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Aliases for NCBP2 Gene

Aliases for NCBP2 Gene

  • Nuclear Cap Binding Protein Subunit 2 2 3 5
  • Nuclear Cap Binding Protein Subunit 2, 20kDa 2 3
  • Nuclear Cap Binding Protein Subunit 2, 20kD 2 3
  • Cell Proliferation-Inducing Gene 55 Protein 3 4
  • 20 KDa Nuclear Cap-Binding Protein 3 4
  • NCBP 20 KDa Subunit 3 4
  • CBP20 3 4
  • NIP1 3 4
  • Nuclear Cap-Binding Protein Subunit 2 3
  • NCBP Interacting Protein 1 3
  • NCBP-Interacting Protein 1 4
  • PIG55 3
  • CBC2 3

External Ids for NCBP2 Gene

Previous GeneCards Identifiers for NCBP2 Gene

  • GC03M192627
  • GC03M197011
  • GC03M198069
  • GC03M197988
  • GC03M198150
  • GC03M196662
  • GC03M193962

Summaries for NCBP2 Gene

Entrez Gene Summary for NCBP2 Gene

  • 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]

GeneCards Summary for NCBP2 Gene

NCBP2 (Nuclear Cap Binding Protein Subunit 2) is a Protein Coding gene. Among its related pathways are mRNA Splicing - Major Pathway and Formation of HIV elongation complex in the absence of HIV Tat. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and RNA binding. An important paralog of this gene is NCBP2L.

UniProtKB/Swiss-Prot for NCBP2 Gene

  • Component of the cap-binding complex (CBC), which binds co-transcriptionally to the 5 cap of pre-mRNAs and is involved in various processes such as pre-mRNA splicing, translation regulation, nonsense-mediated mRNA decay, RNA-mediated gene silencing (RNAi) by microRNAs (miRNAs) and mRNA export. The CBC complex is involved in mRNA export from the nucleus via its interaction with ALYREF/THOC4/ALY, leading to the recruitment of the mRNA export machinery to the 5 end of mRNA and to mRNA export in a 5 to 3 direction through the nuclear pore. The CBC complex is also involved in mediating U snRNA and intronless mRNAs export from the nucleus. The CBC complex is essential for a pioneer round of mRNA translation, before steady state translation when the CBC complex is replaced by cytoplasmic cap-binding protein eIF4E. The pioneer round of mRNA translation mediated by the CBC complex plays a central role in nonsense-mediated mRNA decay (NMD), NMD only taking place in mRNAs bound to the CBC complex, but not on eIF4E-bound mRNAs. The CBC complex enhances NMD in mRNAs containing at least one exon-junction complex (EJC) via its interaction with UPF1, promoting the interaction between UPF1 and UPF2. The CBC complex is also involved in failsafe NMD, which is independent of the EJC complex, while it does not participate in Staufen-mediated mRNA decay (SMD). During cell proliferation, the CBC complex is also involved in microRNAs (miRNAs) biogenesis via its interaction with SRRT/ARS2, thereby being required for miRNA-mediated RNA interference. The CBC complex also acts as a negative regulator of PARN, thereby acting as an inhibitor of mRNA deadenylation. In the CBC complex, NCBP2/CBP20 recognizes and binds capped RNAs (m7GpppG-capped RNA) but requires NCBP1/CBP80 to stabilize the movement of its N-terminal loop and lock the CBC into a high affinity cap-binding state with the cap structure. The conventional cap-binding complex with NCBP2 binds both small nuclear RNA (snRNA) and messenger (mRNA) and is involved in their export from the nucleus (PubMed:26382858).

Additional gene information for NCBP2 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for NCBP2 Gene

Genomics for NCBP2 Gene

GeneHancer (GH) Regulatory Elements for NCBP2 Gene

Promoters and enhancers for NCBP2 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH03I196938 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 561 +0.2 220 7.3 CLOCK MLX DMAP1 IRF4 YY1 SLC30A9 E2F8 ZNF143 SP3 NFYC NCBP2-AS2 NCBP2 PIGZ SENP5 NCBP2-AS1
GH03I196285 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 12.9 +655.3 655328 3.2 HDGF PKNOX1 FOXA2 ARNT ZFP64 ARID4B SIN3A DMAP1 ZNF2 ZBTB7B PCYT1A TM4SF19 WDR53 RNF168 ACAP2 ENSG00000260261 NCBP2 SLC51A ENSG00000231443 ENSG00000228028
GH03I196866 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 11.3 +74.6 74551 2.5 HDGF SMAD1 ARNT ARID4B SIN3A YY1 POLR2B ZNF207 ZNF143 SP5 SENP5 NCBP2-AS2 RPL36P7 NCBP2 NCBP2-AS1 CEP19 GC03M196873
GH03I196567 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 9.8 +373.8 373808 2.6 HDGF SMAD1 ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 POLR2B CBX5 FBXO45 WDR53 SDHAP2 SDHAP1 RNF168 LINC00969 MIR570 CEP19 LINC01063 NCBP2
GH03I196527 Promoter/Enhancer 2 FANTOM5 Ensembl ENCODE dbSUPER 9.5 +414.1 414054 1.8 PKNOX1 ATF1 ARNT SIN3A YY1 GTF3C2 TCF12 ZNF766 GATA2 ZNF143 ENSG00000213358 FBXO45 WDR53 CEP19 NCBP2-AS1 NCBP2 RNF168 MELTF-AS1 TM4SF19 SMCO1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around NCBP2 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the NCBP2 gene promoter:

Genomic Locations for NCBP2 Gene

Genomic Locations for NCBP2 Gene
chr3:196,935,402-196,942,597
(GRCh38/hg38)
Size:
7,196 bases
Orientation:
Minus strand
chr3:196,662,273-196,669,468
(GRCh37/hg19)

Genomic View for NCBP2 Gene

Genes around NCBP2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NCBP2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NCBP2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NCBP2 Gene

Proteins for NCBP2 Gene

  • Protein details for NCBP2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P52298-NCBP2_HUMAN
    Recommended name:
    Nuclear cap-binding protein subunit 2
    Protein Accession:
    P52298
    Secondary Accessions:
    • B2RE91
    • B4DMK7
    • E9PAR5
    • Q14924
    • Q2TS50

    Protein attributes for NCBP2 Gene

    Size:
    156 amino acids
    Molecular mass:
    18001 Da
    Quaternary structure:
    • Component of the nuclear cap-binding complex (CBC), a heterodimer composed of NCBP1/CBP80 and NCBP2/CBP20 that interacts with m7GpppG-capped RNA (PubMed:26382858). Found in a U snRNA export complex with PHAX/RNUXA, NCBP1/CBP80, NCBP2/CBP20, RAN, XPO1 and m7G-capped RNA. Interacts with PHAX/RNUXA, EIF4G1, HNRNPF, HNRNPH1 and ALYREF/THOC4/ALY. Interacts with SRRT/ARS2 and KPNA3 (PubMed:26382858).

    Three dimensional structures from OCA and Proteopedia for NCBP2 Gene

    Alternative splice isoforms for NCBP2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for NCBP2 Gene

Post-translational modifications for NCBP2 Gene

  • Ubiquitination at Lys120 and isoforms=2, 3151

No data available for DME Specific Peptides for NCBP2 Gene

Domains & Families for NCBP2 Gene

Gene Families for NCBP2 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Transporters

Protein Domains for NCBP2 Gene

Graphical View of Domain Structure for InterPro Entry

P52298

UniProtKB/Swiss-Prot:

NCBP2_HUMAN :
  • Belongs to the RRM NCBP2 family.
Family:
  • Belongs to the RRM NCBP2 family.
genes like me logo Genes that share domains with NCBP2: view

Function for NCBP2 Gene

Molecular function for NCBP2 Gene

GENATLAS Biochemistry:
nuclear cap binding protein subunit 2,component of thecap-binding protein complex in association with NCBP2 and other proteins,mediating premRNA splicing and export of U small nuclear RNAs to the cytoplasm
UniProtKB/Swiss-Prot Function:
Component of the cap-binding complex (CBC), which binds co-transcriptionally to the 5 cap of pre-mRNAs and is involved in various processes such as pre-mRNA splicing, translation regulation, nonsense-mediated mRNA decay, RNA-mediated gene silencing (RNAi) by microRNAs (miRNAs) and mRNA export. The CBC complex is involved in mRNA export from the nucleus via its interaction with ALYREF/THOC4/ALY, leading to the recruitment of the mRNA export machinery to the 5 end of mRNA and to mRNA export in a 5 to 3 direction through the nuclear pore. The CBC complex is also involved in mediating U snRNA and intronless mRNAs export from the nucleus. The CBC complex is essential for a pioneer round of mRNA translation, before steady state translation when the CBC complex is replaced by cytoplasmic cap-binding protein eIF4E. The pioneer round of mRNA translation mediated by the CBC complex plays a central role in nonsense-mediated mRNA decay (NMD), NMD only taking place in mRNAs bound to the CBC complex, but not on eIF4E-bound mRNAs. The CBC complex enhances NMD in mRNAs containing at least one exon-junction complex (EJC) via its interaction with UPF1, promoting the interaction between UPF1 and UPF2. The CBC complex is also involved in failsafe NMD, which is independent of the EJC complex, while it does not participate in Staufen-mediated mRNA decay (SMD). During cell proliferation, the CBC complex is also involved in microRNAs (miRNAs) biogenesis via its interaction with SRRT/ARS2, thereby being required for miRNA-mediated RNA interference. The CBC complex also acts as a negative regulator of PARN, thereby acting as an inhibitor of mRNA deadenylation. In the CBC complex, NCBP2/CBP20 recognizes and binds capped RNAs (m7GpppG-capped RNA) but requires NCBP1/CBP80 to stabilize the movement of its N-terminal loop and lock the CBC into a high affinity cap-binding state with the cap structure. The conventional cap-binding complex with NCBP2 binds both small nuclear RNA (snRNA) and messenger (mRNA) and is involved in their export from the nucleus (PubMed:26382858).

Gene Ontology (GO) - Molecular Function for NCBP2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000339 RNA cap binding NAS,IEA 7651522
GO:0000340 RNA 7-methylguanosine cap binding IMP 23793891
GO:0003676 nucleic acid binding IEA --
GO:0003723 NOT RNA binding IDA,IEA 7478990
GO:0003729 mRNA binding IDA 26382858
genes like me logo Genes that share ontologies with NCBP2: view
genes like me logo Genes that share phenotypes with NCBP2: view

Animal Model Products

Inhibitory RNA Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for NCBP2 Gene

Localization for NCBP2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for NCBP2 Gene

Nucleus. Cytoplasm.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for NCBP2 gene
Compartment Confidence
nucleus 5
cytosol 5
extracellular 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for NCBP2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus NAS,IEA 7651522
GO:0005654 nucleoplasm IDA,TAS --
GO:0005737 cytoplasm IEA,IDA 8601613
GO:0005829 cytosol TAS --
GO:0005845 mRNA cap binding complex IDA 7651522
genes like me logo Genes that share ontologies with NCBP2: view

Pathways & Interactions for NCBP2 Gene

genes like me logo Genes that share pathways with NCBP2: view

Gene Ontology (GO) - Biological Process for NCBP2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay TAS --
GO:0000398 mRNA splicing, via spliceosome TAS --
GO:0006366 transcription by RNA polymerase II TAS --
GO:0006368 transcription elongation from RNA polymerase II promoter TAS --
GO:0006369 termination of RNA polymerase II transcription TAS --
genes like me logo Genes that share ontologies with NCBP2: view

No data available for SIGNOR curated interactions for NCBP2 Gene

Drugs & Compounds for NCBP2 Gene

No Compound Related Data Available

Transcripts for NCBP2 Gene

Unigene Clusters for NCBP2 Gene

Nuclear cap binding protein subunit 2, 20kDa:
Representative Sequences:

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for NCBP2 Gene

ExUns: 1a · 1b · 1c · 1d · 1e ^ 2a · 2b ^ 3 ^ 4a · 4b ^ 5 ^ 6a · 6b · 6c · 6d ^ 7a · 7b · 7c · 7d · 7e ^ 8a · 8b · 8c · 8d · 8e · 8f ·
SP1: - - - - - - -
SP2: - - - - - - - - -
SP3: - - - - - - - -
SP4: - - - - - - - - - - - -
SP5: - - - - - - -
SP6: - - - - - -
SP7: - - - -
SP8: - - - - - - - - - - - -
SP9: - - - - - - -
SP10: - -
SP11: - - - - -

ExUns: 8g · 8h
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:

Relevant External Links for NCBP2 Gene

GeneLoc Exon Structure for
NCBP2
ECgene alternative splicing isoforms for
NCBP2

Expression for NCBP2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for NCBP2 Gene

Protein differential expression in normal tissues from HIPED for NCBP2 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (19.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for NCBP2 Gene



Protein tissue co-expression partners for NCBP2 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of NCBP2 Gene:

NCBP2

SOURCE GeneReport for Unigene cluster for NCBP2 Gene:

Hs.591671

Evidence on tissue expression from TISSUES for NCBP2 Gene

  • Nervous system(4.9)
genes like me logo Genes that share expression patterns with NCBP2: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for NCBP2 Gene

Orthologs for NCBP2 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for NCBP2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia NCBP2 33 34
  • 99.57 (n)
dog
(Canis familiaris)
Mammalia NCBP2 33 34
  • 92.52 (n)
oppossum
(Monodelphis domestica)
Mammalia -- 34
  • 92 (a)
ManyToMany
-- 34
  • 90 (a)
ManyToMany
-- 34
  • 90 (a)
ManyToMany
-- 34
  • 88 (a)
ManyToMany
cow
(Bos Taurus)
Mammalia NCBP2 33 34
  • 91.88 (n)
mouse
(Mus musculus)
Mammalia Ncbp2 16 34 33
  • 90.81 (n)
rat
(Rattus norvegicus)
Mammalia LOC100911481 33
  • 89.53 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 55 (a)
OneToMany
chicken
(Gallus gallus)
Aves NCBP2 33 34
  • 75.48 (n)
lizard
(Anolis carolinensis)
Reptilia -- 34
  • 68 (a)
OneToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia ncbp2 33
  • 75.33 (n)
Str.170 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.1644 33
zebrafish
(Danio rerio)
Actinopterygii ncbp2 33 34
  • 71.81 (n)
fruit fly
(Drosophila melanogaster)
Insecta Cbp20 35 34
  • 78 (a)
worm
(Caenorhabditis elegans)
Secernentea F26A3.2 35
  • 65 (a)
ncbp-2 34
  • 58 (a)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes CBC2 36 34
  • 36 (a)
thale cress
(Arabidopsis thaliana)
eudicotyledons CBP20 33
  • 61.5 (n)
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.1040 33
rice
(Oryza sativa)
Liliopsida Os02g0612300 33
  • 61.03 (n)
wheat
(Triticum aestivum)
Liliopsida Ta.2512 33
sea squirt
(Ciona savignyi)
Ascidiacea CSA.10672 34
  • 56 (a)
OneToMany
Species where no ortholog for NCBP2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)

Evolution for NCBP2 Gene

ENSEMBL:
Gene Tree for NCBP2 (if available)
TreeFam:
Gene Tree for NCBP2 (if available)

Paralogs for NCBP2 Gene

Paralogs for NCBP2 Gene

(3) SIMAP similar genes for NCBP2 Gene using alignment to 5 proteins:

genes like me logo Genes that share paralogs with NCBP2: view

Variants for NCBP2 Gene

Sequence variations from dbSNP and Humsavar for NCBP2 Gene

SNP ID Clin Chr 03 pos Variation AA Info Type
rs1000108563 -- 196,941,161(-) G/A intron_variant
rs1000352863 -- 196,936,215(-) AAAAA/AAAA 3_prime_UTR_variant
rs1000807537 -- 196,940,812(-) T/G intron_variant
rs1000859702 -- 196,941,070(-) T/G intron_variant
rs1000883245 -- 196,935,395(-) C/G downstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for NCBP2 Gene

Variant ID Type Subtype PubMed ID
esv2763775 CNV gain+loss 21179565
esv3599293 CNV gain 21293372
nsv1003135 CNV gain 25217958
nsv593086 CNV loss 21841781
nsv819558 CNV loss 19587683

Variation tolerance for NCBP2 Gene

Residual Variation Intolerance Score: 39% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.04; 0.99% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for NCBP2 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
NCBP2

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NCBP2 Gene

Disorders for NCBP2 Gene

Additional Disease Information for NCBP2

No disorders were found for NCBP2 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for NCBP2 Gene

Publications for NCBP2 Gene

  1. A cap-binding protein complex mediating U snRNA export. (PMID: 7651522) Izaurralde E … Mattaj IW (Nature 1995) 2 3 4 22 58
  2. Evidence for a pioneer round of mRNA translation: mRNAs subject to nonsense-mediated decay in mammalian cells are bound by CBP80 and CBP20. (PMID: 11551508) Ishigaki Y … Maquat LE (Cell 2001) 3 4 22 58
  3. Interaction between the human nuclear cap-binding protein complex and hnRNP F. (PMID: 9111328) Gamberi C … Mattaj IW (Molecular and cellular biology 1997) 3 4 22 58
  4. A nuclear cap-binding complex binds Balbiani ring pre-mRNA cotranscriptionally and accompanies the ribonucleoprotein particle during nuclear export. (PMID: 8601613) Visa N … Mattaj IW (The Journal of cell biology 1996) 3 4 22 58
  5. Identification of the factors that interact with NCBP, an 80 kDa nuclear cap binding protein. (PMID: 7478990) Kataoka N … Shimura Y (Nucleic acids research 1995) 2 3 4 58

Products for NCBP2 Gene

Sources for NCBP2 Gene

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