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

    Gene ID: 13047, updated on 3-Dec-2024

    Summary

    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 several processes, including inner ear auditory receptor cell differentiation; lung 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, Nov 2024]
    Expression
    Ubiquitous expression in thymus adult (RPKM 14.0), kidney adult (RPKM 8.1) and 28 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See Cux1 in Genome Data Viewer
    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

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Variation

    Alleles

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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • KIAA4047, MGC102214, mKIAA4047

    Gene Ontology Provided by MGI

    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 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

    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)

    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_001291233.2NP_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:13401393
      Homeobox; Homeobox domain
      pfam00901
      Location:171446
      Orbi_VP5; Orbivirus outer capsid protein VP5
      pfam02376
      Location:12151292
      CUT; CUT domain
      pfam13851
      Location:216437
      GAS; Growth-arrest specific micro-tubule binding
    2. NM_001291234.2NP_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:12311284
      Homeobox; Homeobox domain
      pfam02376
      Location:11061183
      CUT; CUT domain
      pfam13851
      Location:131350
      GAS; Growth-arrest specific micro-tubule binding
      cl23720
      Location:290372
      RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)
      cl23765
      Location:108248
      iSH2_PI3K_IA_R; Inter-Src homology 2 (iSH2) helical domain of Class IA Phosphoinositide 3-kinase Regulatory subunits
    3. NM_001291238.2NP_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:86361
      Orbi_VP5; Orbivirus outer capsid protein VP5
      pfam08172
      Location:423638
      CASP_C; CASP C terminal
      pfam13851
      Location:131352
      GAS; Growth-arrest specific micro-tubule binding
    4. NM_001291239.2NP_001278168.1  protein CASP isoform f

      Status: VALIDATED

      Source sequence(s)
      AC080158, AC083890, AC087329
      UniProtKB/TrEMBL
      Q9JJB6
      Conserved Domains (4) summary
      pfam07851
      Location:390494
      TMPIT; TMPIT-like protein
      pfam08172
      Location:506721
      CASP_C; CASP C terminal
      pfam13851
      Location:216435
      GAS; Growth-arrest specific micro-tubule binding
      pfam15290
      Location:231374
      Syntaphilin; Golgi-localized syntaxin-1-binding clamp
    5. NM_001291240.2NP_001278169.1  protein CASP isoform g

      Status: VALIDATED

      Source sequence(s)
      AC080158, AC083890, AC087329
      UniProtKB/TrEMBL
      Q9JJB6
      Conserved Domains (3) summary
      pfam00901
      Location:171446
      Orbi_VP5; Orbivirus outer capsid protein VP5
      pfam08172
      Location:508723
      CASP_C; CASP C terminal
      pfam13851
      Location:216437
      GAS; Growth-arrest specific micro-tubule binding
    6. NM_001405079.1NP_001392008.1  homeobox protein cut-like 1 isoform h

      Status: VALIDATED

      Source sequence(s)
      AC080158, AC083890, AC087329
      UniProtKB/TrEMBL
      H3BJQ9
    7. NM_001405081.1NP_001392010.1  homeobox protein cut-like 1 isoform i

      Status: VALIDATED

      Source sequence(s)
      AC080158, AC083890, AC087329
      UniProtKB/TrEMBL
      H3BJQ9
    8. NM_001405082.1NP_001392011.1  homeobox protein cut-like 1 isoform j

      Status: VALIDATED

      Source sequence(s)
      AC080158, AC083890, AC087329
      UniProtKB/TrEMBL
      H3BJQ9
      Related
      ENSMUSP00000135370.3, ENSMUST00000176486.9
    9. NM_001405083.1NP_001392012.1  homeobox protein cut-like 1 isoform k

      Status: VALIDATED

      Source sequence(s)
      AC080158, AC083890, AC087329
      UniProtKB/TrEMBL
      Q5BL05
    10. NM_001405084.1NP_001392013.1  homeobox protein cut-like 1 isoform l

      Status: VALIDATED

      Source sequence(s)
      AC080158, AC083890, AC087329
      UniProtKB/TrEMBL
      Q5BL05
    11. NM_001405085.1NP_001392014.1  protein CASP isoform m

      Status: VALIDATED

      Source sequence(s)
      AC080158, AC083890, AC087329
      UniProtKB/TrEMBL
      Q9JJB6
    12. NM_001405086.1NP_001392015.1  protein CASP isoform n

      Status: VALIDATED

      Source sequence(s)
      AC080158, AC083890, AC087329
      UniProtKB/Swiss-Prot
      P70403, Q7TQJ4, Q91WN6
    13. NM_009986.5NP_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:11531206
      Homeobox; Homeobox domain
      pfam00901
      Location:86361
      Orbi_VP5; Orbivirus outer capsid protein VP5
      pfam02376
      Location:10281105
      CUT; CUT domain
      pfam13851
      Location:131352
      GAS; Growth-arrest specific micro-tubule binding
    14. NM_198602.4NP_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:305409
      TMPIT; TMPIT-like protein
      pfam08172
      Location:421636
      CASP_C; CASP C terminal
      pfam15290
      Location:146289
      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_030254113.2XP_030109973.1  homeobox protein cut-like 1 isoform X12

      UniProtKB/TrEMBL
      Q5BL05
      Conserved Domains (4) summary
      PHA03247
      Location:634817
      PHA03247; large tegument protein UL36; Provisional
      TIGR02169
      Location:18368
      SMC_prok_A; chromosome segregation protein SMC, primarily archaeal type
      pfam00046
      Location:11311185
      Homeobox; Homeobox domain
      pfam02376
      Location:10061079
      CUT; CUT domain
    2. XM_036164773.1XP_036020666.1  homeobox protein cut-like 1 isoform X9

      UniProtKB/TrEMBL
      H3BJQ9
      Conserved Domains (4) summary
      PHA03247
      Location:736919
      PHA03247; large tegument protein UL36; Provisional
      COG1196
      Location:16377
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      pfam00046
      Location:12331287
      Homeobox; Homeobox domain
      pfam02376
      Location:11081185
      CUT; CUT domain
    3. XM_030254110.2XP_030109970.1  homeobox protein cut-like 1 isoform X10

      UniProtKB/TrEMBL
      Q5BL05
      Conserved Domains (4) summary
      PHA03247
      Location:680863
      PHA03247; large tegument protein UL36; Provisional
      COG0419
      Location:17430
      SbcC; DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]
      pfam00046
      Location:11771231
      Homeobox; Homeobox domain
      pfam02376
      Location:10521125
      CUT; CUT domain
    4. XM_030254108.2XP_030109968.1  homeobox protein cut-like 1 isoform X5

      UniProtKB/TrEMBL
      H3BJQ9
      Conserved Domains (4) summary
      PHA03247
      Location:760943
      PHA03247; large tegument protein UL36; Provisional
      TIGR04523
      Location:17399
      Mplasa_alph_rch; helix-rich Mycoplasma protein
      pfam00046
      Location:12571311
      Homeobox; Homeobox domain
      pfam02376
      Location:11321205
      CUT; CUT domain
    5. XM_030254106.2XP_030109966.1  homeobox protein cut-like 1 isoform X2

      UniProtKB/TrEMBL
      H3BJQ9
      Conserved Domains (4) summary
      PHA03247
      Location:8451028
      PHA03247; large tegument protein UL36; Provisional
      COG0419
      Location:103482
      SbcC; DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]
      pfam00046
      Location:13421396
      Homeobox; Homeobox domain
      pfam02376
      Location:12171290
      CUT; CUT domain
    6. XM_017320654.3XP_017176143.1  homeobox protein cut-like 1 isoform X1

      UniProtKB/TrEMBL
      H3BJQ9
      Conserved Domains (4) summary
      PHA03247
      Location:8671050
      PHA03247; large tegument protein UL36; Provisional
      COG0419
      Location:103482
      SbcC; DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]
      pfam00046
      Location:13641418
      Homeobox; Homeobox domain
      pfam02376
      Location:12391312
      CUT; CUT domain
    7. XM_006504354.4XP_006504417.1  homeobox protein cut-like 1 isoform X8

      UniProtKB/TrEMBL
      H3BLS0, Q5BL05
      Related
      ENSMUSP00000135892.2, ENSMUST00000176778.8
      Conserved Domains (5) summary
      PHA03247
      Location:739922
      PHA03247; large tegument protein UL36; Provisional
      TIGR02168
      Location:196447
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type
      TIGR04211
      Location:400502
      SH3_and_anchor; SH3 domain protein
      pfam00046
      Location:12361290
      Homeobox; Homeobox domain
      pfam02376
      Location:11111184
      CUT; CUT domain
    8. XM_030254107.2XP_030109967.1  homeobox protein cut-like 1 isoform X4

      UniProtKB/Swiss-Prot
      O08994, P53564, P70301, Q571L6, Q91ZD2
      Conserved Domains (4) summary
      PHA03247
      Location:8191002
      PHA03247; large tegument protein UL36; Provisional
      TIGR02168
      Location:196447
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type
      pfam00046
      Location:13161370
      Homeobox; Homeobox domain
      pfam02376
      Location:11911264
      CUT; CUT domain