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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

CUX2 Gene

protein-coding   GIFtS: 51
GCID: GC12P111471

cut-like homeobox 2

(Previous name: cut-like 2 (Drosophila) )
(Previous symbol: CUTL2)
 Explore 5 diseases affiliated with
CUX2 via our new
 Human Malady Compendium 
Biological research products
for CUX2
    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section

Aliases
Cut-Like Homeobox 21 2     Homeobox Protein Cux-22 3
CUTL21 2 3     Cut-Like 2 (Drosophila)1
CDP21 2     Homeobox Protein Cut-Like 22
KIAA02931 3     

External Ids:    HGNC: 193471   Entrez Gene: 233162   Ensembl: ENSG000001112497   OMIM: 6106485   UniProtKB: O145293   

Export aliases for CUX2 gene to outside databases

Previous GC identifers: GC12P109956 GC12P108667


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Entrez Gene summary for CUX2:
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)

UniProtKB/Swiss-Prot: CUX2_HUMAN, O14529
Function: May be a transcription factor involved in neural specification. Binds to DNA in a sequence-specific manner
(By similarity)




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000012.11  NC_018923.1  NT_009775.17  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the CUX2 gene promoter:
         STAT5B   Pax-5   HTF   IRF-1   HNF-4alpha2   CUTL1   Cdc5   HNF-4alpha1   Ik-2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidCUX2 promoter sequence
   Search SABiosciences Chromatin IP Primers for CUX2

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat CUX2


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 12q24.12   Ensembl cytogenetic band:  12q24.11   HGNC cytogenetic band: 12q24.12

CUX2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CUX2 gene location

GeneLoc information about chromosome 12         GeneLoc Exon Structure

GeneLoc location for GC12P111471:  view genomic region     (about GC identifiers)

Start:
111,471,828 bp from pter      End:
111,788,358 bp from pter
Size:
316,531 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: CUX2_HUMAN, O14529 (See protein sequence)
Recommended Name: Homeobox protein cut-like 2  
Size: 1486 amino acids; 161677 Da
Subcellular location: Nucleus (By similarity)
Sequence caution: Sequence=BAA22962.2; Type=Erroneous initiation; Note=Translation N-terminally shortened;
3 PDB 3D structures from and Proteopedia for CUX2:
1WH6 (3D)        1WH8 (3D)        1X2L (3D)    
Secondary accessions: A7E2Y4

Explore the universe of human proteins at neXtProt for CUX2: NX_O14529

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_O14529

  • CUX2 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_056082.2  
    ENSEMBL proteins: 
     ENSP00000261726   ENSP00000380765  

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    Browse ProSpec Recombinant Proteins
    Uscn Proteins for CUX2

    Gene Ontology (GO): 1 cellular component term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus NAS--


    CUX2 for ontologies           About GeneDecksing



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    Uscn ELISAs and CLIAs for CUX2


    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    CUX2 for domains           About GeneDecksing

    5 InterPro domains/families:
     IPR010982 Lambda_DNA-bd_dom
     IPR003350 Hmoeo_CUT
     IPR017970 Homeobox_CS
     IPR001356 Homeodomain
     IPR009057 Homeodomain-like

    Graphical View of Domain Structure for InterPro Entry O14529

    ProtoNet protein and cluster: O14529

    1 Blocks protein family: IPB003350 Homeodomain protein CUT

    UniProtKB/Swiss-Prot: CUX2_HUMAN, O14529
    Similarity: Belongs to the CUT homeobox family
    Similarity: Contains 3 CUT DNA-binding domains
    Similarity: Contains 1 homeobox DNA-binding domain


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section

    Function Summary:

         UniProtKB/Swiss-Prot: CUX2_HUMAN, O14529
    Function: May be a transcription factor involved in neural specification. Binds to DNA in a sequence-specific manner
    (By similarity)

    miRNA
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    hsa-miR-124* hsa-miR-520e hsa-miR-520f hsa-miR-300 hsa-miR-376b hsa-miR-605 hsa-miR-519a hsa-miR-342-3p
    SwitchGear 3'UTR luciferase reporter plasmidCUX2 3' UTR sequence
    Inhib. RNA
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    OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for CUX2 (see all 4)
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    Gene Ontology (GO): 3 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003677DNA binding ----
    GO:0003700sequence-specific DNA binding transcription factor activity NAS--
    GO:0043565sequence-specific DNA binding IEA--


    CUX2 for ontologies           About GeneDecksing


    Animal Models:
         Mouse knock-out Cux2tm1.1Nieto for CUX2
         5 MGI mutant phenotypes (inferred from 5 alleles(MGI details for Cux2):
     cellular  embryogenesis  mortality/aging  nervous system  no phenotypic analysis 

    CUX2 for phenotypes           About GeneDecksing


    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
    About This Section



    Interactions:

        SABiosciences Gene Network CentralTM Interacting Genes and Proteins Network for CUX2

    STRING Interaction Network Preview (showing 4 interactants - click image to see more details)

    5/6 Interacting proteins for CUX2 (O145293 ENSP000002617264) via UniProtKB, MINT, STRING, and/or I2D (see all 6)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ARP102753, ENSP000003638224I2D: score=1 STRING: ENSP00000363822
    CSNK2A1P684003, ENSP000002172444I2D: score=1 STRING: ENSP00000217244
    ERGP113083, ENSP000003818914I2D: score=1 STRING: ENSP00000381891
    DLG4P783523I2D: score=1 
    HDAC1Q135473I2D: score=1 
    About this table

    Gene Ontology (GO): 4 biological process terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006351transcription, DNA-dependent IEA--
    GO:0006355regulation of transcription, DNA-dependent NAS--
    GO:0045892negative regulation of transcription, DNA-dependent IEA--
    GO:0071310cellular response to organic substance IEA--


    CUX2 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for CUX2
    Search CenterWatch for drugs/clinical trials and news about CUX2 

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for CUX2 gene: 
    NM_015267.3  

    Unigene Cluster for CUX2:

    Cut-like homeobox 2
    Hs.124953  [show with all ESTs]
    Unigene Representative Sequence: BC151245
    3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000261726(uc001tsa.2) ENST00000397643(uc001tsb.2) ENST00000551604


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    hsa-miR-124* hsa-miR-520e hsa-miR-520f hsa-miR-300 hsa-miR-376b hsa-miR-605 hsa-miR-519a hsa-miR-342-3p
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    Inhib. RNA
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    Clone
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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat CUX2
      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat CUX2

    Additional cDNA sequence: 

    AB006631.2 AF234996.1 AF271236.1 BC151245.1 

    3 DOTS entries:

    DT.313213  DT.121110137  DT.92016077 

    24/35 AceView cDNA sequences (see all 35):

    BF446155 AF271236 F02605 F09735 CK300340 AB006631 AA593578 BG060008 
    BX283453 BE255767 BM691900 AF234996 F12097 BM804306 BU728601 Z43134 
    AW948980 H05795 T65238 AI126128 AW023436 AW514237 BQ187120 BQ055126 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    CUX2 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: GGAAGGCTGA

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)

    About this image

    CUX2 expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    Stem Cell Differentiation: 2 LifeMap Cells 
    NameCategory
    Pancreatic endoderm/endocrine precursor-like cells (A scalable, suspensi...)
    Intervertebral disc (IVD) annulus fibrosus (AF) cells (Differentiation of s...)Cartilage
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization

    See CUX2 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for CUX2

    SOURCE GeneReport for Unigene cluster: Hs.124953
        SABiosciences Custom PCR Arrays for CUX2
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CUX2

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

    This gene was present in the common ancestor of eukaryotes.

    Orthologs for CUX2 gene from 8/22 species (see all 22)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Cux21 , 5 cut-like homeobox 21, 5 82.64(n)1
    85.47(a)1
      5 (62.02 cM)5
    130481  NM_007804.21  NP_031830.21 
     1218579635 
    chicken
    (Gallus gallus)
    Aves CUX21 cut-like homeobox 2 74.72(n)
    75.54(a)
      416875  XM_415167.3  XP_415167.3 
    lizard
    (Anolis carolinensis)
    Reptilia CUX26
    --
    70(a)
    1 ↔ 1
    GL343423.1(597202-654956)
    zebrafish
    (Danio rerio)
    Actinopterygii BI867269.12   -- 78.63(n)    BI867269.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta ct6
    cut
    14(a)
    1 ↔ 1
    X(7503181-7572892)
    worm
    (Caenorhabditis elegans)
    Secernentea ceh-446
    Protein CASP
    20(a)
    1 ↔ 1
    III(2530603-2546408)
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons AtCASP6
    protein CASP
    18(a)
    1 → many
    3(6336736-6341788)
    rice
    (Oryza sativa)
    Liliopsida --
    CASP, putative, expressed
    19(a)
    1 → many
    3(28664349-28672103)


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for CUX2 gene
    ONECUT12  ONECUT22  ONECUT32  CUX12  
    2 SIMAP similar genes for CUX2 using alignment to 4 protein entries:     CUX2_HUMAN (see all proteins):
    Nbla10317    CUX1

    CUX2 for paralogs           About GeneDecksing


    1 Pseudogenes.org Pseudogene for CUX2
    PGOHUM00000261080


    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/4925 NCBI SNPs in CUX2 are shown (see all 4925    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 12 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs784374571,2
    F,--108485920(+) TCTTAC/TGCGTC 1 -- us2k11Minor allele frequency- T:0.07WA 118
    rs73166241,2
    C,F,A,H,--108486392(+) TATGTA/GTCAGG 1 -- us2k18Minor allele frequency- G:0.30NS WA CSA 360
    rs761825681,2
    --108486639(+) ACCCCA/GGTTGT 1 -- us2k10--------
    rs110657931,2
    C,H--108486697(+) CTGAAG/AACCCT 1 -- us2k16Minor allele frequency- A:0.00NS EA NA 422
    rs71335801,2
    C,F,--108488962(+) ACCCCG/CTAGGA 1 -- int15Minor allele frequency- C:0.33WA CSA 125
    rs734276081,2
    C,F,--108489289(+) GCACCC/GGCGCC 1 -- int11Minor allele frequency- G:0.13WA 118
    rs765184761,2
    --108490124(+) GATGCA/GTAGAT 1 -- int11Minor allele frequency- G:0.01NA 120
    rs795414831,2
    F,--108490871(+) CTGAGC/TATTAA 1 -- int11Minor allele frequency- T:0.03WA 118
    rs353893051,2
    --108491103(+) TTAATA/GACTTT 1 -- int10--------
    rs1126855831,2
    C,--108491563(+) TTACAC/TAGTAC 1 -- int11Minor allele frequency- T:0.50NA 2

    HapMap Linkage Disequilibrium report for CUX2 (111471828 - 111721828 bp, first 250kb of CUX2)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 2 variations for CUX2
         1 CNV: 71579
         1 Indel: 71580
    Human Gene Mutation Database (HGMD): CUX2

    SABiosciences Cancer Mutation PCR Assays
    QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing CUX2
    DNA2.0 Custom Variant and Variant Library Synthesis for CUX2

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section

    CUX2 for disorders           About GeneDecksing

    OMIM gene information: 610648    OMIM disorders: --

    5 diseases for CUX2:    About MalaCards
    distal hereditary motor neuropathy    fiedler's myocarditis    myocarditis    bipolar disorder
    neuropathy

    1 disease from the University of Copenhagen DISEASES database for CUX2:
    fiedler's myocarditis
    Human Genome Epidemiology (HuGE) Navigator: CUX2 (5 documents)

    Export disorders for CUX2 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for CUX2 gene, integrated from 9 sources (see all 14):
    (articles sorted by number of sources associating them with CUX2)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Construction of expression-ready cDNA clones for KIAA genes: manual curation of 330 KIAA cDNA clones. (PubMed id 12168954)1, 2 Nakajima D.... Nagase T. (2002)
    2. Construction and characterization of human brain cDNA libraries suitable for analysis of cDNA clones encoding relatively large proteins. (PubMed id 9179496)1, 2 Ohara O....Nomura N. (1997)
    3. CUX2, a potential regulator of NCAM expression: genomic characterization and analysis as a positional candidate susceptibility gene for bipolar disorder. (PubMed id 11353453)1, 9 Jacobsen N.J.O.... Owen M.J. (2001)
    4. 1000 Genomes-based imputation identifies novel and ref ined associations for the Wellcome Trust Case Control Consortium phase 1 Data. (PubMed id 22293688)1 Huang J....Li Y. (2012)
    5. Maternal genes and facial clefts in offspring: a comp rehensive search for genetic associations in two population-based cleft studies from Scandinavia. (PubMed id 20634891)1 Jugessur A....Murray J.C. (2010)
    6. 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. (PubMed id 19328558)1 Yosifova A....Nakamura Y. (2009)
    7. 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. (PubMed id 19401682)1 Maestrini E....Monaco A.P. (2009)
    8. A quantitative atlas of mitotic phosphorylation. (PubMed id 18669648)2 Dephoure N.... Gygi S.P. (2008)
    9. The finished DNA sequence of human chromosome 12. (PubMed id 16541075)2 Scherer S.E.... Gibbs R.A. (2006)
    10. Biochemical characterization of the mammalian Cux2 protein. (PubMed id 15656993)1 Gingras H....Nepveu A. (2005)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 23316 HGNC: 19347 AceView: CUTL2 Ensembl:ENSG00000111249 euGenes: HUgn23316
    ECgene: CUX2 H-InvDB: CUX2

    (According to HUGE)
    About This Section
    HUGE: KIAA0293

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for CUX2 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for CUX2 gene:
    Search GeneIP for patents involving CUX2

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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