Mouse Gene Ncbp2 (uc007yxz.2) Description and Page Index
  Description: nuclear cap-binding protein subunit 2
Transcript (Including UTRs)
   Position: mm9 chr16:31,948,632-31,958,558 Size: 9,927 Total Exon Count: 4 Strand: +
Coding Region
   Position: mm9 chr16:31,948,736-31,957,096 Size: 8,361 Coding Exon Count: 4 

Page IndexSequence and LinksUniProtKB CommentsCTDMicroarray ExpressionRNA Structure
Protein StructureOther SpeciesGO AnnotationsmRNA DescriptionsPathwaysOther Names
Model InformationMethods
Data last updated: 2011-03-02

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr16:31,948,632-31,958,558)mRNA (may differ from genome)Protein (156 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAllen Brain Atlas
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkMGIPubMedReactomeStanford SOURCEUniProtKB

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Nuclear cap-binding protein subunit 2; AltName: Full=20 kDa nuclear cap-binding protein; AltName: Full=NCBP 20 kDa subunit; Short=CBP20;
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.
SUBUNIT: Component of the nuclear cap-binding complex (CBC), a heterodimer composed of NCBP1/CBP80 and NCBP2/CBP20 that interacts with m7GpppG-capped RNA. Is part of the exon junction complex (EJC) containing NCBP1, NCBP2, RNPS1, RBM8A, SRRM1, NXF1, UPF3B, UPF2, ALYREF/THOC4 and/or REFBP2. Interacts with EIF4G1, HNRNPF, HNRNPH1 and ALYREF/THOC4/ALY (By similarity). Found in a U snRNA export complex with RNUXA/PHAX, NCBP1/CBP80, NCBP2/CBP20, RAN, XPO1 and m7G-capped RNA. Interaction with RNUXA/PHAX.
SUBCELLULAR LOCATION: Nucleus (By similarity). Cytoplasm (By similarity).
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR (By similarity).
SIMILARITY: Belongs to the RRM NCBP2 family.
SIMILARITY: Contains 1 RRM (RNA recognition motif) domain.

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  Microarray Expression Data
Expression ratio colors:

GNF Expression Atlas 2 Data from GNF1M Mouse Chip


Rinn et. al Sex Gene Expression Data on MOE430A Chip


GNF Expression Atlas Data from U74a Mouse Chip


-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -35.80104-0.344 Picture PostScript Text
3' UTR -422.791462-0.289 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR012677 - Nucleotide-bd_a/b_plait
IPR000504 - RRM_dom

Pfam Domains:
PF00076 - RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)

SCOP Domains:
54928 - RNA-binding domain, RBD

ModBase Predicted Comparative 3D Structure on Q9CQ49
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
HumanRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserGenome BrowserGenome BrowserGenome BrowserGenome Browser
Gene DetailsGene Details Gene DetailsGene DetailsGene Details
Gene SorterGene Sorter Gene SorterGene SorterGene Sorter
Protein SequenceProtein SequenceProtein SequenceProtein SequenceProtein SequenceProtein Sequence

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000339 RNA cap binding
GO:0000340 RNA 7-methylguanosine cap binding
GO:0003676 nucleic acid binding
GO:0003729 mRNA binding
GO:0017069 snRNA binding
GO:0003723 RNA binding

Biological Process:
GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay
GO:0000398 mRNA splicing, via spliceosome
GO:0006397 mRNA processing
GO:0006408 snRNA export from nucleus
GO:0006417 regulation of translation
GO:0006446 regulation of translational initiation
GO:0008380 RNA splicing
GO:0031047 gene silencing by RNA
GO:0031442 positive regulation of mRNA 3'-end processing
GO:0045292 mRNA cis splicing, via spliceosome
GO:0046833 positive regulation of RNA export from nucleus
GO:0051028 mRNA transport
GO:0098789 pre-mRNA cleavage required for polyadenylation

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005845 mRNA cap binding complex
GO:0005846 nuclear cap binding complex
GO:0034518 RNA cap binding complex

-  Descriptions from all associated GenBank mRNAs
  AK008980 - Mus musculus adult male stomach cDNA, RIKEN full-length enriched library, clone:2210418J22 product:nuclear cap binding protein subunit 2, 20kDa, full insert sequence.
AK078181 - Mus musculus adult male olfactory brain cDNA, RIKEN full-length enriched library, clone:6430404F06 product:nuclear cap binding protein subunit 2, 20kDa, full insert sequence.
AK147027 - Mus musculus 17 days pregnant adult female amnion cDNA, RIKEN full-length enriched library, clone:I920089D11 product:nuclear cap binding protein subunit 2, full insert sequence.
AK012659 - Mus musculus 10, 11 days embryo whole body cDNA, RIKEN full-length enriched library, clone:2810003I04 product:nuclear cap binding protein subunit 2, 20kDa, full insert sequence.
AK014016 - Mus musculus 13 days embryo head cDNA, RIKEN full-length enriched library, clone:3110007E06 product:nuclear cap binding protein subunit 2, 20kDa, full insert sequence.
AK135597 - Mus musculus 1 day pregnant adult female ovary cDNA, RIKEN full-length enriched library, clone:7230402I05 product:nuclear cap binding protein subunit 2, full insert sequence.
BC118926 - Mus musculus nuclear cap binding protein subunit 2, mRNA (cDNA clone MGC:143500 IMAGE:40090166), complete cds.
AK077841 - Mus musculus 13 days embryo forelimb cDNA, RIKEN full-length enriched library, clone:5930413E18 product:nuclear cap binding protein subunit 2, 20kDa, full insert sequence.
AK177380 - Mus musculus cDNA, clone:Y0G0102I24, strand:plus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000023460, based on BLAT search.
AK201155 - Mus musculus cDNA, clone:Y1G0137D17, strand:minus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000023460, based on BLAT search.
AK184640 - Mus musculus cDNA, clone:Y0G0130P15, strand:minus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000023460, based on BLAT search.
KY499685 - Mus musculus strain C57BL/6J hypothetical protein mRNA, complete cds.
KY499684 - Mus musculus strain C57BL/6J hypothetical protein mRNA, complete cds.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
mmu03013 - RNA transport
mmu03015 - mRNA surveillance pathway
mmu03040 - Spliceosome

Reactome (by CSHL, EBI, and GO)

Protein Q9CQ49 (Reactome details) participates in the following event(s):

R-MMU-77094 Formation of cap binding complex (CBC)
R-MMU-77095 Recognition and binding of the mRNA cap by the cap-binding complex
R-MMU-6814885 CBCAP complex binds 7-methylguanosine cap of snRNA
R-MMU-112381 Hyperphosphorylation (Ser2) of RNA Pol II CTD by P-TEFb complex
R-MMU-77586 Cleavage of the 3'-end of Replication Dependent Histone Pre-mRNA
R-MMU-77589 Recognition of AAUAAA sequence by CPSF
R-MMU-77592 Cleavage of Intronless Pre-mRNA at 3'-end
R-MMU-191825 Nuclear export of snRNA transcripts
R-MMU-72095 Internal Methylation of mRNA
R-MMU-112383 Hypophosphorylation of RNA Pol II CTD by FCP1P protein
R-MMU-75080 Formation of AT-AC A complex
R-MMU-72180 Cleavage of mRNA at the 3'-end
R-MMU-72185 mRNA polyadenylation
R-MMU-159101 NXF1:NXT1 (TAP:p15) binds capped mRNA:CBC:EJC:TREX (minus DDX39B)
R-MMU-77584 Binding of SLBP to Replication-Dependent Histone Pre-mRNA
R-MMU-111438 Recruitment of U7 snRNP:ZFP100 complex to the Histone Pre-mRNA
R-MMU-77593 Cleavage and polyadenylation of Intronless Pre-mRNA
R-MMU-111437 Cleavage of the 3'-end of the Histone Pre-mRNA
R-MMU-113407 DSIF complex binds to RNA Pol II (hypophosphorylated)
R-MMU-6803523 PTB and hnRNPA1 bind FGFR2 pre-mRNA to repress IIIb splicing and promote formation of FGFR2c mRNA
R-MMU-6803527 ESRP1 and 2 bind FGFR2 pre-mRNA to promote FGFR2b maturation and expression
R-MMU-77590 Recruitment of CstF to the CPSF Bound Pre-mRNA
R-MMU-75098 mRNP complex dissociates from cytosolic face of NPC
R-MMU-72127 Formation of the Spliceosomal B Complex
R-MMU-72139 Formation of the active Spliceosomal C (B*) complex
R-MMU-72143 Lariat Formation and 5'-Splice Site Cleavage
R-MMU-75081 Formation of AT-AC B Complex
R-MMU-75082 ATAC spliceosome mediated Lariat formation,5' splice site cleavage
R-MMU-156661 Formation of Exon Junction Complex
R-MMU-77585 Recruitment of U7 snRNP:ZFP100 complex to the SLBP Bound Pre-mRNA
R-MMU-113402 Formation of DSIF:NELF:early elongation complex
R-MMU-77591 Binding of Cleavage factors and Poly(A)Polymerase to the CstF:CPSF:Pre-mRNA Complex
R-MMU-113409 Abortive termination of early transcription elongation by DSIF:NELF
R-MMU-72086 mRNA Capping
R-MMU-6807505 RNA polymerase II transcribes snRNA genes
R-MMU-112382 Formation of RNA Pol II elongation complex
R-MMU-109688 Cleavage of Growing Transcript in the Termination Region
R-MMU-77588 SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs
R-MMU-77595 Processing of Intronless Pre-mRNAs
R-MMU-8953854 Metabolism of RNA
R-MMU-191859 snRNP Assembly
R-MMU-72203 Processing of Capped Intron-Containing Pre-mRNA
R-MMU-113418 Formation of the Early Elongation Complex
R-MMU-72165 mRNA Splicing - Minor Pathway
R-MMU-72187 mRNA 3'-end processing
R-MMU-159236 Transport of Mature mRNA derived from an Intron-Containing Transcript
R-MMU-111367 SLBP independent Processing of Histone Pre-mRNAs
R-MMU-6803529 FGFR2 alternative splicing
R-MMU-73857 RNA Polymerase II Transcription
R-MMU-75955 RNA Polymerase II Transcription Elongation
R-MMU-73856 RNA Polymerase II Transcription Termination
R-MMU-75067 Processing of Capped Intronless Pre-mRNA
R-MMU-975957 Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC)
R-MMU-194441 Metabolism of non-coding RNA
R-MMU-72163 mRNA Splicing - Major Pathway
R-MMU-72172 mRNA Splicing
R-MMU-72202 Transport of Mature Transcript to Cytoplasm
R-MMU-5654738 Signaling by FGFR2
R-MMU-74160 Gene expression (Transcription)
R-MMU-927802 Nonsense-Mediated Decay (NMD)
R-MMU-674695 RNA Polymerase II Pre-transcription Events
R-MMU-190236 Signaling by FGFR
R-MMU-9006934 Signaling by Receptor Tyrosine Kinases
R-MMU-162582 Signal Transduction

-  Other Names for This Gene
  Alternate Gene Symbols: Cbp20, NCBP2_MOUSE, NM_026554, NP_080830, Q0VF93, Q3UI86, Q9CQ49, uc007yxz.1
UCSC ID: uc007yxz.2
RefSeq Accession: NM_026554
Protein: Q9CQ49 (aka NCBP2_MOUSE)
CCDS: CCDS28110.1

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: NM_026554.4
exon count: 4CDS single in 3' UTR: no RNA size: 2054
ORF size: 471CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1142.00frame shift in genome: no % Coverage: 99.17
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.