Human Gene CUX1 (uc003uyx.4)
  Description: Homo sapiens cut-like homeobox 1 (CUX1), transcript variant 1, mRNA.
RefSeq Summary (NM_181552): 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 chr7:101,460,882-101,901,513 Size: 440,632 Total Exon Count: 24 Strand: +
Coding Region
   Position: hg19 chr7:101,460,920-101,892,322 Size: 431,403 Coding Exon Count: 24 

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

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr7:101,460,882-101,901,513)mRNA (may differ from genome)Protein (1505 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSCGAPEnsemblEntrez GeneExonPrimer

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Homeobox protein cut-like 1; AltName: Full=CCAAT displacement protein; Short=CDP; AltName: Full=Homeobox protein cux-1;
FUNCTION: Probably has a broad role in mammalian development as a repressor of developmentally regulated gene expression. May act by preventing binding of positively-activing CCAAT factors to promoters. Component of nf-munr repressor; binds to the matrix attachment regions (MARs) (5' and 3') of the immunoglobulin heavy chain enhancer. Represses T-cell receptor (TCR) beta enhancer function by binding to MARbeta, an ATC-rich DNA sequence located upstream of the TCR beta enhancer (By similarity).
SUBUNIT: Interacts with BANP (By similarity).
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR.
MISCELLANEOUS: Asn-1290 may participate in regulating DNA-binding activity by promoting homo- and heterodimerization.
SIMILARITY: Belongs to the CUT homeobox family.
SIMILARITY: Contains 3 CUT DNA-binding domains.
SIMILARITY: Contains 1 homeobox DNA-binding domain.

-  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 -16.2038-0.426 Picture PostScript Text
3' UTR -3044.999191-0.331 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
IPR003350 - Hmoeo_CUT
IPR017970 - Homeobox_CS
IPR001356 - Homeodomain
IPR009057 - Homeodomain-like
IPR010982 - Lambda_DNA-bd_dom

Pfam Domains:
PF00046 - Homeobox domain
PF02376 - CUT domain
PF05920 - Homeobox KN domain

SCOP Domains:
46689 - Homeodomain-like

ModBase Predicted Comparative 3D Structure on P39880
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 orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 Protein Sequence    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding
GO:0003677 DNA binding
GO:0004713 protein tyrosine kinase activity
GO:0030674 protein binding, bridging
GO:0043565 sequence-specific DNA binding

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0000301 retrograde transport, vesicle recycling within Golgi
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0007275 multicellular organism development
GO:0018108 peptidyl-tyrosine phosphorylation
GO:0048193 Golgi vesicle transport
GO:0050775 positive regulation of dendrite morphogenesis

Cellular Component:
GO:0000139 Golgi membrane
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005794 Golgi apparatus
GO:0005829 cytosol

-  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.
JD408328 - Sequence 389352 from Patent EP1572962.
JD394606 - Sequence 375630 from Patent EP1572962.
JD209944 - Sequence 190968 from Patent EP1572962.
JD457975 - Sequence 438999 from Patent EP1572962.
JD423222 - Sequence 404246 from Patent EP1572962.
JD129598 - Sequence 110622 from Patent EP1572962.
JD288848 - Sequence 269872 from Patent EP1572962.
JD505041 - Sequence 486065 from Patent EP1572962.
JD168192 - Sequence 149216 from Patent EP1572962.
JD040463 - Sequence 21487 from Patent EP1572962.
JD566122 - Sequence 547146 from Patent EP1572962.
JD048888 - Sequence 29912 from Patent EP1572962.
JD428764 - Sequence 409788 from Patent EP1572962.
JD503740 - Sequence 484764 from Patent EP1572962.
JD548797 - Sequence 529821 from Patent EP1572962.
JD176796 - Sequence 157820 from Patent EP1572962.
JD375010 - Sequence 356034 from Patent EP1572962.
JD106724 - Sequence 87748 from Patent EP1572962.
JD176180 - Sequence 157204 from Patent EP1572962.
JD355475 - Sequence 336499 from Patent EP1572962.
JD307917 - Sequence 288941 from Patent EP1572962.
JD288880 - Sequence 269904 from Patent EP1572962.
JD206215 - Sequence 187239 from Patent EP1572962.
JD377072 - Sequence 358096 from Patent EP1572962.
JD232086 - Sequence 213110 from Patent EP1572962.
JD166421 - Sequence 147445 from Patent EP1572962.
JD438223 - Sequence 419247 from Patent EP1572962.
JD419119 - Sequence 400143 from Patent EP1572962.
JD440235 - Sequence 421259 from Patent EP1572962.
JD048968 - Sequence 29992 from Patent EP1572962.
AK056307 - Homo sapiens cDNA FLJ31745 fis, clone NT2RI2007303.
JD532995 - Sequence 514019 from Patent EP1572962.
JD409479 - Sequence 390503 from Patent EP1572962.
JD302088 - Sequence 283112 from Patent EP1572962.
JD078947 - Sequence 59971 from Patent EP1572962.
JD150956 - Sequence 131980 from Patent EP1572962.
JD302674 - Sequence 283698 from Patent EP1572962.
JD329267 - Sequence 310291 from Patent EP1572962.
JD211700 - Sequence 192724 from Patent EP1572962.
JD154195 - Sequence 135219 from Patent EP1572962.
JD299511 - Sequence 280535 from Patent EP1572962.
JD270018 - Sequence 251042 from Patent EP1572962.
JD161188 - Sequence 142212 from Patent EP1572962.
JD181124 - Sequence 162148 from Patent EP1572962.
JD337032 - Sequence 318056 from Patent EP1572962.
JD232183 - Sequence 213207 from Patent EP1572962.
JD375492 - Sequence 356516 from Patent EP1572962.
JD429389 - Sequence 410413 from Patent EP1572962.
JD278570 - Sequence 259594 from Patent EP1572962.
BC040199 - Homo sapiens cDNA clone IMAGE:4816860.
BC045562 - Homo sapiens cDNA clone IMAGE:4815142.
JD153961 - Sequence 134985 from Patent EP1572962.
JD261363 - Sequence 242387 from Patent EP1572962.
JD555772 - Sequence 536796 from Patent EP1572962.
JD118964 - Sequence 99988 from Patent EP1572962.
JD461666 - Sequence 442690 from Patent EP1572962.
JD347776 - Sequence 328800 from Patent EP1572962.
JD338373 - Sequence 319397 from Patent EP1572962.
JD345107 - Sequence 326131 from Patent EP1572962.
JD149739 - Sequence 130763 from Patent EP1572962.
JD229645 - Sequence 210669 from Patent EP1572962.
JD062516 - Sequence 43540 from Patent EP1572962.
JD266082 - Sequence 247106 from Patent EP1572962.
JD554733 - Sequence 535757 from Patent EP1572962.
JD393955 - Sequence 374979 from Patent EP1572962.
JD325546 - Sequence 306570 from Patent EP1572962.
JD347349 - Sequence 328373 from Patent EP1572962.
JD499148 - Sequence 480172 from Patent EP1572962.
BC007204 - Homo sapiens, clone IMAGE:3605822, mRNA.
JD254288 - Sequence 235312 from Patent EP1572962.
JD271810 - Sequence 252834 from Patent EP1572962.
JD109517 - Sequence 90541 from Patent EP1572962.
JD545392 - Sequence 526416 from Patent EP1572962.
JD064289 - Sequence 45313 from Patent EP1572962.
JD038298 - Sequence 19322 from Patent EP1572962.
JD361864 - Sequence 342888 from Patent EP1572962.
JD045502 - Sequence 26526 from Patent EP1572962.
JD160065 - Sequence 141089 from Patent EP1572962.
JD303337 - Sequence 284361 from Patent EP1572962.
JD524286 - Sequence 505310 from Patent EP1572962.
JD402961 - Sequence 383985 from Patent EP1572962.
JD475631 - Sequence 456655 from Patent EP1572962.
JD042774 - Sequence 23798 from Patent EP1572962.
JD057429 - Sequence 38453 from Patent EP1572962.
JD240541 - Sequence 221565 from Patent EP1572962.
JD080545 - Sequence 61569 from Patent EP1572962.
JD449435 - Sequence 430459 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein P39880 (Reactome details) participates in the following event(s):

R-HSA-1839031 Dimerization of cytosolic FGFR1 fusion proteins
R-HSA-1839039 Tyrosine kinase inhibitors bind and inhibit cytosolic FGFR1 fusion dimer phosphorylation
R-HSA-1839065 Phosphorylation of cytosolic FGFR1 fusion dimers
R-HSA-1839080 Activated cytosolic FGFR1 fusions bind PIK3CA
R-HSA-1839112 Phosphorylation of STAT5 by cytosolic FGFR1 fusions
R-HSA-1839094 Activated FGFR1 mutants and fusions bind PLCG1
R-HSA-1839100 p-4Y- PLCG1 dissociates from activated FGFR1 mutants and fusions
R-HSA-1839091 Cytosolic FGFR1 fusion protein-associated PI3K phosphorylates PIP2 to PIP3
R-HSA-1839098 Activated FGFR1 mutants and fusions phosphorylate PLCG1
R-HSA-1839117 Signaling by cytosolic FGFR1 fusion mutants
R-HSA-1839124 FGFR1 mutant receptor activation
R-HSA-5655302 Signaling by FGFR1 in disease
R-HSA-1226099 Signaling by FGFR in disease
R-HSA-5663202 Diseases of signal transduction
R-HSA-1643685 Disease

-  Other Names for This Gene
  Alternate Gene Symbols: CUTL1, CUX1_HUMAN, NM_181552, NP_853530, P39880, Q6NYH4, Q75LE5, Q75MT2, Q75MT3, Q86UJ7, Q9UEV5
UCSC ID: uc003uyx.4
RefSeq Accession: NM_181552
Protein: P39880 (aka CUX1_HUMAN)
CCDS: CCDS5721.1, CCDS56498.1

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: NM_181552.3
exon count: 24CDS single in 3' UTR: no RNA size: 13760
ORF size: 4518CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 9136.00frame shift in genome: no % Coverage: 99.91
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.