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    NCBP2 nuclear cap binding protein subunit 2 [ Homo sapiens (human) ]

    Gene ID: 22916, updated on 11-Apr-2024

    Summary

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    Official Symbol
    NCBP2provided by HGNC
    Official Full Name
    nuclear cap binding protein subunit 2provided by HGNC
    Primary source
    HGNC:HGNC:7659
    See related
    Ensembl:ENSG00000114503 MIM:605133; AllianceGenome:HGNC:7659
    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
    CBC2; NIP1; CBP20; PIG55
    Summary
    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 has an RNP domain commonly found in RNA binding proteins, and contains the cap-binding activity. The CBC promotes pre-mRNA splicing, 3'-end processing, RNA nuclear export, and nonsense-mediated mRNA decay. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in brain (RPKM 25.7), thyroid (RPKM 22.3) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    3q29
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (196935406..196942528, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (199661457..199668578, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (196662277..196669399, complement)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene p21 (RAC1) activated kinase 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:196513771-196514477 Neighboring gene RNA, U6 small nuclear 42, pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr3:196568870-196569024 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15073 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:196595799-196596300 Neighboring gene SUMO specific peptidase 5 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:196625459-196625966 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:196668731-196669404 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:196669405-196670078 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr3:196670753-196671426 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:196674955-196675702 Neighboring gene NCBP2 antisense RNA 1 Neighboring gene Sharpr-MPRA regulatory region 11589 Neighboring gene NCBP2 antisense 2 (head to head) Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:196695281-196695816 Neighboring gene phosphatidylinositol glycan anchor biosynthesis class Z

    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. Binding properties and dynamic localization of an alternative isoform of the cap-binding complex subunit CBP20. Pabis M, et al. Nucleus, 2010 Sep-Oct. PMID 21326824, Free PMC Article
    2. Nonsense-mediated mRNA decay: splicing, translation and mRNP dynamics. Maquat LE. Nat Rev Mol Cell Biol, 2004 Feb. PMID 15040442
    3. Large-scale induced fit recognition of an m(7)GpppG cap analogue by the human nuclear cap-binding complex. Mazza C, et al. EMBO J, 2002 Oct 15. PMID 12374755, Free PMC Article
    4. Crystal structure of the human nuclear cap binding complex. Mazza C, et al. Mol Cell, 2001 Aug. PMID 11545740
    5. A nuclear cap-binding complex binds Balbiani ring pre-mRNA cotranscriptionally and accompanies the ribonucleoprotein particle during nuclear export. Visa N, et al. J Cell Biol, 1996 Apr. PMID 8601613, Free PMC Article

    See all (108) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. m7G-related genes-NCBP2 and EIF4E3 determine immune contexture in head and neck squamous cell carcinoma by regulating CCL4/CCL5 expression.
      Title: m7G-related genes-NCBP2 and EIF4E3 determine immune contexture in head and neck squamous cell carcinoma by regulating CCL4/CCL5 expression.
    2. Affinity proteomic dissection of the human nuclear cap-binding complex interactome.
      Title: Affinity proteomic dissection of the human nuclear cap-binding complex interactome.
    3. NCBP2 is not required for cell viability and poly(A) RNA export.
      Title: mRNA export through an additional cap-binding complex consisting of NCBP1 and NCBP3.
    4. A novel alternative splice variant of CBP20, termed CBP20S, has an in-frame deletion, leading to the translation of a protein lacking most of the RNA recognition motif (RRM).
      Title: Binding properties and dynamic localization of an alternative isoform of the cap-binding complex subunit CBP20.
    5. determined how importin-beta binds to the cap-binding complex (CBC) through its CBP20 subunit
      Title: The molecular basis for the regulation of the cap-binding complex by the importins.
    6. a new MIF4G domain-containing protein, CTIF (CBP80/20-dependent translation initiation factor) that interacts directly with CBP80 and is part of the CBP80/20-dependent translation initiation complex
      Title: A new MIF4G domain-containing protein, CTIF, directs nuclear cap-binding protein CBP80/20-dependent translation.
    7. We show that NELF interacts with the nuclear cap binding complex (CBC), a heterodimeric, multifunctional factor that plays important roles in several mRNA processing steps, and the two factors together participate in the 3' end processing of histone mRNAs
      Title: NELF interacts with CBC and participates in 3' end processing of replication-dependent histone mRNAs.
    8. crystal structure at 2.1 A resolution of CBP20 and CBP80 bound to an m(7)GpppG cap analogue
      Title: Large-scale induced fit recognition of an m(7)GpppG cap analogue by the human nuclear cap-binding complex.
    9. Structural basis of m7GpppG binding to the nuclear cap-binding protein complex.
      Title: Structural basis of m7GpppG binding to the nuclear cap-binding protein complex.
    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

    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 DNA binding EXP
    Inferred from Experiment
    more info
    		 PubMed 
    enables RNA 7-methylguanosine cap binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables RNA 7-methylguanosine cap binding IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables RNA binding HDA PubMed 
    NOT enables RNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables RNA cap binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA cap binding NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    enables mRNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables snRNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in RNA splicing ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in alternative mRNA splicing, via spliceosome NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in cap-dependent translational initiation NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in histone mRNA metabolic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in mRNA 3'-end processing NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in mRNA cis splicing, via spliceosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in mRNA export from nucleus IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    involved_in mRNA metabolic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in mRNA splicing, via spliceosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in mRNA splicing, via spliceosome NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in mRNA transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in miRNA-mediated post-transcriptional gene silencing NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in nuclear-transcribed mRNA catabolic process, nonsense-mediated decay IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in nuclear-transcribed mRNA catabolic process, nonsense-mediated decay IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in nuclear-transcribed mRNA catabolic process, nonsense-mediated decay NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in positive regulation of RNA export from nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in positive regulation of mRNA 3'-end processing IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of transcription elongation by RNA polymerase II NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in primary miRNA processing NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in regulation of translational initiation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulatory ncRNA-mediated post-transcriptional gene silencing NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in snRNA export from nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in snRNA export from nucleus NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of RNA cap binding complex IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytoplasm NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    part_of nuclear cap binding complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of nuclear cap binding complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of nuclear cap binding complex IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus NAS
    Non-traceable Author Statement
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    nuclear cap-binding protein subunit 2
    Names
    20 kDa nuclear cap-binding protein
    NCBP 20 kDa subunit
    NCBP interacting protein 1
    cell proliferation-inducing gene 55 protein
    nuclear cap binding protein subunit 2, 20kD
    nuclear cap binding protein subunit 2, 20kDa

    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.

    mRNA and Protein(s)

    1. NM_001042540.2 → NP_001036005.1  nuclear cap-binding protein subunit 2 isoform 2

      See identical proteins and their annotated locations for NP_001036005.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. The encoded isoform (2) is shorter compared to isoform 1.
      Source sequence(s)
      AC011322
      Consensus CDS
      CCDS46986.1
      UniProtKB/Swiss-Prot
      P52298
      Related
      ENSP00000397619.2, ENST00000427641.2
      Conserved Domains (1) summary
      cl17169
      Location:41 → 66
      RRM_SF; RNA recognition motif (RRM) superfamily

    2. NM_001308036.2 → NP_001294965.1  nuclear cap-binding protein subunit 2 isoform 3

      See identical proteins and their annotated locations for NP_001294965.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an alternate 5' exon and contains an alternate 5' terminal exon, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (3) has a shorter and distinct N-terminus, compared to isoform 1.
      Source sequence(s)
      AC011322
      Consensus CDS
      CCDS77878.1
      UniProtKB/Swiss-Prot
      P52298
      Related
      ENSP00000412785.2, ENST00000452404.6
      Conserved Domains (1) summary
      cd12240
      Location:24 → 101
      RRM_NCBP2; RNA recognition motif found in nuclear cap-binding protein subunit 2 (CBP20) and similar proteins

    3. NM_001410857.1 → NP_001397786.1  nuclear cap-binding protein subunit 2 isoform 4

      Status: REVIEWED

      Source sequence(s)
      AC011322
      Consensus CDS
      CCDS93446.1
      UniProtKB/TrEMBL
      A0A9K3Y7M6, D3DXB7, F6WVI0
      Related
      ENSP00000413518.1, ENST00000447325.5

    4. NM_007362.5 → NP_031388.2  nuclear cap-binding protein subunit 2 isoform 1

      See identical proteins and their annotated locations for NP_031388.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AC011322
      Consensus CDS
      CCDS3323.1
      UniProtKB/Swiss-Prot
      B2RE91, B4DMK7, E9PAR5, P52298, Q14924, Q2TS50
      Related
      ENSP00000326806.5, ENST00000321256.10
      Conserved Domains (1) summary
      cd12240
      Location:42 → 119
      RRM_NCBP2; RNA recognition motif (RRM) found in nuclear cap-binding protein subunit 2 (CBP20) and similar proteins

    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_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      196935406..196942528 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      199661457..199668578 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P52298.1 GenPept UniProtKB/Swiss-Prot:P52298

    Gene LinkOut

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

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