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NCBP1 Gene

protein-coding   GIFtS: 59

GC09P099435
nuclear cap binding protein subunit 1, 80kDa
(Previous names: nuclear cap binding protein subunit 1, 80kD )
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database
(Previous symbol: NCBP)
Services    
(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc , and/or 7Ensembl, 8miRBase)
About This Section

Aliases
CBP80 1, 2, 3
MGC2087 2
NCBP 2, 3
OTTHUMP00000021753 2
Descriptions
80 kDa nuclear cap-binding protein 3
NCBP 80 kDa subunit 3
nuclear cap binding protein subunit 1, 80kD 1
nuclear cap binding protein subunit 1, 80kDa 2
External Ids
HGNC: 76581
Entrez Gene: 46862
UniProtKB: Q091613
Ensembl: ENSG000001369377
Search outside databases for aliases for NCBP1 gene

Previous GC identifers: GC09P091221 GC09P092139 GC09P093853 GC09P095775 GC09P097475

(According to Entrez Gene, Wikipedia's Gene Wiki,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

EntrezGene summary for NCBP1:
The product of this gene is a component of the nuclear cap-binding protein complex (CBC), which
binds to the monomethylated 5' cap of nascent pre-mRNA in the nucleoplasm. The encoded
protein promotes high-affinity mRNA-cap binding and associates with the CTD of RNA polymerase II.
The CBC promotes pre-mRNA splicing, 3'-end processing, RNA nuclear export, and
nonsense-mediated mRNA decay. [provided by RefSeq]

UniProtKB/Swiss-Prot: NCBP1_HUMAN, Q09161
Function: Involved in mediating U snRNA export from the nucleus. Binds to 5' capped mRNA

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 36),
and/or miRBase,
Genomic Views according to UCSC and Ensembl, Transcription factor binding sites according to SABiosciences)
About This Section

Genomic View:
UCSC Golden Path with GeneCards custom track

 Transcription factor binding sites upstream to the NCBP1 gene  

Entrez Gene cytogenetic band: 9q34.1   Ensembl cytogenetic band:  9q22.33   HGNC cytogenetic band: 9q34.1

NCBP1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)

GeneLoc gene densities for chromosome 9         GeneLoc Exon Structure

GeneLoc location for GC09P099435:     (about GC identifiers)

Start:
99,435,526 bp from pter
End:
99,475,851 bp from pter
Size:
40,326 bases
Orientation:
plus strand
RefSeq DNA sequence:
NC_000009.10  NT_008470.18  
(According to 1UniProtKB, and/or Ensembl, Phosphorylation sites according to 2Phosphosite, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Enzo Life Sciences, Abnova, OriGene and/or, Abcam,
Biochemical Assays by Invitrogen, Millipore, R&D Systems, Cell Signaling Technology, and/or Enzo Life Sciences, Ontologies according to Gene Ontology Consortium 01 Apr 2009 and Entrez Gene, Antibodies by Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Cell Signaling Technology, Abcam, Abnova, and/or Novus Biologicals)
About This Section

UniProtKB/Swiss-Prot: NCBP1_HUMAN, Q09161 (See protein sequence)
Recommended Name: Nuclear cap-binding protein subunit 1  
Size: 790 amino acids; 91839 Da
Subunit: Found in a U snRNA export complex with RNUXA/PHAX, CBP20, CBP80, RAN, XPO1 and m7G-capped
RNA. Interaction with RNUXA/PHAX (By similarity). Heterodimer with NCBP2. Is part of the exon
junction complex (EJC) containing NCBP1, NCBP2, RNPS1, RBM8A, SRRM1, NXF1, UPF3B, UPF2, THOC4
and/or REFBP2
Subcellular location: Nucleus
PDB structures from and Proteopedia :
1H2T (3D)    1H2U (3D)    1H2V (3D)    1H6K (3D)    1N52 (3D)    1N54 (3D)    
Secondary accessions: Q59G76 Q5T1V0

Post-translational modifications:

  • View phosphorylation sites using PhosphoSite2


  • REFSEQ proteins: NP_002477.1  

    ENSEMBL proteins: 
    ENSP00000364272 ENSP00000364274 ENSP00000364289 


    Human Recombinant Proteins 
    Browse Drug Discovery Central at Invitrogen for human recombinant proteins
    Browse Purified and Recombinant Proteins at Millipore
    Browse Human Recombinant Proteins at Sigma-Aldrich  
    Browse R&D Systems for human recombinant proteins
    Browse recombinant and purified proteins available from Enzo Life Sciences
    Recombinant Proteins from Abcam (NCBP1)
    Human Recombinant Proteins from Abnova (NCBP1)
                    Browse Origene for full length recombinant human proteins expressed in human HEK293 cells 

    4 Gene Ontology (GO) cellular component terms (links to tree view):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634 nucleus IDA9342333
    GO:0005654 nucleoplasm TAS7937105
    GO:0005829 cytosol EXP11333016
    GO:0005845 mRNA cap binding complex IDA7651522 9342333
    About this table

    Antibodies for NCBP1: 
    Browse Antibodies Central at Invitrogen
    Browse Millipore's Extensive Line of Mono- and Polyclonal Antibodies
    Sigma-Aldrich Antibodies for NCBP1
    Browse R&D Systems for Antibodies
    Antibodies from Abcam (NCBP1), each with their AbpromiseSM
    Monoclonal and Polyclonal Antibodies from Abnova (NCBP1)
    Novus Biologicals Antibodies for NCBP1

    Assays for NCBP1: 
    Browse Invitrogen for biochemical assays
    Browse Kits and Assays available from Millipore
    Browse R&D Systems for biochemical assays
    Browse biochemical assays available from Enzo Life Sciences

    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    4 InterPro domains/families:
     IPR015172 MIF4G-like_typ-1
     IPR003890 MIF4G-like_typ-3
     IPR016021 MIF4-like_typ_1/2/3
     IPR015174 MIF4G-like_typ-2


       GeneDecks  NCBP1 for the domains selected above  
    About GeneDecksing

    Graphical View of Domain Structure for InterPro Entry Q09161

    ProtoNet protein and cluster: Q09161

    1 Blocks protein family: IPB003890 Initiation factor eIF-4 gamma

    UniProtKB/Swiss-Prot: NCBP1_HUMAN, Q09161
    Similarity: Belongs to the NCBP1 family
    Similarity: Contains 1 MIF4G domain

    (According to MGI Jun 06 2009, UniProtKB, IUBMB,and/or Genatlas,
    shRNA from OriGene, Sigma-Aldrich, RNAi from Sigma-Aldrich,
    RNAi Products, Clones, and Q-PCR Products from Invitrogen, Millipore, OriGene, and/or Abnova, siRNAs from Applied Biosystems, SYBR primers from OriGene, Cell-based Assays from Millipore, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
    About This Section

    Inhib.
    RNA:
    Invitrogen RNAi Products for gene knock-down (NCBP1)
    Browse for Gene Knock-down Tools from Millipore
    Abnova Chimera RNAi Products for Gene knock-down (NCBP1)
                  OriGene 29mer shRNA kit in GFP-retroviral vector: NM_002486

                  Applied Biosystems Silencer® siRNAs for NCBP1

                  Sigma-Aldrich siRNA for NCBP1  
                         Sigma-Aldrich shRNA for NCBP1  
                         Explore Sigma-Aldrich super-pooled esiRNAs  

    Clones:Invitrogen Clones for NCBP1
    Browse Clones for the Expression of Recombinant Proteins Available from Millipore
                  OriGene GFP tagged cDNA clone in CMV expression vector: NM_002486
                                     Myc/DDK tagged cDNA clone in CMV expression vector: NM_002486
                                     untagged cDNA clone in CMV expression vector: NM_002486 

    Primers: Browse Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers
                  OriGene genome-wide validated SYBR primer pairs: NM_002486

    UniProtKB/Swiss-Prot: NCBP1_HUMAN, Q09161
    Function: Involved in mediating U snRNA export from the nucleus. Binds to 5' capped mRNA

    Genatlas biochemistry entry for NCBP1:
    nuclear cap binding protein 1,component of the cap-binding protein complex in association with
    NCBP2 and other proteins,mediating premRNA splicing and export of U small nuclear RNAs to the
    cytoplasm

    2 Gene Ontology (GO) molecular function terms (links to tree view):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000339 RNA cap binding TAS8069914
    GO:0005515 protein binding IPI7478990 9111328
    About this table

    (Pathways according to Invitrogen (maps by GeneGo), Millipore, Cell Signaling Technology, Sigma-Aldrich, KEGG and/or UniProtKB,
    Sets of similar genes according to GeneDecks, Proteins Network according to SABiosciences, Interactions according to 1UniProtKB, 2MINT, and/or 3STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
    About This Section


     Gene Network CentralTM Interacting Genes and Proteins Network for  NCBP1 


    5/162 Interacting proteins for NCBP1 (ENSP000003642893 Q091611, 2) via UniProtKB, MINT, and/or STRING (see all 162 )
    InteractantInteraction Details
    GeneCardExternal ID(s)
    EIF4G3O434321STRING (score=.739) EBI-464743, EBI-464766
    EIF4EP067302STRING (score=.975) MINT-4791425
    EIF4G1Q046372STRING (score=.91) MINT-4791425
    SF3A2Q154282STRING (score=.949) MINT-5205917
    NCBP2P522981, 2STRING (score=.999) EBI-464743, EBI-464729 MINT-24994 EBI-464743, EBI-464729 MINT-24994
    About this table

    5/7 Gene Ontology (GO) biological process terms (links to tree view) (see all 7 ):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000387 spliceosomal snRNP biogenesis EXP15130578
    GO:0006379 mRNA cleavage IDA9342333
    GO:0006810 transport IEA--
    GO:0008380 RNA splicing TAS8069914
    GO:0016070 RNA metabolic process IEA--
    About this table
    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, Sigma-Aldrich, Tocris Bioscience, and/or Novoseek and Drugs according to Enzo Life Sciences and/or PharmGKB)
    About This Section

    Browse drugs & compounds from Enzo Life Sciences
    Browse Small Molecules at Sigma-Aldrich

    Browse Tocris compounds for NCBP1

    (GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 219 Homo sapiens; Jun 2 2009) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView,
    non coding RNAs according to RNAdb,
    ESTs according to GeneTide,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from Invitrogen, Millipore, and/or Abnova,
    siRNAs from Applied Biosystems, Sigma-Aldrich,
    shRNA from Sigma-Aldrich, OriGene,
    Tagged/untagged cDNA clones from OriGene,
    Expression Assays from Applied Biosystems)
    About This Section

    Inhib.
    RNA:
    Invitrogen RNAi Products for gene knock-down (NCBP1)
    Browse for Gene Knock-down Tools from Millipore
    Abnova Chimera RNAi Products for Gene knock-down (NCBP1)
                  OriGene 29mer shRNA kit in GFP-retroviral vector: NM_002486

                  Sigma-Aldrich siRNA for NCBP1  
                         Sigma-Aldrich shRNA for NCBP1  
                         Explore Sigma-Aldrich super-pooled esiRNAs  

    Applied Biosystems Silencer® siRNAs: 

    NM_002486  

    REFSEQ mRNAs for NCBP1 gene: 

    NM_002486.4   

    Applied Biosystems TaqMan ® Gene Expression Assays: 

    NM_002486  

                  OriGene GFP tagged cDNA clone in CMV expression vector: NM_002486
                                     Myc/DDK tagged cDNA clone in CMV expression vector: NM_002486
                                     untagged cDNA clone in CMV expression vector: NM_002486 

    Additional cDNA sequence: 

    AB209233.1 AK312807.1 BC001450.2 D32002.1 X80030.1 

    20 DOTS entries:

    DT.95369662  DT.101961008  DT.86841494  DT.447205  DT.95369671  DT.102835149  DT.412404  DT.100693312 
    DT.121158370  DT.65285061  DT.121158243  DT.95336094  DT.121158266  DT.121158356  DT.121158364  DT.75140851 
    DT.95369664  DT.100685586  DT.100786207  DT.97785246 

    24/200 AceView cDNA sequences (see all 200 ):

    AA468545 AU138969 AA076305 BX365349 BU176513 BU949532 AI868113 BX116966 
    BU624686 BG392612 AI081311 BC001450 AU135678 AA804812 BX099181 CB121904 
    AA905723 AA912932 BQ709253 AA262509 BM714312 BM802780 BQ063845 AA255663 

    highest scoring ESTs for NCBP1:

    D32002 AI391649 AI799881 AI926237 AL522497 AL562000 AU149980 BC001450 BE087734 BE781615 

    Unigene Cluster for NCBP1:

    Nuclear cap binding protein subunit 1, 80kDa
    Hs.595669  [show with all ESTs]
    Unigene Representative Sequence: NM_002486


    GeneLoc Exon Structure

    4 Alternative Splicing Database (ASD) splice patterns (SP) for NCBP1

    ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3a · 3b · 3c ^ 4 ^ 5a · 5b ^ 6 ^ 7 ^ 8 ^ 9a · 9b ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^
    SP1:                                      -     -                                                                                                               
    SP2:                                      -     -     -                 -                                                                                       
    SP3:                                            -                                                                                                               
    SP4:                                                                                                                                                            

    ExUns: 20 ^ 21 ^ 22 ^ 23
    SP1:                        
    SP2:                        
    SP3:                        
    SP4:                        

    About this scheme

    ECgene alternative splicing isoforms for NCBP1

    3 Ensembl transcripts including schematic representations:
    ENST00000375130  ENST00000375132  ENST00000375147  
    (Experimental results according to 1GeneNote and GNF BioGPS,
    probe sets-to-genes annotations according to 2GeneAnnot , 3GeneTide , Sets of similar genes according to GeneDecks, Electronic Northern calculations according to data from UniGene (Build 219 Homo sapiens), SAGE tags according to CGAP, plus additional links to SOURCE, and/or GNF BioGPS, and/or EXPOLDB, and/or UniProtKB,
    Expression Assays from Applied Biosystems )
    About This Section

    NCBP1 expression in normal and diseased human tissues

     Applied Biosystems TaqMan ® Gene Expression Assays for NCBP1

    1 / 2 / 3

    5 probe-sets matching NCBP1 gene


    Affymetrix
    probe-set
    Array  GeneAnnot data GeneNote data GeneTide data
    # genes Sensitivity Specificity Correlation Length Gb_Accession Consensus Uniqueness Score Rank

    37987_at2, 3 U95-A 1 1.00 1.00 1.00 1.00 D32002 1.00 1.00 1.00 1

    209520_s_at2, 3 U133-A 1 1.00 1.00 -- -- BC001450 0.80 1.00 0.91 1

    209519_at2, 3 U133-A 1 1.00 1.00 -- -- BG108193 0.60 1.00 0.82 1

    209520_s_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --

    209519_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --
    About this table
    Data from (Publications) and GNF BioGPS
        About these images
    About these images

    CGAP SAGE TAG: AAGAGAGGAC

    SOURCE GeneReport for Unigene cluster: Hs.595669

    Expression variation in blood from EXPOLDB for NCBP1

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD and/or 5MGI Jun 06 2009, with possible further links to Flybase and/or WormBase, Gene Trees according to Ensembl)
    About This Section


    Orthologs for NCBP1 gene from 5/15 species (see all 15 )
    Organism Gene Locus Description Human
    Similarity
    NCBI accessions
    dog
    (Canis familiaris)
    NCBP11   -- nuclear cap binding protein subunit 1, 80kDa 94.52(n)
    99.36(a)
    474772  XM_862016.1  XP_867109.1 
    chimpanzee
    (Pan troglodytes)
    NCBP11   -- nuclear cap binding protein subunit 1, 80kDa 99.83(n)
    100(a)
    464601  XM_520138.2  XP_520138.2 
    rat
    (Rattus norvegicus)
    Ncbp11   -- nuclear cap binding protein subunit 1, 80kDa 89.96(n)
    98.1(a)
    298075  NM_001014785.1  NP_001014785.1 
    mouse
    (Mus musculus)
    Ncbp15
    AU0146451
    4 (21.50 cM)5
    nuclear cap binding protein subunit 15
    expressed sequence AU0146451
    89.54(n)1
    97.97(a)1
    4337021  NM_001033201.31  NP_001028373.21 
    chicken
    (Gallus gallus)
    RCJMB04_14d71   -- nuclear cap binding protein subunit 1, 80kDa 80.89(n)
    90.63(a)
    427379  NM_001031440.1  NP_001026611.1 
    About this table        Species with no ortholog for NCBP1

    ENSEMBL Gene Tree for NCBP1
    (Paralogs according to 1HomoloGene
    and 2Ensembl, Pseudogenes according to 3Pseudogene.org)
    About This Section

      --
    (According to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, and UniProtKB, Linkage Disequilibrium by HapMap, Genotyping Reagents from Applied Biosystems)
    About This Section


    10/187 NCBI SNPs in NCBP1 are shown (see all 187 )
    (Click for Applied Biosystems TaqMan ® Genotyping Assay)  (see all 104)
    ABGenomic DataTranscription DataAllele Frequencies
    SNP IDValidChr 9 posSequenceRecsAA
    Chg
    TypeMoreRecsAllele
    freq
    PopTotal
    sample
    More
    ------------
    rs78623561,2
    A,C,F,H99475974(+) AACTGG/ATAAGG 1 -- ng318Minor allele frequency- A:0.14EU EA WA 836
    rs133004351,2
    H99475905(+) AAGGGA/CCCTTG 1 -- ng314Minor allele frequency- C:0.00EU EA WA 414
    --
    rs31767611,2
    F99476248(-) ATTAT-/GGCGGGGG 1 -- ng311Minor allele frequency- GGC:0.06NS 152
    rs11318351,2
    C99475769(+) AGATGG/TCATGT 1 -- ut310--------
    --
    rs31767621,2
    F99476243(-) GGGGGC/GGGGGA 1 -- ng311Minor allele frequency- G:0.14NS 152
    rs22971551,2
    C,F,H99460797(-) GGACAC/TAGAGC 1 L/L syn1 ese39Minor allele frequency- A:0.01EA NA EU WA 2140
    rs101151491,2
    F,H99470963(+) GATGAC/TGACAG 1 D/D syn1 ese34Minor allele frequency- T:0.01EU EA WA 414
    rs346757771,2
    F99445448(+) TATAAT/CGAAGC 1 N/N syn11Minor allele frequency- C:0.03NA 78
    rs20261321,2
    A,C,F,H,O99455661(-) TTATTT/CGATCT 1 -- int119Minor allele frequency- C:0.41EU EA WA NA 1758
    rs28058371,2
    A,C,F,H,O99473054(-) AGGAAT/CAATGG 1 -- int18Minor allele frequency- C:0.44EU EA WA NA 2050
    About this table

    HapMap Linkage Disequilibrium images for NCBP1 (up to first 250kb)

    (in which this Gene is Involved, According to OMIM, UniProtKB, PharmGKB, Genatlas, GeneTests, Blood group antigen gene mutations by BGMUT, HGMD, GAD, HuGE Navigator, BCGD, and/or TGDB.)
    About This Section

    OMIM: 600469

    (Possibly Related Articles in Doctor's Guide)
    About This Section

      --

    (in PubMed. Associations of this gene to articles via 1Novoseek, 2HGNC, 3Entrez Gene, 4UniProtKB/Swiss-Prot, 5UniProtKB/TrEMBL, 6GAD, and/or 7PharmGKB)
    About This Section

    10/46 PubMed articles for NCBP1 gene (see all 46 ):
    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section

     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, and/or H-InvDB)
    About This Section

    Entrez Gene: 4686 HGNC: 7658 AceView: NCBP1 Ensembl:ENSG00000136937 euGenes: HUgn4686
    ECgene: NCBP1 H-InvDB: NCBP1
    (According to HUGE)
    About This Section

      --
    (According to ATLAS, HORDE, IMGT, MTDB, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section

      --
    (Available from WIS Yeda, Salk, Tufts)
    About This Section

      --
    (Reagents available from Applied Biosystems, Antibodies and assays by Cell Signaling Technology, Abcam, Novus Biologicals,
    Sigma-Aldrich, R&D Systems, Millipore, Abnova, and/or Invitrogen, Clones available from OriGene,and/or Invitrogen, Drugs and/or compounds by Sigma-Aldrich,
    Enzo Life Sciences, and/or Tocris Bioscience)
    About This Section



    Products for NCBP1:
     TaqMan ® Gene Expression Assays
     TaqMan ® Genotyping Assays
      Free SNP selection tool



      Invitrogen iPath Pathways  Invitrogen BLOCK-iT™ RNAi
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     Predesigned and custom siRNAs for NCBP1 Antibodies for NCBP1
     Explore super-pooled esiRNAs Browse proteins at Sigma-Aldrich
     Lentivirus-delivered shRNAs for NCBP1 Browse small molecules at Sigma-Aldrich
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