Human Gene NKAP (uc004esh.3) Description and Page Index
  Description: Homo sapiens NFKB activating protein (NKAP), mRNA.
RefSeq Summary (NM_024528): This gene encodes a protein that is involved in the activation of the ubiquitous transcription factor NF-kappaB. This protein is associated with the the histone deacetylase HDAC3 and with the Notch corepressor complex, and it thereby acts as a transcriptional repressor of Notch target genes. It is also required for alphabeta T cell development. A related pseudogene has been identified on chromosome X, while a related and intronless retrocopy, which has an intact CDS and may be functional, is located on chromosome 6. [provided by RefSeq, May 2010]. ##Evidence-Data-START## Transcript exon combination :: AK026279.1, AY388958.1 [ECO:0000332] RNAseq introns :: mixed/partial sample support SAMEA1965299, SAMEA1966682 [ECO:0000350] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000371410.5/ ENSP00000360464.3 RefSeq Select criteria :: based on conservation, expression, longest protein ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chrX:119,059,013-119,077,735 Size: 18,723 Total Exon Count: 9 Strand: -
Coding Region
   Position: hg19 chrX:119,059,183-119,077,568 Size: 18,386 Coding Exon Count: 9 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chrX:119,059,013-119,077,735)mRNA (may differ from genome)Protein (415 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedStanford SOURCETreefamUniProtKB
Wikipedia

-  Comments and Description Text from UniProtKB
  ID: NKAP_HUMAN
DESCRIPTION: RecName: Full=NF-kappa-B-activating protein;
FUNCTION: Acts as a transcriptional repressor. Plays a role as a transcriptional corepressor of the Notch-mediated signaling required for T-cell development. Also involved in the TNF and IL-1 induced NF-kappa-B activation. Associates with chromatin at the Notch-regulated SKP2 promoter.
SUBUNIT: Component of the Notch corepressor complex. Interacts with CIR1 and HDAC3.
SUBCELLULAR LOCATION: Nucleus.
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR.
SIMILARITY: Belongs to the UPF0396 family.
SEQUENCE CAUTION: Sequence=AAH71686.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence;

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): NKAP
CDC HuGE Published Literature: NKAP

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 7.77 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 203.64 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -71.40167-0.428 Picture PostScript Text
3' UTR -23.10170-0.136 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR009269 - DUF926

Pfam Domains:
PF06047 - Ras-induced vulval development antagonist
PF15692 - NF-kappa-B-activating protein

ModBase Predicted Comparative 3D Structure on Q8N5F7
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserNo orthologGenome BrowserGenome BrowserNo ortholog
Gene DetailsGene Details Gene DetailsGene Details 
Gene SorterGene Sorter Gene SorterGene Sorter 
 RGDEnsemblFlyBaseWormBase 
 Protein Sequence Protein SequenceProtein Sequence 
 Alignment AlignmentAlignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003682 chromatin binding
GO:0003723 RNA binding
GO:0005515 protein binding
GO:0031490 chromatin DNA binding

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0007219 Notch signaling pathway
GO:0019827 stem cell population maintenance
GO:0030097 hemopoiesis
GO:0030851 granulocyte differentiation
GO:0033077 T cell differentiation in thymus
GO:0045892 negative regulation of transcription, DNA-templated
GO:0046638 positive regulation of alpha-beta T cell differentiation
GO:0071425 hematopoietic stem cell proliferation

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005829 cytosol


-  Descriptions from all associated GenBank mRNAs
  BC015354 - Homo sapiens NFKB activating protein, mRNA (cDNA clone MGC:21454 IMAGE:3450847), complete cds.
AK094446 - Homo sapiens cDNA FLJ37127 fis, clone BRACE2022848.
BC032442 - Homo sapiens NFKB activating protein, mRNA (cDNA clone MGC:40260 IMAGE:5139142), complete cds.
BC012770 - Homo sapiens NF-kappaB activating protein, mRNA (cDNA clone IMAGE:3830231), partial cds.
AL832118 - Homo sapiens mRNA; cDNA DKFZp686K18103 (from clone DKFZp686K18103).
JD079935 - Sequence 60959 from Patent EP1572962.
JD375285 - Sequence 356309 from Patent EP1572962.
AK026279 - Homo sapiens cDNA: FLJ22626 fis, clone HSI06109.
AY388958 - Homo sapiens nuclear NF-kappaB activating protein mRNA, complete cds.
BC000940 - Homo sapiens cDNA clone IMAGE:3445361.
JD313158 - Sequence 294182 from Patent EP1572962.
HQ448222 - Synthetic construct Homo sapiens clone IMAGE:100071623; CCSB000445_02 NF-kappaB activating protein (NKAP) gene, encodes complete protein.
KJ894686 - Synthetic construct Homo sapiens clone ccsbBroadEn_04080 NKAP gene, encodes complete protein.
KJ899538 - Synthetic construct Homo sapiens clone ccsbBroadEn_08932 NKAP gene, encodes complete protein.
DQ575095 - Homo sapiens piRNA piR-43207, complete sequence.
BC016783 - Homo sapiens NFKB activating protein, mRNA (cDNA clone IMAGE:4132258), partial cds.
CU689374 - Synthetic construct Homo sapiens gateway clone IMAGE:100018239 5' read NKAP mRNA.
CU677277 - Synthetic construct Homo sapiens gateway clone IMAGE:100017215 5' read NKAP mRNA.
JD346052 - Sequence 327076 from Patent EP1572962.
BC018968 - Homo sapiens NFKB activating protein, mRNA (cDNA clone IMAGE:3925709), partial cds.
BC071686 - Homo sapiens NFKB activating protein, mRNA (cDNA clone IMAGE:4537519), partial cds.
JD382022 - Sequence 363046 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: NKAP_HUMAN, NM_024528, NP_078804, Q6IPW6, Q8N5F7, Q96BQ2, Q9H638
UCSC ID: uc004esh.3
RefSeq Accession: NM_024528
Protein: Q8N5F7 (aka NKAP_HUMAN)
CCDS: CCDS14592.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_024528.3
exon count: 9CDS single in 3' UTR: no RNA size: 1600
ORF size: 1248CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2696.00frame shift in genome: no % Coverage: 99.06
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.