mutLBSgeneDB

mutLBSgeneDB
mutated Ligand Binding Site gene DataBase

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Gene Summary

Ligand Binding Site Mutation Information

Protein Structure Related Information

Gene Expression and Gene-Gene Network

Phenotype Information

Pharmacological Information

Conservation Information for LBS

Gene summary for NCBP1
Gene summary
Basic gene Info.Gene symbolNCBP1
Gene namenuclear cap binding protein subunit 1, 80kDa
SynonymsCBP80|NCBP|Sto1
CytomapUCSC genome browser: 9q34.1
Type of geneprotein-coding
RefGenesNM_002486.4,
Description80 kDa nuclear cap-binding proteinNCBP 80 kDa subunitnuclear cap binding protein subunit 1, 80kDnuclear cap-binding protein subunit 1
Modification date20141207
dbXrefs MIM : 600469
HGNC : HGNC
Ensembl : ENSG00000136937
HPRD : 02717
Vega : OTTHUMG00000020332
ProteinUniProt: Q09161
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_NCBP1
BioGPS: 4686
PathwayNCI Pathway Interaction Database: NCBP1
KEGG: NCBP1
REACTOME: NCBP1
Pathway Commons: NCBP1
ContextiHOP: NCBP1
ligand binding site mutation search in PubMed: NCBP1
UCL Cancer Institute: NCBP1
Assigned class in mutLBSgeneDBC: This gene just belongs to mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO IDGO TermPubMed ID
GO:0000184nuclear-transcribed mRNA catabolic process, nonsense-mediated decay11551508
GO:00063707-methylguanosine mRNA capping12434151
GO:0006379mRNA cleavage9342333
GO:0006446regulation of translational initiation11551508
GO:0031442positive regulation of mRNA 3'-end processing9342333


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Ligand binding site mutations for NCBP1
Lollipop-style diagram of mutations at LBS in amino-acid sequence.
We represented ligand binding site mutations only. (You can see big image via clicking.)
 
: non-synonymous mutation on LBS, Circle size denotes number of samples.

Cancer type specific mutLBS sorted by frequency
LBSAAchange of nsSNVCancer type# samples
Y761Q760HLUAD1
cf) Cancer type abbreviation. BLCA: Bladder urothelial carcinoma, BRCA: Breast invasive carcinoma, CESC: Cervical squamous cell carcinoma and endocervical adenocarcinoma, COAD: Colon adenocarcinoma, GBM: Glioblastoma multiforme, LGG: Brain lower grade glioma, HNSC: Head and neck squamous cell carcinoma, KICH: Kidney chromophobe, KIRC: Kidney renal clear cell carcinoma, KIRP: Kidney renal papillary cell carcinoma, LAML: Acute myeloid leukemia, LUAD: Lung adenocarcinoma, LUSC: Lung squamous cell carcinoma, OV: Ovarian serous cystadenocarcinoma, PAAD: Pancreatic adenocarcinoma, PRAD: Prostate adenocarcinoma, SKCM: Skin cutaneous melanoma, STAD: Stomach adenocarcinoma, THCA: Thyroid carcinoma, UCEC: Uterine corpus endometrial carcinoma.


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Protein structure related information for NCBP1
Relative protein structure stability change (ΔΔE) using Mupro 1.1
Mupro score denotes assessment of the effect of mutations on thermodynamic stability.
  (ΔΔE<0: mutation decreases stability, ΔΔE>0: mutation increases stability)
: nsSNV at non-LBS: nsSNV at LBS

nsSNVs sorted by the relative stability change of protein structure by each mutation
Blue: mutations of positive stability change. and red : the most recurrent mutation for this gene.
LBSAAchange of nsSNVRelative stability change
Y761Q760H-1.2705908
(MuPro1.1: Jianlin Cheng et al., Prediction of Protein Stability Changes for Single-Site Mutations Using Support Vector Machines, PROTEINS: Structure, Function, and Bioinformatics. 2006, 62:1125-1132)

Structure image for NCBP1 from PDB

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Differential gene expression and gene-gene network for NCBP1
Differential gene expression between mutated and non-mutated LBS samples in all 16 major cancer types

Differential co-expressed gene network based on protein-protein interaction data (CePIN)
* Left PPI network was created from samples with mutations in the LBS of NCBP1 and the right PPI network was created from samples without mutations in the LBS of NCBP1. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.


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Phenotype information for NCBP1
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type

Mutation level pathogenic information (ClinVar annotation)
Allele IDAA changeClinical significanceOriginPhenotype IDs

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Pharmacological information for NCBP1
Gene expression profile of anticancer drug treated cell-lines (CCLE)
Heatmap showing the correlation between gene expression and drug response across all the cell-lines. We chose the top 20 among 138 drugs.We used Pearson's correlation coefficient.
Drug information targeting mutLBSgene (Approved drugs only)
Drug statusDrugBank IDNameTypeDrug structure

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of NCBP1 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
MGMAGNESIUM(2+)1n52AY761


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Conservation information for LBS of NCBP1
Multiple alignments for Q09161 in multiple species
LBSAA sequence# speciesSpecies
K707AQSEQKNLFLV5Homo sapiens, Xenopus tropicalis, Gallus gallus, Mus musculus, Rattus norvegicus
K707ALSETEVLLLL1Arabidopsis thaliana
K707GLEESKELLRL1Oryza sativa subsp. japonica
K707NKEKLERMVT-1Caenorhabditis elegans
K707ANVNQKRLFLI1Drosophila melanogaster
K707AYVDQKRLFLI1Anopheles gambiae
T764QQYMVTLENLL4Homo sapiens, Xenopus tropicalis, Mus musculus, Rattus norvegicus
T764WPHMEKLESEV1Arabidopsis thaliana
T764WSHIAMLDQEI1Oryza sativa subsp. japonica
T764LKHSSNIADEV1Caenorhabditis elegans
T764QQYMVTFENLL1Gallus gallus
T764QKYSSTLETLL1Drosophila melanogaster
T764QKYSSTLESLL1Anopheles gambiae
V763IQQYMVTLENL4Homo sapiens, Xenopus tropicalis, Mus musculus, Rattus norvegicus
V763IWPHMEKLESE1Arabidopsis thaliana
V763IWSHIAMLDQE1Oryza sativa subsp. japonica
V763LLKHSSNIADE1Caenorhabditis elegans
V763IQQYMVTFENL1Gallus gallus
V763VQKYSSTLETL1Drosophila melanogaster
V763VQKYSSTLESL1Anopheles gambiae
Y761QIIQQYMVTLE3Homo sapiens, Xenopus tropicalis, Rattus norvegicus
Y761EQVQKYSSTLE2Drosophila melanogaster, Anopheles gambiae
Y761SEIWPHMEKLE1Arabidopsis thaliana
Y761TEIWSHIAMLD1Oryza sativa subsp. japonica
Y761ETLLKHSSNIA1Caenorhabditis elegans
Y761QIIQQYMVTFE1Gallus gallus
Y761QTIQQYMVTLE1Mus musculus


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