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

Summary

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

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_000071.7 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?

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.
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.
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.
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.
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.
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.
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.
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.
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.
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)

Endonuclease-mediated (2)
Gene trapped (1) 1 citation
Targeted (6) 1 citation

General gene information

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Markers

Cux2 (e-PCR), detects polymorphism
- UniSTS:547859

Cux2 (e-PCR), detects polymorphism
- UniSTS:530681

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

Status: REVIEWED

Source sequence(s)

AC113302, AC140353
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
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
NM_001428518.1 → NP_001415447.1 homeobox protein cut-like 2 isoform 3

Status: REVIEWED

Source sequence(s)

AC113302, AC124189
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

NC_000071.7 Reference GRCm39 C57BL/6J

Range

121996025..122188522 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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