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

Gene ID: 13047, updated on 12-May-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 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
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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 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

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_001291233.2NP_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
  7. NM_001405081.1NP_001392010.1  homeobox protein cut-like 1 isoform i

    Status: VALIDATED

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

    Status: VALIDATED

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

    Status: VALIDATED

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

    Status: VALIDATED

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

    Status: VALIDATED

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

    Status: VALIDATED

    Source sequence(s)
    AC080158, AC083890, AC087329
  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