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NCBP1 nuclear cap binding protein subunit 1 [ Homo sapiens (human) ]

Gene ID: 4686, updated on 23-Nov-2023

Summary

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Official Symbol
NCBP1provided by HGNC
Official Full Name
nuclear cap binding protein subunit 1provided by HGNC
Primary source
HGNC:HGNC:7658
See related
Ensembl:ENSG00000136937 MIM:600469; AllianceGenome:HGNC:7658
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
NCBP; Sto1; CBP80
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 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, Jul 2008]
Expression
Ubiquitous expression in testis (RPKM 9.3), lymph node (RPKM 7.9) and 25 other tissues See more
Orthologs
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Genomic context

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See NCBP1 in Genome Data Viewer
Location:
9q22.33
Exon count:
23
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (97633821..97673748)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (109805762..109845689)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (100396103..100436030)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105376168 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:100278102-100278602 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28665 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28666 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:100293128-100293286 Neighboring gene tropomodulin 1 Neighboring gene Sharpr-MPRA regulatory region 7780 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:100318031-100318532 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:100319241-100319742 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28667 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28668 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:100335093-100335332 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28669 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28670 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28671 Neighboring gene Sharpr-MPRA regulatory region 9871 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:100396128-100396963 Neighboring gene thiosulfate sulfurtransferase like domain containing 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28674 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28675 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28676 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20102 Neighboring gene XPA, DNA damage recognition and repair factor Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:100465986-100467185 Neighboring gene keratin 18 pseudogene 13 Neighboring gene papillary thyroid carcinoma susceptibility candidate 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28678 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:100520047-100521246 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr9:100534165-100534666 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr9:100534667-100535166 Neighboring gene VISTA enhancer hs1595 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20103 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:100571176-100572375 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:100589760-100589981 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:100613975-100614476 Neighboring gene forkhead box E1

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. CBP80-promoted mRNP rearrangements during the pioneer round of translation, nonsense-mediated mRNA decay, and thereafter. Maquat LE, et al. Cold Spring Harb Symp Quant Biol, 2010. PMID 21447822, Free PMC Article
  2. Cellular cap-binding proteins associate with influenza virus mRNAs. Bier K, et al. J Gen Virol, 2011 Jul. PMID 21402597
  3. Diverse role of three tyrosines in binding of the RNA 5' cap to the human nuclear cap binding complex. Worch R, et al. J Mol Biol, 2009 Jan 16. PMID 19026660
  4. Cotranscriptional mRNP assembly: from the DNA to the nuclear pore. Aguilera A. Curr Opin Cell Biol, 2005 Jun. PMID 15901492
  5. Cloning of a complementary DNA encoding an 80 kilodalton nuclear cap binding protein. Kataoka N, et al. Nucleic Acids Res, 1994 Sep 25. PMID 7937105, Free PMC Article

See all (199) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Translation mediated by the nuclear cap-binding complex is confined to the perinuclear region via a CTIF-DDX19B interaction.
    Title: Translation mediated by the nuclear cap-binding complex is confined to the perinuclear region via a CTIF-DDX19B interaction.
  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. NCBP1 promotes the development of lung adenocarcinoma through up-regulation of CUL4B.
    Title: NCBP1 promotes the development of lung adenocarcinoma through up-regulation of CUL4B.
  4. Results suggest that rev protein, HIV-1 (Rev) regulates the association of nuclear cap-binding protein NCBP 80 kDa subunit (CBP80) and eukaryotic translation initiation factor 4A1 (eIF4AI) with the unspliced mRNA in the cytoplasm and the nucleus, respectively, during HIV-1 replication.
    Title: A Rev-CBP80-eIF4AI complex drives Gag synthesis from the HIV-1 unspliced mRNA.
  5. Study proposes the existence of an alternative cap-binding complex involving NCBP1 and NCBP3 that plays a key role in mRNA biogenesis.
    Title: mRNA export through an additional cap-binding complex consisting of NCBP1 and NCBP3.
  6. down-regulation of CTIF using a small interfering RNA causes a redistribution of CBP80 from polysome fractions to subpolysome fractions, without significant consequence to eIF4E distribution
    Title: Translation initiation on mRNAs bound by nuclear cap-binding protein complex CBP80/20 requires interaction between CBP80/20-dependent translation initiation factor and eukaryotic translation initiation factor 3g.
  7. Cellular processes by which CBP80-CBP20 -bound messenger ribonucleoproteins (mRNPs) are remodeled to eIF4E-bound mRNPs, are overviewed.
    Title: CBP80-promoted mRNP rearrangements during the pioneer round of translation, nonsense-mediated mRNA decay, and thereafter.
  8. Viral mRNA associates with the influenza virus A NS1 and the cellular NCBP1 of the nuclear cap-binding complex.
    Title: Cellular cap-binding proteins associate with influenza virus mRNAs.
  9. UPF1 binds PTC-containing mRNA more efficiently than the corresponding PTC-free mRNA in a way that is promoted by the UPF1-CBP80 interaction.
    Title: UPF1 association with the cap-binding protein, CBP80, promotes nonsense-mediated mRNA decay at two distinct steps.
  10. resolution X-ray structure for a cap-binding complex (CBC)-importin-alpha complex that provides a detailed picture for how importin-alpha binds to the CBP80 subunit of the CBC.
    Title: The molecular basis for the regulation of the cap-binding complex by the importins.
Submit: New GeneRIF Correction See all GeneRIFs (18)

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

EBI GWAS Catalog

Description
The FOXE1 locus is a major genetic determinant for radiation-related thyroid carcinoma in Chernobyl.
EBI GWAS Catalog

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

Clone Names

  • MGC2087

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA 7-methylguanosine cap binding IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables RNA binding HDA PubMed 
enables RNA cap binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables mRNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables molecular adaptor activity EXP
Inferred from Experiment
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in 7-methylguanosine mRNA capping IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in RNA catabolic process IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in RNA splicing TAS
Traceable Author Statement
more info
 PubMed 
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 defense response to virus IMP
Inferred from Mutant Phenotype
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 export from nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in mRNA export from nucleus IMP
Inferred from Mutant Phenotype
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 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 mRNA transcription by RNA polymerase II NAS
Non-traceable Author Statement
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 IBA
Inferred from Biological aspect of Ancestor
more info
  
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 binding IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of cell growth IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of mRNA 3'-end processing IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of mRNA splicing, via spliceosome 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 mRNA processing IBA
Inferred from Biological aspect of Ancestor
more info
  
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 IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in snRNA export from nucleus NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in spliceosomal complex assembly IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
part_of RNA cap binding complex IMP
Inferred from Mutant Phenotype
more info
 PubMed 
part_of RNA cap binding complex TAS
Traceable Author Statement
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 IDA
Inferred from Direct Assay
more info
  
located_in cytosol TAS
Traceable Author Statement
more info
  
part_of mRNA cap binding complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of mRNA cap binding complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of mRNA cap binding complex IPI
Inferred from Physical Interaction
more info
 PubMed 
located_in mitochondrion IDA
Inferred from Direct Assay
more info
  
part_of nuclear cap binding complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of nuclear cap binding complex IPI
Inferred from Physical Interaction
more info
 PubMed 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
part_of ribonucleoprotein complex IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
nuclear cap-binding protein subunit 1
Names
80 kDa nuclear cap-binding protein
NCBP 80 kDa subunit
nuclear cap binding protein subunit 1, 80kDa

NCBI Reference Sequences (RefSeq)

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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_001351504.2 → NP_001338433.1  nuclear cap-binding protein subunit 1 isoform 2

    Status: REVIEWED

    Source sequence(s)
    AL445531, BC001450, CA418527, DA885233
    Conserved Domains (3) summary
    smart00543
    Location:9 → 173
    MIF4G; Middle domain of eukaryotic initiation factor 4G (eIF4G)
    pfam09088
    Location:284 → 403
    MIF4G_like; MIF4G like
    pfam09090
    Location:418 → 693
    MIF4G_like_2; MIF4G like

  2. NM_001351505.2 → NP_001338434.1  nuclear cap-binding protein subunit 1 isoform 3

    Status: REVIEWED

    Source sequence(s)
    AL445531, BC001450, CA418527, CN266899
    Conserved Domains (2) summary
    pfam09088
    Location:161 → 280
    MIF4G_like; MIF4G like
    pfam09090
    Location:295 → 570
    MIF4G_like_2; MIF4G like

  3. NM_001351506.2 → NP_001338435.1  nuclear cap-binding protein subunit 1 isoform 3

    Status: REVIEWED

    Source sequence(s)
    AL445531, BC001450, CA418527, CN266899, DA885233
    Conserved Domains (2) summary
    pfam09088
    Location:161 → 280
    MIF4G_like; MIF4G like
    pfam09090
    Location:295 → 570
    MIF4G_like_2; MIF4G like

  4. NM_001351507.2 → NP_001338436.1  nuclear cap-binding protein subunit 1 isoform 4

    Status: REVIEWED

    Source sequence(s)
    AL445531, BC001450, CA418527
    Conserved Domains (2) summary
    pfam09088
    Location:2 → 100
    MIF4G_like; MIF4G like
    pfam09090
    Location:115 → 389
    MIF4G_like_2; MIF4G like

  5. NM_002486.5 → NP_002477.1  nuclear cap-binding protein subunit 1 isoform 1

    See identical proteins and their annotated locations for NP_002477.1

    Status: REVIEWED

    Source sequence(s)
    AL445531, BC001450, CA418527
    Consensus CDS
    CCDS6728.1
    UniProtKB/Swiss-Prot
    B2R718, Q09161, Q59G76, Q5T1V0, Q5T7X2
    Related
    ENSP00000364289.3, ENST00000375147.8
    Conserved Domains (3) summary
    smart00543
    Location:28 → 240
    MIF4G; Middle domain of eukaryotic initiation factor 4G (eIF4G)
    pfam09088
    Location:351 → 470
    MIF4G_like; MIF4G like
    pfam09090
    Location:485 → 760
    MIF4G_like_2; MIF4G like

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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    97633821..97673748
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    109805762..109845689
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q09161.1 GenPept UniProtKB/Swiss-Prot:Q09161

Gene LinkOut

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

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