Cux1 cut-like homeobox 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Cux1provided by RGD
Official Full Name: cut-like homeobox 1provided by RGD
Primary source: RGD:620618
See related: Ensembl:ENSRNOG00000001424 AllianceGenome:RGD:620618
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: CDP; CDP2; Cutl1
Summary: Enables protein-macromolecule adaptor activity. Involved in retrograde transport, vesicle recycling within Golgi. Located in Golgi membrane. Orthologous to human CUX1 (cut like homeobox 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Thymus (RPKM 235.8), Kidney (RPKM 177.0) and 9 other tissues See more
Orthologs: human mouse all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

Location:: 12q12

Exon count:: 36

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	12	NC_086030.1 (25728393..26062497)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	12	NC_051347.1 (20107062..20425868)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	12	NC_005111.4 (23150886..23470095)

Chromosome 12 - NC_086030.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

hyperoxia resulted in a reduction of neurons expressing Cux1
Title: Oxygen flux reduces Cux1 positive neurons and cortical growth in a gestational rodent model of growth restriction.
In arcuate nucleus of hypothalamus, CUX1 gene was co-expressed in the kisspeptin neurons.
Title: Expression of EAP1 and CUX1 in the hypothalamus of female rats and relationship with KISS1 and GnRH.
Cux1 functions as a negative regulator of dendritic complexity for cortical pyramidal neurons.
Title: The transcription factor Cux1 regulates dendritic morphology of cortical pyramidal neurons.
characterization of the golgin-84-CASP tether binding to coat protein complex I (COPI) vesicles.
Title: Golgin tethers define subpopulations of COPI vesicles.

Submit: New GeneRIF Correction

General gene information

Go to the top of the page Help

Markers

BF411168 (e-PCR)
- UniSTS:247557

BE120355 (e-PCR)
- UniSTS:247311

RH133068 (e-PCR)
- UniSTS:216351

AU047743 (e-PCR)
- UniSTS:110208

RH130111 (e-PCR)
- UniSTS:213399

D12Got43 (e-PCR)
- UniSTS:114621

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

RH139585 (e-PCR)
- UniSTS:221669

AU049974 (e-PCR)
- UniSTS:146416

BF412746 (e-PCR)
- UniSTS:248304

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA binding	ISO Inferred from Sequence Orthology more info
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	ISO Inferred from Sequence Orthology 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	ISO Inferred from Sequence Orthology more info
enables chromatin binding	ISO Inferred from Sequence Orthology more info
enables protein-macromolecule adaptor activity	IPI Inferred from Physical Interaction more info	PubMed
enables sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables sequence-specific double-stranded DNA binding	IEA Inferred from Electronic Annotation 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	ISO Inferred from Sequence Orthology more info
involved_in intra-Golgi vesicle-mediated transport	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within kidney development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within lung development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of dendrite morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in retrograde transport, vesicle recycling within Golgi	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in Golgi apparatus	IEA Inferred from Electronic Annotation more info
located_in Golgi apparatus	ISO Inferred from Sequence Orthology more info
located_in Golgi membrane	IDA Inferred from Direct Assay more info	PubMed
located_in Golgi membrane	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in neuron projection	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
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	IEA Inferred from Electronic Annotation more info
located_in nucleus	ISO Inferred from Sequence Orthology more info

General protein information

Go to the top of the page Help

Preferred Names: homeobox protein cut-like 1

Names: CCAAT displacement protein; cut-like 1; homeobox protein cux-1

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

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)

NM_001415774.1 → NP_001402703.1 homeobox protein cut-like 1 isoform 2

Status: VALIDATED

Source sequence(s)

JAXUCZ010000012
NM_001415775.1 → NP_001402704.1 homeobox protein cut-like 1 isoform 3

Status: VALIDATED

Source sequence(s)

JAXUCZ010000012
NM_053860.1 → NP_446312.1 homeobox protein cut-like 1 isoform 1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000012

UniProtKB/Swiss-Prot

F1LRC5, P53565

UniProtKB/TrEMBL

A0A8I6AM13

Related

ENSRNOP00000056243.3, ENSRNOT00000059486.6

Conserved Domains (6) summary

PHA03307
Location:1300 → 1497

PHA03307; transcriptional regulator ICP4; Provisional

PRK10263
Location:676 → 941

PRK10263; DNA translocase FtsK; Provisional

TIGR02168
Location:18 → 356

SMC_prok_B; chromosome segregation protein SMC, common bacterial type

TIGR04211
Location:296 → 422

SH3_and_anchor; SH3 domain protein

pfam00046
Location:1231 → 1285

Homeobox; Homeobox domain

pfam02376
Location:1106 → 1179

CUT; CUT domain

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086030.1 Reference GRCr8

Range

25728393..26062497

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063270998.1 → XP_063127068.1 homeobox protein cut-like 1 isoform X8
XM_063270996.1 → XP_063127066.1 homeobox protein cut-like 1 isoform X5
XM_063271001.1 → XP_063127071.1 homeobox protein cut-like 1 isoform X12
XM_063271003.1 → XP_063127073.1 homeobox protein cut-like 1 isoform X14
XM_003751160.6 → XP_003751208.1 homeobox protein cut-like 1 isoform X6

See identical proteins and their annotated locations for XP_003751208.1

UniProtKB/TrEMBL

A0A8I6AM13, A0A8I6G4D0

Related

ENSRNOP00000080302.1

Conserved Domains (4) summary

pfam00046
Location:1255 → 1308

Homeobox; Homeobox domain

pfam00901
Location:86 → 361

Orbi_VP5; Orbivirus outer capsid protein VP5

pfam02376
Location:1130 → 1207

CUT; CUT domain

pfam13851
Location:131 → 352

GAS; Growth-arrest specific micro-tubule binding
XM_003751161.5 → XP_003751209.1 homeobox protein cut-like 1 isoform X16

See identical proteins and their annotated locations for XP_003751209.1

UniProtKB/TrEMBL

A0A8I6AM13

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
XM_063270997.1 → XP_063127067.1 homeobox protein cut-like 1 isoform X7
XM_063271005.1 → XP_063127075.1 homeobox protein cut-like 1 isoform X17
XM_063271006.1 → XP_063127076.1 homeobox protein cut-like 1 isoform X18
XM_063271000.1 → XP_063127070.1 homeobox protein cut-like 1 isoform X9
XM_063271002.1 → XP_063127072.1 homeobox protein cut-like 1 isoform X13
XM_063271011.1 → XP_063127081.1 homeobox protein cut-like 1 isoform X24
XM_063271010.1 → XP_063127080.1 homeobox protein cut-like 1 isoform X23
XM_063271009.1 → XP_063127079.1 homeobox protein cut-like 1 isoform X22
XM_008769167.3 → XP_008767389.1 homeobox protein cut-like 1 isoform X21

See identical proteins and their annotated locations for XP_008767389.1

UniProtKB/TrEMBL

A0A8I5ZR58

Conserved Domains (4) summary

pfam07851
Location:390 → 494

TMPIT; TMPIT-like protein

pfam08172
Location:506 → 721

CASP_C; CASP C terminal

pfam10212
Location:240 → 437

TTKRSYEDQ; Predicted coiled-coil domain-containing protein

pfam13851
Location:216 → 435

GAS; Growth-arrest specific micro-tubule binding
XM_063270995.1 → XP_063127065.1 homeobox protein cut-like 1 isoform X4
XM_006249202.4 → XP_006249264.1 homeobox protein cut-like 1 isoform X2

See identical proteins and their annotated locations for XP_006249264.1

UniProtKB/TrEMBL

A0A8I6AM13

Conserved Domains (6) summary

pfam00046
Location:1338 → 1391

Homeobox; Homeobox domain

pfam02376
Location:1213 → 1290

CUT; CUT domain

pfam13851
Location:216 → 435

GAS; Growth-arrest specific micro-tubule binding

cd16269
Location:328 → 338

GBP_C; coiled coil [structural motif]

cl20817
Location:212 → 355

GBP_C; Guanylate-binding protein, C-terminal domain

cl23720
Location:375 → 457

RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)
XM_347163.9 → XP_347164.4 homeobox protein cut-like 1 isoform X1

See identical proteins and their annotated locations for XP_347164.4

UniProtKB/TrEMBL

A0A8I6AM13

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
XM_063271004.1 → XP_063127074.1 homeobox protein cut-like 1 isoform X15
XM_039089023.2 → XP_038944951.1 homeobox protein cut-like 1 isoform X11

UniProtKB/TrEMBL

A0A8I6AM13

Conserved Domains (5) summary

PHA03307
Location:1305 → 1502

PHA03307; transcriptional regulator ICP4; Provisional

COG1196
Location:104 → 459

Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]

PRK10263
Location:681 → 946

PRK10263; DNA translocase FtsK; Provisional

pfam00046
Location:1236 → 1290

Homeobox; Homeobox domain

pfam02376
Location:1111 → 1188

CUT; CUT domain
XM_063270994.1 → XP_063127064.1 homeobox protein cut-like 1 isoform X3
XM_006249204.4 → XP_006249266.1 homeobox protein cut-like 1 isoform X10

See identical proteins and their annotated locations for XP_006249266.1

UniProtKB/TrEMBL

A0A8I6AM13

Conserved Domains (4) summary

pfam00046
Location:1238 → 1291

Homeobox; Homeobox domain

pfam00901
Location:171 → 446

Orbi_VP5; Orbivirus outer capsid protein VP5

pfam02376
Location:1113 → 1190

CUT; CUT domain

pfam13851
Location:216 → 437

GAS; Growth-arrest specific micro-tubule binding
XM_008769166.3 → XP_008767388.1 homeobox protein cut-like 1 isoform X20

See identical proteins and their annotated locations for XP_008767388.1

UniProtKB/TrEMBL

A0A8I5ZR58, F1M8J7

Related

ENSRNOP00000040645.6

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
XM_063271008.1 → XP_063127078.1 homeobox protein cut-like 1 isoform X19