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NCBP2 nuclear cap binding protein subunit 2 [ Homo sapiens (human) ]

Gene ID: 22916, updated on 5-Jul-2020

Summary

Official Symbol
NCBP2provided by HGNC
Official Full Name
nuclear cap binding protein subunit 2provided by HGNC
Primary source
HGNC:HGNC:7659
See related
Ensembl:ENSG00000114503 MIM:605133
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
CBC2; NIP1; CBP20; PIG55
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 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]
Expression
Ubiquitous expression in brain (RPKM 25.7), thyroid (RPKM 22.3) and 25 other tissues See more
Orthologs

Genomic context

See NCBP2 in Genome Data Viewer
Location:
3q29
Exon count:
5
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 3 NC_000003.12 (196932729..196942593, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (196662273..196669464, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene RNA, U4 small nuclear 89, pseudogene Neighboring gene p21 (RAC1) activated kinase 2 Neighboring gene RNA, U6 small nuclear 42, pseudogene Neighboring gene SUMO specific peptidase 5 Neighboring gene NCBP2 antisense RNA 1 Neighboring gene NCBP2 antisense 2 (head to head) Neighboring gene phosphatidylinositol glycan anchor biosynthesis class Z

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
RNA 7-methylguanosine cap binding IDA
Inferred from Direct Assay
more info
PubMed 
RNA 7-methylguanosine cap binding IMP
Inferred from Mutant Phenotype
more info
PubMed 
RNA binding HDA PubMed 
NOT RNA binding IDA
Inferred from Direct Assay
more info
PubMed 
RNA cap binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
RNA cap binding NAS
Non-traceable Author Statement
more info
PubMed 
mRNA binding IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
snRNA binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
7-methylguanosine mRNA capping TAS
Traceable Author Statement
more info
 
RNA export from nucleus TAS
Traceable Author Statement
more info
 
RNA metabolic process TAS
Traceable Author Statement
more info
 
RNA splicing ISS
Inferred from Sequence or Structural Similarity
more info
 
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 IDA
Inferred from Direct Assay
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 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 export from nucleus ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of mRNA 3'-end processing 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 translational initiation IDA
Inferred from Direct Assay
more info
PubMed 
snRNA export from nucleus ISS
Inferred from Sequence or Structural Similarity
more info
 
snRNA export from nucleus NAS
Non-traceable Author Statement
more info
PubMed 
snRNA transcription by RNA polymerase II TAS
Traceable Author Statement
more info
 
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 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytosol TAS
Traceable Author Statement
more info
 
mRNA cap binding complex IDA
Inferred from Direct Assay
more info
PubMed 
nuclear cap binding complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleoplasm IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
nucleus NAS
Non-traceable Author Statement
more info
PubMed 

General protein information

Preferred Names
nuclear cap-binding protein subunit 2
Names
20 kDa nuclear cap-binding protein
NCBP 20 kDa subunit
NCBP interacting protein 1
cell proliferation-inducing gene 55 protein
nuclear cap binding protein subunit 2, 20kD
nuclear cap binding protein subunit 2, 20kDa

NCBI Reference Sequences (RefSeq)

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)

  1. NM_001042540.1NP_001036005.1  nuclear cap-binding protein subunit 2 isoform 2

    See identical proteins and their annotated locations for NP_001036005.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. The encoded isoform (2) is shorter compared to isoform 1.
    Source sequence(s)
    AC011322, AW440347, BC001255, BP248419, CN421262
    Consensus CDS
    CCDS46986.1
    UniProtKB/Swiss-Prot
    P52298
    Related
    ENSP00000397619.2, ENST00000427641.2
    Conserved Domains (1) summary
    cl17169
    Location:4166
    RRM_SF; RNA recognition motif (RRM) superfamily
  2. NM_001308036.1NP_001294965.1  nuclear cap-binding protein subunit 2 isoform 3

    See identical proteins and their annotated locations for NP_001294965.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an alternate 5' exon and contains an alternate 5' terminal exon, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (3) has a shorter and distinct N-terminus, compared to isoform 1.
    Source sequence(s)
    AK297506, AW440347, BC001255, DC375323
    Consensus CDS
    CCDS77878.1
    UniProtKB/Swiss-Prot
    P52298
    Related
    ENSP00000412785.2, ENST00000452404.6
    Conserved Domains (1) summary
    cd12240
    Location:24101
    RRM_NCBP2; RNA recognition motif found in nuclear cap-binding protein subunit 2 (CBP20) and similar proteins
  3. NM_007362.5NP_031388.2  nuclear cap-binding protein subunit 2 isoform 1

    See identical proteins and their annotated locations for NP_031388.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AC011322
    Consensus CDS
    CCDS3323.1
    UniProtKB/Swiss-Prot
    P52298
    Related
    ENSP00000326806.5, ENST00000321256.10
    Conserved Domains (1) summary
    cd12240
    Location:42119
    RRM_NCBP2; RNA recognition motif found in nuclear cap-binding protein subunit 2 (CBP20) and similar proteins

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p13 Primary Assembly

    Range
    196932729..196942593 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011512556.3XP_011510858.1  nuclear cap-binding protein subunit 2 isoform X1

    See identical proteins and their annotated locations for XP_011510858.1

    UniProtKB/TrEMBL
    B3KSB0
    Related
    ENSP00000389315.1, ENST00000411704.1
    Conserved Domains (1) summary
    cd12240
    Location:149
    RRM_NCBP2; RNA recognition motif found in nuclear cap-binding protein subunit 2 (CBP20) and similar proteins
  2. XM_011512557.3XP_011510859.1  nuclear cap-binding protein subunit 2 isoform X1

    See identical proteins and their annotated locations for XP_011510859.1

    UniProtKB/TrEMBL
    B3KSB0
    Related
    ENSP00000413518.1, ENST00000447325.5
    Conserved Domains (1) summary
    cd12240
    Location:149
    RRM_NCBP2; RNA recognition motif found in nuclear cap-binding protein subunit 2 (CBP20) and similar proteins
  3. XM_011512558.3XP_011510860.1  nuclear cap-binding protein subunit 2 isoform X1

    See identical proteins and their annotated locations for XP_011510860.1

    UniProtKB/TrEMBL
    B3KSB0
    Related
    ENSP00000394105.1, ENST00000422610.5
    Conserved Domains (1) summary
    cd12240
    Location:149
    RRM_NCBP2; RNA recognition motif found in nuclear cap-binding protein subunit 2 (CBP20) and similar proteins
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