Human Gene CUX1 (uc003uyw.3) Description and Page Index
  Description: Homo sapiens cut-like homeobox 1 (CUX1), transcript variant 6, mRNA.
RefSeq Summary (NM_001202545): The protein encoded by this gene is a member of the homeodomain family of DNA binding proteins. It may regulate gene expression, morphogenesis, and differentiation and it may also play a role in the cell cycle progession. Several alternatively spliced transcript variants encoding different isoforms have been identified.[provided by RefSeq, Feb 2011].
Transcript (Including UTRs)
   Position: hg19 chr7:101,459,184-101,927,250 Size: 468,067 Total Exon Count: 22 Strand: +
Coding Region
   Position: hg19 chr7:101,459,311-101,926,382 Size: 467,072 Coding Exon Count: 22 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated: 2013-06-15

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr7:101,459,184-101,927,250)mRNA (may differ from genome)Protein (632 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsH-INV

-  Comments and Description Text from UniProtKB
DESCRIPTION: SubName: Full=Protein CASP;
CAUTION: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered as preliminary data.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): CUX1
CDC HuGE Published Literature: CUX1
Positive Disease Associations: Inflammatory Bowel Diseases , Myocardial Infarction , Stroke
Related Studies:
  1. Inflammatory Bowel Diseases
    Richard H Duerr et al. Science (New York, N.Y.) 2006, A genome-wide association study identifies IL23R as an inflammatory bowel disease gene., Science (New York, N.Y.). [PubMed 17068223]
  2. Myocardial Infarction
    , , . [PubMed 0]
  3. Myocardial Infarction
    , , . [PubMed 0]
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: CUX1
Diseases sorted by gene-association score: fiedler's myocarditis (9), norrie disease (7), dirofilariasis (7), histidinemia (6), histidine metabolism disease (6), leiomyoma (3)

-  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: 15.96 RPKM in Uterus
Total median expression: 342.93 RPKM

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

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -51.44127-0.405 Picture PostScript Text
3' UTR -302.58868-0.349 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
IPR012955 - CASP_C

Pfam Domains:
PF08172 - CASP C terminal

ModBase Predicted Comparative 3D Structure on J3KQV9
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 orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     

-  Descriptions from all associated GenBank mRNAs
  AK125076 - Homo sapiens cDNA FLJ43086 fis, clone BRTHA3019048, highly similar to Protein CASP.
AK303151 - Homo sapiens cDNA FLJ57247 complete cds, highly similar to Protein CASP.
AK222832 - Homo sapiens mRNA for CCAAT displacement protein isoform b variant, clone: HEP07381.
AK125097 - Homo sapiens cDNA FLJ43107 fis, clone CTONG2020108, highly similar to Protein CASP.
BC066592 - Homo sapiens cut-like homeobox 1, mRNA (cDNA clone MGC:75164 IMAGE:5740343), complete cds.
L12579 - Human alternatively spliced CUTL1 mRNA, complete cds.
AK297548 - Homo sapiens cDNA FLJ57747 complete cds, highly similar to Protein CASP.
BC012323 - Homo sapiens cDNA clone IMAGE:4550607, containing frame-shift errors.
AK122726 - Homo sapiens cDNA FLJ16230 fis, clone FEBRA2025249, highly similar to Protein CASP.
BC025422 - Homo sapiens cut-like homeobox 1, mRNA (cDNA clone IMAGE:4864729), complete cds.
AB462994 - Synthetic construct DNA, clone: pF1KB9775, Homo sapiens CUTL1 gene for cut-like homeobox 1, without stop codon, in Flexi system.
M74099 - Human displacement protein (CCAAT) mRNA.
AB075522 - Homo sapiens neuroblastoma cDNA, clone:Nbla10317, full insert sequence.
KF421948 - Homo sapiens CUX1/RET fusion (CUX1/RET fusion) mRNA, partial cds.
BC036852 - Homo sapiens mRNA similar to cut-like 1, CCAAT displacement protein (Drosophila) (cDNA clone IMAGE:5415882).
JD123985 - Sequence 105009 from Patent EP1572962.
JD226573 - Sequence 207597 from Patent EP1572962.
JD442338 - Sequence 423362 from Patent EP1572962.
JD335725 - Sequence 316749 from Patent EP1572962.
JD392070 - Sequence 373094 from Patent EP1572962.
JD465448 - Sequence 446472 from Patent EP1572962.
JD367823 - Sequence 348847 from Patent EP1572962.
JD067690 - Sequence 48714 from Patent EP1572962.
JD397594 - Sequence 378618 from Patent EP1572962.
JD123637 - Sequence 104661 from Patent EP1572962.
JD387326 - Sequence 368350 from Patent EP1572962.
JD382235 - Sequence 363259 from Patent EP1572962.
JD112797 - Sequence 93821 from Patent EP1572962.
JD228488 - Sequence 209512 from Patent EP1572962.
JD209277 - Sequence 190301 from Patent EP1572962.
JD275191 - Sequence 256215 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: J3KQV9, J3KQV9_HUMAN, NM_001202545, NP_001189474
UCSC ID: uc003uyw.3
RefSeq Accession: NM_001202545
Protein: J3KQV9 CCDS: CCDS56499.1

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: NM_001202545.1
exon count: 22CDS single in 3' UTR: no RNA size: 2901
ORF size: 1899CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3362.00frame shift in genome: no % Coverage: 99.76
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.