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NBPF6 Gene

protein-coding   GIFtS: 30
GCID: GC01P108919

Neuroblastoma Breakpoint Family, Member 6

  See NBPF6-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 61 2
Neuroblastoma Breakpoint Family Member 62

External Ids:    HGNC: 319881   Entrez Gene: 6531492   Ensembl: ENSG000001860867   OMIM: 6139965   UniProtKB: Q5VWK03   

Export aliases for NBPF6 gene to outside databases

Previous GC identifers: GC01U901190 GC01P108720 GC01P108794


(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 NBPF6 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. Alternative splicing of this gene results in multiple
transcript variants encoding distinct isoforms. (provided by RefSeq, Mar 2013)

GeneCards Summary for NBPF6 Gene:
NBPF6 (neuroblastoma breakpoint family, member 6) is a protein-coding gene. Diseases associated with NBPF6 include neuroblastoma, and schizophrenia. An important paralog of this gene is NBPF3.




(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 NBPF6 gene promoter:
         AP-4   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for NBPF6

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat NBPF6


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

Entrez Gene cytogenetic band: 1p13.3   Ensembl cytogenetic band:  1p13.3   HGNC cytogenetic band: 1p13.3

NBPF6 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
NBPF6 gene location

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01P108919:  view genomic region     (about GC identifiers)

Start:
108,918,421 bp from pter      End:
109,013,624 bp from pter
Size:
95,204 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, Cloud-Clone Corp., and/or eBioscience,
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UniProtKB/Swiss-Prot: NBPF6_HUMAN, Q5VWK0 (See protein sequence)
Recommended Name: Neuroblastoma breakpoint family member 6  
Size: 638 amino acids; 72239 Da
Miscellaneous: Encoded by one of the numerous copies of NBPF genes clustered in the p36, p12 and q21 region of the
chromosome 1
Sequence caution: Sequence=CAH70399.1; Type=Erroneous initiation; Sequence=CAI23469.1; Type=Erroneous initiation;
Secondary accessions: A4QN25
Alternative splicing: 2 isoforms:  Q5VWK0-1   Q5VWK0-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for NBPF6: NX_Q5VWK0

Explore proteomics data for NBPF6 at MOPED


See NBPF6 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins (2 alternative transcripts): 
NP_001137459.1  NP_001137460.1  

ENSEMBL proteins: 
 ENSP00000417277   ENSP00000434735   ENSP00000402703   ENSP00000359057   ENSP00000294652  

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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 Q5VWK0

ProtoNet protein and cluster: Q5VWK0

UniProtKB/Swiss-Prot: NBPF6_HUMAN, Q5VWK0
Similarity: Belongs to the NBPF family
Similarity: Contains 3 NBPF domains


Find genes that share domains with NBPF6           About GenesLikeMe


(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, 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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Animal Models:
   inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for NBPF6
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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
NBPF6_HUMAN, Q5VWK0: Cytoplasm (Probable)
Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
cytosol2
nucleus2

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

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

Find genes that share ontologies with NBPF6           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 NBPF6
Interactions:

    Search GeneGlobe Interaction Network for NBPF6

(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 compounds at ApexBio 

Browse Tocris compounds for NBPF6



(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 NBPF6 gene (2 alternative transcripts): 
NM_001143987.1  NM_001143988.1  

5 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000495380 ENST00000531446 ENST00000444143 ENST00000370040(uc009wep.3 uc009weq.3)
ENST00000294652
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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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NBPF6 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: CTGAGAGTGC
NBPF6 Expression
About this image

NBPF6 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

NBPF6 Protein Expression
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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 NBPF6 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
40(a)
1 → many
17(57512543-57515264)


ENSEMBL Gene Tree for NBPF6 (if available)
TreeFam Gene Tree for NBPF6 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for NBPF6 gene
NBPF41 2  NBPF32  NBPF202  NBPF82  ENSG000002038362  NBPF92  NBPF112  NBPF152  
NBPF12  NBPF142  NBPF102  NBPF122  ENSG000002038272  
17 SIMAP similar genes for NBPF6 using alignment to 3 protein entries:     NBPF6_HUMAN (see all proteins):
NBPF5P    NBPF4    NBPF21    NBPF20    NBPF1    NBPF7
NBPF11    NBPF8    NBPF12    NBPF3    NBPF9    NBPF10
NBPF15    NBPF16    NBPF24    AL592307.2    NBPF14

Find genes that share paralogs with NBPF6           About GenesLikeMe


Selected Pseudogenes.org Pseudogenes for NBPF6 (see all 6)
PGOHUM00000244134 PGOHUM00000259478 PGOHUM00000251119 PGOHUM00000259589 PGOHUM00000259590


(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 NBPF6 (see all 104)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 1 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1995322491,2
C--108990981(+) TAGTGA/CATTAA 2 -- us2k10--------
rs1818707551,2
--108991639(+) CTGTCA/GCTACA 2 -- us2k10--------
rs1873689991,2
--108991645(+) CTACAC/TAGTGT 2 -- us2k10--------
rs1387349531,2
C--108992034(+) TTAGAA/GCAACT 2 -- us2k10--------
rs772194751,2
F--108992040(+) CAACTC/ATATAT 2 -- us2k11Minor allele frequency- A:0.00NA 2
rs795588801,2
F--108992046(+) TATATG/ATATAT 2 -- us2k11Minor allele frequency- A:0.00NA 2
rs1807777521,2
--108992054(+) TATATA/GTATAT 2 -- us2k10--------
rs769174071,2
F--108992066(+) TATATG/ATATAT 2 -- us2k11Minor allele frequency- A:0.50NA 2
rs2019988721,2
F--108993329(+) AGTTCC/TGAGAC 4 R * stg11Minor allele frequency- T:0.04EU 541
rs781060551,2
F--108993954(+) AGTGAG/AAGGGA 2 -- int11Minor allele frequency- A:0.00NA 2

HapMap Linkage Disequilibrium report for NBPF6 (108918421 - 109013624 bp)

Structural Variations
     Database of Genomic Variants (DGV) 10 variations for NBPF6:    About this table    
Variant IDTypeSubtypePubMed ID
nsv821488CNV Deletion20802225
nsv10606CNV Loss18304495
nsv2276CNV Loss18451855
nsv498679CNV Loss21111241
nsv428179CNV Gain18775914
nsv823886CNV Gain20364138
nsv872137CNV Gain21882294
esv23343CNV Gain+Loss19812545
dgv85e1CNV Complex17122850
dgv83e1CNV Complex17122850

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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: 613996    OMIM disorders: --

2 diseases for NBPF6:    
About MalaCards
neuroblastoma    schizophrenia


Find genes that share disorders with NBPF6           About GenesLikeMe


Export disorders for NBPF6 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 NBPF6 gene integrated from 10 sources:
(articles sorted by number of sources associating them with NBPF6)
    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, 3 Vandepoele K.... van Roy F. (Mol. Biol. Evol. 2005)
  2. Evolutionary history and genome organization of DUF1220 protein domains. (PubMed id 22973535)1 O'Bleness M.S....Sikela J.M. (G3 (Bethesda) 2012)
  3. The DNA sequence and biological annotation of human chromosome 1. (PubMed id 16710414)2 Gregory S.G.... Bentley D.R. (Nature 2006)
  4. 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)
  5. 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: 653149 HGNC: 31988 Ensembl:ENSG00000186086 euGenes: HUgn653149 ECgene: NBPF6
H-InvDB: NBPF6

(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 NBPF6 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 NBPF6 gene:
Search GeneIP for patents involving NBPF6

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, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, 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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 Search Vector BioLabs for ready-to-use adenovirus/AAV for human, mouse, rat NBPF6
 inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for NBPF6
 inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for NBPF6
 LSBio Antibodies in human, mouse, rat for NBPF6
Customized transgenic rodents for:
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 Browse compounds at ApexBio
 Search Addgene for plasmids for NBPF6
  Search eBioscience for proteins for NBPF6
  Search eBioscience for elisas for NBPF6
  eBioscience FlowRNA Probe Sets
       
GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014 , 21 Aug 2014 , 8 Sep 2014

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