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

    Gene ID: 22916, updated on 17-Jun-2024

    Summary

    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
    NEW
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    Genomic context

    See NCBP2 in Genome Data Viewer
    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

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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

    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)

    NEW Try the new Transcript table

    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_001042540.2NP_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:4166
      RRM_SF; RNA recognition motif (RRM) superfamily
    2. NM_001308036.2NP_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:24101
      RRM_NCBP2; RNA recognition motif found in nuclear cap-binding protein subunit 2 (CBP20) and similar proteins
    3. NM_001410857.1NP_001397786.1  nuclear cap-binding protein subunit 2 isoform 4

      Status: REVIEWED

      Source sequence(s)
      AC011322
      Consensus CDS
      CCDS93446.1
      UniProtKB/TrEMBL
      A0A9K3Y7M6, C9JQX9, D3DXB7, F6WVI0
      Related
      ENSP00000413518.1, ENST00000447325.5
    4. NM_007362.5NP_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:42119
      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)