Human Gene NUCKS1 (uc001hdb.3)
  Description: Homo sapiens nuclear casein kinase and cyclin-dependent kinase substrate 1 (NUCKS1), mRNA.
RefSeq Summary (NM_022731): This gene encodes a nuclear protein that is highly conserved in vertebrates. The conserved regions of the protein contain several consensus phosphorylation sites for casein kinase II and cyclin-dependent kinases, two putative nuclear localization signals, and a basic DNA-binding domain. It is phosphorylated in vivo by Cdk1 during mitosis of the cell cycle. [provided by RefSeq, Aug 2010]. Sequence Note: This RefSeq record was created from transcript and genomic sequence data to make the sequence consistent with the reference genome assembly. The genomic coordinates used for the transcript record were based on transcript alignments.
Transcript (Including UTRs)
   Position: hg19 chr1:205,681,947-205,719,372 Size: 37,426 Total Exon Count: 7 Strand: -
Coding Region
   Position: hg19 chr1:205,687,408-205,719,101 Size: 31,694 Coding Exon Count: 7 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:205,681,947-205,719,372)mRNA (may differ from genome)Protein (243 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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neXtProtOMIMPubMedTreefamUniProtKBWikipedia
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: NUCKS_HUMAN
DESCRIPTION: RecName: Full=Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1; AltName: Full=P1;
SUBCELLULAR LOCATION: Nucleus.
TISSUE SPECIFICITY: Widely expressed, with highest levels in thyroid gland, prostate and uterus and in fetal liver, thymus and lung.
PTM: Phosphorylated by CDK1 and casein kinase. Phosphorylated upon DNA damage, probably by ATM or ATR.
SEQUENCE CAUTION: Sequence=BAB15076.1; Type=Erroneous termination; Positions=164; Note=Translated as Arg; Sequence=CAC20412.1; Type=Erroneous gene model prediction;

-  Primer design for this transcript
 

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Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
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To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): NUCKS1
CDC HuGE Published Literature: NUCKS1
Positive Disease Associations: Cystatins , Glucose , Mental Competency , Parkinson Disease , Parkinson's disease
Related Studies:
  1. Cystatins
    Shih-Jen Hwang et al. BMC medical genetics 2007, A genome-wide association for kidney function and endocrine-related traits in the NHLBI's Framingham Heart Study., BMC medical genetics. [PubMed 17903292]
    Kidney function traits and TSH are associated with SNPs on the Affymetrix GeneChip Human Mapping 100K SNP set. These data will serve as a valuable resource for replication as more SNPs associated with kidney function and endocrine traits are identified.
  2. Glucose
    James B Meigs et al. BMC medical genetics 2007, Genome-wide association with diabetes-related traits in the Framingham Heart Study., BMC medical genetics. [PubMed 17903298]
    Framingham 100K SNP data is a resource for association tests of known and novel genes with diabetes and related traits posted at http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?id=phs000007 webcite. Framingham 100K data replicate the TCF7L2 association with diabetes.
  3. Mental Competency
    Kathryn L Lunetta et al. BMC medical genetics 2007, Genetic correlates of longevity and selected age-related phenotypes: a genome-wide association study in the Framingham Study., BMC medical genetics. [PubMed 17903295]
    Longevity and aging traits are associated with SNPs on the Affymetrix 100K GeneChip. None of the associations achieved genome-wide significance. These data generate hypotheses and serve as a resource for replication as more genes and biologic pathways are proposed as contributing to longevity and healthy aging.
           more ... click here to view the complete list

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 118.13 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 2523.49 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 -114.80271-0.424 Picture PostScript Text
3' UTR -1478.135461-0.271 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
IPR026633 - NUCKS1

ModBase Predicted Comparative 3D Structure on Q9H1E3
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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 BrowserGenome BrowserNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGDEnsembl   
 Protein SequenceProtein Sequence   
 AlignmentAlignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0001077 transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding
GO:0003682 chromatin binding
GO:0003690 double-stranded DNA binding
GO:0003697 single-stranded DNA binding
GO:0003723 RNA binding
GO:0008134 transcription factor binding

Biological Process:
GO:0000724 double-strand break repair via homologous recombination
GO:0001678 cellular glucose homeostasis
GO:0006275 regulation of DNA replication
GO:0006325 chromatin organization
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0006366 transcription from RNA polymerase II promoter
GO:0019046 release from viral latency
GO:0031297 replication fork processing
GO:0035822 gene conversion
GO:0036297 interstrand cross-link repair
GO:0042593 glucose homeostasis
GO:0043923 positive regulation by host of viral transcription
GO:0044829 positive regulation by host of viral genome replication
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0046626 regulation of insulin receptor signaling pathway
GO:0046628 positive regulation of insulin receptor signaling pathway
GO:0060382 regulation of DNA strand elongation
GO:0071481 cellular response to X-ray
GO:1990968 modulation by host of RNA binding by virus
GO:1990969 modulation by host of viral RNA-binding transcription factor activity

Cellular Component:
GO:0000785 chromatin
GO:0000790 nuclear chromatin
GO:0005634 nucleus
GO:0005730 nucleolus
GO:0005737 cytoplasm


-  Descriptions from all associated GenBank mRNAs
  BC007568 - Homo sapiens cDNA clone IMAGE:3028427, **** WARNING: chimeric clone ****.
BC039469 - Homo sapiens cDNA clone IMAGE:4513453, partial cds.
BC067224 - Homo sapiens cDNA clone IMAGE:4099512, partial cds.
AK056578 - Homo sapiens cDNA FLJ32016 fis, clone NTONG1000064.
BC016311 - Homo sapiens cDNA clone IMAGE:4074138, partial cds.
BC107728 - Homo sapiens cDNA clone IMAGE:4603817.
BC025313 - Homo sapiens nuclear casein kinase and cyclin-dependent kinase substrate 1, mRNA (cDNA clone IMAGE:4860149), with apparent retained intron.
AK095855 - Homo sapiens cDNA FLJ38536 fis, clone HCHON2001200.
AK311186 - Homo sapiens cDNA, FLJ18228.
DL492522 - Novel nucleic acids.
DL490991 - Novel nucleic acids.
JD026135 - Sequence 7159 from Patent EP1572962.
JD035767 - Sequence 16791 from Patent EP1572962.
AK300416 - Homo sapiens cDNA FLJ61403 complete cds, highly similar to Nuclear ubiquitous casein andcyclin-dependent kinases substrate.
JD033093 - Sequence 14117 from Patent EP1572962.
AK025133 - Homo sapiens cDNA: FLJ21480 fis, clone COL05034.
JD091006 - Sequence 72030 from Patent EP1572962.
JD174255 - Sequence 155279 from Patent EP1572962.
JD326483 - Sequence 307507 from Patent EP1572962.
JD263173 - Sequence 244197 from Patent EP1572962.
BC000805 - Homo sapiens nuclear casein kinase and cyclin-dependent kinase substrate 1, mRNA (cDNA clone MGC:5494 IMAGE:3452665), complete cds.
AY823399 - Homo sapiens nuclear ubiquitous casein kinase and cyclin-dependent kinase substrate variant (NUCKS) mRNA, complete cds, alternatively spliced.
AJ012584 - Homo sapiens mRNA for nuclear ubiquitous casein kinase and cyclin-dependent kinase substrate (NUCKS gene).
AK225228 - Homo sapiens mRNA for nuclear ubiquitous casein kinase and cyclin-dependent kinase substrate variant, clone: COL05034.
AB049824 - Homo sapiens mRNA for JC7, complete cds.
JD212139 - Sequence 193163 from Patent EP1572962.
JD061868 - Sequence 42892 from Patent EP1572962.
DQ891218 - Synthetic construct clone IMAGE:100003848; FLH170248.01X; RZPDo839D0498D nuclear casein kinase and cyclin-dependent kinase substrate 1 (NUCKS1) gene, encodes complete protein.
DQ894401 - Synthetic construct Homo sapiens clone IMAGE:100008861; FLH170244.01L; RZPDo839D0497D nuclear casein kinase and cyclin-dependent kinase substrate 1 (NUCKS1) gene, encodes complete protein.
AB528490 - Synthetic construct DNA, clone: pF1KB3778, Homo sapiens NUCKS1 gene for nuclear casein kinase and cyclin-dependent kinase substrate 1, without stop codon, in Flexi system.
JD174232 - Sequence 155256 from Patent EP1572962.
JD251830 - Sequence 232854 from Patent EP1572962.
JD202575 - Sequence 183599 from Patent EP1572962.
JD214288 - Sequence 195312 from Patent EP1572962.
JD079394 - Sequence 60418 from Patent EP1572962.
CR457339 - Homo sapiens full open reading frame cDNA clone RZPDo834B0310D for gene NUCKS, nuclear ubiquitous casein kinase and cyclin-dependent kinase substrate; complete cds, incl. stopcodon.
AF212045 - Homo sapiens potential LAG1 interactor mRNA, partial cds.
LG070620 - KR 1020150124006-A/5: NUCKS1, Novel Coactivator regulating the transcriptional activity of HIV-1 Tat.
LG070618 - KR 1020150124006-A/3: NUCKS1, Novel Coactivator regulating the transcriptional activity of HIV-1 Tat.

-  Other Names for This Gene
  Alternate Gene Symbols: JC7, NM_022731, NP_073568, NUCKS, NUCKS_HUMAN, Q54AC0, Q5PXE7, Q9H1D6, Q9H1E3, Q9H723
UCSC ID: uc001hdb.3
RefSeq Accession: NM_022731
Protein: Q9H1E3 (aka NUCKS_HUMAN or NUKS_HUMAN)
CCDS: CCDS30987.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_022731.4
exon count: 7CDS single in 3' UTR: no RNA size: 6471
ORF size: 732CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1664.00frame shift in genome: no % Coverage: 99.89
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
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.