CUX1 cut like homeobox 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: CUX1provided by HGNC
Official Full Name: cut like homeobox 1provided by HGNC
Primary source: HGNC:HGNC:2557
See related: Ensembl:ENSG00000257923 MIM:116896; AllianceGenome:HGNC:2557
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: CDP; CUX; p75; CASP; CDP1; COY1; Clox; GDDI; p100; p110; p200; CUTL1; GOLIM6; CDP/Cut; Cux/CDP; Nbla10317
Summary: The protein encoded by this gene is a member of the homeodomain family of DNA binding proteins. It may regulate gene expression, morphogenesis, and differentiation and it may also play a role in the cell cycle progession. Several alternatively spliced transcript variants encoding different isoforms have been identified.[provided by RefSeq, Feb 2011]
Expression: Ubiquitous expression in endometrium (RPKM 11.3), thyroid (RPKM 8.5) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 7q22.1

Exon count:: 34

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	7	NC_000007.14 (101816007..102283958)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	7	NC_060931.1 (103136249..103601363)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	7	NC_000007.13 (101459287..101927250)

Chromosome 7 - NC_000007.14 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: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Post-GWAS functional analysis identifies CUX1 as a regulator of p16[INK4a] and cellular senescence.
Title: Post-GWAS functional analysis identifies CUX1 as a regulator of p16(INK4a) and cellular senescence.
Clinically Significant CUX1 Mutations Are Frequently Subclonal and Common in Myeloid Disorders With a High Number of Co-mutated Genes and Dysplastic Features.
Title: Clinically Significant CUX1 Mutations Are Frequently Subclonal and Common in Myeloid Disorders With a High Number of Co-mutated Genes and Dysplastic Features.
Genomic studies controvert the existence of the CUX1 p75 isoform.
Title: Genomic studies controvert the existence of the CUX1 p75 isoform.
p113 isoform encoded by CUX1 circular RNA drives tumor progression via facilitating ZRF1/BRD4 transactivation.
Title: p113 isoform encoded by CUX1 circular RNA drives tumor progression via facilitating ZRF1/BRD4 transactivation.
N6-methyladenosine modification of circCUX1 confers radioresistance of hypopharyngeal squamous cell carcinoma through caspase1 pathway.
Title: N6-methyladenosine modification of circCUX1 confers radioresistance of hypopharyngeal squamous cell carcinoma through caspase1 pathway.
Overexpressed P75CUX1 promotes EMT in glioma infiltration by activating beta-catenin.
Title: Overexpressed P75CUX1 promotes EMT in glioma infiltration by activating β-catenin.
Cut-like homeobox 1 (CUX1) tumor suppressor gene haploinsufficiency induces apoptosis evasion to sustain myeloid leukemia.
Title: Cut-like homeobox 1 (CUX1) tumor suppressor gene haploinsufficiency induces apoptosis evasion to sustain myeloid leukemia.
Regulation of Janus Kinase 2 by an Inflammatory Bowel Disease Causal Non-coding Single Nucleotide Polymorphism.
Title: Regulation of Janus Kinase 2 by an Inflammatory Bowel Disease Causal Non-coding Single Nucleotide Polymorphism.
In fibroblasts, IL-17A response depends on CUX1 and IkappaBzeta to engage the NF-kappaB complex to produce chemoattractants for neutrophil and monocyte recruitment.
Title: CUX1 and IκBζ (NFKBIZ) mediate the synergistic inflammatory response to TNF and IL-17A in stromal fibroblasts.
These functional findings may explain why samples with either CUX1 (MT) or low CUX1 expression coincided with significantly higher numbers of somatic hits by whole-exome sequencing. Our findings implicate the DNA repair dysfunction resulting from CUX1 lesions in the pathogenesis of MNs, in which they lead to a mutator phenotype.
Title: Distinct clinical and biological implications of CUX1 in myeloid neoplasms.

Submit: New GeneRIF Correction See all GeneRIFs (72)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Global developmental delay with or without impaired intellectual development MedGen: C5193032 OMIM: 618330 GeneReviews: Not available	Compare labs

EBI GWAS Catalog

Description
Possible association of CUX1 gene polymorphisms with antidepressant response in major depressive disorder. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH69797 (e-PCR)
- UniSTS:14338

GDB:4585377 (e-PCR)
- UniSTS:78870

CUTL1 (e-PCR)
- UniSTS:24857

GDB:4585601 (e-PCR)
- UniSTS:27419

STS-N22942 (e-PCR)
- UniSTS:75561

RH123864 (e-PCR)
- UniSTS:136239

RH48359 (e-PCR)
- UniSTS:13615

SHGC-148514 (e-PCR)
- UniSTS:176434

SHGC-172596 (e-PCR)
- UniSTS:184628

D7S518 (e-PCR), detects polymorphism
- UniSTS:26935

RH123877 (e-PCR)
- UniSTS:136252

WI-21075 (e-PCR)
- UniSTS:50237

RH104044 (e-PCR)
- UniSTS:98369

D7S666 (e-PCR), detects polymorphism
- UniSTS:49218

D7S666 (e-PCR), detects polymorphism
- UniSTS:49219

RH16539 (e-PCR)
- UniSTS:23624

RH118854 (e-PCR)
- UniSTS:138835

GDB:4585345 (e-PCR)
- UniSTS:34397

PMC133930P1 (e-PCR)
- UniSTS:270691

GDB:1317368 (e-PCR)
- UniSTS:41061

WI-21899 (e-PCR)
- UniSTS:78951

RH12633 (e-PCR)
- UniSTS:7790

D7S515 (e-PCR), detects polymorphism
- UniSTS:53871

RH44454 (e-PCR)
- UniSTS:53362

GDB:1318673 (e-PCR)
- UniSTS:10359

D7S2433 (e-PCR)
- UniSTS:70776

WI-17166 (e-PCR)
- UniSTS:17279

D7S546E (e-PCR)
- UniSTS:51074

D7S2433 (e-PCR)
- UniSTS:37264

RH48012 (e-PCR)
- UniSTS:49562

D7S518 (e-PCR), detects polymorphism
- UniSTS:72868

GDB:4584979 (e-PCR)
- UniSTS:55972

GDB:1317346 (e-PCR)
- UniSTS:22184

MARC_4357-4358:991938494:5 (e-PCR)
- UniSTS:231083

MARC_4357-4358:996679565:1 (e-PCR)
- UniSTS:231083

D12S1228E (e-PCR)
- UniSTS:151475

D7S1616 (e-PCR)
- UniSTS:53950

D7S740 (e-PCR)
- UniSTS:24255

D7S2686 (e-PCR)
- UniSTS:27330

SHGC-84975 (e-PCR)
- UniSTS:104901

RH36434 (e-PCR)
- UniSTS:55761

D7S666 (e-PCR), detects polymorphism
- UniSTS:33238

GDB:4585337 (e-PCR)
- UniSTS:68568

WI-13779 (e-PCR)
- UniSTS:56300

D7S543E (e-PCR)
- UniSTS:68089

AF007375 (e-PCR)
- UniSTS:13564

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
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	ISA Inferred from Sequence Alignment more info
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	ISS Inferred from Sequence or Structural Similarity more info
enables sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables sequence-specific double-stranded DNA binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in negative regulation of transcription by RNA polymerase II	TAS Traceable Author Statement more info	PubMed
involved_in positive regulation of dendrite morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in Golgi apparatus	IDA Inferred from Direct Assay more info
part_of chromatin	ISA Inferred from Sequence Alignment more info
located_in cytosol	TAS Traceable Author Statement more info
located_in nucleoplasm	IDA Inferred from Direct Assay 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

General protein information

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Preferred Names: protein CASP; Homeobox protein cut-like 1

Names: CCAAT displacement protein; CDP/Cux p200; CUX1 gene Alternatively Spliced Product; cut homolog; golgi integral membrane protein 6; homeobox protein cux-1; mutant CUX1; putative protein product of Nbla10317

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.

Genomic

NG_029476.2 RefSeqGene

Range

5104..473055

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_1123

mRNA and Protein(s)

NM_001202543.2 → NP_001189472.1 Homeobox protein cut-like 1 isoform d

See identical proteins and their annotated locations for NP_001189472.1

Status: REVIEWED

Description

Transcript Variant: This variant (4) encodes the longest isoform (d).

Source sequence(s)

AC005088, BC040199, BC066592, DC410774

Consensus CDS

CCDS56498.1

UniProtKB/TrEMBL

A0A2R8Y852

Related

ENSP00000353401.3, ENST00000360264.7

Conserved Domains (5) summary

pfam05887
Location:1314 → 1412

Trypan_PARP; Procyclic acidic repetitive protein (PARP)

pfam00046
Location:1258 → 1311

Homeobox; Homeobox domain

pfam00901
Location:86 → 361

Orbi_VP5; Orbivirus outer capsid protein VP5

pfam02376
Location:1133 → 1210

CUT; CUT domain

pfam13851
Location:131 → 352

GAS; Growth-arrest specific micro-tubule binding
NM_001202544.3 → NP_001189473.1 protein CASP isoform e

Status: REVIEWED

Description

Transcript Variant: This variant (5) lacks an in-frame exon in the 5' region and has an alternate 3' sequence including the coding region, as compared to variant 1. The resulting isoform (e) lacks an internal segment and has a shorter and distinct C-terminus, as compared to isoform d.

Source sequence(s)

AC091390, AK125097, BC012323, BC066592, DC410774, L12579

Consensus CDS

CCDS56500.1

UniProtKB/Swiss-Prot

P39880, Q13948

Related

ENSP00000449371.2, ENST00000547394.6

Conserved Domains (3) summary

pfam00901
Location:70 → 345

Orbi_VP5; Orbivirus outer capsid protein VP5

pfam08172
Location:407 → 622

CASP_C; CASP C terminal

pfam13851
Location:115 → 336

GAS; Growth-arrest specific micro-tubule binding
NM_001202545.3 → NP_001189474.1 protein CASP isoform f

Status: REVIEWED

Description

Transcript Variant: This variant (6) lacks an in-frame exon in the 5' region and has an alternate 3' sequence including the coding region, as compared to variant 1. The resulting isoform (f) lacks an internal segment and has a shorter and distinct C-terminus, as compared to isoform d.

Source sequence(s)

AC091390, AK122726, BC012323, DC410774, L12579

Consensus CDS

CCDS56499.1

UniProtKB/Swiss-Prot

P39880, Q13948

Related

ENSP00000409745.2, ENST00000425244.6

Conserved Domains (3) summary

pfam07851
Location:261 → 336

TMPIT; TMPIT-like protein

pfam08172
Location:377 → 592

CASP_C; CASP C terminal

pfam15290
Location:101 → 240

Syntaphilin; Golgi-localized syntaxin-1-binding clamp
NM_001202546.3 → NP_001189475.1 protein CASP isoform g

Status: REVIEWED

Description

Transcript Variant: This variant (7) lacks an in-frame exon in the 5' region and has an alternate 3' sequence including the coding region, as compared to variant 1. The resulting isoform (g) lacks an internal segment and has a shorter and distinct C-terminus, as compared to isoform d.

Source sequence(s)

AC005096, AC091390, AK303151, BC012323, L12579

Consensus CDS

CCDS59071.1

UniProtKB/Swiss-Prot

Q13948

Related

ENSP00000377410.3, ENST00000393824.7

Conserved Domains (3) summary

pfam00901
Location:49 → 322

Orbi_VP5; Orbivirus outer capsid protein VP5

pfam08172
Location:384 → 599

CASP_C; CASP C terminal

pfam13851
Location:94 → 313

GAS; Growth-arrest specific micro-tubule binding
NM_001913.5 → NP_001904.2 protein CASP isoform b

See identical proteins and their annotated locations for NP_001904.2

Status: REVIEWED

Description

Transcript Variant: This variant (2) has an alternate 3' sequence including the coding region, as compared to variant 4. The resulting isoform (b) has a shorter and distinct C-terminus, as compared to isoform d.

Source sequence(s)

AC091390, AK222832, BC012323, DC410774, L12579

Consensus CDS

CCDS5720.1

UniProtKB/Swiss-Prot

B3KWH3, B3KWH8, B4DZZ2, G3V1Z6, J3KPQ6, Q13948, Q53GU9, Q8TBS3

Related

ENSP00000484760.2, ENST00000622516.6

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_181500.4 → NP_852477.1 protein CASP isoform c

See identical proteins and their annotated locations for NP_852477.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) lacks a 6 nt segment at an alternate splice site and has an alternate 3' sequence including the coding region, as compared to variant 4. The resulting isoform (c) lacks two internal amino acids and has a shorter and distinct C-terminus, as compared to isoform d.

Source sequence(s)

AB075522, AC091390, BC012323, BC025422, BC066592, DC410774

Consensus CDS

CCDS47672.1

UniProtKB/Swiss-Prot

P39880, Q13948

UniProtKB/TrEMBL

Q3LIA3

Related

ENSP00000414091.5, ENST00000437600.9

Conserved Domains (2) summary

pfam00901
Location:86 → 359

Orbi_VP5; Orbivirus outer capsid protein VP5

pfam08172
Location:421 → 636

CASP_C; CASP C terminal
NM_181552.4 → NP_853530.2 Homeobox protein cut-like 1 isoform a

See identical proteins and their annotated locations for NP_853530.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) has an alternate 5' exon, as compared to variant 4. The resulting isoform (a) has a shorter and distinct N-terminus, as compared to isoform d.

Source sequence(s)

AC005088, AC005096, BC040199, BC066592, M74099

Consensus CDS

CCDS5721.1

UniProtKB/Swiss-Prot

B3KV79, J3KQV9, P39880, Q6NYH4, Q75LE5, Q75MT2, Q75MT3, Q86UJ7, Q9UEV5

UniProtKB/TrEMBL

A0A2R8Y852

Related

ENSP00000292535.7, ENST00000292535.12

Conserved Domains (5) summary

pfam05887
Location:1303 → 1401

Trypan_PARP; Procyclic acidic repetitive protein (PARP)

pfam00046
Location:1247 → 1300

Homeobox; Homeobox domain

pfam00901
Location:75 → 350

Orbi_VP5; Orbivirus outer capsid protein VP5

pfam02376
Location:1122 → 1199

CUT; CUT domain

pfam13851
Location:120 → 341

GAS; Growth-arrest specific micro-tubule binding

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000007.14 Reference GRCh38.p14 Primary Assembly

Range

101816007..102283958

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047419908.1 → XP_047275864.1 Homeobox protein cut-like 1 isoform X5
XM_047419912.1 → XP_047275868.1 Homeobox protein cut-like 1 isoform X10

Related

ENSP00000496653.1, ENST00000645010.1
XM_047419913.1 → XP_047275869.1 Homeobox protein cut-like 1 isoform X11
XM_011515825.3 → XP_011514127.1 Homeobox protein cut-like 1 isoform X13

UniProtKB/TrEMBL

A0A2R8YDI1

Conserved Domains (5) summary

PHA03247
Location:656 → 842

PHA03247; large tegument protein UL36; Provisional

PHA03307
Location:1223 → 1296

PHA03307; transcriptional regulator ICP4; Provisional

TIGR02169
Location:18 → 368

SMC_prok_A; chromosome segregation protein SMC, primarily archaeal type

pfam00046
Location:1156 → 1210

Homeobox; Homeobox domain

pfam02376
Location:1031 → 1104

CUT; CUT domain
XM_047419914.1 → XP_047275870.1 Homeobox protein cut-like 1 isoform X14
XM_047419916.1 → XP_047275872.1 Homeobox protein cut-like 1 isoform X16

Related

ENSP00000494610.1, ENST00000646649.1
XM_047419917.1 → XP_047275873.1 Homeobox protein cut-like 1 isoform X17
XM_047419909.1 → XP_047275865.1 Homeobox protein cut-like 1 isoform X6
XM_047419910.1 → XP_047275866.1 Homeobox protein cut-like 1 isoform X7
XM_017011760.3 → XP_016867249.1 Homeobox protein cut-like 1 isoform X12

UniProtKB/TrEMBL

A0A2R8Y852

Conserved Domains (5) summary

PHA03247
Location:734 → 920

PHA03247; large tegument protein UL36; Provisional

PHA03307
Location:1301 → 1374

PHA03307; transcriptional regulator ICP4; Provisional

TIGR02168
Location:18 → 362

SMC_prok_B; chromosome segregation protein SMC, common bacterial type

pfam00046
Location:1234 → 1288

Homeobox; Homeobox domain

pfam02376
Location:1109 → 1182

CUT; CUT domain
XM_047419915.1 → XP_047275871.1 Homeobox protein cut-like 1 isoform X15
XM_005250154.4 → XP_005250211.2 protein CASP isoform X18

Related

ENST00000560541.5
XM_005250150.4 → XP_005250207.2 Homeobox protein cut-like 1 isoform X1
XM_006715854.3 → XP_006715917.2 Homeobox protein cut-like 1 isoform X4

Related

ENSP00000446630.2, ENST00000549414.6
XM_047419906.1 → XP_047275862.1 Homeobox protein cut-like 1 isoform X2
XM_047419907.1 → XP_047275863.1 Homeobox protein cut-like 1 isoform X3
XM_024446668.2 → XP_024302436.2 Homeobox protein cut-like 1 isoform X8
XM_047419911.1 → XP_047275867.1 Homeobox protein cut-like 1 isoform X9