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mutLBSgeneDB |
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| Gene summary for NCBP2 |
 Gene summary |
| Basic gene Info. | Gene symbol | NCBP2 |
| Gene name | nuclear cap binding protein subunit 2, 20kDa | |
| Synonyms | CBC2|CBP20|NIP1 | |
| Cytomap | UCSC genome browser: 3q29 | |
| Type of gene | protein-coding | |
| RefGenes | NM_001042540.1, NM_007362.3, | |
| Description | 20 kDa nuclear cap-binding proteinNCBP 20 kDa subunitNCBP interacting protein 1NCBP-interacting protein 1cell proliferation-inducing gene 55 proteinnuclear cap binding protein subunit 2, 20kDnuclear cap-binding protein subunit 2 | |
| Modification date | 20141207 | |
| dbXrefs | MIM : 605133 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000114503 | ||
| HPRD : 05503 | ||
| Vega : OTTHUMG00000155520 | ||
| Protein | UniProt: P52298 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_NCBP2 | |
| BioGPS: 22916 | ||
| Pathway | NCI Pathway Interaction Database: NCBP2 | |
| KEGG: NCBP2 | ||
| REACTOME: NCBP2 | ||
| Pathway Commons: NCBP2 | ||
| Context | iHOP: NCBP2 | |
| ligand binding site mutation search in PubMed: NCBP2 | ||
| UCL Cancer Institute: NCBP2 | ||
| Assigned class in mutLBSgeneDB | C: This gene just belongs to mutLBSgenes. | |
| Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez |
| GO ID | GO Term | PubMed ID | GO:0000184 | nuclear-transcribed mRNA catabolic process, nonsense-mediated decay | 11551508 | GO:0006370 | 7-methylguanosine mRNA capping | 12434151 | GO:0006446 | regulation of translational initiation | 11551508 | GO:0045292 | mRNA cis splicing, via spliceosome | 18426921 |
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| Ligand binding site mutations for NCBP2 |
| 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. |
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| Cancer type specific mutLBS sorted by frequency |
| LBS | AAchange of nsSNV | Cancer type | # samples | R112 | I110M | HNSC | 1 | G126 | G126S | UCEC | 1 | R135 | R135W | UCEC | 1 |
| 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 NCBP2 |
| 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 |
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| 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. |
| LBS | AAchange of nsSNV | Relative stability change | R112 | I110M | -1.0039774 | G126 | G126S | -0.58422169 | R135 | R135W | -0.46808214 |
| (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 NCBP2 from PDB |
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| Differential gene expression and gene-gene network for NCBP2 |
| 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) |
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| Phenotype information for NCBP2 |
| Gene level disease information (DisGeNet) |
| Disease ID | Disease name | # PubMed | Association type |
| Mutation level pathogenic information (ClinVar annotation) |
| Allele ID | AA change | Clinical significance | Origin | Phenotype IDs |
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| Pharmacological information for NCBP2 |
| 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. |
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| Drug information targeting mutLBSgene (Approved drugs only) |
| Drug status | DrugBank ID | Name | Type | Drug structure |
| Gene-centered ligand-gene interaction network |
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| Ligands binding to mutated ligand binding site of NCBP2 go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | 7MG | 7N-METHYL-8-HYDROGUANOSINE-5'-MONOPHOSPHATE | 1h2t | Z | R112 | GTG | 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE | 1n52 | B | R112 | 7MG | 7N-METHYL-8-HYDROGUANOSINE-5'-MONOPHOSPHATE | 1h2u | X | R112 G126 R135 | 7MG | 7N-METHYL-8-HYDROGUANOSINE-5'-MONOPHOSPHATE | 1h2u | Y | R112 G126 R135 | GDP | GUANOSINE-5'-DIPHOSPHATE | 1h2t | Z | R135 | GDP | GUANOSINE-5'-DIPHOSPHATE | 1h2u | X | R135 | GDP | GUANOSINE-5'-DIPHOSPHATE | 1h2u | Y | R135 |
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| Conservation information for LBS of NCBP2 |
| Multiple alignments for P52298 in multiple species |
| LBS | AA sequence | # species | Species | D114 | RIIRTDWDAGF | 6 | Homo sapiens, Danio rerio, Bos taurus, Mus musculus, Rattus norvegicus, Xenopus tropicalis | D114 | RPIRVDFDWGF | 2 | Arabidopsis thaliana, Oryza sativa subsp. japonica | D116 | IRTDWDAGFKE | 6 | Homo sapiens, Danio rerio, Bos taurus, Mus musculus, Rattus norvegicus, Xenopus tropicalis | D116 | IRVDFDWGFQE | 1 | Arabidopsis thaliana | D116 | IRVDFDWGFEE | 1 | Oryza sativa subsp. japonica | D22 | LSQYRDQHFRG | 3 | Homo sapiens, Bos taurus, Xenopus tropicalis | D22 | LSEYRDQHFRG | 2 | Mus musculus, Rattus norvegicus | D22 | VSQYRDQHFKG | 1 | Danio rerio | D22 | LSAYRDRRFSG | 1 | Arabidopsis thaliana | D22 | LSAYRDRRFTG | 1 | Oryza sativa subsp. japonica | F83 | KTACGFCFVEY | 6 | Homo sapiens, Danio rerio, Bos taurus, Mus musculus, Rattus norvegicus, Xenopus tropicalis | F83 | KTPCGFCFVLF | 1 | Arabidopsis thaliana | F83 | KTPCGFCFILY | 1 | Oryza sativa subsp. japonica | G126 | EGRQYGRGRSG | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | G126 | EGRQYGRGKSG | 2 | Danio rerio, Xenopus tropicalis | G126 | EGRQWGRGRSG | 2 | Arabidopsis thaliana, Oryza sativa subsp. japonica | G128 | RQYGRGRSGGQ | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | G128 | RQYGRGKSGGQ | 2 | Danio rerio, Xenopus tropicalis | G128 | RQWGRGRSGGQ | 2 | Arabidopsis thaliana, Oryza sativa subsp. japonica | Q133 | GRSGGQVRDEY | 6 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus, Arabidopsis thaliana, Oryza sativa subsp. japonica | Q133 | GKSGGQVRDEY | 2 | Danio rerio, Xenopus tropicalis | R112 | DDRIIRTDWDA | 6 | Homo sapiens, Danio rerio, Bos taurus, Mus musculus, Rattus norvegicus, Xenopus tropicalis | R112 | DDRPIRVDFDW | 2 | Arabidopsis thaliana, Oryza sativa subsp. japonica | R123 | GFKEGRQYGRG | 6 | Homo sapiens, Danio rerio, Bos taurus, Mus musculus, Rattus norvegicus, Xenopus tropicalis | R123 | GFQEGRQWGRG | 1 | Arabidopsis thaliana | R123 | GFEEGRQWGRG | 1 | Oryza sativa subsp. japonica | R127 | GRQYGRGRSGG | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | R127 | GRQYGRGKSGG | 2 | Danio rerio, Xenopus tropicalis | R127 | GRQWGRGRSGG | 2 | Arabidopsis thaliana, Oryza sativa subsp. japonica | R135 | SGGQVRDEYRQ | 4 | Homo sapiens, Danio rerio, Bos taurus, Xenopus tropicalis | R135 | SGGQVRDEYRE | 2 | Mus musculus, Rattus norvegicus | R135 | SGGQVRDEYRT | 2 | Arabidopsis thaliana, Oryza sativa subsp. japonica | V134 | RSGGQVRDEYR | 6 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus, Arabidopsis thaliana, Oryza sativa subsp. japonica | V134 | KSGGQVRDEYR | 2 | Danio rerio, Xenopus tropicalis | W115 | IIRTDWDAGFK | 6 | Homo sapiens, Danio rerio, Bos taurus, Mus musculus, Rattus norvegicus, Xenopus tropicalis | W115 | PIRVDFDWGFQ | 1 | Arabidopsis thaliana | W115 | PIRVDFDWGFE | 1 | Oryza sativa subsp. japonica | Y125 | KEGRQYGRGRS | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | Y125 | KEGRQYGRGKS | 2 | Danio rerio, Xenopus tropicalis | Y125 | QEGRQWGRGRS | 1 | Arabidopsis thaliana | Y125 | EEGRQWGRGRS | 1 | Oryza sativa subsp. japonica | Y138 | QVRDEYRQDYD | 4 | Homo sapiens, Danio rerio, Bos taurus, Xenopus tropicalis | Y138 | QVRDEYREDYD | 2 | Mus musculus, Rattus norvegicus | Y138 | QVRDEYRTDYD | 2 | Arabidopsis thaliana, Oryza sativa subsp. japonica | Y20 | VELSQYRDQHF | 3 | Homo sapiens, Bos taurus, Xenopus tropicalis | Y20 | VELSEYRDQHF | 2 | Mus musculus, Rattus norvegicus | Y20 | VDVSQYRDQHF | 1 | Danio rerio | Y20 | AKLSAYRDRRF | 1 | Arabidopsis thaliana | Y20 | TKLSAYRDRRF | 1 | Oryza sativa subsp. japonica | Y43 | KSCTLYVGNLS | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | Y43 | QSATLYVGNLS | 1 | Danio rerio | Y43 | HSCTLYVGNLS | 1 | Xenopus tropicalis | Y43 | ASTTVYIGNVS | 1 | Arabidopsis thaliana | Y43 | ASVTVYVGNMS | 1 | Oryza sativa subsp. japonica |
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