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
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

Genomic context

Location:: 9q22.33

Exon count:: 23

Annotation release	Status	Assembly	Chr	Location
109.20200522	current	GRCh38.p13 (GCF_000001405.39)	9	NC_000009.12 (97633423..97673748)
105	previous assembly	GRCh37.p13 (GCF_000001405.25)	9	NC_000009.11 (100395705..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?

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.
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.
The authors could distinguish two tyrosines, Y43 and Y20, in stabilization of the cap inside the cap-binding complex binding pocket.
Title: Diverse role of three tyrosines in binding of the RNA 5' cap to the human nuclear cap binding complex.
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.

Submit: New GeneRIF Correction See all GeneRIFs (15)

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

NHGRI GWAS Catalog

Description
The FOXE1 locus is a major genetic determinant for radiation-related thyroid carcinoma in Chernobyl. NHGRI GWA Catalog NHGRI GWA 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: 306 organisms have orthologs with human gene NCBP1
Orthologs

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
RNA 7-methylguanosine cap binding	IMP Inferred from Mutant Phenotype more info	PubMed
RNA binding	HDA more info	PubMed
RNA cap binding	IBA Inferred from Biological aspect of Ancestor more info	PubMed
mRNA binding	IBA Inferred from Biological aspect of Ancestor more info	PubMed
protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
7-methylguanosine mRNA capping	IDA Inferred from Direct Assay more info	PubMed
7-methylguanosine mRNA capping	TAS Traceable Author Statement more info
RNA catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
RNA export from nucleus	TAS Traceable Author Statement more info
RNA metabolic process	TAS Traceable Author Statement more info
RNA splicing	TAS Traceable Author Statement more info	PubMed
fibroblast growth factor receptor signaling pathway	TAS Traceable Author Statement more info
gene silencing by RNA	IEA Inferred from Electronic Annotation more info
histone mRNA metabolic process	TAS Traceable Author Statement more info
mRNA 3'-end processing	TAS Traceable Author Statement more info
mRNA cis splicing, via spliceosome	IEA Inferred from Electronic Annotation more info
mRNA export from nucleus	IBA Inferred from Biological aspect of Ancestor more info	PubMed
mRNA export from nucleus	IMP Inferred from Mutant Phenotype more info	PubMed
mRNA export from nucleus	TAS Traceable Author Statement more info
mRNA splicing, via spliceosome	IBA Inferred from Biological aspect of Ancestor more info	PubMed
mRNA splicing, via spliceosome	TAS Traceable Author Statement more info
nuclear export	TAS Traceable Author Statement more info
nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	IBA Inferred from Biological aspect of Ancestor more info	PubMed
nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	IDA Inferred from Direct Assay more info	PubMed
nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	IMP Inferred from Mutant Phenotype more info	PubMed
nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	TAS Traceable Author Statement more info
positive regulation of RNA binding	IMP Inferred from Mutant Phenotype more info	PubMed
positive regulation of cell growth	IMP Inferred from Mutant Phenotype more info	PubMed
positive regulation of mRNA 3'-end processing	IMP Inferred from Mutant Phenotype more info	PubMed
positive regulation of mRNA splicing, via spliceosome	IMP Inferred from Mutant Phenotype more info	PubMed
pre-mRNA cleavage required for polyadenylation	IMP Inferred from Mutant Phenotype more info	PubMed
NOT regulation of mRNA polyadenylation	IMP Inferred from Mutant Phenotype more info	PubMed
regulation of mRNA processing	IBA Inferred from Biological aspect of Ancestor more info	PubMed
regulation of translational initiation	IDA Inferred from Direct Assay more info	PubMed
snRNA transcription by RNA polymerase II	TAS Traceable Author Statement more info
spliceosomal complex assembly	IMP Inferred from Mutant Phenotype more info	PubMed
termination of RNA polymerase II transcription	TAS Traceable Author Statement more info
transcription by RNA polymerase II	TAS Traceable Author Statement more info
transcription elongation from RNA polymerase II promoter	TAS Traceable Author Statement more info

Component	Evidence Code	Pubs
RNA cap binding complex	IMP Inferred from Mutant Phenotype more info	PubMed
RNA cap binding complex	TAS Traceable Author Statement more info	PubMed
cytosol	IDA Inferred from Direct Assay more info
cytosol	TAS Traceable Author Statement more info
mRNA cap binding complex	IBA Inferred from Biological aspect of Ancestor more info	PubMed
mRNA cap binding complex	IDA Inferred from Direct Assay more info	PubMed
mitochondrion	IDA Inferred from Direct Assay more info
nuclear cap binding complex	IBA Inferred from Biological aspect of Ancestor more info	PubMed
nucleoplasm	IDA Inferred from Direct Assay more info
nucleoplasm	TAS Traceable Author Statement more info
nucleus	IBA Inferred from Biological aspect of Ancestor more info	PubMed
nucleus	IDA Inferred from Direct Assay more info	PubMed
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_001351504.1 → NP_001338433.1 nuclear cap-binding protein subunit 1 isoform 2

Status: REVIEWED

Source sequence(s)

AL445531, BC001450, CA418527, DA885233, DB086376

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 → 692

MIF4G_like_2; MIF4G like
NM_001351505.1 → NP_001338434.1 nuclear cap-binding protein subunit 1 isoform 3

Status: REVIEWED

Source sequence(s)

AL445531, BC001450, CA418527, CN266899, DB086376

Conserved Domains (2) summary

pfam09088
Location:161 → 280

MIF4G_like; MIF4G like

pfam09090
Location:295 → 569

MIF4G_like_2; MIF4G like
NM_001351506.1 → NP_001338435.1 nuclear cap-binding protein subunit 1 isoform 3

Status: REVIEWED

Source sequence(s)

AL445531, BC001450, CA418527, CN266899, DA885233, DB086376

Conserved Domains (2) summary

pfam09088
Location:161 → 280

MIF4G_like; MIF4G like

pfam09090
Location:295 → 569

MIF4G_like_2; MIF4G like
NM_001351507.1 → NP_001338436.1 nuclear cap-binding protein subunit 1 isoform 4

Status: REVIEWED

Source sequence(s)

AL445531, BC001450, CA418527, DB086376

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

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 → 759

MIF4G_like_2; MIF4G like