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NBPF4 Gene

protein-coding   GIFtS: 35
GCID: GC01M108765

Neuroblastoma Breakpoint Family, Member 4

  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 41 2
Neuroblastoma Breakpoint Family Member 42

External Ids:    HGNC: 265501   Entrez Gene: 1485452   Ensembl: ENSG000001964277   OMIM: 6139945   UniProtKB: Q96M433   

Export aliases for NBPF4 gene to outside databases

Previous GC identifers: GC01M108478 GC01M106711


(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 NBPF4 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, Mar 2013)

GeneCards Summary for NBPF4 Gene:
NBPF4 (neuroblastoma breakpoint family, member 4) is a protein-coding gene. Diseases associated with NBPF4 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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RefSeq DNA sequence:
NC_000001.11  NT_032977.10  NC_018912.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the NBPF4 gene promoter:
         AP-4   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat NBPF4


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

NBPF4 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
NBPF4 gene location

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01M108765:  view genomic region     (about GC identifiers)

Start:
108,765,963 bp from pter      End:
108,786,703 bp from pter
Size:
20,741 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, 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: NBPF4_HUMAN, Q96M43 (See protein sequence)
Recommended Name: Neuroblastoma breakpoint family member 4  
Size: 638 amino acids; 72053 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=BAB71469.1; Type=Miscellaneous discrepancy; Note=Aberrant splicing;
Secondary accessions: Q5T483

Explore the universe of human proteins at neXtProt for NBPF4: NX_Q96M43

Explore proteomics data for NBPF4 at MOPED


See NBPF4 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_001137461.1  
ENSEMBL proteins: 
 ENSP00000389237  

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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 Q96M43

ProtoNet protein and cluster: Q96M43

UniProtKB/Swiss-Prot: NBPF4_HUMAN, Q96M43
Similarity: Belongs to the NBPF family
Similarity: Contains 3 NBPF domains


NBPF4 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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Phenotypes:
     1 GenomeRNAi human phenotype for NBPF4:
 Decreased Hepatitis C virus re 

Animal Models:
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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
NBPF4_HUMAN, Q96M43: 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--

NBPF4 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 NBPF4
Interactions:

    Search GeneGlobe Interaction Network for NBPF4

(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 NBPF4



(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 NBPF4 gene (2 alternative transcripts): 
NM_001143989.2  NM_152488.1  

Unigene Cluster for NBPF4:

Neuroblastoma breakpoint family, member 4
Hs.511849  [show with all ESTs]
Unigene Representative Sequence: NM_001143989
1 Ensembl transcript including schematic representation, and UCSC links where relevant:
ENST00000415641(uc009weo.2 uc001dvo.2 uc009wen.2)
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Additional mRNA sequence: 

AK302318.1 AK316438.1 BC125162.1 

4 DOTS entries:

DT.121451377  DT.121352631  DT.95148305  DT.75150941 

2 AceView cDNA sequences:

AK057395 NM_152488 

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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NBPF4 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: --
NBPF4 Expression
About this image

NBPF4 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

NBPF4 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.511849

UniProtKB/Swiss-Prot: NBPF4_HUMAN, Q96M43
Tissue specificity: Expressed in testis

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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 NBPF4 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 NBPF4 (if available)
TreeFam Gene Tree for NBPF4 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for NBPF4 gene
NBPF61 2  NBPF32  NBPF202  NBPF82  ENSG000002038362  NBPF92  NBPF112  NBPF152  
NBPF12  NBPF142  NBPF102  NBPF122  ENSG000002038272  
17 SIMAP similar genes for NBPF4 using alignment to 2 protein entries:     NBPF4_HUMAN (see all proteins):
NBPF5P    NBPF6    NBPF21    NBPF20    NBPF1    NBPF11
NBPF3    NBPF7    NBPF8    NBPF12    NBPF9    NBPF15
NBPF16    NBPF24    AL592307.2    NBPF10    NBPF14

NBPF4 for paralogs           About GeneDecksing


5 Pseudogenes.org Pseudogenes for NBPF4
PGOHUM00000251082 PGOHUM00000251126 PGOHUM00000244972 PGOHUM00000251129 PGOHUM00000250233


(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 NBPF4 (see all 80)    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 1 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs29195161,2
F,H--108765532(-) ccccaG/Atgcgg 1 -- ds50014Minor allele frequency- A:0.00NS EA 418
rs29195151,2
--108765572(-) ctcagC/Tccatc 1 -- ds50010--------
rs1869887161,2
--108765936(+) TTACCG/TCCTAT 1 -- ds50010--------
rs1917977781,2
--108766039(+) GCTGCA/GGACTC 1 -- ut310--------
rs29927691,2
C--108766087(-) TTGACA/C/TGGCGT 2 -- ut311NA 2
rs1434229881,2
C--108766094(+) TCAATG/TCTATT 1 -- ut310--------
rs38707371,2
C,A,H--108766133(-) TGTGAC/TCAATA 1 -- ut310--------
rs2008346551,2
C--108766319(+) TTGTGA/TCATTC 1 -- ut311Minor allele frequency- T:0.00EU 593
rs22593111,2
C,F,H--108766334(+) ATCCTG/ACCATC 2 /A /V mis17Minor allele frequency- A:0.33EA NS NA 842
rs1835986971,2
C--108766348(+) TGCGTC/ACTTCC 2 /R /S mis11Minor allele frequency- A:0.00EU 593

HapMap Linkage Disequilibrium report for NBPF4 (108765963 - 108786703 bp)

Structural Variations
     Database of Genomic Variants (DGV) 7 variations for NBPF4:    About this table    
Variant IDTypeSubtypePubMed ID
nsv821352CNV Deletion20802225
nsv10550CNV Loss18304495
nsv526757CNV Loss19592680
nsv428179CNV Gain18775914
esv23343CNV Gain+Loss19812545
dgv83e1CNV Complex17122850
dgv84e1CNV 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: 613994    OMIM disorders: --

4 diseases for NBPF4:    
About MalaCards
neuroblastoma    microcephaly    schizophrenia    mental retardation


NBPF4 for disorders           About GeneDecksing


Export disorders for NBPF4 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 NBPF4 gene integrated from 10 sources:
(articles sorted by number of sources associating them with NBPF4)
    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. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
  3. The DNA sequence and biological annotation of human chromosome 1. (PubMed id 16710414)2 Gregory S.G.... Bentley D.R. (Nature 2006)
  4. 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: 148545 HGNC: 26550 AceView: FLJ32833 Ensembl:ENSG00000196427 euGenes: HUgn148545
ECgene: NBPF4 H-InvDB: NBPF4

(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 NBPF4 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 NBPF4 gene:
Search GeneIP for patents involving NBPF4

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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The GeneCards human gene database gene index: 1 3 5 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z 


Developed at the Crown Human Genome Center, Department of Molecular Genetics, the Weizmann Institute of Science

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