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

Summary

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: mouse all
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Genomic context

Location:: 9q22.33

Exon count:: 23

Annotation release	Status	Assembly	Chr	Location
110	current	GRCh38.p14 (GCF_000001405.40)	9	NC_000009.12 (97633821..97673748)
110	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_000009.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
Affinity proteomic dissection of the human nuclear cap-binding complex interactome.
Title: Affinity proteomic dissection of the human nuclear cap-binding complex interactome.
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.
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.
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.
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.
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.
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.
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.
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 EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

NCBP1_4020 (e-PCR)
- UniSTS:462366

RH122051 (e-PCR)
- UniSTS:134687

RH68376 (e-PCR)
- UniSTS:47138

SHGC-12947 (e-PCR)
- UniSTS:79671

RH102496 (e-PCR)
- UniSTS:96830

RH71150 (e-PCR)
- UniSTS:3672

SHGC-36266 (e-PCR)
- UniSTS:77955

SHGC-143489 (e-PCR)
- UniSTS:171931

STS-AA035493 (e-PCR)
- UniSTS:21493

STS-AA011612 (e-PCR)
- UniSTS:13303

Homology

Homologs of the NCBP1 gene: The NCBP1 gene is conserved in chimpanzee, Rhesus monkey, dog, cow, mouse, rat, chicken, fruit fly, mosquito, C.elegans, A.thaliana, rice, and frog.
Orthologs from Annotation Pipeline: 428 organisms have orthologs with human gene NCBP1
Orthologs

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 more info	PubMed
enables RNA cap binding	IBA Inferred from Biological aspect of Ancestor more info	PubMed
enables mRNA binding	IBA Inferred from Biological aspect of Ancestor more info	PubMed
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	IC Inferred by Curator more info	PubMed
involved_in cap-dependent translational initiation	IC Inferred by Curator 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	IC Inferred by Curator more info	PubMed
involved_in mRNA export from nucleus	IBA Inferred from Biological aspect of Ancestor more info	PubMed
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 splicing, via spliceosome	IC Inferred by Curator more info	PubMed
involved_in mRNA transcription by RNA polymerase II	EXP Inferred from Experiment more info	PubMed
involved_in mRNA transcription by RNA polymerase II	IC Inferred by Curator more info	PubMed
involved_in miRNA-mediated gene silencing	IC Inferred by Curator more info	PubMed
involved_in nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	IC Inferred by Curator 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 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 phosphorylation of RNA polymerase II C-terminal domain	IC Inferred by Curator more info	PubMed
involved_in positive regulation of transcription elongation by RNA polymerase II	IC Inferred by Curator more info	PubMed
involved_in pre-mRNA cleavage required for polyadenylation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in primary miRNA processing	IC Inferred by Curator more info	PubMed
NOT involved_in regulation of mRNA polyadenylation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of mRNA processing	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in regulation of translational initiation	IDA Inferred from Direct Assay more info	PubMed
involved_in snRNA export from nucleus	IC Inferred by Curator more info	PubMed
involved_in snRNA export from nucleus	IMP Inferred from Mutant Phenotype 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	IC Inferred by Curator more info	PubMed
located_in cytoplasm	IDA Inferred from Direct Assay 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	PubMed
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	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
located_in nucleoplasm	TAS Traceable Author Statement more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info	PubMed
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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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)

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
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
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
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
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

Q09161, Q5T7X2

UniProtKB/TrEMBL

A0A024R179

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