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NAPSB Gene

pseudogene   GIFtS: 32
GCID: GC19M050837

Napsin B Aspartic Peptidase, Pseudogene

  Search for NAPSB
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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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This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3

Aliases
Napsin B Aspartic Peptidase, Pseudogene1 2
NAP1L2
NAP22
NAPB2
NAPSBP2

External Ids:    HGNC: 133961   Entrez Gene: 2562362   Ensembl: ENSG000001314017   
ORGUL members:         

Export aliases for NAPSB gene to outside databases

Previous GC identifers: GC19M055530 GC19M055531 GC19M047175


(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 NAPSB Gene:
NAPSB (napsin B aspartic peptidase, pseudogene) is a pseudogene, and is affiliated with the lncRNA class.


(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 at NCBI GenBank:
NC_000019.9  NC_018930.2  NT_011109.17  
Regulatory elements:
   Regulatory transcription factor binding sites in the NAPSB gene promoter:
         CREB   TBP   Brachyury   Bach2   NF-kappaB   NF-kappaB1   E47   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidNAPSB promoter sequence
   Search Chromatin IP Primers for NAPSB

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


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

Entrez Gene cytogenetic band: 19q13.33   Ensembl cytogenetic band:  19q13.33   HGNC cytogenetic band: 19q13.33

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

GeneLoc information about chromosome 19         GeneLoc Exon Structure

GeneLoc location for GC19M050837:  view genomic region     (about GC identifiers)

Start:
50,837,053 bp from pter      End:
50,848,024 bp from pter
Size:
10,972 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., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, 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: --


(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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(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:
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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 COMPARTMENTS: 

CompartmentConfidence
endoplasmic reticulum3
lysosome2
extracellular1

(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 NAPSB
Interactions:

    Search GeneGlobe Interaction Network for NAPSB

(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 NAPSB



(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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Unigene Cluster for NAPSB:

Napsin B aspartic peptidase, pseudogene
Hs.636624  [show with all ESTs]
Unigene Representative Sequence: NR_002798
6 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000531692 ENST00000527780(uc002prw.3) ENST00000562112 ENST00000534096
ENST00000534789 ENST00000525179
miRNA
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Additional mRNA sequence: 

AF090387.1 AF098485.1 AF200344.1 AK300884.1 AK310134.1 BC006149.1 BC019048.2 BC032360.1 
BC040958.1 BC053864.1 BC065203.1 BC085008.1 BC111705.1 NR_002798.1 

6 DOTS entries:

DT.115036  DT.121420480  DT.95244708  DT.40262867  DT.91952801  DT.99998492 

Selected AceView cDNA sequences (see all 215):

BQ712631 BM993071 AI005080 BI823670 AF090386 BC065203 CA307403 BI764577 
NM_004851 BC019048 AW183525 BU541597 BM996247 BP340501 AA485027 BX111968 
BQ019267 AF098485 BE675393 AI218262 BC006149 BM988961 AF200344 AF098484 

GeneLoc Exon Structure

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

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


ECgene alternative splicing isoforms for NAPSB

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


NAPSB expression in embryonic tissues and stem cells    About this table
Data from LifeMap, the Embryonic Development and Stem Cells Database
 selected tissues (see all 4) fully expand
 
 Blood (Cardiovascular System)    fully expand to see all 7 entries
         Mature B-Cells Peripheral Blood
         CD19+ B Cells   
 
 Thymus (Hematopoietic System)
         T Helper Cells Thymus
 
 Umbilical Cord (Extraembryonic Tissues)
         Cord Blood Monocytes (CD14+)   
 
 Tonsil (Hematopoietic System)
NAPSB Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

NAPSB Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.636624
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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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  --

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

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

(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 NAPSB (see all 274)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 19 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1821103981,2
--50836666(+) ACAGGA/GGACGA 1 -- int10--------
rs104113451,2
C,F--50836684(+) GGGAAC/GGGTAT 1 -- int15Minor allele frequency- G:0.22WA NA CSA 244
rs1869403451,2
--50836790(+) GCATGC/TTGTGG 1 -- int10--------
rs558299371,2
C--50836849(+) CGTGAT/AGCTCC 1 -- int13Minor allele frequency- A:0.27NA EA 242
rs730705361,2
--50836868(+) AGGAGA/CCTTTG 1 -- int10--------
rs802706031,2
C--50836985(+) CTCAAC/TTCCGT 1 -- int10--------
rs104186861,2
C,F--50836986(+) TCAACT/CCCGTG 1 -- int14Minor allele frequency- C:0.06NA WA 242
rs1925007091,2
--50836994(+) GTGGGA/TCCATG 1 -- int10--------
rs617305221,2
C--50837098(+) AGCTCT/GGCTAC 1 -- nc-transcript-variant2Minor allele frequency- G:0.02NS WA 190
rs1435366691,2
--50837130(+) TGGGCA/GGCACC 1 -- nc-transcript-variant0--------

HapMap Linkage Disequilibrium report for NAPSB (50837053 - 50848024 bp)

Structural Variations
     Database of Genomic Variants (DGV) 3 variations for NAPSB:    About this table    
Variant IDTypeSubtypePubMed ID
nsv2529CNV Insertion18451855
dgv3976n71CNV Loss21882294
nsv523948CNV Gain19592680

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

(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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  --

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

  1. Membrane-anchored aspartyl protease with Alzheimer's disease beta- secretase activity. (PubMed id 10591213)1, 3 Yan R.... Gurney M.E. (Nature 1999)
  2. Napsins: new human aspartic proteinases. Distinction between two closely related genes. (PubMed id 9877162)1, 3 Tatnell P.J.... Kay J. (FEBS Lett. 1998)
  3. Pronapsin A and B gene expression in normal and malignant human lung and mononuclear blood cells. (PubMed id 12151090)1, 9 Cook M....Kay J. (Biochim. Biophys. Acta 2002)
  4. Structural and phylogenetic comparison of napsin genes: the duplication, loss of function and human-specific pseudogenization of napsin B. (PubMed id 23333608)1 Nishishita K....Tsukuba T. (Gene 2013)
  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: 256236 HGNC: 13396 AceView: NAPSAandNAPSB Ensembl:ENSG00000131401 euGenes: HUgn256236
ECgene: NAPSB H-InvDB: NAPSB

(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 NAPSB 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 NAPSB gene:
Search GeneIP for patents involving NAPSB

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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