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    Cux2 cut-like homeobox 2 [ Mus musculus (house mouse) ]

    Gene ID: 13048, updated on 24-Dec-2024

    Summary

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    Official Symbol
    Cux2provided by MGI
    Official Full Name
    cut-like homeobox 2provided by MGI
    Primary source
    MGI:MGI:107321
    See related
    Ensembl:ENSMUSG00000042589 AllianceGenome:MGI:107321
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    Cutl2; Cux-2; 1700051K22Rik
    Summary
    This gene is a member of the Cut family of transcription factors that have multiple DNA binding domains and regulate cell proliferation and differentiation. This gene is primarily expressed in nervous tissues where it controls the proliferation of neuronal precursors, and may play a role in organogenesis earlier during embryonic development. Mice lacking the encoded protein exhibit smaller spinal cords with deficits in neural progenitor development as well as in neuroblast and interneuron differentiation. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2015]
    Expression
    Biased expression in cortex adult (RPKM 10.2), frontal lobe adult (RPKM 7.6) and 14 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Cux2 in Genome Data Viewer
    Location:
    5 F; 5 62.02 cM
    Exon count:
    29
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 5 NC_000071.7 (121996025..122188522, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 5 NC_000071.6 (121857962..122050415, complement)

    Chromosome 5 - NC_000071.7Genomic Context describing neighboring genes Neighboring gene STARR-positive B cell enhancer mm9_chr5:122298757-122299058 Neighboring gene predicted gene, 32422 Neighboring gene PH domain containing endocytic trafficking adaptor 1 Neighboring gene predicted gene, 52785 Neighboring gene uncharacterized LOC118568726 Neighboring gene predicted gene, 52786 Neighboring gene VISTA enhancer mm77 Neighboring gene myosin, light polypeptide 2, regulatory, cardiac, slow Neighboring gene coiled-coil domain containing 63

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. Reinforcement Learning Recruits Somata and Apical Dendrites across Layers of Primary Sensory Cortex. Lacefield CO, et al. Cell Rep, 2019 Feb 19. PMID 30784583, Free PMC Article
    2. Imaging of Evoked Cortical Depolarizations Using Either ASAP2s, or chi-VSFP, or Di-4-Anepps, or Autofluorescence Optical Signals. Milicevic KD, et al. J Integr Neurosci, 2023 Nov 6. PMID 38176939
    3. Responses to Pattern-Violating Visual Stimuli Evolve Differently Over Days in Somata and Distal Apical Dendrites. Gillon CJ, et al. J Neurosci, 2024 Jan 31. PMID 37989593, Free PMC Article
    4. Cux2 serves as a novel lineage marker of granule cell layer neurons from the rhombic lip in mouse and chick embryos. Capaldo E, et al. Dev Dyn, 2016 Aug. PMID 27198720
    5. Temporal controls over inter-areal cortical projection neuron fate diversity. Klingler E, et al. Nature, 2021 Nov. PMID 34754107

    See all (195) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. LHX2 binding site in Cux2-E1 enhancer is evolutionally conserved.Lhx2 regulates Cux2 expression in cortical layer II-IV during brain development.
      Title: Cux2 expression regulated by Lhx2 in the upper layer neurons of the developing cortex.
    2. homeobox TF Lmx1a can activate the Cux2 enhancer through activation of a conserved intronic enhancer
      Title: Lmx1a drives Cux2 expression in the cortical hem through activation of a conserved intronic enhancer.
    3. CUX2 inhibited HNF6 transcriptional regulation of the sex-specific gene promoters CYP2C11 and CYP2C12, blocking HNF6 repression of CYP2C11 and HNF6 activation of CYP2C12.
      Title: Cross Talk Between GH-Regulated Transcription Factors HNF6 and CUX2 in Adult Mouse Liver.
    4. results suggest that the persistent expression of CUX2 in postmitotic neurons contributes to the maintenance of genome integrity through its stimulation of oxidative DNA damage repair.
      Title: CUX2 protein functions as an accessory factor in the repair of oxidative DNA damage.
    5. Results suggest that Cux2 expression reflects hippocampal neurogenesis and identifies non-self-renewing neural progenitors in the subgranular zone of the dentate gyrus
      Title: Cux2 activity defines a subpopulation of perinatal neurogenic progenitors in the hippocampus.
    6. Results suggest that by their differential effects on basal and apical dendrites, Cux1 and Cux2 can promote the integration of layer II-III neurons in the intracortical networks in highly specific ways
      Title: Cux1 and Cux2 selectively target basal and apical dendritic compartments of layer II-III cortical neurons.
    7. Cux2-positive radial glial cells generate diverse subtypes of neocortical projection neurons and macroglia
      Title: Cux2-positive radial glial cells generate diverse subtypes of neocortical projection neurons and macroglia.
    8. Cux2 activity plays an important role for ongoing neurogenesis in the olfactory epithelium
      Title: Cux2 acts as a critical regulator for neurogenesis in the olfactory epithelium of vertebrates.
    9. The downregulation of CUX2 in male liver at puberty contributes to the developmental changes establishing adult patterns of sex-specific gene expression.
      Title: Impact of CUX2 on the female mouse liver transcriptome: activation of female-biased genes and repression of male-biased genes.
    10. Cux2 is expressed and may participate in development of a specific subtype of myelinated TrkA(+) nociceptors.
      Title: The transcription factor Cux2 marks development of an A-delta sublineage of TrkA sensory neurons.
    Submit: New GeneRIF Correction See all GeneRIFs (17)

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables DNA-binding transcription repressor activity, RNA polymerase II-specific IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables RNA polymerase II transcription regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA polymerase II transcription regulatory region sequence-specific DNA binding IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables sequence-specific double-stranded DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in cognition ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within negative regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of dendrite morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of dendritic spine morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of excitatory postsynaptic potential IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of gene expression IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of synapse assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in short-term memory IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    homeobox protein cut-like 2
    Names
    homeobox protein Cux-2

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001312908.2 → NP_001299837.1  homeobox protein cut-like 2 isoform 1

      Status: REVIEWED

      Source sequence(s)
      AC113302, AC140353
      Consensus CDS
      CCDS39251.1
      UniProtKB/Swiss-Prot
      P70298, Q6P1E6
      Related
      ENSMUSP00000107381.3, ENSMUST00000111752.10
      Conserved Domains (3) summary
      COG1196
      Location:121 → 315
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      pfam00046
      Location:1116 → 1170
      Homeobox; Homeobox domain
      pfam02376
      Location:988 → 1064
      CUT; CUT domain

    2. NM_001415780.2 → NP_001402709.1  homeobox protein cut-like 2 isoform 2

      Status: REVIEWED

      Source sequence(s)
      AC113302, AC140353

    3. NM_001428516.1 → NP_001415445.1  homeobox protein cut-like 2 isoform 1

      Status: REVIEWED

      Source sequence(s)
      AC113302, AC140353
      UniProtKB/Swiss-Prot
      P70298, Q6P1E6

    4. NM_001428517.1 → NP_001415446.1  homeobox protein cut-like 2 isoform 1

      Status: REVIEWED

      Source sequence(s)
      AC113302, AC124189
      UniProtKB/Swiss-Prot
      P70298, Q6P1E6

    5. NM_001428518.1 → NP_001415447.1  homeobox protein cut-like 2 isoform 3

      Status: REVIEWED

      Source sequence(s)
      AC113302, AC124189

    6. NM_007804.3 → NP_031830.2  homeobox protein cut-like 2 isoform 1

      See identical proteins and their annotated locations for NP_031830.2

      Status: REVIEWED

      Source sequence(s)
      AC113302, AC140353
      Consensus CDS
      CCDS39251.1
      UniProtKB/Swiss-Prot
      P70298, Q6P1E6
      Related
      ENSMUSP00000083497.6, ENSMUST00000086317.12
      Conserved Domains (3) summary
      COG1196
      Location:121 → 315
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      pfam00046
      Location:1116 → 1170
      Homeobox; Homeobox domain
      pfam02376
      Location:988 → 1064
      CUT; CUT domain

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000071.7 Reference GRCm39 C57BL/6J

      Range
      121996025..122188522 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011248166.4 → XP_011246468.1  homeobox protein cut-like 2 isoform X4

      Conserved Domains (3) summary
      COG1196
      Location:199 → 393
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      pfam00046
      Location:1205 → 1259
      Homeobox; Homeobox domain
      pfam02376
      Location:1077 → 1150
      CUT; CUT domain

    2. XM_030254117.2 → XP_030109977.1  homeobox protein cut-like 2 isoform X3

      Conserved Domains (3) summary
      COG1196
      Location:274 → 505
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      pfam00046
      Location:1265 → 1319
      Homeobox; Homeobox domain
      pfam02376
      Location:1137 → 1210
      CUT; CUT domain

    3. XM_030254116.2 → XP_030109976.1  homeobox protein cut-like 2 isoform X2

      Conserved Domains (3) summary
      COG1196
      Location:279 → 473
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      pfam00046
      Location:1274 → 1328
      Homeobox; Homeobox domain
      pfam02376
      Location:1146 → 1219
      CUT; CUT domain

    4. XM_011248171.4 → XP_011246473.2  homeobox protein cut-like 2 isoform X1

      Conserved Domains (3) summary
      COG1196
      Location:279 → 473
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      pfam00046
      Location:1285 → 1339
      Homeobox; Homeobox domain
      pfam02376
      Location:1157 → 1230
      CUT; CUT domain

    5. XM_011248173.3 → XP_011246475.1  homeobox protein cut-like 2 isoform X6

      See identical proteins and their annotated locations for XP_011246475.1

      Conserved Domains (3) summary
      COG1196
      Location:121 → 315
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      pfam00046
      Location:1127 → 1181
      Homeobox; Homeobox domain
      pfam02376
      Location:999 → 1072
      CUT; CUT domain

    6. XM_030254118.2 → XP_030109978.1  homeobox protein cut-like 2 isoform X7

      UniProtKB/Swiss-Prot
      P70298, Q6P1E6
      Conserved Domains (3) summary
      COG1196
      Location:121 → 315
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      pfam00046
      Location:1116 → 1170
      Homeobox; Homeobox domain
      pfam02376
      Location:988 → 1064
      CUT; CUT domain

    7. XM_011248167.3 → XP_011246469.1  homeobox protein cut-like 2 isoform X6

      See identical proteins and their annotated locations for XP_011246469.1

      Conserved Domains (3) summary
      COG1196
      Location:121 → 315
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      pfam00046
      Location:1127 → 1181
      Homeobox; Homeobox domain
      pfam02376
      Location:999 → 1072
      CUT; CUT domain

    8. XM_030254119.2 → XP_030109979.1  homeobox protein cut-like 2 isoform X7

      UniProtKB/Swiss-Prot
      P70298, Q6P1E6
      Conserved Domains (3) summary
      COG1196
      Location:121 → 315
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      pfam00046
      Location:1116 → 1170
      Homeobox; Homeobox domain
      pfam02376
      Location:988 → 1064
      CUT; CUT domain

    9. XM_011248168.4 → XP_011246470.1  homeobox protein cut-like 2 isoform X6

      See identical proteins and their annotated locations for XP_011246470.1

      Conserved Domains (3) summary
      COG1196
      Location:121 → 315
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      pfam00046
      Location:1127 → 1181
      Homeobox; Homeobox domain
      pfam02376
      Location:999 → 1072
      CUT; CUT domain

    10. XM_011248169.4 → XP_011246471.1  homeobox protein cut-like 2 isoform X6

      See identical proteins and their annotated locations for XP_011246471.1

      Conserved Domains (3) summary
      COG1196
      Location:121 → 315
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      pfam00046
      Location:1127 → 1181
      Homeobox; Homeobox domain
      pfam02376
      Location:999 → 1072
      CUT; CUT domain

    11. XM_011248170.4 → XP_011246472.1  homeobox protein cut-like 2 isoform X6

      See identical proteins and their annotated locations for XP_011246472.1

      Conserved Domains (3) summary
      COG1196
      Location:121 → 315
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      pfam00046
      Location:1127 → 1181
      Homeobox; Homeobox domain
      pfam02376
      Location:999 → 1072
      CUT; CUT domain

    12. XM_011248172.4 → XP_011246474.1  homeobox protein cut-like 2 isoform X6

      See identical proteins and their annotated locations for XP_011246474.1

      Conserved Domains (3) summary
      COG1196
      Location:121 → 315
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      pfam00046
      Location:1127 → 1181
      Homeobox; Homeobox domain
      pfam02376
      Location:999 → 1072
      CUT; CUT domain

    13. XM_036164774.1 → XP_036020667.1  homeobox protein cut-like 2 isoform X7

      Conserved Domains (3) summary
      COG1196
      Location:121 → 315
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      pfam00046
      Location:1116 → 1170
      Homeobox; Homeobox domain
      pfam02376
      Location:988 → 1064
      CUT; CUT domain

    14. XM_011248176.4 → XP_011246478.1  homeobox protein cut-like 2 isoform X6

      See identical proteins and their annotated locations for XP_011246478.1

      Conserved Domains (3) summary
      COG1196
      Location:121 → 315
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      pfam00046
      Location:1127 → 1181
      Homeobox; Homeobox domain
      pfam02376
      Location:999 → 1072
      CUT; CUT domain

    15. XM_036164775.1 → XP_036020668.1  homeobox protein cut-like 2 isoform X8

      Conserved Domains (3) summary
      COG1196
      Location:121 → 315
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      pfam00046
      Location:1096 → 1150
      Homeobox; Homeobox domain
      pfam02376
      Location:968 → 1044
      CUT; CUT domain

    16. XM_017320655.3 → XP_017176144.1  homeobox protein cut-like 2 isoform X9

      Conserved Domains (3) summary
      COG1196
      Location:4 → 132
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      pfam00046
      Location:948 → 1002
      Homeobox; Homeobox domain
      pfam02376
      Location:820 → 893
      CUT; CUT domain

    17. XM_030254120.2 → XP_030109980.1  homeobox protein cut-like 2 isoform X9

      Conserved Domains (3) summary
      COG1196
      Location:4 → 132
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      pfam00046
      Location:948 → 1002
      Homeobox; Homeobox domain
      pfam02376
      Location:820 → 893
      CUT; CUT domain
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P70298.2 GenPept UniProtKB/Swiss-Prot:P70298

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