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Aliases for CUX2 Gene

Aliases for CUX2 Gene

  • Cut Like Homeobox 2 2 3 5
  • Homeobox Protein Cux-2 3 4
  • CUTL2 3 4
  • Homeobox Protein Cut-Like 2 3
  • Cut-Like 2 (Drosophila) 2
  • Cut-Like Homeobox 2 2
  • KIAA0293 4
  • CDP2 3

External Ids for CUX2 Gene

Previous HGNC Symbols for CUX2 Gene

  • CUTL2

Previous GeneCards Identifiers for CUX2 Gene

  • GC12P109956
  • GC12P111471
  • GC12P108667

Summaries for CUX2 Gene

Entrez Gene Summary for CUX2 Gene

  • This gene encodes a protein which contains three CUT domains and a homeodomain; both domains are DNA-binding motifs. A similar gene, whose gene product possesses different DNA-binding activities, is located on chromosome on chromosome 7. Two pseudogenes of this gene have been identified on chromosomes 10 and 4. [provided by RefSeq, Jan 2013]

GeneCards Summary for CUX2 Gene

CUX2 (Cut Like Homeobox 2) is a Protein Coding gene. Diseases associated with CUX2 include Fiedler's Myocarditis and Alcohol-Related Neurodevelopmental Disorder. Gene Ontology (GO) annotations related to this gene include sequence-specific DNA binding and RNA polymerase II regulatory region sequence-specific DNA binding. An important paralog of this gene is CUX1.

UniProtKB/Swiss-Prot for CUX2 Gene

  • May be a transcription factor involved in neural specification. Binds to DNA in a sequence-specific manner (By similarity).

Additional gene information for CUX2 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CUX2 Gene

Genomics for CUX2 Gene

GeneHancer (GH) Regulatory Elements for CUX2 Gene

Promoters and enhancers for CUX2 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH12J111035 Enhancer 0.8 FANTOM5 659.4 +1.6 1647 0.5 CTCF ZNF362 YY2 ZNF398 ZBTB8A ZNF2 ZNF335 GLIS2 ZNF366 ZNF692 CUX2 GC12M111175
GH12J111033 Enhancer 0.7 ENCODE 650.7 -0.3 -252 0.2 CTCF MXI1 SIN3A ZNF335 GLIS2 PATZ1 EZH2 ZBTB20 ZBTB10 ZNF362 CUX2 LOC105369981
GH12J111034 Enhancer 0.7 ENCODE 650.7 +1.0 978 0.3 SUZ12 ZNF2 ZNF335 ZNF664 GLIS2 ZNF366 ZNF600 KLF8 ZBTB20 ZBTB10 CUX2 GC12M111175
GH12J111039 Promoter 0.6 EPDnew 650.7 -0.1 -74 0.1 ZBTB26 CUX2 LOC105369981
GH12J111037 Enhancer 0.5 ENCODE 650.7 +0.7 668 0.2 POLR2A CTBP2 ZNF398 ZBTB26 CUX2 GC12M111175
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CUX2 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CUX2 gene promoter:
  • CUTL1
  • STAT5B
  • HNF-4alpha2
  • HNF-4alpha1
  • Ik-2
  • HTF
  • Pax-5
  • IRF-1
  • Cdc5

Genomic Locations for CUX2 Gene

Genomic Locations for CUX2 Gene
316,531 bases
Plus strand
316,531 bases
Plus strand

Genomic View for CUX2 Gene

Genes around CUX2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CUX2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CUX2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CUX2 Gene

Proteins for CUX2 Gene

  • Protein details for CUX2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Homeobox protein cut-like 2
    Protein Accession:
    Secondary Accessions:
    • A7E2Y4

    Protein attributes for CUX2 Gene

    1486 amino acids
    Molecular mass:
    161677 Da
    Quaternary structure:
    No Data Available
    • Sequence=BAA22962.2; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for CUX2 Gene

neXtProt entry for CUX2 Gene

Post-translational modifications for CUX2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for CUX2 Gene

No data available for DME Specific Peptides for CUX2 Gene

Domains & Families for CUX2 Gene

Gene Families for CUX2 Gene

Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins
  • Predicted membrane proteins
  • Transcription factors

Protein Domains for CUX2 Gene

Suggested Antigen Peptide Sequences for CUX2 Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the CUT homeobox family.
  • Belongs to the CUT homeobox family.
genes like me logo Genes that share domains with CUX2: view

Function for CUX2 Gene

Molecular function for CUX2 Gene

UniProtKB/Swiss-Prot Function:
May be a transcription factor involved in neural specification. Binds to DNA in a sequence-specific manner (By similarity).

Phenotypes From GWAS Catalog for CUX2 Gene

Gene Ontology (GO) - Molecular Function for CUX2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding IEA,ISS --
GO:0000978 RNA polymerase II proximal promoter sequence-specific DNA binding IEA --
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding NAS 19274049
GO:0001078 transcriptional repressor activity, RNA polymerase II proximal promoter sequence-specific DNA binding IEA --
GO:0003677 DNA binding IEA --
genes like me logo Genes that share ontologies with CUX2: view
genes like me logo Genes that share phenotypes with CUX2: view

Animal Models for CUX2 Gene

MGI Knock Outs for CUX2:
  • Cux2 Cux2<tm1.1Nieto>

Animal Model Products

miRNA for CUX2 Gene

Targeted motifs for CUX2 Gene
HOMER Transcription Factor Regulatory Elements motif CUX2
  • Consensus sequence: HNRAATCAAT Submotif: canonical Cell Type: Liver GEO ID: GSE35985

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology and Transcription Factor Targets for CUX2 Gene

Localization for CUX2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CUX2 Gene

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CUX2 gene
Compartment Confidence
extracellular 5
nucleus 5
golgi apparatus 3

Gene Ontology (GO) - Cellular Components for CUX2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000139 Golgi membrane IBA --
GO:0005634 nucleus IEA,IDA 15656993
GO:0070062 extracellular exosome HDA 19056867
genes like me logo Genes that share ontologies with CUX2: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for CUX2 Gene

Pathways & Interactions for CUX2 Gene

No Data Available

Gene Ontology (GO) - Biological Process for CUX2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II IDA 15656993
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0007275 multicellular organism development IBA --
GO:0007614 short-term memory ISS,IEA --
genes like me logo Genes that share ontologies with CUX2: view

No data available for Pathways by source and SIGNOR curated interactions for CUX2 Gene

Drugs & Compounds for CUX2 Gene

(1) Drugs for CUX2 Gene - From: PharmGKB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Rifampicin Approved Pharma Agonist, Inhibition, Inhibitor Pregnane X receptor agonist; antibiotic 376
genes like me logo Genes that share compounds with CUX2: view

Transcripts for CUX2 Gene

mRNA/cDNA for CUX2 Gene

Unigene Clusters for CUX2 Gene

Cut-like homeobox 2:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for CUX2 Gene

No ASD Table

Relevant External Links for CUX2 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CUX2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CUX2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CUX2 Gene

This gene is overexpressed in Liver (x11.2), Brain - Cortex (x9.4), Brain - Frontal Cortex (BA9) (x8.1), and Brain - Anterior cingulate cortex (BA24) (x5.3).

Protein differential expression in normal tissues from HIPED for CUX2 Gene

This gene is overexpressed in Rectum (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for CUX2 Gene

Protein tissue co-expression partners for CUX2 Gene

NURSA nuclear receptor signaling pathways regulating expression of CUX2 Gene:


SOURCE GeneReport for Unigene cluster for CUX2 Gene:


Evidence on tissue expression from TISSUES for CUX2 Gene

  • Nervous system(4.4)
genes like me logo Genes that share expression patterns with CUX2: view

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for CUX2 Gene

Orthologs for CUX2 Gene

This gene was present in the common ancestor of animals.

Orthologs for CUX2 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia CUX2 34 33
  • 99.43 (n)
(Bos Taurus)
Mammalia CUX2 34 33
  • 88.99 (n)
(Canis familiaris)
Mammalia CUX2 34 33
  • 88.83 (n)
(Rattus norvegicus)
Mammalia Cux2 33
  • 81.84 (n)
(Mus musculus)
Mammalia Cux2 16 34 33
  • 81.45 (n)
(Ornithorhynchus anatinus)
Mammalia CUX2 34
  • 77 (a)
(Monodelphis domestica)
Mammalia CUX2 34
  • 75 (a)
(Gallus gallus)
Aves CUX2 34 33
  • 74.12 (n)
(Anolis carolinensis)
Reptilia CUX2 34
  • 70 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia cux2 33
  • 64.08 (n)
(Danio rerio)
Actinopterygii cux2 33
  • 64.28 (n)
cux2b 34
  • 57 (a)
fruit fly
(Drosophila melanogaster)
Insecta ct 34
  • 17 (a)
(Caenorhabditis elegans)
Secernentea ceh-44 34
  • 24 (a)
Species where no ortholog for CUX2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for CUX2 Gene

Gene Tree for CUX2 (if available)
Gene Tree for CUX2 (if available)
Evolutionary constrained regions (ECRs) for CUX2: view image

Paralogs for CUX2 Gene

Paralogs for CUX2 Gene

(2) SIMAP similar genes for CUX2 Gene using alignment to 4 proteins:

  • Q9BZX3_HUMAN Pseudogenes for CUX2 Gene

genes like me logo Genes that share paralogs with CUX2: view

Variants for CUX2 Gene

Sequence variations from dbSNP and Humsavar for CUX2 Gene

SNP ID Clin Chr 12 pos Variation AA Info Type
rs1000003475 -- 111,224,117(+) A/C/G intron_variant
rs1000014126 -- 111,309,599(+) T/C intron_variant
rs1000016037 -- 111,249,913(+) A/G/T intron_variant
rs1000047869 -- 111,235,202(+) G/A intron_variant
rs1000054527 -- 111,061,391(+) G/T genic_upstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for CUX2 Gene

Variant ID Type Subtype PubMed ID
dgv2861n54 CNV loss 21841781
dgv2862n54 CNV loss 21841781
dgv2863n54 CNV gain+loss 21841781
dgv2864n54 CNV loss 21841781
dgv2865n54 CNV loss 21841781
esv22627 CNV loss 19812545
esv25829 CNV loss 19812545
esv2659278 CNV deletion 23128226
esv2665858 CNV deletion 23128226
esv2667290 CNV deletion 23128226
esv2746357 CNV deletion 23290073
esv2746358 CNV deletion 23290073
esv3333168 CNV duplication 20981092
esv3630747 CNV loss 21293372
esv3630748 CNV loss 21293372
esv3630749 CNV loss 21293372
esv3630750 CNV loss 21293372
esv3630751 CNV loss 21293372
esv3630752 CNV loss 21293372
nsv1069694 CNV deletion 25765185
nsv1069695 CNV deletion 25765185
nsv1131045 CNV deletion 24896259
nsv1145621 CNV deletion 24896259
nsv1145622 CNV deletion 24896259
nsv455714 CNV loss 19166990
nsv475674 CNV novel sequence insertion 20440878
nsv513366 CNV insertion 21212237
nsv560155 CNV gain 21841781
nsv560160 CNV gain 21841781
nsv560161 CNV loss 21841781
nsv560166 CNV gain 21841781
nsv560169 CNV loss 21841781
nsv832513 CNV gain 17160897
nsv952478 CNV deletion 24416366

Variation tolerance for CUX2 Gene

Residual Variation Intolerance Score: 5.45% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.35; 63.29% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CUX2 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CUX2 Gene

Disorders for CUX2 Gene

MalaCards: The human disease database

(3) MalaCards diseases for CUX2 Gene - From: HGMD and DISEASES

Disorder Aliases PubMed IDs
fiedler's myocarditis
  • fiedler myocarditis
alcohol-related neurodevelopmental disorder
  • arnd
fetal alcohol spectrum disorder
  • fetal alcohol syndrome
- elite association - COSMIC cancer census association via MalaCards
Search CUX2 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for CUX2

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with CUX2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CUX2 Gene

Publications for CUX2 Gene

  1. 1000 Genomes-based imputation identifies novel and refined associations for the Wellcome Trust Case Control Consortium phase 1 Data. (PMID: 22293688) Huang J … Li Y (European journal of human genetics : EJHG 2012) 3 44 58
  2. Maternal genes and facial clefts in offspring: a comprehensive search for genetic associations in two population-based cleft studies from Scandinavia. (PMID: 20634891) Jugessur A … Murray JC (PloS one 2010) 3 44 58
  3. High-density SNP association study and copy number variation analysis of the AUTS1 and AUTS5 loci implicate the IMMP2L-DOCK4 gene region in autism susceptibility. (PMID: 19401682) Maestrini E … IMGSAC (Molecular psychiatry 2010) 3 44 58
  4. Case-control association study of 65 candidate genes revealed a possible association of a SNP of HTR5A to be a factor susceptible to bipolar disease in Bulgarian population. (PMID: 19328558) Yosifova A … Nakamura Y (Journal of affective disorders 2009) 3 44 58
  5. Construction of expression-ready cDNA clones for KIAA genes: manual curation of 330 KIAA cDNA clones. (PMID: 12168954) Nakajima D … Nagase T (DNA research : an international journal for rapid publication of reports on genes and genomes 2002) 3 4 58

Products for CUX2 Gene

Sources for CUX2 Gene

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