CUX2 Gene (Protein Coding)

Cut Like Homeobox 2

GC12P111034
GIFtS:
40
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] See more...

Aliases for CUX2 Gene

Aliases for CUX2 Gene

  • Cut Like Homeobox 2 2 3 5
  • Homeobox Protein Cut-Like 2 3 4
  • Homeobox Protein Cux-2 3 4
  • KIAA0293 2 4
  • CUTL2 3 4
  • CDP2 2 3
  • Cut-Like 2 (Drosophila) 2
  • Cut-Like Homeobox 2 2
  • EIEE67 3
  • CUX2 5

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 Epileptic Encephalopathy, Early Infantile, 67 and Lennox-Gastaut Syndrome. 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 Summary for CUX2 Gene

  • Transcription factor involved in the control of neuronal proliferation and differentiation in the brain. Regulates dendrite development and branching, dendritic spine formation, and synaptogenesis in cortical layers II-III. Binds to DNA in a sequence-specific manner.

Additional gene information for CUX2 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for CUX2 Gene

Genomics for CUX2 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for CUX2 Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH12J111033 Promoter/Enhancer 2 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas 609.3 +0.6 635 3.2 CTCF TEAD4 ZNF692 PRDM1 PATZ1 EZH2 ZNF600 YY1 ZNF341 ZNF561 CUX2 HSALNG0094027 PHETA1
GH12J111055 Enhancer 1.7 VISTA UCNEbase FANTOM5 ENCODE 13.8 +23.0 23026 2.9 CREB1 ETV6 GABPA ZNF776 PKNOX1 ZNF600 KLF9 SP2 ELK1 CTBP1 ADAM1A ATXN2 IFT81 MAPKAPK5 PCNPP1 CUX2 BRAP ATXN2-AS ANAPC7 MYL2
GH12J111285 Enhancer 0.6 Ensembl ENCODE 11.5 +250.3 250335 2.6 PRDM10 ZIC2 ZKSCAN1 GLIS1 CUX2 MYL2 TMEM116 RF00017-1273 piR-48759-070 lnc-FAM109A-3 LOC105369983 PHETA1 RF00017-1272
GH12J111093 Enhancer 0.6 Ensembl 11.5 +59.5 59536 1.4 PKNOX1 EED RUNX3 CBFB TCF12 GATA3 RXRA MTA3 HNF4A GATA2 CUX2 PHETA1 RF00951-026 piR-32325-045
GH12J111353 Enhancer 0.6 Ensembl ENCODE 10.2 +319.9 319869 0.5 KDM1A RFX1 BCOR ZNF16 ZMYM3 ZFP36 MAPKAPK5 NAA25 CUX2 ALDH2 lnc-CUX2-1 piR-44974-002 PHETA1 RF00017-1272
- 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 the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for CUX2

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

Genomic Locations for CUX2 Gene

Genomic Locations for CUX2 Gene
chr12:111,034,165-111,350,556
(GRCh38/hg38)
Size:
316,392 bases
Orientation:
Plus strand
chr12:111,471,828-111,788,358
(GRCh37/hg19)
Size:
316,531 bases
Orientation:
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 Structure • Gene Density

RefSeq DNA sequence for CUX2 Gene

Proteins for CUX2 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

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

    Protein Symbol:
    O14529-CUX2_HUMAN
    Recommended name:
    Homeobox protein cut-like 2
    Protein Accession:
    O14529
    Secondary Accessions:
    • A7E2Y4

    Protein attributes for CUX2 Gene

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

    Three dimensional structures from OCA and Proteopedia for CUX2 Gene

neXtProt entry for CUX2 Gene

Protein Expression for CUX2 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for CUX2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for CUX2 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for CUX2 Gene

Domains & Families for CUX2 Gene

Gene Families for CUX2 Gene

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

Protein Domains for CUX2 Gene

InterPro:
Blocks:
  • Homeodomain protein CUT
ProtoNet:

Suggested Antigen Peptide Sequences for CUX2 Gene

GenScript: Design optimal peptide antigens:
  • Homeobox protein cux-2 (CUX2_HUMAN)
  • Transcription factor CUX2 (Q9BZV4_HUMAN)
  • Neuron specific transcription factor (Q9BZX3_HUMAN)

Graphical View of Domain Structure for InterPro Entry

O14529

UniProtKB/Swiss-Prot:

CUX2_HUMAN :
  • Belongs to the CUT homeobox family.
Family:
  • Belongs to the CUT homeobox family.
genes like me logo Genes that share domains with CUX2: view

Function for CUX2 Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
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  6. Cell Line

Molecular function for CUX2 Gene

UniProtKB/Swiss-Prot Function:
Transcription factor involved in the control of neuronal proliferation and differentiation in the brain. Regulates dendrite development and branching, dendritic spine formation, and synaptogenesis in cortical layers II-III. Binds to DNA in a sequence-specific manner.

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 DNA-binding transcription factor activity, RNA polymerase II-specific ISM 19274049
GO:0001227 DNA-binding transcription repressor activity, RNA polymerase II-specific 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

Human Phenotype Ontology for CUX2 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for CUX2 Gene

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

Animal Model Products

CRISPR Products

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

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CUX2

No data available for Enzyme Numbers (IUBMB) and Transcription Factor Targets for CUX2 Gene

Localization for CUX2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CUX2 Gene

Nucleus.

Subcellular locations from

COMPARTMENTS
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
nucleus 5
extracellular 4
golgi apparatus 3
plasma membrane 1
cytoskeleton 1
mitochondrion 1
peroxisome 1
endoplasmic reticulum 1
cytosol 1

Gene Ontology (GO) - Cellular Components for CUX2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000139 Golgi membrane IBA 21873635
GO:0000790 nuclear chromatin ISA --
GO:0005634 nucleus IBA,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

PathCards logo

SuperPathways 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 IEA,IDA 15656993
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0007614 short-term memory IEA,ISS --
GO:0010628 positive regulation of gene expression IEA,ISS --
GO:0045892 negative regulation of transcription, DNA-templated 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

Products:

  1. Drug

(1) Drugs for CUX2 Gene - From: PharmGKB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Rifampicin Approved Pharma Agonist, Inhibitor, Inhibition Pregnane X receptor agonist; antibiotic 456
genes like me logo Genes that share compounds with CUX2: view

Transcripts for CUX2 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for CUX2 Gene

2 REFSEQ mRNAs :
4 NCBI additional mRNA sequence :
3 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CUX2

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

No ASD Table

Relevant External Links for CUX2 Gene

GeneLoc Exon Structure for
CUX2

Expression for CUX2 Gene

Products:

  1. Primer
  2. Gene Expression Assay

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

mRNA expression in normal human tissues for CUX2 Gene
mRNA expression by BioGPS for CUX2 GenemRNA expression by GTEx 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

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for CUX2

SOURCE GeneReport for Unigene cluster for CUX2 Gene:

Hs.124953

Evidence on tissue expression from TISSUES for CUX2 Gene

  • Nervous system(4.5)
  • Liver(2.3)
  • Blood(2.1)
  • Skin(2.1)
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
Chimpanzee
(Pan troglodytes)
 Mammalia CUX2 30 31
  • 99.43 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia CUX2 30 31
  • 88.99 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia CUX2 30 31
  • 88.83 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Cux2 30
  • 81.84 (n)
Mouse
(Mus musculus)
 Mammalia Cux2 30 17 31
  • 81.45 (n)
 OneToOne
Platypus
(Ornithorhynchus anatinus)
 Mammalia CUX2 31
  • 77 (a)
 OneToOne
Oppossum
(Monodelphis domestica)
 Mammalia CUX2 31
  • 75 (a)
 OneToOne
Chicken
(Gallus gallus)
 Aves CUX2 30 31
  • 74.12 (n)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia CUX2 31
  • 70 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia cux2 30
  • 64.08 (n)
Zebrafish
(Danio rerio)
 Actinopterygii cux2 30
  • 64.28 (n)
cux2b 31
  • 57 (a)
 OneToOne
Fruit Fly
(Drosophila melanogaster)
 Insecta ct 31
  • 17 (a)
 OneToMany
Worm
(Caenorhabditis elegans)
 Secernentea ceh-44 31
  • 24 (a)
 OneToMany
Species where no ortholog for CUX2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (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

ENSEMBL:
Gene Tree for CUX2 (if available)
TreeFam:
Gene Tree for CUX2 (if available)
Aminode:
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:

  • CUX2_HUMAN
  • F5GWR6_HUMAN
  • Q9BZV4_HUMAN
  • Q9BZX3_HUMAN

Pseudogenes.org Pseudogenes for CUX2 Gene

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

Variants for CUX2 Gene

Products:

  1. SNP Genotyping and Copy Number Assay

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for CUX2 Gene

SNP ID Clinical significance and condition Chr 12 pos Variation AA Info Type
710707 Likely Benign: not provided 111,307,070(+) C/T SYNONYMOUS_VARIANT
710752 Benign: not provided 111,320,652(+) G/A SYNONYMOUS_VARIANT
713817 Benign: not provided 111,214,217(+) C/T SYNONYMOUS_VARIANT,FIVE_PRIME_UTR_VARIANT
714570 Benign: not provided 111,310,035(+) T/C INTRON_VARIANT
716175 Likely Benign: not provided 111,347,874(+) G/A MISSENSE_VARIANT

Additional dbSNP identifiers (rs#s) for CUX2 Gene

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)
CUX2
SNPedia medical, phenotypic, and genealogical associations of SNPs for
CUX2

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

(6) MalaCards diseases for CUX2 Gene - From: UniProtKB/Swiss-Prot, OMIM, GTR, Orphanet, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search CUX2 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

CUX2_HUMAN
  • Epileptic encephalopathy, early infantile, 67 (EIEE67) [MIM:618141]: A form of epileptic encephalopathy, a heterogeneous group of severe childhood onset epilepsies characterized by refractory seizures, neurodevelopmental impairment, and poor prognosis. Development is normal prior to seizure onset, after which cognitive and motor delays become apparent. EIEE67 is an autosomal dominant form characterized by onset of seizures in infancy. Later onset of seizures in childhood may occur in some patients. {ECO:0000269 PubMed:29630738, ECO:0000269 PubMed:29795476}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for CUX2

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with CUX2: view

No data available for Genatlas for CUX2 Gene

Publications for CUX2 Gene

  1. A recurrent de novo CUX2 missense variant associated with intellectual disability, seizures, and autism spectrum disorder. (PMID: 29795476) Barington M … Ostergaard E (European journal of human genetics : EJHG 2018) 3 4
  2. The epilepsy phenotypic spectrum associated with a recurrent CUX2 variant. (PMID: 29630738) Chatron N … Lesca G (Annals of neurology 2018) 3 4
  3. 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 41
  4. 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 41
  5. 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 41

ExternalLinks

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