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NPDC1 Gene

protein-coding   GIFtS: 50
GCID: GC09M139933

Neural Proliferation, Differentiation And Control, 1

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(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Neural Proliferation, Differentiation And Control, 11 2     CAB-2
NPDC-12 3     CAB-12
CAB12 5     Neural Proliferation Differentiation And Control Protein 12
CAB2     

External Ids:    HGNC: 78991   Entrez Gene: 566542   Ensembl: ENSG000001072817   OMIM: 6057985   UniProtKB: Q9NQX53   

Export aliases for NPDC1 gene to outside databases

Previous GC identifers: GC09M131083 GC09M131623 GC09M133373 GC09M135291 GC09M137209 GC09M139053 GC09M109393


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for NPDC1 Gene:
NPDC1 (neural proliferation, differentiation and control, 1) is a protein-coding gene.

UniProtKB/Swiss-Prot: NPDC1_HUMAN, Q9NQX5
Function: Suppresses oncogenic transformation in neural and non-neural cells and down-regulates neural cell
proliferation. Might be involved in transcriptional regulation (By similarity)

Gene Wiki entry for NPDC1 Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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Regulatory elements:
   Regulatory transcription factor binding sites in the NPDC1 gene promoter:
         RFX1   GATA-3   NRSF form 1   SEF-1 (1)   NRSF form 2   GATA-1   GATA-2   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for NPDC1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat NPDC1


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 9q34.3   Ensembl cytogenetic band:  9q34.3   HGNC cytogenetic band: 9q34.3

NPDC1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
NPDC1 gene location

GeneLoc information about chromosome 9         GeneLoc Exon Structure

GeneLoc location for GC09M139933:  view genomic region     (about GC identifiers)

Start:
139,933,909 bp from pter      End:
139,940,676 bp from pter
Size:
6,768 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: NPDC1_HUMAN, Q9NQX5 (See protein sequence)
Recommended Name: Neural proliferation differentiation and control protein 1 precursor  
Size: 325 amino acids; 34516 Da
Secondary accessions: Q5SPY8 Q9BTD6 Q9BXT3 Q9NQS2 Q9Y434

Explore the universe of human proteins at neXtProt for NPDC1: NX_Q9NQX5

Explore proteomics data for NPDC1 at MOPED

Post-translational modifications: 

  • Glycosylation2 at Ser114, Thr115, Thr130, Ser134
  • Modification sites at PhosphoSitePlus

  • See NPDC1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_056207.3  
    ENSEMBL proteins: 
     ENSP00000360659   ENSP00000360660  

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    antibodies-online peptides for NPDC1

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    1 InterPro protein domain:
     IPR009635 NPDC1

    Graphical View of Domain Structure for InterPro Entry Q9NQX5

    ProtoNet protein and cluster: Q9NQX5

    UniProtKB/Swiss-Prot: NPDC1_HUMAN, Q9NQX5
    Similarity: Belongs to the NPDC1/cab-1 family


    Find genes that share domains with NPDC1           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: NPDC1_HUMAN, Q9NQX5
    Function: Suppresses oncogenic transformation in neural and non-neural cells and down-regulates neural cell
    proliferation. Might be involved in transcriptional regulation (By similarity)

    Phenotypes:
         1 MGI mutant phenotype (inferred from 1 allele(MGI details for Npdc1):

     normal 

    Find genes that share phenotypes with NPDC1           About GenesLikeMe

    Animal Models:
         MGI mouse knock-out Npdc1tm1Ce for NPDC1

       genOway: Develop your customized and physiologically relevant rodent model for NPDC1

    miRNA
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    miRTarBase miRNAs that target NPDC1:
    hsa-mir-99b-5p (MIRT044185)

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    2 qRT-PCR Assays for microRNAs that regulate NPDC1:
    hsa-miR-3119 hsa-miR-145
    SwitchGear 3'UTR luciferase reporter plasmidNPDC1 3' UTR sequence
    Inhib. RNA
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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    NPDC1_HUMAN, Q9NQX5: Membrane; Single-pass membrane protein (Potential)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    extracellular2
    plasma membrane2
    chloroplast1
    cytosol1
    endoplasmic reticulum1
    golgi apparatus1
    nucleus1

    Gene Ontology (GO): 1 cellular component term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0016021integral component of membrane IEA--

    Find genes that share ontologies with NPDC1           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for NPDC1
    Interactions:

        GeneGlobe Interaction Network for NPDC1

    STRING Interaction Network Preview (showing 5 interactants - click image to see 16)

    Selected Interacting proteins for NPDC1 (Q9NQX53 ENSP000003606604) via UniProtKB, MINT, STRING, and/or I2D (see all 16)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    CCND3P302813, ENSP000003620824I2D: score=2 STRING: ENSP00000362082
    CDK2P249413, ENSP000002669704I2D: score=2 STRING: ENSP00000266970
    E2F1Q010943, ENSP000003455714I2D: score=2 STRING: ENSP00000345571
    UBCP0CG483, ENSP000003448184I2D: score=1 STRING: ENSP00000344818
    MADDQ8WXG63, ENSP000003109334I2D: score=1 STRING: ENSP00000310933
    About this table

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for NPDC1



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for NPDC1 gene: 
    NM_015392.3  

    6 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000371600(uc004cks.2) ENST00000371601(uc004ckt.2) ENST00000496498
    ENST00000472668 ENST00000488145 ENST00000485589
    miRNA
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    hsa-miR-3119 hsa-miR-145
    SwitchGear 3'UTR luciferase reporter plasmidNPDC1 3' UTR sequence
    Inhib. RNA
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      QuantiTect SYBR Green Assays in human, mouse, rat NPDC1
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    Selected AceView cDNA sequences (see all 413):

    CB242775 BX366082 CA312110 CR626507 CB153286 BC004217 CF126142 CR605121 
    CD723142 BI918359 AK074793 AI923915 CR621502 BQ575630 AI799722 BQ050832 
    CR597998 BM822565 BI488915 H06128 BQ777616 CR595396 BU607324 BF725309 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for NPDC1 (see all 8)    About this scheme

    ExUns: 1a · 1b · 1c ^ 2a · 2b · 2c · 2d ^ 3a · 3b ^ 4 ^ 5 ^ 6a · 6b ^ 7 ^ 8 ^ 9a · 9b ^ 10 ^ 11
    SP1:                    -                 -                                                     -                     
    SP2:                    -     -           -                                                     -                     
    SP3:                                      -                                                     -                     
    SP4:                                                                                            -           -         
    SP5:                                      -     -                                                                     


    ECgene alternative splicing isoforms for NPDC1

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    NPDC1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GAGAACCGTA
    NPDC1 Expression
    About this image


    NPDC1 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 5) fully expand
     
     Blood (Hematopoietic System)
             Hematopoietic Stem Cells Hematopoietic Bone Marrow
     
     Neural Tube (Nervous System)
             Telencephalon
     
     Adipose (Muscoskeletal System)
     
     Stomach (Gastrointestinal Tract)
     
     Prostate (Endocrine System)
    NPDC1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    NPDC1 Protein Expression

    UniProtKB/Swiss-Prot: NPDC1_HUMAN, Q9NQX5
    Tissue specificity: Strongly expressed in adult brain; especially in hippocampus, frontal lobe and temporal lobe

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    In Situ
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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of animals.

    Orthologs for NPDC1 gene from Selected species (see all 12)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Npdc11 , 5 neural proliferation, differentiation and control gene more5
    neural proliferation, differentiation and control 11
    79(n)1
    79.87(a)1
      2 (17.23 cM)5
    181461  NM_008721.41  NP_032747.21 
     253993515 
    chicken
    (Gallus gallus)
    Aves NPDC11 neural proliferation, differentiation and control, more 62.98(n)
    54.94(a)
      770620  XM_001233958.3  XP_001233959.3 
    lizard
    (Anolis carolinensis)
    Reptilia NPDC16
    neural proliferation, differentiation and control,...
    63(a)
    1 ↔ 1
    AAWZ02039732(3830-6786)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia Str.106202 Transcribed sequence with weak similarity to protein more 75.64(n)    AL972580.2 
    zebrafish
    (Danio rerio)
    Actinopterygii sbcb10302 sbcb1030 77.44(n)   387312  BG307328.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta Atf-26
    Activating transcription factor-2
    11(a)
    1 ↔ 1
    2R(20757590-20768744)
    worm
    (Caenorhabditis elegans)
    Secernentea cab-16
    Protein CAB-1 (cab-1) mRNA, complete cds
    15(a)
    1 ↔ 1
    X(12199655-12213049) WBGene00000277


    ENSEMBL Gene Tree for NPDC1 (if available)
    TreeFam Gene Tree for NPDC1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for NPDC1 gene

    Find genes that share paralogs with NPDC1           About GenesLikeMe


    1 Pseudogenes.org Pseudogene for NPDC1
    PGOHUM00000238707


    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for NPDC1 (see all 258)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 9 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1445565981,2
    --139933431(+) CACACA/GGGTAC 1 -- int10--------
    rs107815341,2
    C,F,A--139933589(+) CAGCCT/CTCTTT 1 -- int110Minor allele frequency- C:0.28NA WA EA 372
    rs1177527881,2
    F--139933604(+) CACAGG/CATGGG 1 -- int11Minor allele frequency- C:0.01NA 120
    rs70265041,2
    C,F,A,H--139933617(+) CTTCCG/AGGCCG 1 -- int110Minor allele frequency- A:0.09NA WA CSA EA 373
    rs1474264681,2
    --139933698(+) GCAGGA/GGTGAG 1 -- int10--------
    rs1831479221,2
    C--139933842(+) CAGGGA/GTCCGT 1 -- int10--------
    rs2005755281,2
    C--139933882(-) AATCTC/TCCACC 1 -- int10--------
    rs1870753921,2
    --139933976(+) CCTGCA/GCTCTA 1 -- ut310--------
    rs1484621851,2
    C--139933984(+) CTACGA/GTTCTC 1 -- ut310--------
    rs66051,2
    C,F,A,H--139934020(-) CTGTTC/TGGTTT 1 -- ut3122Minor allele frequency- T:0.19EA MN NA NS 3655

    HapMap Linkage Disequilibrium report for NPDC1 (139933909 - 139940676 bp)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for NPDC1 (see all 29):    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2422220CNV Deletion17116639
    nsv894483CNV Loss21882294
    nsv894567CNV Loss21882294
    dgv8416n71CNV Loss21882294
    dgv8439n71CNV Loss21882294
    dgv8440n71CNV Loss21882294
    dgv8441n71CNV Loss21882294
    dgv8428n71CNV Loss21882294
    nsv894521CNV Loss21882294
    nsv894503CNV Loss21882294

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing NPDC1
    DNA2.0 Custom Variant and Variant Library Synthesis for NPDC1

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 605798    OMIM disorders: --


    Find genes that share disorders with NPDC1           About GenesLikeMe


    Export disorders for NPDC1 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for NPDC1 gene, integrated from 10 sources (see all 22):
    (articles sorted by number of sources associating them with NPDC1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Characterization and tissue expression of a novel human gene npdc1. (PubMed id 11245976)1, 2, 3 Qu X.... He F. (Gene 2001)
    2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    3. Functional analysis of the NPDC-1 gene. (PubMed id 15563841)1, 9 Evrard C....Rouget P. (Gene 2004)
    4. Toward an understanding of the protein interaction network of the human liver. (PubMed id 21988832)1 Wang J....Yang X. (Mol. Syst. Biol. 2011)
    5. Systematic and quantitative assessment of the ubiquitin-modified proteome. (PubMed id 21906983)1 Kim W....Gygi S.P. (Mol. Cell 2011)
    6. Ubiquitin ligase substrate identification through quantitative proteomics at both the protein and peptide levels. (PubMed id 21987572)1 Lee K.A....Doedens J.R. (J. Biol. Chem. 2011)
    7. Mass spectrometric analysis of lysine ubiquitylation reveals promiscuity at site level. (PubMed id 21139048)1 Danielsen J.M....Nielsen M.L. (amp 2011)
    8. Global identification of modular cullin-RING ligase substrates. (PubMed id 21963094)1 Emanuele M.J....Elledge S.J. (Cell 2011)
    9. Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis. (PubMed id 20068231)2 Olsen J.V....Mann M. (Sci. Signal. 2010)
    10. The interactome of the histone gene regulatory factor HiNF-P suggests novel cell cycle related roles in transcriptional control and RNA processing. (PubMed id 17577209)1 Miele A....Stein J.L. (J. Cell. Biochem. 2007)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 56654 HGNC: 7899 AceView: NPDC1 Ensembl:ENSG00000107281 euGenes: HUgn56654
    ECgene: NPDC1 H-InvDB: NPDC1

    (According to HUGE)
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    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for NPDC1 Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for NPDC1 Genetics and Cytogenetics in Oncology and Haematology

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for NPDC1 gene:
    Search GeneIP for patents involving NPDC1

    GeneCards and IP:
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