129083 euGenes: HUgn1315
    ECgene: COPB1 H-InvDB: COPB1

    (According to HUGE)
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    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
    About This Section

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    NameDescription
    PharmGKB entry for COPB1 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section

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    Patent Information for COPB1 gene:
    Search GeneIP for patents involving COPB1

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, eBioscience, antibodies-online, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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