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NBPF10 Gene

protein-coding   GIFtS: 36
GCID: GC01P145297

Neuroblastoma Breakpoint Family, Member 10

  See related diseases
at  

(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
Neuroblastoma Breakpoint Family, Member 101 2
AB62
AG12
NBPF92
Neuroblastoma Breakpoint Family Member 102

External Ids:    HGNC: 319921   Entrez Gene: 1001324062   Ensembl: ENSG000001633867   OMIM: 6140005   UniProtKB: Q6P3W63   

Export aliases for NBPF10 gene to outside databases

Previous GC identifers: GC01P142784 GC01M016761 GC01P144001 GC01P145293 GC01M120910 GC01P145294


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for NBPF10 Gene:
This gene is a member of the neuroblastoma breakpoint family (NBPF) which consists of dozens of recently
duplicated genes primarily located in segmental duplications on human chromosome 1. This gene family has
experienced its greatest expansion within the human lineage and has expanded, to a lesser extent, among primates
in general. Members of this gene family are characterized by tandemly repeated copies of DUF1220 protein domains.
Gene copy number variations in the human chromosomal region 1q21.1, where most DUF1220 domains are located, have
been implicated in a number of developmental and neurogenetic diseases such as microcephaly, macrocephaly,
autism, schizophrenia, mental retardation, congenital heart disease, neuroblastoma, and congenital kidney and
urinary tract anomalies. Altered expression of some gene family members is associated with several types of
cancer. This gene family contains numerous pseudogenes. (provided by RefSeq, Apr 2013)

GeneCards Summary for NBPF10 Gene:
NBPF10 (neuroblastoma breakpoint family, member 10) is a protein-coding gene. Diseases associated with NBPF10 include neuroblastoma, and microcephaly. An important paralog of this gene is NBPF6.




(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 NBPF10 gene promoter:
         HFH-3   Elk-1   Sox5   Pax-2   Pax-2a   AP-4   AREB6   FOXI1   PPAR-gamma1   Pax-2b   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for NBPF10

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat NBPF10


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

Entrez Gene cytogenetic band: 1q21.1   Ensembl cytogenetic band:  1q21.1   HGNC cytogenetic band: 1q21.1

NBPF10 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
NBPF10 gene location

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01P145297:  view genomic region     (about GC identifiers)

Start:
145,289,772 bp from pter      End:
145,370,303 bp from pter
Size:
80,532 bases      Orientation:
plus 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, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: NBPFA_HUMAN, Q6P3W6 (See protein sequence)
Recommended Name: Neuroblastoma breakpoint family member 10  
Size: 841 amino acids; 96426 Da
Miscellaneous: Encoded by one of the numerous copies of NBPF genes clustered in the p36, p12 and q21 region of the
chromosome 1
Secondary accessions: Q5RHC0 Q9NWN6
Alternative splicing: 2 isoforms:  Q6P3W6-1   Q6P3W6-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for NBPF10: NX_Q6P3W6

Explore proteomics data for NBPF10 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See NBPF10 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_001034792.4  
    ENSEMBL proteins: 
     ENSP00000358345   ENSP00000473920   ENSP00000414194   ENSP00000358344   ENSP00000474625  
     ENSP00000474856   ENSP00000345684  

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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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    HGNC Gene Families:
    NBPF: neuroblastoma breakpoint family

    1 InterPro protein domain:
     IPR010630 NBPF_dom

    Graphical View of Domain Structure for InterPro Entry Q6P3W6

    ProtoNet protein and cluster: Q6P3W6

    UniProtKB/Swiss-Prot: NBPFA_HUMAN, Q6P3W6
    Similarity: Belongs to the NBPF family
    Similarity: Contains 6 NBPF domains


    NBPF10 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, 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, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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         Gene Ontology (GO): 1 molecular function term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0044822poly(A) RNA binding IDA--
         
    NBPF10 for ontologies           About GeneDecksing


    Phenotypes:
         2 GenomeRNAi human phenotypes for NBPF10:
     Increased S DNA content  Increased number of mitotic ce 

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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
    NBPFA_HUMAN, Q6P3W6: Cytoplasm (Probable)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus3
    cytosol2
    plasma membrane1

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005737cytoplasm IEA--

    NBPF10 for ontologies           About GeneDecksing


    (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 NBPF10
    Interactions:

        Search GeneGlobe Interaction Network for NBPF10

    (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 NBPF10 (NBPFA)



    (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, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for NBPF10 gene: 
    NM_001039703.5  

    7 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000369339 ENST00000464433 ENST00000448873(uc001emq.1) ENST00000369338
    ENST00000490598 ENST00000605176 ENST00000342960(uc021oun.1 uc021oup.1 uc021oum.1 uc010oyp.1 uc021ouo.1 uc001enc.2 uc021ouq.1 uc021oul.1 uc010oyi.2 uc010oyj.2 uc010oyl.2)

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    GeneLoc Exon Structure

    4 Alternative Splicing Database (ASD) splice patterns (SP) for NBPF10    About this scheme

    ExUns: 1a · 1b ^ 2a · 2b ^ 3a · 3b · 3c · 3d ^ 4a · 4b · 4c ^ 5
    SP1:                                                                        
    SP2:              -                                                         
    SP3:                                                                        
    SP4:                                                                        


    ECgene alternative splicing isoforms for NBPF10

    (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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    NBPF10 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    NBPF10 Expression
    About this image

    NBPF10 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    NBPF10 Protein Expression
        Custom PCR Arrays for NBPF10
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    In Situ
    Assay Products:
     

     
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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 mammals.

    Orthologs for NBPF10 gene from Selected species (see all 3)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    dog
    (Canis familiaris)
    Mammalia --
    Uncharacterized protein
    36(a)
    1 → many
    17(57512543-57515264)


    ENSEMBL Gene Tree for NBPF10 (if available)
    TreeFam Gene Tree for NBPF10 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for NBPF10 gene
    NBPF141 2  NBPF111 2  NBPF91 2  NBPF81 2  NBPF151 2  NBPF121 2  NBPF19  NBPF11 2  
    NBPF201 2  LOC102724250  NBPF26  NBPF62  NBPF32  ENSG000002038362  NBPF42  ENSG000002038272  
    17 SIMAP similar genes for NBPF10 using alignment to 11 protein entries:     NBPFA_HUMAN (see all proteins):
    NBPF21    NBPF20    NBPF8    NBPF15    NBPF16    NBPF11
    NBPF1    AL592307.2    NBPF9    NBPF14    NBPF12    NBPF24
    NBPF3    NBPF7    NBPF5P    NBPF6    NBPF4

    NBPF10 for paralogs           About GeneDecksing


    1 Pseudogenes.org Pseudogene for NBPF10
    PGOHUM00000259457


    (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 NBPF10 (see all 41)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 1 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs40681131,2
    C,F--145296372(+) GTCCTG/AGTTCA 2 /L syn13Minor allele frequency- A:0.38NA 8
    rs50001391,2
    C,F--145312157(-) GACTAG/CGAAGA 1 -- int17Minor allele frequency- C:0.39NA 18
    rs712549611,2
    C,F--145312175(-) GCCACA/GGGCAT 1 -- int16Minor allele frequency- G:0.39NA 18
    rs757335201,2
    C--145312195(+) CTACTC/G/TTCAAG 1 -- int11NA 2
    rs776285491,2
    C,F--145312205(+) GATGTT/GGGATC 1 -- int13Minor allele frequency- G:0.39NA WA 126
    rs795315061,2
    F--145312254(+) CTCAAT/GTTTGT 1 -- int12Minor allele frequency- G:0.25NA 8
    rs712145121,2
    C,F--145312266(-) TCTACA/GAGATC 1 -- int16Minor allele frequency- G:0.44NA 16
    rs19743171,2
    F--145312268(-) AAATCC/G/TCCAAG 1 -- int15NA 12
    rs39288721,2
    --145312268(-) AATCTA/C/GCAAGA 1 -- int12NA 4
    rs39288371,2
    C--145312270(-) GAAATC/G/TTACAA 1 -- int10--------

    HapMap Linkage Disequilibrium report for NBPF10 (145289772 - 145370303 bp)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for NBPF10 (see all 37):    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2717407CNV Deletion23290073
    esv2667344CNV Deletion23128226
    dgv66e199CNV Deletion23128226
    esv2248028CNV Deletion18987734
    dgv46e201CNV Deletion23290073
    esv2717206CNV Deletion23290073
    nsv435814CNV Deletion17901297
    dgv15n16CNV Deletion17901297
    esv2422428CNV Duplication17116639
    nsv24CNV Insertion15895083

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    (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: 614000    OMIM disorders: --

    4 diseases for NBPF10:    
    About MalaCards
    neuroblastoma    microcephaly    schizophrenia    mental retardation

    1 disease from the University of Copenhagen DISEASES database for NBPF10:
    Cancer

    NBPF10 for disorders           About GeneDecksing


    Export disorders for NBPF10 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 NBPF10 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with NBPF10)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. The DNA sequence and biological annotation of human chromosome 1. (PubMed id 16710414)1, 2 Gregory S.G.... Bentley D.R. (Nature 2006)
    2. A novel gene family NBPF: intricate structure generated by gene duplications during primate evolution. (PubMed id 16079250)1, 3 Vandepoele K.... van Roy F. (Mol. Biol. Evol. 2005)
    3. 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)
    4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    5. Why do cellular proteins linked to K63-polyubiquitin chains not associate with proteasomes? (PubMed id 23314748)1 Nathan J.A....Goldberg A.L. (EMBO J. 2013)
    6. Systematic and quantitative assessment of the ubiquitin-modified proteome. (PubMed id 21906983)1 Kim W....Gygi S.P. (Mol. Cell 2011)
    7. Automated phosphoproteome analysis for cultured cancer cells by two-dimensional nanoLC-MS using a calcined titania/C18 biphasic column. (PubMed id 18187866)1 Imami K....Ishihama Y. (Anal Sci 2008)
    8. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 100132406 HGNC: 31992 Ensembl:ENSG00000163386 euGenes: HUgn100132406 ECgene: NBPF10
    H-InvDB: NBPF10

    (According to HUGE)
    About This Section

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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 NBPF10 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for NBPF10 gene:
    Search GeneIP for patents involving NBPF10

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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    GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014

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