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NBPF1 Gene

protein-coding   GIFtS: 40
GCID: GC01M016888

Neuroblastoma Breakpoint Family, Member 1

  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 11 2     AD22
KIAA16933 5     NBG2
AB132     NBPF2
AB142     Neuroblastoma Breakpoint Family Member 12
AB232     

External Ids:    HGNC: 260881   Entrez Gene: 556722   Ensembl: ENSG000002194817   OMIM: 6105015   UniProtKB: Q3BBV03   

Export aliases for NBPF1 gene to outside databases

Previous GC identifers: GC01M016666 GC01M016764 GC01M015383


(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 NBPF1 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 NBPF1 Gene:
NBPF1 (neuroblastoma breakpoint family, member 1) is a protein-coding gene. Diseases associated with NBPF1 include shipyard eye, and neuroblastoma. 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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RefSeq DNA sequence:
NC_000001.11  NC_018912.2  NT_032977.10  
Regulatory elements:
   Regulatory transcription factor binding sites in the NBPF1 gene promoter:
         SRF   Pax-5   SRF (504 AA)   MyoD   Olf-1   LUN-1   XBP-1   NF-E2 p45   ZID   NF-E2   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for NBPF1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat NBPF1


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

Entrez Gene cytogenetic band: 1p36.13   Ensembl cytogenetic band:  1p36.13   HGNC cytogenetic band: 1p36.13

NBPF1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
NBPF1 gene location

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01M016888:  view genomic region     (about GC identifiers)

Start:
16,888,814 bp from pter      End:
16,940,057 bp from pter
Size:
51,244 bases      Orientation:
minus strand
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for NBPF1

(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: NBPF1_HUMAN, Q3BBV0 (See protein sequence)
Recommended Name: Neuroblastoma breakpoint family member 1  
Size: 1214 amino acids; 139343 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: Q8N4E8 Q9C0H0

Explore the universe of human proteins at neXtProt for NBPF1: NX_Q3BBV0

Explore proteomics data for NBPF1 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See NBPF1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_060410.2  
    ENSEMBL proteins: 
     ENSP00000474456   ENSP00000473795   ENSP00000473697   ENSP00000474352   ENSP00000474816  

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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 Q3BBV0

    ProtoNet protein and cluster: Q3BBV0

    UniProtKB/Swiss-Prot: NBPF1_HUMAN, Q3BBV0
    Similarity: Belongs to the NBPF family
    Similarity: Contains 8 NBPF domains


    NBPF1 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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    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for NBPF1
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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
    NBPF1_HUMAN, Q3BBV0: Cytoplasm
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus3
    cytosol2

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

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

    NBPF1 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 NBPF1
    Interactions:

        Search GeneGlobe Interaction Network for NBPF1

    (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 NBPF1



    (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 NBPF1 gene: 
    NM_017940.4  

    Unigene Clusters for NBPF1:

    Neuroblastoma breakpoint family, member 1
    Hs.467587  [show with all ESTs], Hs.523572  [show with all ESTs]
    Unigene Representative Sequences: AY894575, NM_001102663
    9 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000430580(uc001ayz.1 uc010oce.1 uc009vos.1) ENST00000392963(uc009vot.1)
    ENST00000420513 ENST00000599069 ENST00000599908 ENST00000449853(uc001azb.1 uc001aza.4 uc001azc.1)
    ENST00000432949 ENST00000420031 ENST00000287968
    miRNA
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      QuantiFast Probe-based Assays in human, mouse, rat NBPF1

    Additional mRNA sequence: 

    AF379619.1 AF379620.1 AF420437.1 

    Selected DOTS entries (see all 48):

    DT.413237  DT.121346666  DT.102843346  DT.121346674  DT.306616  DT.436721  DT.75101477  DT.100646648 
    DT.102843345  DT.121346529  DT.121346575  DT.449222  DT.100058829  DT.102843950  DT.121346678  DT.121346552 
    DT.121346559  DT.121346596  DT.121451694  DT.121460219  DT.451039  DT.91786973  DT.100059221  DT.100858688 

    Selected AceView cDNA sequences (see all 219):

    AA577102 BM665124 AI373099 AA478452 D31148 BM454751 AI671614 AA447033 
    BG771660 BQ682424 AI094039 CA427727 BV190399 BV184110 AW474946 AK055895 
    BP373673 F09484 AA954844 AV724737 AF379618 W17223 AF379617 BE274740 

    GeneLoc Exon Structure


    (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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    NBPF1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TTGGCTTTTC
    NBPF1 Expression
    About this image

    NBPF1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    NBPF1 Protein Expression

    SOURCE GeneReport for Unigene clusters: Hs.467587 Hs.523572

    UniProtKB/Swiss-Prot: NBPF1_HUMAN, Q3BBV0
    Tissue specificity: Widely expressed. The only tissue which shows a weak expression is kidney

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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for NBPF1

    (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 NBPF1 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
    35(a)
    1 → many
    17(57512543-57515264)


    ENSEMBL Gene Tree for NBPF1 (if available)
    TreeFam Gene Tree for NBPF1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for NBPF1 gene
    LOC102724250  NBPF111 2  NBPF151 2  NBPF91 2  NBPF121 2  NBPF81 2  NBPF101 2  NBPF141 2  
    NBPF26  NBPF19  NBPF201 2  NBPF62  NBPF32  ENSG000002038362  NBPF42  ENSG000002038272  
    17 SIMAP similar genes for NBPF1 using alignment to 7 protein entries:     NBPF1_HUMAN (see all proteins):
    NBPF21    NBPF15    NBPF16    NBPF14    NBPF20    NBPF24
    NBPF8    AL592307.2    NBPF10    NBPF12    NBPF11    NBPF9
    NBPF3    NBPF7    NBPF5P    NBPF6    NBPF4

    NBPF1 for paralogs           About GeneDecksing



    (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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    10 SNPs for NBPF1    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 1 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs39016801,2,4
    ----see VAR_0323702 mis40--------
    rs37386611,2,4
    ----see VAR_0323672 mis40--------
    rs6816231,2,4
    ----see VAR_0323662 mis40--------
    rs6728121,2,4
    ----see VAR_0323682 mis40--------
    rs97270801,2,4
    ----see VAR_0323722 mis40--------
    rs39016791,2,4
    ----see VAR_0323712 mis40--------
    rs97300771,2,4
    ----see VAR_0323652 mis40--------
    rs115819261,2,4
    ----see VAR_0323732 mis40--------
    rs97300801,2,4
    ----see VAR_0323642 mis40--------
    rs284530111,2,4
    ----see VAR_0323692 mis40--------

    HapMap Linkage Disequilibrium report for NBPF1 (16888814 - 16940057 bp)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for NBPF1 (see all 47):    About this table    
    Variant IDTypeSubtypePubMed ID
    dgv20e201CNV Deletion23290073
    dgv1n16CNV Deletion17901297
    esv2744463CNV Deletion23290073
    esv2678817CNV Deletion23128226
    dgv21e199CNV Deletion23128226
    nsv471344CNV Duplication19718026
    nsv821511CNV Duplication20802225
    nsv471343CNV Duplication19718026
    nsv3632CNV Insertion18451855
    nsv435932CNV Insertion17901297

    Human Gene Mutation Database (HGMD): NBPF1
    Site Specific Mutation Identification with PCR Assays
    Search QIAGEN SeqTarget long-range PCR primers for resequencing NBPF1
    DNA2.0 Custom Variant and Variant Library Synthesis for NBPF1

    (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: 610501    OMIM disorders: --

    6 diseases for NBPF1:    
    About MalaCards
    shipyard eye    neuroblastoma    microcephaly    gastroenteritis
    schizophrenia    mental retardation


    NBPF1 for disorders           About GeneDecksing


    Export disorders for NBPF1 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 NBPF1 gene, integrated from 10 sources (see all 12):
    (articles sorted by number of sources associating them with NBPF1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. A novel gene family NBPF: intricate structure generated by gene duplications during primate evolution. (PubMed id 16079250)1, 2, 3 Vandepoele K.... van Roy F. (Mol. Biol. Evol. 2005)
    2. Prediction of the coding sequences of unidentified human genes. XIX. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PubMed id 11214970)1, 2, 3 Nagase T.... Ohara O. (DNA Res. 2000)
    3. 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)
    4. Evolutionary history and genome organization of DUF1220 protein domains. (PubMed id 22973535)1 O'Bleness M.S....Sikela J.M. (G3 (Bethesda) 2012)
    5. Systematic and quantitative assessment of the ubiquitin-modified proteome. (PubMed id 21906983)1 Kim W....Gygi S.P. (Mol. Cell 2011)
    6. Chibby interacts with NBPF1 and clusterin, two candidate tumor suppressors linked to neuroblastoma. (PubMed id 20096688)1 Vandepoele K....van Roy F. (Exp. Cell Res. 2010)
    7. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    8. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1 Ota T.... Sugano S. (Nat. Genet. 2004)
    9. 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)
    10. Constitutional translocation t(1;17)(p36.31-p36.13;q11.2-q12.1) in a neuroblastoma patient. Establishment of somatic cell hybrids and identification of PND/A12M2 on chromosome 1 and NF1/SCYA7 on chromosome 17 as breakpoint flanking single copy markers. (PubMed id 7700633)1 Laureys G.... Van Roy N. (Oncogene 1995)

    (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: 55672 HGNC: 26088 AceView: FLJ20719 Ensembl:ENSG00000219481 euGenes: HUgn55672
    ECgene: NBPF1 H-InvDB: NBPF1

    (According to HUGE)
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    HUGE: KIAA1693

    (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 NBPF1 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 NBPF1 gene:
    Search GeneIP for patents involving NBPF1

    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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