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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
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Genomic context

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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

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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

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