Human Gene NCBP2 (ENST00000452404.6) Description and Page Index
  Description: Homo sapiens nuclear cap binding protein subunit 2 (NCBP2), transcript variant 3, mRNA. (from RefSeq NM_001308036)
RefSeq Summary (NM_001308036): 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].
Gencode Transcript: ENST00000452404.6
Gencode Gene: ENSG00000114503.11
Transcript (Including UTRs)
   Position: hg38 chr3:196,936,777-196,942,440 Size: 5,664 Total Exon Count: 4 Strand: -
Coding Region
   Position: hg38 chr3:196,937,011-196,941,958 Size: 4,948 Coding Exon Count: 4 

Page IndexSequence and LinksUniProtKB CommentsCTDRNA-Seq ExpressionMicroarray Expression
RNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA DescriptionsPathways
Other NamesMethods
Data last updated: 2019-09-04

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr3:196,936,777-196,942,440)mRNA (may differ from genome)Protein (138 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsHGNC
ReactomeStanford 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=Cell proliferation-inducing gene 55 protein; AltName: Full=NCBP 20 kDa subunit; Short=CBP20; AltName: Full=NCBP-interacting protein 1; Short=NIP1;
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. Found in a U snRNA export complex with RNUXA/PHAX, NCBP1/CBP80, NCBP2/CBP20, RAN, XPO1 and m7G-capped RNA. Interaction with RNUXA/PHAX. 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.
INTERACTION: Q09161:NCBP1; NbExp=5; IntAct=EBI-464729, EBI-464743;
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR.
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

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 42.52 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 922.92 RPKM

View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -210.80482-0.437 Picture PostScript Text
3' UTR -53.90234-0.230 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)

Protein Data Bank (PDB) 3-D Structure
MuPIT help

- X-ray MuPIT

- X-ray MuPIT

- X-ray MuPIT
To conserve bandwidth, only the images from the first 3 structures are shown.
1H6K - X-ray MuPIT 1N52 - X-ray MuPIT 1N54 - X-ray MuPIT
3FEX - X-ray MuPIT 3FEY - X-ray MuPIT

ModBase Predicted Comparative 3D Structure on P52298
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.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserNo orthologNo orthologNo orthologNo orthologGenome Browser
Gene Details    Gene Details
Gene Sorter    Gene Sorter
Protein Sequence    Protein Sequence
Alignment    Alignment

-  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:0003723 RNA binding
GO:0003729 mRNA binding
GO:0005515 protein binding
GO:0017069 snRNA binding

Biological Process:
GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay
GO:0000398 mRNA splicing, via spliceosome
GO:0006366 transcription from RNA polymerase II promoter
GO:0006368 transcription elongation from RNA polymerase II promoter
GO:0006369 termination of RNA polymerase II transcription
GO:0006370 7-methylguanosine mRNA capping
GO:0006397 mRNA processing
GO:0006405 RNA export from nucleus
GO:0006406 mRNA export from nucleus
GO:0006408 snRNA export from nucleus
GO:0006417 regulation of translation
GO:0006446 regulation of translational initiation
GO:0008334 histone mRNA metabolic process
GO:0008380 RNA splicing
GO:0008543 fibroblast growth factor receptor signaling pathway
GO:0016070 RNA metabolic process
GO:0031047 gene silencing by RNA
GO:0031124 mRNA 3'-end processing
GO:0031442 positive regulation of mRNA 3'-end processing
GO:0042795 snRNA transcription from RNA polymerase II promoter
GO:0045292 mRNA cis splicing, via spliceosome
GO:0046833 positive regulation of RNA export from nucleus
GO:0051028 mRNA transport
GO:0051168 nuclear export
GO:0098789 pre-mRNA cleavage required for polyadenylation
GO:1900363 regulation of mRNA polyadenylation

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005845 mRNA cap binding complex
GO:0005846 nuclear cap binding complex
GO:0034518 RNA cap binding complex

-  Descriptions from all associated GenBank mRNAs
  AK093216 - Homo sapiens cDNA FLJ35897 fis, clone TESTI2009502, highly similar to Nuclear cap-binding protein subunit 2.
BC001255 - Homo sapiens nuclear cap binding protein subunit 2, 20kDa, mRNA (cDNA clone MGC:4991 IMAGE:3458927), complete cds.
BX537372 - Homo sapiens mRNA; cDNA DKFZp686G18222 (from clone DKFZp686G18222).
BX647994 - Homo sapiens mRNA; cDNA DKFZp686P0552 (from clone DKFZp686P0552).
AK315903 - Homo sapiens cDNA, FLJ78802 complete cds, highly similar to Nuclear cap-binding protein subunit 2.
AK296144 - Homo sapiens cDNA FLJ52508 complete cds, highly similar to Nuclear cap-binding protein subunit 2.
AK308192 - Homo sapiens cDNA, FLJ98140.
AK297506 - Homo sapiens cDNA FLJ52517 complete cds, highly similar to Nuclear cap-binding protein subunit 2.
D59253 - Homo sapiens mRNA for NCBP interacting protein 1, complete cds.
X84157 - H.sapiens mRNA for CBP20.
AY644767 - Homo sapiens cell proliferation-inducing gene 55 mRNA, complete cds.
JD338367 - Sequence 319391 from Patent EP1572962.
AK316601 - Homo sapiens cDNA, FLJ96704, Homo sapiens nuclear cap binding protein subunit 2, 20kDa (NCBP2), mRNA.
CU674628 - Synthetic construct Homo sapiens gateway clone IMAGE:100020612 5' read NCBP2 mRNA.
BT006842 - Homo sapiens nuclear cap binding protein subunit 2, 20kDa mRNA, complete cds.
DQ890703 - Synthetic construct clone IMAGE:100003333; FLH165300.01X; RZPDo839A08160D nuclear cap binding protein subunit 2, 20kDa (NCBP2) gene, encodes complete protein.
DQ893887 - Synthetic construct Homo sapiens clone IMAGE:100008347; FLH165296.01L; RZPDo839A08159D nuclear cap binding protein subunit 2, 20kDa (NCBP2) gene, encodes complete protein.
AB528874 - Synthetic construct DNA, clone: pF1KE0603, Homo sapiens NCBP2 gene for nuclear cap binding protein subunit 2, 20kDa, without stop codon, in Flexi system.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa03040 - Spliceosome

Reactome (by CSHL, EBI, and GO)

Protein P52298 (Reactome details) participates in the following event(s):

R-HSA-77094 Formation of cap binding complex (CBC)
R-HSA-77587 Docking of Mature Replication Dependent Histone mRNA with the NPC
R-HSA-77095 Recognition and binding of the mRNA cap by the cap-binding complex
R-HSA-167089 Recognition and binding of the HIV-1 mRNA cap by the cap-binding complex
R-HSA-6814885 CBCAP complex binds 7-methylguanosine cap of snRNA
R-HSA-77594 Docking of the Mature intronless derived transcript derived mRNA, TAP and Aly/Ref at the NPC
R-HSA-111439 Docking of Mature Histone mRNA complex:TAP at the NPC
R-HSA-112381 Hyperphosphorylation (Ser2) of RNA Pol II CTD by P-TEFb complex
R-HSA-167084 Hyperphosphorylation (Ser2) of RNA Pol II CTD by P-TEFb complex
R-HSA-167191 Hyperphosphorylation (Ser2) of RNA Pol II CTD by the P-TEFb(Cyclin T1:Cdk9) complex
R-HSA-77586 Cleavage of the 3'-end of Replication Dependent Histone Pre-mRNA
R-HSA-77589 Recognition of AAUAAA sequence by CPSF
R-HSA-77592 Cleavage of Intronless Pre-mRNA at 3'-end
R-HSA-191825 Nuclear export of snRNA transcripts
R-HSA-72103 Formation of pre-mRNPs
R-HSA-75080 Formation of AT-AC A complex
R-HSA-72095 Internal Methylation of mRNA
R-HSA-8849157 TREX complex binds spliced, capped mRNA:CBC:EJC cotranscriptionally
R-HSA-72185 mRNA polyadenylation
R-HSA-72180 Cleavage of mRNA at the 3'-end
R-HSA-112383 Hypophosphorylation of RNA Pol II CTD by FCP1P protein
R-HSA-77584 Binding of SLBP to Replication-Dependent Histone Pre-mRNA
R-HSA-111438 Recruitment of U7 snRNP:ZFP100 complex to the Histone Pre-mRNA
R-HSA-77593 Cleavage and polyadenylation of Intronless Pre-mRNA
R-HSA-113407 DSIF complex binds to RNA Pol II (hypophosphorylated)
R-HSA-75096 Docking of the TAP:EJC Complex with the NPC
R-HSA-159101 NXF1:NXT1 (TAP:p15) binds capped mRNA:CBC:EJC:TREX (minus DDX39B)
R-HSA-111437 Cleavage of the 3'-end of the Histone Pre-mRNA
R-HSA-167072 Hypophosphorylation of RNA Pol II CTD by FCP1P protein
R-HSA-167083 DSIF complex binds to RNA Pol II (hypophosphorylated)
R-HSA-6803523 PTB and hnRNPA1 bind FGFR2 pre-mRNA to repress IIIb splicing and promote formation of FGFR2c mRNA
R-HSA-6803527 ESRP1 and 2 bind FGFR2 pre-mRNA to promote FGFR2b maturation and expression
R-HSA-77590 Recruitment of CstF to the CPSF Bound Pre-mRNA
R-HSA-75098 mRNP complex dissociates from cytosolic face of NPC
R-HSA-72107 Formation of the Spliceosomal E complex
R-HSA-72143 Lariat Formation and 5'-Splice Site Cleavage
R-HSA-72139 Formation of the active Spliceosomal C (B*) complex
R-HSA-72124 Formation of the Spliceosomal A Complex
R-HSA-72127 Formation of the Spliceosomal B Complex
R-HSA-72130 Formation of an intermediate Spliceosomal C (Bact) complex
R-HSA-75081 Formation of AT-AC B Complex
R-HSA-75082 ATAC spliceosome mediated Lariat formation,5' splice site cleavage
R-HSA-75079 Formation of AT-AC C complex
R-HSA-75083 ATAC spliceosome mediated 3' splice site cleavage, exon ligation
R-HSA-156661 Formation of Exon Junction Complex
R-HSA-77585 Recruitment of U7 snRNP:ZFP100 complex to the SLBP Bound Pre-mRNA
R-HSA-113402 Formation of DSIF:NELF:early elongation complex
R-HSA-167085 Formation of DSIF:NELF:HIV-1 early elongation complex
R-HSA-77591 Binding of Cleavage factors and Poly(A)Polymerase to the CstF:CPSF:Pre-mRNA Complex
R-HSA-927832 UPF1 binds an mRNP with a termination codon preceding an Exon Junction Complex
R-HSA-927789 Formation of UPF1:eRF3 complex on mRNA with a premature termination codon and no Exon Junction Complex
R-HSA-113409 Abortive termination of early transcription elongation by DSIF:NELF
R-HSA-167087 Limited elongation of the HIV-1 transcript
R-HSA-167478 Abortive termination of HIV-1 early transcription elongation by DSIF:NELF
R-HSA-167147 Separation of abortive HIV-1 transcript from template
R-HSA-927889 SMG1 phosphorylates UPF1 (enhanced by Exon Junction Complex)
R-HSA-72086 mRNA Capping
R-HSA-159230 Transport of the SLBP Dependant Mature mRNA
R-HSA-167158 Formation of the HIV-1 Early Elongation Complex
R-HSA-6807505 RNA polymerase II transcribes snRNA genes
R-HSA-159231 Transport of Mature mRNA Derived from an Intronless Transcript
R-HSA-159227 Transport of the SLBP independent Mature mRNA
R-HSA-112382 Formation of RNA Pol II elongation complex
R-HSA-167152 Formation of HIV elongation complex in the absence of HIV Tat
R-HSA-167200 Formation of HIV-1 elongation complex containing HIV-1 Tat
R-HSA-77588 SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs
R-HSA-109688 Cleavage of Growing Transcript in the Termination Region
R-HSA-77595 Processing of Intronless Pre-mRNAs
R-HSA-8953854 Metabolism of RNA
R-HSA-159234 Transport of Mature mRNAs Derived from Intronless Transcripts
R-HSA-9010553 Regulation of expression of SLITs and ROBOs
R-HSA-191859 snRNP Assembly
R-HSA-975957 Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC)
R-HSA-72203 Processing of Capped Intron-Containing Pre-mRNA
R-HSA-72165 mRNA Splicing - Minor Pathway
R-HSA-72187 mRNA 3'-end processing
R-HSA-72163 mRNA Splicing - Major Pathway
R-HSA-113418 Formation of the Early Elongation Complex
R-HSA-111367 SLBP independent Processing of Histone Pre-mRNAs
R-HSA-159236 Transport of Mature mRNA derived from an Intron-Containing Transcript
R-HSA-6803529 FGFR2 alternative splicing
R-HSA-8851708 Signaling by FGFR2 IIIa TM
R-HSA-167169 HIV Transcription Elongation
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-75955 RNA Polymerase II Transcription Elongation
R-HSA-167172 Transcription of the HIV genome
R-HSA-167246 Tat-mediated elongation of the HIV-1 transcript
R-HSA-75067 Processing of Capped Intronless Pre-mRNA
R-HSA-73856 RNA Polymerase II Transcription Termination
R-HSA-72202 Transport of Mature Transcript to Cytoplasm
R-HSA-376176 Signaling by ROBO receptors
R-HSA-194441 Metabolism of non-coding RNA
R-HSA-927802 Nonsense-Mediated Decay (NMD)
R-HSA-72172 mRNA Splicing
R-HSA-5654738 Signaling by FGFR2
R-HSA-1839126 FGFR2 mutant receptor activation
R-HSA-74160 Gene expression (Transcription)
R-HSA-162599 Late Phase of HIV Life Cycle
R-HSA-975956 Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)
R-HSA-422475 Axon guidance
R-HSA-674695 RNA Polymerase II Pre-transcription Events
R-HSA-167242 Abortive elongation of HIV-1 transcript in the absence of Tat
R-HSA-190236 Signaling by FGFR
R-HSA-5655253 Signaling by FGFR2 in disease
R-HSA-162587 HIV Life Cycle
R-HSA-1266738 Developmental Biology
R-HSA-9006934 Signaling by Receptor Tyrosine Kinases
R-HSA-1226099 Signaling by FGFR in disease
R-HSA-162906 HIV Infection
R-HSA-162582 Signal Transduction
R-HSA-5663202 Diseases of signal transduction
R-HSA-5663205 Infectious disease
R-HSA-1643685 Disease

-  Other Names for This Gene
  Alternate Gene Symbols: B2RE91, B4DMK7, CBP20, NCBP2_HUMAN, NM_001308036, P52298, PIG55, Q14924, Q2TS50, uc011btz.1, uc011btz.2
UCSC ID: uc011btz.2
RefSeq Accession: NM_001308036
Protein: P52298 (aka NCBP2_HUMAN)
CCDS: CCDS77878.1

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