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Cux1 cut-like homeobox 1 [ Mus musculus (house mouse) ]

Gene ID: 13047, updated on 11-Apr-2024

Summary

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Official Symbol
Cux1provided by MGI
Official Full Name
cut-like homeobox 1provided by MGI
Primary source
MGI:MGI:88568
See related
Ensembl:ENSMUSG00000029705 AllianceGenome:MGI:88568
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
CDP; Cux; Cutl1; Cux-1
Summary
Enables RNA polymerase II cis-regulatory region sequence-specific DNA binding activity and chromatin binding activity. Involved in positive regulation of dendrite morphogenesis. Acts upstream of or within animal organ development and negative regulation of transcription by RNA polymerase II. Located in cytoplasm; neuron projection; and nucleus. Is expressed in several structures, including alimentary system; genitourinary system; nervous system; respiratory system; and sensory organ. Orthologous to human CUX1 (cut like homeobox 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in thymus adult (RPKM 14.0), kidney adult (RPKM 8.1) and 28 other tissues See more
Orthologs
human all
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Genomic context

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Location:
5 G2; 5 75.96 cM
Exon count:
34
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 5 NC_000071.7 (136276989..136596429, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 5 NC_000071.6 (136248135..136567590, complement)

Chromosome 5 - NC_000071.7Genomic Context describing neighboring genes Neighboring gene ribosomal protein L7A pseudogene Neighboring gene SH2B adaptor protein 2 Neighboring gene predicted gene, 30408 Neighboring gene predicted gene, 16599 Neighboring gene CapStarr-seq enhancer MGSCv37_chr5:136886527-136886728 Neighboring gene microRNA 721 Neighboring gene STARR-seq mESC enhancer starr_14619 Neighboring gene STARR-seq mESC enhancer starr_14620 Neighboring gene predicted gene, 54307 Neighboring gene CapStarr-seq enhancer MGSCv37_chr5:137026660-137026843 Neighboring gene STARR-seq mESC enhancer starr_14621 Neighboring gene STARR-positive B cell enhancer ABC_E4794 Neighboring gene CapStarr-seq enhancer MGSCv37_chr5:137093643-137093839 Neighboring gene CapStarr-seq enhancer MGSCv37_chr5:137093950-137094103 Neighboring gene CapStarr-seq enhancer MGSCv37_chr5:137099197-137099306 Neighboring gene predicted gene, 38722 Neighboring gene myosin, light chain 10, regulatory

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. CUX1 promotes epithelial-mesenchymal transition (EMT) in renal fibrosis of UUO model by targeting MMP7. Teng S, et al. Biochem Biophys Res Commun, 2022 Jun 11. PMID 35397425
  2. Loss of a 7q gene, CUX1, disrupts epigenetically driven DNA repair and drives therapy-related myeloid neoplasms. Imgruet MK, et al. Blood, 2021 Sep 2. PMID 34473231, Free PMC Article
  3. The function of CUX1 in oxidative DNA damage repair is needed to prevent premature senescence of mouse embryo fibroblasts. Ramdzan ZM, et al. Oncotarget, 2015 Feb 28. PMID 25682875, Free PMC Article
  4. CUX1 transcription factor is required for optimal ATM/ATR-mediated responses to DNA damage. Vadnais C, et al. Nucleic Acids Res, 2012 May. PMID 22319212, Free PMC Article
  5. Asynchronous expression of the homeodomain protein CUX1 in Sertoli cells and spermatids during spermatogenesis in mice. Kroll MR, et al. Biol Reprod, 2011 Mar. PMID 20980687, Free PMC Article

See all (536) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. CUX1-related neurodevelopmental disorder: deep insights into phenotype-genotype spectrum and underlying pathology.
    Title: CUX1-related neurodevelopmental disorder: deep insights into phenotype-genotype spectrum and underlying pathology.
  2. CUX1 promotes epithelial-mesenchymal transition (EMT) in renal fibrosis of UUO model by targeting MMP7.
    Title: CUX1 promotes epithelial-mesenchymal transition (EMT) in renal fibrosis of UUO model by targeting MMP7.
  3. Loss of a 7q gene, CUX1, disrupts epigenetically driven DNA repair and drives therapy-related myeloid neoplasms.
    Title: Loss of a 7q gene, CUX1, disrupts epigenetically driven DNA repair and drives therapy-related myeloid neoplasms.
  4. To determine the role for CUX1 in hematopoiesis, this study generated 2 short hairpin RNA-based mouse models with approximately 54% (Cux1(mid)) or approximately 12% (Cux1(low)) residual CUX1 protein. Cux1(mid) mice develop myelodysplastic syndrome (MDS) with anemia and trilineage dysplasia, whereas CUX1(low) mice developed MDS/myeloproliferative neoplasms and anemia.
    Title: Gene dosage effect of CUX1 in a murine model disrupts HSC homeostasis and controls the severity and mortality of MDS.
  5. reduction of VAV2 in absence of CUX1 was associated with a significant decrease of RAC1 activity in response to epithelial wounding. Our results identify a novel pathway by which CUX1 regulates normal intestinal epithelial cell restitution
    Title: Transcription factor CUX1 is required for intestinal epithelial wound healing and targets the VAV2-RAC1 Signalling complex.
  6. Cux1 expression in polycystic kidney disease is not directly involved in cystogenesis but promotes cell proliferation required for expansion of existing cysts, primarily by repression of p27.
    Title: Cux1 promotes cell proliferation and polycystic kidney disease progression in an ADPKD mouse model.
  7. Cux1 is essential for the developmental modulation of intrinsic excitability and the switch to a Kv1-dependent firing mode necessary for interhemispheric innervation.
    Title: Cux1 Enables Interhemispheric Connections of Layer II/III Neurons by Regulating Kv1-Dependent Firing.
  8. Findings reinforce the link between oxidative DNA damage and cellular senescence and suggest that the role of CUX1 as an accessory factor in DNA repair will be critical in physiological situations that generate higher levels of reactive oxygen species.
    Title: The function of CUX1 in oxidative DNA damage repair is needed to prevent premature senescence of mouse embryo fibroblasts.
  9. 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.
  10. Results show that Cux1 is expressed in cerebellar granule cell precursors and downregulated as they terminally differentiate; suggests some limitations of established medulloblastoma cell lines and mouse models
    Title: The transcription factor Cux1 in cerebellar granule cell development and medulloblastoma pathogenesis.
Submit: New GeneRIF Correction See all GeneRIFs (42)

Variation

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Alleles

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

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • KIAA4047, MGC102214, mKIAA4047

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 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 chromatin binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein-macromolecule adaptor activity ISO
Inferred from Sequence Orthology
more info
  
enables sequence-specific DNA binding IDA
Inferred from Direct Assay
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
acts_upstream_of_or_within inner ear auditory receptor cell differentiation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in intra-Golgi vesicle-mediated transport IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within kidney development IGI
Inferred from Genetic Interaction
more info
 PubMed 
acts_upstream_of_or_within lung development IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within multicellular organism development IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of dendrite morphogenesis IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in retrograde transport, vesicle recycling within Golgi ISO
Inferred from Sequence Orthology
more info
  
Component Evidence Code Pubs
located_in Golgi apparatus ISO
Inferred from Sequence Orthology
more info
  
located_in Golgi membrane ISO
Inferred from Sequence Orthology
more info
  
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in membrane IEA
Inferred from Electronic Annotation
more info
  
located_in neuron projection IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleoplasm ISO
Inferred from Sequence Orthology
more info
  
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
protein CASP; homeobox protein cut-like 1
Names
CCAAT displacement protein
Cux/CDP homeoprotein
cut-like 1
homeobox protein cux-1

NCBI Reference Sequences (RefSeq)

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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_001291233.2 → NP_001278162.1  homeobox protein cut-like 1 isoform c

    Status: VALIDATED

    Source sequence(s)
    AC080158, AC083890, AC087329
    UniProtKB/TrEMBL
    H3BJQ9
    Related
    ENSMUSP00000135086.2, ENSMUST00000176172.8
    Conserved Domains (4) summary
    pfam00046
    Location:1340 → 1393
    Homeobox; Homeobox domain
    pfam00901
    Location:171 → 446
    Orbi_VP5; Orbivirus outer capsid protein VP5
    pfam02376
    Location:1215 → 1292
    CUT; CUT domain
    pfam13851
    Location:216 → 437
    GAS; Growth-arrest specific micro-tubule binding

  2. NM_001291234.2 → NP_001278163.1  homeobox protein cut-like 1 isoform d

    Status: VALIDATED

    Source sequence(s)
    AC080158, AC083890, AC087329
    Consensus CDS
    CCDS71684.1
    UniProtKB/Swiss-Prot
    O08994, P53564, P70301, Q571L6, Q91ZD2
    UniProtKB/TrEMBL
    H3BK24
    Related
    ENSMUSP00000135223.3, ENSMUST00000175975.9
    Conserved Domains (5) summary
    pfam00046
    Location:1231 → 1284
    Homeobox; Homeobox domain
    pfam02376
    Location:1106 → 1183
    CUT; CUT domain
    pfam13851
    Location:131 → 350
    GAS; Growth-arrest specific micro-tubule binding
    cl23720
    Location:290 → 372
    RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)
    cl23765
    Location:108 → 248
    iSH2_PI3K_IA_R; Inter-Src homology 2 (iSH2) helical domain of Class IA Phosphoinositide 3-kinase Regulatory subunits

  3. NM_001291238.2 → NP_001278167.1  protein CASP isoform e

    Status: VALIDATED

    Source sequence(s)
    AC080158, AC083890, AC087329
    Consensus CDS
    CCDS71685.1
    UniProtKB/Swiss-Prot
    P70403, Q7TQJ4, Q91WN6
    UniProtKB/TrEMBL
    H3BJN3
    Related
    ENSMUSP00000135054.2, ENSMUST00000176216.9
    Conserved Domains (3) summary
    pfam00901
    Location:86 → 361
    Orbi_VP5; Orbivirus outer capsid protein VP5
    pfam08172
    Location:423 → 638
    CASP_C; CASP C terminal
    pfam13851
    Location:131 → 352
    GAS; Growth-arrest specific micro-tubule binding

  4. NM_001291239.2 → NP_001278168.1  protein CASP isoform f

    Status: VALIDATED

    Source sequence(s)
    AC080158, AC083890, AC087329
    UniProtKB/TrEMBL
    Q9JJB6
    Conserved Domains (4) summary
    pfam07851
    Location:390 → 494
    TMPIT; TMPIT-like protein
    pfam08172
    Location:506 → 721
    CASP_C; CASP C terminal
    pfam13851
    Location:216 → 435
    GAS; Growth-arrest specific micro-tubule binding
    pfam15290
    Location:231 → 374
    Syntaphilin; Golgi-localized syntaxin-1-binding clamp

  5. NM_001291240.2 → NP_001278169.1  protein CASP isoform g

    Status: VALIDATED

    Source sequence(s)
    AC080158, AC083890, AC087329
    UniProtKB/TrEMBL
    Q9JJB6
    Conserved Domains (3) summary
    pfam00901
    Location:171 → 446
    Orbi_VP5; Orbivirus outer capsid protein VP5
    pfam08172
    Location:508 → 723
    CASP_C; CASP C terminal
    pfam13851
    Location:216 → 437
    GAS; Growth-arrest specific micro-tubule binding

  6. NM_001405079.1 → NP_001392008.1  homeobox protein cut-like 1 isoform h

    Status: VALIDATED

    Source sequence(s)
    AC080158, AC083890, AC087329

  7. NM_001405081.1 → NP_001392010.1  homeobox protein cut-like 1 isoform i

    Status: VALIDATED

    Source sequence(s)
    AC080158, AC083890, AC087329

  8. NM_001405082.1 → NP_001392011.1  homeobox protein cut-like 1 isoform j

    Status: VALIDATED

    Source sequence(s)
    AC080158, AC083890, AC087329
    Related
    ENSMUSP00000135370.3, ENSMUST00000176486.9

  9. NM_001405083.1 → NP_001392012.1  homeobox protein cut-like 1 isoform k

    Status: VALIDATED

    Source sequence(s)
    AC080158, AC083890, AC087329

  10. NM_001405084.1 → NP_001392013.1  homeobox protein cut-like 1 isoform l

    Status: VALIDATED

    Source sequence(s)
    AC080158, AC083890, AC087329

  11. NM_001405085.1 → NP_001392014.1  protein CASP isoform m

    Status: VALIDATED

    Source sequence(s)
    AC080158, AC083890, AC087329

  12. NM_001405086.1 → NP_001392015.1  protein CASP isoform n

    Status: VALIDATED

    Source sequence(s)
    AC080158, AC083890, AC087329

  13. NM_009986.5 → NP_034116.3  homeobox protein cut-like 1 isoform a

    Status: VALIDATED

    Source sequence(s)
    AC080158, AC083890, AC087329
    Consensus CDS
    CCDS39328.1
    UniProtKB/TrEMBL
    E9QKE9, Q5BL05
    Related
    ENSMUSP00000004097.9, ENSMUST00000004097.16
    Conserved Domains (4) summary
    pfam00046
    Location:1153 → 1206
    Homeobox; Homeobox domain
    pfam00901
    Location:86 → 361
    Orbi_VP5; Orbivirus outer capsid protein VP5
    pfam02376
    Location:1028 → 1105
    CUT; CUT domain
    pfam13851
    Location:131 → 352
    GAS; Growth-arrest specific micro-tubule binding

  14. NM_198602.4 → NP_941004.2  protein CASP isoform b

    Status: VALIDATED

    Source sequence(s)
    AC080158, AC083890, AC087329
    Consensus CDS
    CCDS57391.1
    UniProtKB/Swiss-Prot
    P70403, Q7TQJ4, Q91WN6
    UniProtKB/TrEMBL
    H3BKT0
    Related
    ENSMUSP00000135512.2, ENSMUST00000176745.8
    Conserved Domains (3) summary
    pfam07851
    Location:305 → 409
    TMPIT; TMPIT-like protein
    pfam08172
    Location:421 → 636
    CASP_C; CASP C terminal
    pfam15290
    Location:146 → 289
    Syntaphilin; Golgi-localized syntaxin-1-binding clamp

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
    136276989..136596429 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_030254113.2 → XP_030109973.1  homeobox protein cut-like 1 isoform X12

    UniProtKB/TrEMBL
    Q5BL05
    Conserved Domains (4) summary
    PHA03247
    Location:634 → 817
    PHA03247; large tegument protein UL36; Provisional
    TIGR02169
    Location:18 → 368
    SMC_prok_A; chromosome segregation protein SMC, primarily archaeal type
    pfam00046
    Location:1131 → 1185
    Homeobox; Homeobox domain
    pfam02376
    Location:1006 → 1079
    CUT; CUT domain

  2. XM_036164773.1 → XP_036020666.1  homeobox protein cut-like 1 isoform X9

    UniProtKB/TrEMBL
    H3BJQ9
    Conserved Domains (4) summary
    PHA03247
    Location:736 → 919
    PHA03247; large tegument protein UL36; Provisional
    COG1196
    Location:16 → 377
    Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
    pfam00046
    Location:1233 → 1287
    Homeobox; Homeobox domain
    pfam02376
    Location:1108 → 1185
    CUT; CUT domain

  3. XM_030254110.2 → XP_030109970.1  homeobox protein cut-like 1 isoform X10

    UniProtKB/TrEMBL
    Q5BL05
    Conserved Domains (4) summary
    PHA03247
    Location:680 → 863
    PHA03247; large tegument protein UL36; Provisional
    COG0419
    Location:17 → 430
    SbcC; DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]
    pfam00046
    Location:1177 → 1231
    Homeobox; Homeobox domain
    pfam02376
    Location:1052 → 1125
    CUT; CUT domain

  4. XM_030254108.2 → XP_030109968.1  homeobox protein cut-like 1 isoform X5

    UniProtKB/TrEMBL
    H3BJQ9
    Conserved Domains (4) summary
    PHA03247
    Location:760 → 943
    PHA03247; large tegument protein UL36; Provisional
    TIGR04523
    Location:17 → 399
    Mplasa_alph_rch; helix-rich Mycoplasma protein
    pfam00046
    Location:1257 → 1311
    Homeobox; Homeobox domain
    pfam02376
    Location:1132 → 1205
    CUT; CUT domain

  5. XM_030254106.2 → XP_030109966.1  homeobox protein cut-like 1 isoform X2

    UniProtKB/TrEMBL
    H3BJQ9
    Conserved Domains (4) summary
    PHA03247
    Location:845 → 1028
    PHA03247; large tegument protein UL36; Provisional
    COG0419
    Location:103 → 482
    SbcC; DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]
    pfam00046
    Location:1342 → 1396
    Homeobox; Homeobox domain
    pfam02376
    Location:1217 → 1290
    CUT; CUT domain

  6. XM_017320654.3 → XP_017176143.1  homeobox protein cut-like 1 isoform X1

    UniProtKB/TrEMBL
    H3BJQ9
    Conserved Domains (4) summary
    PHA03247
    Location:867 → 1050
    PHA03247; large tegument protein UL36; Provisional
    COG0419
    Location:103 → 482
    SbcC; DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]
    pfam00046
    Location:1364 → 1418
    Homeobox; Homeobox domain
    pfam02376
    Location:1239 → 1312
    CUT; CUT domain

  7. XM_006504354.4 → XP_006504417.1  homeobox protein cut-like 1 isoform X8

    UniProtKB/TrEMBL
    H3BLS0, Q5BL05
    Related
    ENSMUSP00000135892.2, ENSMUST00000176778.8
    Conserved Domains (5) summary
    PHA03247
    Location:739 → 922
    PHA03247; large tegument protein UL36; Provisional
    TIGR02168
    Location:196 → 447
    SMC_prok_B; chromosome segregation protein SMC, common bacterial type
    TIGR04211
    Location:400 → 502
    SH3_and_anchor; SH3 domain protein
    pfam00046
    Location:1236 → 1290
    Homeobox; Homeobox domain
    pfam02376
    Location:1111 → 1184
    CUT; CUT domain

  8. XM_030254107.2 → XP_030109967.1  homeobox protein cut-like 1 isoform X4

    UniProtKB/Swiss-Prot
    O08994, P53564, P70301, Q571L6, Q91ZD2
    Conserved Domains (4) summary
    PHA03247
    Location:819 → 1002
    PHA03247; large tegument protein UL36; Provisional
    TIGR02168
    Location:196 → 447
    SMC_prok_B; chromosome segregation protein SMC, common bacterial type
    pfam00046
    Location:1316 → 1370
    Homeobox; Homeobox domain
    pfam02376
    Location:1191 → 1264
    CUT; CUT domain
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P53564.3 GenPept UniProtKB/Swiss-Prot:P53564
P70403.2 GenPept UniProtKB/Swiss-Prot:P70403

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