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

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: human all
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Genomic context

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_000071.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
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.
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.
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.
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.
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)

Endonuclease-mediated (3) 1 citation
Targeted (5) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

BE120355 (e-PCR)
- UniSTS:247311

D5Mit265 (e-PCR), detects polymorphism
- UniSTS:130401

PMC133930P1 (e-PCR)
- UniSTS:270691

RH125658 (e-PCR)
- UniSTS:162444

Cutl1 (e-PCR), detects polymorphism
- UniSTS:506827

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 factor activity, RNA polymerase II-specific	IEA Inferred from Electronic Annotation 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
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 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 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 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)

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

Status: VALIDATED

Source sequence(s)

AC080158, AC083890, AC087329
NM_001405081.1 → NP_001392010.1 homeobox protein cut-like 1 isoform i

Status: VALIDATED

Source sequence(s)

AC080158, AC083890, AC087329
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
NM_001405083.1 → NP_001392012.1 homeobox protein cut-like 1 isoform k

Status: VALIDATED

Source sequence(s)

AC080158, AC083890, AC087329
NM_001405084.1 → NP_001392013.1 homeobox protein cut-like 1 isoform l

Status: VALIDATED

Source sequence(s)

AC080158, AC083890, AC087329
NM_001405085.1 → NP_001392014.1 protein CASP isoform m

Status: VALIDATED

Source sequence(s)

AC080158, AC083890, AC087329
NM_001405086.1 → NP_001392015.1 protein CASP isoform n

Status: VALIDATED

Source sequence(s)

AC080158, AC083890, AC087329
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
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

NC_000071.7 Reference GRCm39 C57BL/6J

Range

136276989..136596429 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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
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
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
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
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
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
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