NCBP3 Gene

Name nuclear cap binding subunit 3
Description Enables RNA 7-methylguanosine cap binding activity and mRNA binding activity. Involved in defense response to virus; mRNA export from nucleus; and snRNA export from nucleus. Located in cytoplasm and nuclear speck. Part of nuclear cap binding activity complex. [provided by Alliance of Genome Resources, Mar 2025]
Summary
{"type": "root", "children": [{"type": "p", "children": [{"type": "t", "text": "\nNCBP3 is a novel cap‐binding protein that functions as part of an alternative nuclear cap‐binding complex (CBC) with NCBP1. This alternative CBC is capable of binding the 5′‐cap of RNA polymerase II transcripts and aids in mRNA biogenesis by promoting polyadenylated RNA export under normal conditions; however, its role becomes particularly crucial during cellular stress such as viral infection, when the canonical NCBP2-dependent complex is insufficient."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "1"}]}, {"type": "t", "text": "NCBP3 also exhibits a distinct interaction profile compared to its canonical partners by preferentially associating with components of the Exon Junction Complex (EJC) and the TREX complex. Through these interactions, NCBP3 stabilizes multi-exonic transcripts by competing with RNA degradation factors and thereby facilitates proper mRNA processing and nuclear export."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "2"}]}, {"type": "t", "text": "Further quantitative interactome screenings have refined our understanding of NCBP3’s associations within ribonucleoprotein assemblies, underscoring its role in mRNA fate decisions while interacting selectively with factors influencing RNA maturation."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "3"}]}, {"type": "t", "text": "In addition to its general role in RNA processing, NCBP3 has been implicated in glioma progression. It is upregulated in glioma tissues and cells, where it binds and stabilizes the small nucleolar RNA host gene 6 (SNHG6). This interaction promotes the repression of the transcription factor GBX2 via polycomb repressive complex 2-mediated H3K27me3 modification, ultimately leading to enhanced expression of oncogenic targets such as FLOT1 and facilitating malignant progression."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "4"}]}, {"type": "t", "text": ""}]}, {"type": "rg", "children": [{"type": "r", "ref": 1, "children": [{"type": "t", "text": "Anna Gebhardt, Matthias Habjan, Christian Benda, et al. "}, {"type": "b", "children": [{"type": "t", "text": "mRNA export through an additional cap-binding complex consisting of NCBP1 and NCBP3."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Nat Commun (2015)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/ncomms9192"}], "href": "https://doi.org/10.1038/ncomms9192"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "26382858"}], "href": "https://pubmed.ncbi.nlm.nih.gov/26382858"}]}, {"type": "r", "ref": 2, "children": [{"type": "t", "text": "Yuhui Dou, Isabelle Barbosa, Hua Jiang, et al. "}, {"type": "b", "children": [{"type": "t", "text": "NCBP3 positively impacts mRNA biogenesis."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Nucleic Acids Res (2020)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1093/nar/gkaa744"}], "href": "https://doi.org/10.1093/nar/gkaa744"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "32960271"}], "href": "https://pubmed.ncbi.nlm.nih.gov/32960271"}]}, {"type": "r", "ref": 3, "children": [{"type": "t", "text": "Yuhui Dou, Svetlana Kalmykova, Maria Pashkova, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Affinity proteomic dissection of the human nuclear cap-binding complex interactome."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Nucleic Acids Res (2020)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1093/nar/gkaa743"}], "href": "https://doi.org/10.1093/nar/gkaa743"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "32960270"}], "href": "https://pubmed.ncbi.nlm.nih.gov/32960270"}]}, {"type": "r", "ref": 4, "children": [{"type": "t", "text": "Xiwen Li, Fangfang Zhang, Jun Ma, et al. "}, {"type": "b", "children": [{"type": "t", "text": "NCBP3/SNHG6 inhibits GBX2 transcription in a histone modification manner to facilitate the malignant biological behaviour of glioma cells."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "RNA Biol (2021)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1080/15476286.2020.1790140"}], "href": "https://doi.org/10.1080/15476286.2020.1790140"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "32618493"}], "href": "https://pubmed.ncbi.nlm.nih.gov/32618493"}]}]}]}
NCBI Gene ID 55421
API
Download Associations
Predicted Functions View NCBP3's ARCHS4 Predicted Functions.
Co-expressed Genes View NCBP3's ARCHS4 Predicted Functions.
Expression in Tissues and Cell Lines View NCBP3's ARCHS4 Predicted Functions.

Functional Associations

NCBP3 has 1,344 functional associations with biological entities spanning 6 categories (functional term, phrase or reference, disease, phenotype or trait, chemical, cell line, cell type or tissue, gene, protein or microRNA, sequence feature) extracted from 29 datasets.

Click the + buttons to view associations for NCBP3 from the datasets below.

If available, associations are ranked by standardized value

Dataset Summary
CCLE Cell Line Proteomics Cell lines associated with NCBP3 protein from the CCLE Cell Line Proteomics dataset.
CellMarker Gene-Cell Type Associations cell types associated with NCBP3 gene from the CellMarker Gene-Cell Type Associations dataset.
ChEA Transcription Factor Targets 2022 transcription factors binding the promoter of NCBP3 gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets 2022 dataset.
COMPARTMENTS Curated Protein Localization Evidence Scores 2025 cellular components containing NCBP3 protein from the COMPARTMENTS Curated Protein Localization Evidence Scores 2025 dataset.
COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025 cellular components co-occuring with NCBP3 protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025 dataset.
DepMap CRISPR Gene Dependency cell lines with fitness changed by NCBP3 gene knockdown relative to other cell lines from the DepMap CRISPR Gene Dependency dataset.
DISEASES Text-mining Gene-Disease Association Evidence Scores 2025 diseases co-occuring with NCBP3 gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores 2025 dataset.
GO Biological Process Annotations 2023 biological processes involving NCBP3 gene from the curated GO Biological Process Annotations 2023 dataset.
GO Biological Process Annotations 2025 biological processes involving NCBP3 gene from the curated GO Biological Process Annotations2025 dataset.
GO Cellular Component Annotations 2023 cellular components containing NCBP3 protein from the curated GO Cellular Component Annotations 2023 dataset.
GO Cellular Component Annotations 2025 cellular components containing NCBP3 protein from the curated GO Cellular Component Annotations 2025 dataset.
GO Molecular Function Annotations 2023 molecular functions performed by NCBP3 gene from the curated GO Molecular Function Annotations 2023 dataset.
GO Molecular Function Annotations 2025 molecular functions performed by NCBP3 gene from the curated GO Molecular Function Annotations 2025 dataset.
GTEx eQTL 2025 SNPs regulating expression of NCBP3 gene from the GTEx eQTL 2025 dataset.
GTEx Tissue Gene Expression Profiles 2023 tissues with high or low expression of NCBP3 gene relative to other tissues from the GTEx Tissue Gene Expression Profiles 2023 dataset.
IMPC Knockout Mouse Phenotypes phenotypes of mice caused by NCBP3 gene knockout from the IMPC Knockout Mouse Phenotypes dataset.
LINCS L1000 CMAP Chemical Perturbation Consensus Signatures small molecule perturbations changing expression of NCBP3 gene from the LINCS L1000 CMAP Chemical Perturbations Consensus Signatures dataset.
LINCS L1000 CMAP CRISPR Knockout Consensus Signatures gene perturbations changing expression of NCBP3 gene from the LINCS L1000 CMAP CRISPR Knockout Consensus Signatures dataset.
MGI Mouse Phenotype Associations 2023 phenotypes of transgenic mice caused by NCBP3 gene mutations from the MGI Mouse Phenotype Associations 2023 dataset.
NIBR DRUG-seq U2OS MoA Box Gene Expression Profiles drug perturbations changing expression of NCBP3 gene from the NIBR DRUG-seq U2OS MoA Box dataset.
PFOCR Pathway Figure Associations 2024 pathways involving NCBP3 protein from the Wikipathways PFOCR 2024 dataset.
Replogle et al., Cell, 2022 K562 Essential Perturb-seq Gene Perturbation Signatures gene perturbations changing expression of NCBP3 gene from the Replogle et al., Cell, 2022 K562 Essential Perturb-seq Gene Perturbation Signatures dataset.
Replogle et al., Cell, 2022 K562 Genome-wide Perturb-seq Gene Perturbation Signatures gene perturbations changing expression of NCBP3 gene from the Replogle et al., Cell, 2022 K562 Genome-wide Perturb-seq Gene Perturbation Signatures dataset.
Replogle et al., Cell, 2022 RPE1 Essential Perturb-seq Gene Perturbation Signatures gene perturbations changing expression of NCBP3 gene from the Replogle et al., Cell, 2022 RPE1 Essential Perturb-seq Gene Perturbation Signatures dataset.
RummaGEO Drug Perturbation Signatures drug perturbations changing expression of NCBP3 gene from the RummaGEO Drug Perturbation Signatures dataset.
RummaGEO Gene Perturbation Signatures gene perturbations changing expression of NCBP3 gene from the RummaGEO Gene Perturbation Signatures dataset.
TISSUES Curated Tissue Protein Expression Evidence Scores 2025 tissues with high expression of NCBP3 protein from the TISSUES Curated Tissue Protein Expression Evidence Scores 2025 dataset.
TISSUES Experimental Tissue Protein Expression Evidence Scores 2025 tissues with high expression of NCBP3 protein in proteomics datasets from the TISSUES Experimental Tissue Protein Expression Evidence Scores 2025 dataset.
TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025 tissues co-occuring with NCBP3 protein in abstracts of biomedical publications from the TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025 dataset.