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NKAPP1 Gene

pseudogene   GIFtS: 26
GCID: GC0XM119258

NFKB Activating Protein Pseudogene 1

(Previous name: chromosome X open reading frame 42)
(Previous symbol: CXorf42)
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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): antisense

Quality score for the ORGUL clustered with this gene is 3

Aliases
NFKB Activating Protein Pseudogene 11 2
CXorf421 2 3
Chromosome X Open Reading Frame 421
NF-Kappa-B-Activating Protein Pseudogene 13

External Ids:    HGNC: 267061   Entrez Gene: 1588012   Ensembl: ENSG000002333827   UniProtKB: Q8N9T23   
ORGUL members:         

Export aliases for NKAPP1 gene to outside databases

Previous GC identifers: GC0XM119371 GC0XM108822 GC0XM119255


(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 NKAPP1 Gene:
NKAPP1 (NFKB activating protein pseudogene 1) is a pseudogene, and is affiliated with the antisense RNA 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_000023.10  NC_018934.2  NT_011786.17  
Regulatory elements:
   Search for regulatory transcription factor binding sites for NKAPP1
         Other transcription factors

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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat NKAPP1


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

Entrez Gene cytogenetic band: Xq24   Ensembl cytogenetic band:  Xq24   HGNC cytogenetic band: Xq24

NKAPP1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
NKAPP1 gene location

GeneLoc information about chromosome X         GeneLoc Exon Structure

GeneLoc location for GC0XM119258:  view genomic region     (about GC identifiers)

Start:
119,254,863 bp from pter      End:
119,379,122 bp from pter
Size:
124,260 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., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: CX042_HUMAN, Q8N9T2 (See protein sequence)
Recommended Name: Putative uncharacterized protein CXorf42  
Size: 125 amino acids; 14163 Da
Caution: Could be the product of a pseudogene. Related to NKAP
Sequence caution: Sequence=CAD97792.1; Type=Miscellaneous discrepancy; Note=Cloning artifact;
Secondary accessions: Q05CP2 Q14CJ5 Q7Z3P3

Explore the universe of human proteins at neXtProt for NKAPP1: NX_Q8N9T2


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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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ProtoNet protein and cluster: Q8N9T2


(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, 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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Phenotypes:
     2 GenomeRNAi human phenotypes for NKAPP1:
 G0/1 arrest  Increased G1 DNA content 

Animal Models:
   genOway: Develop your customized and physiologically relevant rodent model for NKAPP1

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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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(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 NKAPP1
Interactions:

    Search GeneGlobe Interaction Network for NKAPP1

(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
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Browse Tocris compounds for NKAPP1 (CX042)



(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 NKAPP1 gene: 
NM_173522.1  

Unigene Cluster for NKAPP1:

NFKB activating protein pseudogene 1
Hs.442518  [show with all ESTs]
Unigene Representative Sequence: NR_027131
7 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000555168 ENST00000554109 ENST00000554946 ENST00000452254(uc004esm.3)
ENST00000592037 ENST00000585790 ENST00000536487
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Additional mRNA sequence: 

BC022359.1 BC113730.1 BC113732.1 NR_027131.1 

2 DOTS entries:

DT.97789251  DT.121298812 

Selected AceView cDNA sequences (see all 27):

BC022359 BX490669 AW013941 NM_173522 AK093895 AX748357 BM798637 AI632568 
BX490448 AW002536 AI017557 AW237101 BF591912 BX537594 AI989963 BM511996 
AI371752 CK905715 AW611964 BF057644 BM512235 BQ638190 BG527810 BX490668 

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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NKAPP1 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: GATTTTGGTA
NKAPP1 Expression
About this image

NKAPP1 Protein expression data from MOPED1, PaxDb2 and MaxQB3 --

SOURCE GeneReport for Unigene cluster: Hs.442518
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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 NKAPP1 (if available)
TreeFam Gene Tree for NKAPP1 (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 NKAPP1 (see all 120)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr X posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1863434321,2
--119369941(+) TTTAGA/TTATAT 1 -- int10--------
rs736076361,2
C,F--119370036(+) GTTCTT/AGTAGT 1 -- int11Minor allele frequency- A:0.50WA 2
rs1903959861,2
--119370040(+) TTGTAG/TTGCCA 1 -- int10--------
rs736076381,2
C,F--119370533(+) ATATGA/GGGGGC 1 -- nc-transcript-variant2Minor allele frequency- G:0.33WA CSA 3
rs1163033661,2
--119370626(+) TCTGTA/TTTGTG 1 -- nc-transcript-variant0--------
rs1816373141,2
--119370708(+) TATGAA/GCTGAC 1 -- nc-transcript-variant0--------
rs1864371951,2
--119370890(+) ACTCAC/TAGGGC 1 -- nc-transcript-variant0--------
rs1471518501,2
C--119370909(+) AAGGTA/GGCAGC 1 -- nc-transcript-variant0--------
rs1913398071,2
--119371594(+) ACTGAA/GTGAGT 1 -- nc-transcript-variant0--------
rs1395923961,2
C--119371753(+) AATCA-/AT    
   T
/TAT
ATACC
2 -- nc-transcript-variant0--------

HapMap Linkage Disequilibrium report for NKAPP1 (119254863 - 119379122 bp)

Structural Variations
     Database of Genomic Variants (DGV) 3 variations for NKAPP1:    About this table    
Variant IDTypeSubtypePubMed ID
esv2676041CNV Deletion23128226
esv2740431CNV Deletion23290073
esv2740432CNV Deletion23290073

Site Specific Mutation Identification with PCR Assays
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DNA2.0 Custom Variant and Variant Library Synthesis for NKAPP1

(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 NKAPP1 gene integrated from 10 sources:
(articles sorted by number of sources associating them with NKAPP1)
    Utopia: connect your pdf to the dynamic
world of online information

  1. 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)
  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 full-ORF clone resource of the German cDNA consortium. (PubMed id 17974005)2 Bechtel S.... Schupp I. (BMC Genomics 2007)
  4. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (Genome Res. 2006)
  5. The DNA sequence of the human X chromosome. (PubMed id 15772651)2 Ross M.T.... Bentley D.R. (Nature 2005)
  6. 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: 158801 HGNC: 26706 AceView: CXorf42 Ensembl:ENSG00000233382 euGenes: HUgn158801
ECgene: NKAPP1 H-InvDB: NKAPP1

(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 NKAPP1 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 NKAPP1 gene:
Search GeneIP for patents involving NKAPP1

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, eBioscience, antibodies-online, 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 genOway)
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