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NIN ninein (GSK3B interacting protein)

Written2004-09José Luis Vizmanos
Departamento de Genética, Facultad de Ciencias, Universidad de Navarra, 31008 Pamplona, Navarra, Espana

(Note : for Links provided by Atlas : click)

Identity

Alias_namesninein (GSK3B interacting protein)
Other aliasGSK3B-interacting protein
Glycogen synthase kinase 3 beta-interacting protein
KIAA1565
Ninein centrosomal protein.
HGNC (Hugo) NIN
LocusID (NCBI) 51199
Atlas_Id 176
Location 14q22.1  [Link to chromosome band 14q22]
Location_base_pair Starts at 50725829 and ends at 50831121 bp from pter ( according to hg19-Feb_2009)  [Mapping NIN.png]
Local_order SAV1 (SAlvador homolog 1 Drosophila) is more centromeric.
C14orf29 (Chromosome 14 Open Reading Frame 29) is more telomeric.
 
  Genomic structure of NIN. Black boxes indicate exons.
Fusion genes
(updated 2017)		Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
GTPBP4 (10p15.3) / NIN (14q22.1)MAP4K5 (14q21.3) / NIN (14q22.1)MAP4K5 (14q22.1) / NIN (14q22.1)
NIN (14q22.1) / ABHD12B (14q22.1)NIN (14q22.1) / DOK3 (5q35.3)NIN (14q22.1) / NIN (14q22.1)
NIN (14q22.1) / PDGFRB (5q32)NIN (14q22.1) / TAGLN (11q23.3)NIN (14q22.1) / TMX1 (14q22.1)
NIN (14q22.1) / TOGARAM1 (14q21.2)PDGFRB (5q32) / NIN (14q22.1)TAGLN (11q23.3) / NIN (14q22.1)

DNA/RNA

Description 31 exons spanning 111.3 Kb on 14q22.1. Transcription is from telomere to centromere.
Transcription 5 alternative transcripts:
  • Variant 2 encodes de longest isoform
  • Variant 1 contains a different 3' terminal region and the resulting protein has a distinct and shorter C-terminus.
  • Variant 3 contains also a different 3' terminal region and it encodes isoform 3 , with a shorter and distinct C-terminus than variant 2.
  • Variant 4 differs in the 5' and 3' UTRs, and has multiple differences in the coding region. The resulting isoform 4 contains an additional internal segment, when compared to isoform 2, has a longer and distinct N-terminus, and has a shorter and distinct C-terminus.
  • Variant 5 has multiple differences in the coding region and 3' UTR, the resulting isoform 5 contains an additional internal segment and has a distinct and shorter C-terminus. Isoform 5 has also been referred to as hNinein-Lm.

    4 alternative transcripts in EnsEMBL 1:

  • Q9HCK7 corresponding to RefSeq variant 4.
  • NIN corresponding to RefSeq variant 5.
  • NIN corresponding to RefSeq variant 4.
  • NM_182944 corresponding to RefSeq variant 1.

    • Protein

    Note Ninein (GSK3B interacting protein)
     
      Schematic representation of NIN. LZ: leuzine-zipper domain. Coiled-coil domains are indicated with asterisks.
    Description Homooligomer. Interacts with GSK3B (GSK3-beta) via its C-terminus domain, ait also interacts with C14ORF166 preventing its phosphorylation by GSK3-beta. NIN is a component of the core centrosome. Arranged in a tubular conformation with an open and a closed end within the centrosome. In the mother centrosome, it localizes at both ends of the centrosome tube, including the site of centrosome duplication, while in the daughter centrosome it is present only at the closed end. Requires PCM1 for centrosome localization. In interphase cells, it is localized in the centrosome. Decreases in metaphase and anaphase and reappears in telophase.
    Expression Ubiquitous. Highly expressed in heart and skeletal muscle.
    Localisation Centrosome.
    Function The centrosome is the major microtubulin-organizing center (MTOC) in most vertebrate cells. In a typical somatic cell, the centrosome is composed of a pair of centrioles surrounded by a mass of amorphous pericentriolar material (PCM) that may be involved in the complex of Y-tubulin, centrin, pericentrin and ninein. This protein play an important role as a microtubule minus-end capping, centriole position, anchoring factor and as a centrosome maturation factor. Localization of this protein to the centrosome requires three of its four leucine zippers in the central coiled-coil domain. In addition it has been suggested that ninein could play a role to ensure equal chromosome segregation prior to telophase/cytokinesis in the division cycle.
    Homology It presents homology in various species. It also belongs to ENSF00000001557 protein family.

    Mutations

    Somatic t(5;14)(q33;q24) 5' NIN-PDGFRB 3' fusion in a chronic myeloprolifetrative disorder with eosinophilia

    Implicated in

    Note
      
    Entity t(5;14)(q33;q24) , 5q33 myeloproliferative disease.
    Disease Chronic myeloproliferative disorder with eosinophilia and skin lesions ( "Atypical CML").
    Prognosis Good. Relative mild disease course over at least 13 years. Imatinib mesylate responsive disease.
    Cytogenetics t(5;14)(q33;q24)
    Hybrid/Mutated Gene 5' NIN-PDGFRB 3'
    Abnormal Protein NIN-PDGFRB
     
    Schematic representation of the fusion NIN-PDGFRB consecuence of the t(5;14)(q33;q24) in a chronic myeloprolifetrative disorder with eosinophilia. From up to down: PDGFRB, NIN and the putative chimeric NIN-PDGFRB structure. TM, transmembrane domain; TK, tyrosine kinase domain; LZ, leuzine-zipper domain. Coiled coil domains on NIN and NIN-PDGFRB are indicated with asterisks.
      

    Bibliography

    Molecular characterisation of ninein, a new coiled-coil protein of the centrosome.
    Bouckson-Castaing V, Moudjou M, Ferguson DJ, Mucklow S, Belkaid Y, Milon G, Crocker PR
    Journal of cell science. 1996 ; 109 ( Pt 1) : 179-190.
    PMID 8834802
     
    Molecular characterization of human ninein protein: two distinct subdomains required for centrosomal targeting and regulating signals in cell cycle.
    Chen CH, Howng SL, Cheng TS, Chou MH, Huang CY, Hong YR
    Biochemical and biophysical research communications. 2003 ; 308 (4) : 975-983.
    PMID 12927815
     
    Assembly of centrosomal proteins and microtubule organization depends on PCM-1.
    Dammermann A, Merdes A
    The Journal of cell biology. 2002 ; 159 (2) : 255-266.
    PMID 12403812
     
    Re-evaluating centrosome function.
    Doxsey S
    Nature reviews. Molecular cell biology. 2001 ; 2 (9) : 688-698.
    PMID 11533726
     
    Pericentrin, a highly conserved centrosome protein involved in microtubule organization.
    Doxsey SJ, Stein P, Evans L, Calarco PD, Kirschner M
    Cell. 1994 ; 76 (4) : 639-650.
    PMID 8124707
     
    Genomic organization and molecular characterization of the human ninein gene.
    Hong YR, Chen CH, Chuo MH, Liou SY, Howng SL
    Biochemical and biophysical research communications. 2000 ; 279 (3) : 989-995.
    PMID 11162463
     
    A novel ninein-interaction protein, CGI-99, blocks ninein phosphorylation by GSK3beta and is highly expressed in brain tumors.
    Howng SL, Hsu HC, Cheng TS, Lee YL, Chang LK, Lu PJ, Hong YR
    FEBS letters. 2004 ; 566 (1-3) : 162-168.
    PMID 15147888
     
    Microtubule minus-end anchorage at centrosomal and non-centrosomal sites: the role of ninein.
    Mogensen MM, Malik A, Piel M, Bouckson-Castaing V, Bornens M
    Journal of cell science. 2000 ; 113 ( Pt 17) : 3013-3023.
    PMID 10934040
     
    A subset of centrosomal proteins are arranged in a tubular conformation that is reproduced during centrosome duplication.
    Ou Y, Rattner JB
    Cell motility and the cytoskeleton. 2000 ; 47 (1) : 13-24.
    PMID 11002307
     
    CEP110 and ninein are located in a specific domain of the centrosome associated with centrosome maturation.
    Ou YY, Mack GJ, Zhang M, Rattner JB
    Journal of cell science. 2002 ; 115 (Pt 9) : 1825-1835.
    PMID 11956314
     
    Human ninein is a centrosomal autoantigen recognized by CREST patient sera and plays a regulatory role in microtubule nucleation.
    Stillwell EE, Zhou J, Joshi HC
    Cell cycle (Georgetown, Tex.). 2004 ; 3 (7) : 923-930.
    PMID 15190203
     
    NIN, a gene encoding a CEP110-like centrosomal protein, is fused to PDGFRB in a patient with a t(5;14)(q33;q24) and an imatinib-responsive myeloproliferative disorder.
    Vizmanos JL, Novo FJ, Rom´n JP, Baxter EJ, Lahortiga I, Larr´yoz MJ, Odero MD, Giraldo P, Calasanz MJ, Cross NC
    Cancer research. 2004 ; 64 (8) : 2673-2676.
    PMID 15087377
     

    Citation

    This paper should be referenced as such :
    Vizmanos, JL
    NIN (ninein (GSK3B interacting protein))
    Atlas Genet Cytogenet Oncol Haematol. 2004;8(4):300-302.
    Free journal version : [ pdf ]   [ DOI ]
    On line version : http://AtlasGeneticsOncology.org/Genes/NINID176.html

    Other Leukemias implicated (Data extracted from papers in the Atlas) [ 3 ]
      t(5;14)(q33;q24) NIN/PDGFRB
    t(14;14)(q22;q22) NIN/TMX1
    t(14;14)(q22;q32) NIN/UNC79

    Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 1 ]
      MAP4K5/NIN (14q22)

    External links

    Nomenclature
    HGNC (Hugo)NIN   14906
    Cards
    AtlasNINID176
    Entrez_Gene (NCBI)NIN  51199  ninein
    AliasesSCKL7
    GeneCards (Weizmann)NIN
    Ensembl hg19 (Hinxton)ENSG00000100503 [Gene_View]
    Ensembl hg38 (Hinxton)ENSG00000100503 [Gene_View]  ENSG00000100503 [Sequence]  chr14:50725829-50831121 [Contig_View]  NIN [Vega]
    ICGC DataPortalENSG00000100503
    TCGA cBioPortalNIN
    AceView (NCBI)NIN
    Genatlas (Paris)NIN
    WikiGenes51199
    SOURCE (Princeton)NIN
    Genetics Home Reference (NIH)NIN
    Genomic and cartography
    GoldenPath hg38 (UCSC)NIN  -     chr14:50725829-50831121 -  14q22.1   [Description]    (hg38-Dec_2013)
    GoldenPath hg19 (UCSC)NIN  -     14q22.1   [Description]    (hg19-Feb_2009)
    GoldenPathNIN - 14q22.1 [CytoView hg19]  NIN - 14q22.1 [CytoView hg38]
    ImmunoBaseENSG00000100503
    Mapping of homologs : NCBININ [Mapview hg19]  NIN [Mapview hg38]
    OMIM608684   614851   
    Gene and transcription
    Genbank (Entrez)AA742651 AB046785 AF186776 AF212162 AF223937
    RefSeq transcript (Entrez)NM_016350 NM_020921 NM_182944 NM_182945 NM_182946
    RefSeq genomic (Entrez)
    Consensus coding sequences : CCDS (NCBI)NIN
    Cluster EST : UnigeneHs.569387 [ NCBI ]
    CGAP (NCI)Hs.569387
    Alternative Splicing GalleryENSG00000100503
    Gene ExpressionNIN [ NCBI-GEO ]   NIN [ EBI - ARRAY_EXPRESS ]   NIN [ SEEK ]   NIN [ MEM ]
    Gene Expression Viewer (FireBrowse)NIN [ Firebrowse - Broad ]
    SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
    GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
    BioGPS (Tissue expression)51199
    GTEX Portal (Tissue expression)NIN
    Human Protein AtlasENSG00000100503-NIN [pathology]   [cell]   [tissue]
    Protein : pattern, domain, 3D structure
    UniProt/SwissProtQ8N4C6   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
    NextProtQ8N4C6  [Sequence]  [Exons]  [Medical]  [Publications]
    With graphics : InterProQ8N4C6
    Splice isoforms : SwissVarQ8N4C6
    PhosPhoSitePlusQ8N4C6
    Domaine pattern : Prosite (Expaxy)EF_HAND_2 (PS50222)   
    Domains : Interpro (EBI)EF-hand-dom_pair    EF_hand_dom    NIN   
    Domain families : Pfam (Sanger)
    Domain families : Pfam (NCBI)
    Conserved Domain (NCBI)NIN
    DMDM Disease mutations51199
    Blocks (Seattle)NIN
    SuperfamilyQ8N4C6
    Human Protein Atlas [tissue]ENSG00000100503-NIN [tissue]
    Peptide AtlasQ8N4C6
    HPRD09785
    IPIIPI00441952   IPI00171791   IPI00329695   IPI00921003   IPI00441955   IPI00441959   IPI00971005   IPI00984029   IPI00441960   IPI00982681   IPI00883941   IPI00978213   
    Protein Interaction databases
    DIP (DOE-UCLA)Q8N4C6
    IntAct (EBI)Q8N4C6
    FunCoupENSG00000100503
    BioGRIDNIN
    STRING (EMBL)NIN
    ZODIACNIN
    Ontologies - Pathways
    QuickGOQ8N4C6
    Ontology : AmiGOpericentriolar material  pericentriolar material  spindle pole  calcium ion binding  protein binding  GTP binding  nucleus  nucleolus  centrosome  centrosome  centriole  centriole  plasma membrane  protein localization  centriole-centriole cohesion  kinase binding  corpus callosum morphogenesis  corticospinal tract morphogenesis  dendrite  positive regulation of microtubule polymerization  microtubule anchoring at centrosome  microtubule anchoring at centrosome  microtubule minus-end  axonal growth cone  apical part of cell  collateral sprouting  positive regulation of axonogenesis  centrosome localization  centrosome localization  mitotic spindle  centrosome-templated microtubule nucleation  mitotic spindle pole  ciliary transition fiber  centriolar subdistal appendage  
    Ontology : EGO-EBIpericentriolar material  pericentriolar material  spindle pole  calcium ion binding  protein binding  GTP binding  nucleus  nucleolus  centrosome  centrosome  centriole  centriole  plasma membrane  protein localization  centriole-centriole cohesion  kinase binding  corpus callosum morphogenesis  corticospinal tract morphogenesis  dendrite  positive regulation of microtubule polymerization  microtubule anchoring at centrosome  microtubule anchoring at centrosome  microtubule minus-end  axonal growth cone  apical part of cell  collateral sprouting  positive regulation of axonogenesis  centrosome localization  centrosome localization  mitotic spindle  centrosome-templated microtubule nucleation  mitotic spindle pole  ciliary transition fiber  centriolar subdistal appendage  
    NDEx NetworkNIN
    Atlas of Cancer Signalling NetworkNIN
    Wikipedia pathwaysNIN
    Orthology - Evolution
    OrthoDB51199
    GeneTree (enSembl)ENSG00000100503
    Phylogenetic Trees/Animal Genes : TreeFamNIN
    HOGENOMQ8N4C6
    Homologs : HomoloGeneNIN
    Homology/Alignments : Family Browser (UCSC)NIN
    Gene fusions - Rearrangements
    Fusion : MitelmanMAP4K5/NIN [14q21.3/14q22.1]  [t(14;14)(q22;q22)]  
    Fusion : MitelmanNIN/FAM179B [14q22.1/14q21.2]  [t(14;14)(q21;q22)]  
    Fusion : MitelmanNIN/PDGFRB [14q22.1/5q32]  [t(5;14)(q32;q22)]  
    Fusion PortalMAP4K5 14q21.3 NIN 14q22.1 BRCA
    Fusion PortalNIN 14q22.1 FAM179B 14q21.2 BRCA
    Fusion : TICdbNIN [14q22.1]  -  PDGFRB [5q32]
    Fusion : FusionGDB15677    20913    24363    24364    24365    24366    24367    24368    24369    24370    24371    37148   
    Fusion : Fusion_HubETV6--NIN    FRYL--NIN    GTPBP4--NIN    MAP4K5--NIN    NIN--ABHD12B    NIN--ATP5S    NIN--CABLES1    NIN--DOK3    NIN--FAM179B    NIN--GCA    NIN--GNG2    NIN--HERC4    NIN--IDE    NIN--JAK1    NIN--KLC1   
    NIN--MRPL52    NIN--NIN    NIN--PDGFRB    NIN--PMEL    NIN--RBX1    NIN--SAV1    NIN--SF1    NIN--SNRPN    NIN--SNURF    NIN--STXBP6    NIN--TAGLN    NIN--TG    NIN--WDR20    NIN--ZMYND11    PDGFRB--NIN   
    PGS1--NIN    TAGLN--NIN   
    Fusion : QuiverNIN
    Polymorphisms : SNP and Copy number variants
    NCBI Variation ViewerNIN [hg38]
    dbSNP Single Nucleotide Polymorphism (NCBI)NIN
    dbVarNIN
    ClinVarNIN
    1000_GenomesNIN 
    Exome Variant ServerNIN
    ExAC (Exome Aggregation Consortium)ENSG00000100503
    GNOMAD BrowserENSG00000100503
    Varsome BrowserNIN
    Genetic variants : HAPMAP51199
    Genomic Variants (DGV)NIN [DGVbeta]
    DECIPHERNIN [patients]   [syndromes]   [variants]   [genes]  
    CONAN: Copy Number AnalysisNIN 
    Mutations
    ICGC Data PortalNIN 
    TCGA Data PortalNIN 
    Broad Tumor PortalNIN
    OASIS PortalNIN [ Somatic mutations - Copy number]
    Somatic Mutations in Cancer : COSMICNIN  [overview]  [genome browser]  [tissue]  [distribution]  
    Somatic Mutations in Cancer : COSMIC3DNIN
    Mutations and Diseases : HGMDNIN
    LOVD (Leiden Open Variation Database)Whole genome datasets
    LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
    LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
    BioMutasearch NIN
    DgiDB (Drug Gene Interaction Database)NIN
    DoCM (Curated mutations)NIN (select the gene name)
    CIViC (Clinical Interpretations of Variants in Cancer)NIN (select a term)
    intoGenNIN
    NCG5 (London)NIN
    Cancer3DNIN(select the gene name)
    Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
    Diseases
    OMIM608684    614851   
    Orphanet21691   
    DisGeNETNIN
    MedgenNIN
    Genetic Testing Registry NIN
    NextProtQ8N4C6 [Medical]
    TSGene51199
    GENETestsNIN
    Target ValidationNIN
    Huge Navigator NIN [HugePedia]
    snp3D : Map Gene to Disease51199
    BioCentury BCIQNIN
    ClinGenNIN
    Clinical trials, drugs, therapy
    Chemical/Protein Interactions : CTD51199
    Chemical/Pharm GKB GenePA31630
    Clinical trialNIN
    Miscellaneous
    canSAR (ICR)NIN (select the gene name)
    DataMed IndexNIN
    Probes
    Litterature
    PubMed60 Pubmed reference(s) in Entrez
    GeneRIFsGene References Into Functions (Entrez)
    CoreMineNIN
    EVEXNIN
    GoPubMedNIN
    iHOPNIN
    REVIEW articlesautomatic search in PubMed
    Last year publicationsautomatic search in PubMed

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