Cux2 cut-like homeobox 2 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Cux2provided by RGD
Official Full Name: cut-like homeobox 2provided by RGD
Primary source: RGD:1305967
See related: EnsemblRapid:ENSRNOG00000001259 AllianceGenome:RGD:1305967
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: Cutl2
Summary: Predicted to enable DNA-binding transcription repressor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in several processes, including positive regulation of nervous system development; regulation of gene expression; and short-term memory. Predicted to act upstream of or within negative regulation of DNA-templated transcription. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in developmental and epileptic encephalopathy 67. Orthologous to human CUX2 (cut like homeobox 2). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Adrenal (RPKM 36.5), Liver (RPKM 35.8) and 8 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 12q16

Exon count:: 31

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	12	NC_086030.1 (40168402..40368303)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	12	NC_051347.1 (34507723..34707581)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	12	NC_005111.4 (40016774..40221067)

Chromosome 12 - NC_086030.1 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: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages 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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.

Submit: New GeneRIF Correction

General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
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 repressor activity, RNA polymerase II-specific	ISO Inferred from Sequence Orthology 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 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	ISO Inferred from Sequence Orthology more info
involved_in 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 positive regulation of dendritic spine morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of excitatory postsynaptic potential	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of gene expression	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of synapse assembly	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 short-term memory	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
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: cut-like 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_001271380.1 → NP_001258309.1 homeobox protein cut-like 2 isoform 1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000012

UniProtKB/TrEMBL

F1M048

Related

ENSRNOP00000001697.8, ENSRNOT00000001697.9

Conserved Domains (2) summary

pfam00046
Location:1116 → 1169

Homeobox; Homeobox domain

pfam02376
Location:988 → 1064

CUT; CUT domain
NM_001415781.1 → NP_001402710.1 homeobox protein cut-like 2 isoform 2

Status: VALIDATED

Source sequence(s)

JAXUCZ010000012

Related

ENSRNOP00000100533.1, ENSRNOT00000164301.1

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

40168402..40368303

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039089254.2 → XP_038945182.1 homeobox protein cut-like 2 isoform X6

Conserved Domains (3) summary

TIGR02168
Location:107 → 310

SMC_prok_B; chromosome segregation protein SMC, common bacterial type

pfam00046
Location:1134 → 1188

Homeobox; Homeobox domain

pfam02376
Location:1006 → 1082

CUT; CUT domain
XM_039089256.2 → XP_038945184.1 homeobox protein cut-like 2 isoform X6

Conserved Domains (3) summary

TIGR02168
Location:107 → 310

SMC_prok_B; chromosome segregation protein SMC, common bacterial type

pfam00046
Location:1134 → 1188

Homeobox; Homeobox domain

pfam02376
Location:1006 → 1082

CUT; CUT domain
XM_039089257.2 → XP_038945185.1 homeobox protein cut-like 2 isoform X6

Conserved Domains (3) summary

TIGR02168
Location:107 → 310

SMC_prok_B; chromosome segregation protein SMC, common bacterial type

pfam00046
Location:1134 → 1188

Homeobox; Homeobox domain

pfam02376
Location:1006 → 1082

CUT; CUT domain
XM_039089247.2 → XP_038945175.1 homeobox protein cut-like 2 isoform X2

Conserved Domains (3) summary

TIGR02168
Location:184 → 387

SMC_prok_B; chromosome segregation protein SMC, common bacterial type

pfam00046
Location:1211 → 1265

Homeobox; Homeobox domain

pfam02376
Location:1083 → 1159

CUT; CUT domain
XM_039089246.2 → XP_038945174.1 homeobox protein cut-like 2 isoform X1

Conserved Domains (3) summary

TIGR02168
Location:185 → 388

SMC_prok_B; chromosome segregation protein SMC, common bacterial type

pfam00046
Location:1212 → 1266

Homeobox; Homeobox domain

pfam02376
Location:1084 → 1160

CUT; CUT domain
XM_039089248.2 → XP_038945176.1 homeobox protein cut-like 2 isoform X3

Conserved Domains (3) summary

TIGR02168
Location:185 → 388

SMC_prok_B; chromosome segregation protein SMC, common bacterial type

pfam00046
Location:1205 → 1259

Homeobox; Homeobox domain

pfam02376
Location:1077 → 1153

CUT; CUT domain
XM_039089249.2 → XP_038945177.1 homeobox protein cut-like 2 isoform X4

Conserved Domains (3) summary

TIGR02168
Location:185 → 388

SMC_prok_B; chromosome segregation protein SMC, common bacterial type

pfam00046
Location:1201 → 1255

Homeobox; Homeobox domain

pfam02376
Location:1073 → 1149

CUT; CUT domain
XM_039089252.2 → XP_038945180.1 homeobox protein cut-like 2 isoform X6

Conserved Domains (3) summary

TIGR02168
Location:107 → 310

SMC_prok_B; chromosome segregation protein SMC, common bacterial type

pfam00046
Location:1134 → 1188

Homeobox; Homeobox domain

pfam02376
Location:1006 → 1082

CUT; CUT domain
XM_039089255.2 → XP_038945183.1 homeobox protein cut-like 2 isoform X6

Conserved Domains (3) summary

TIGR02168
Location:107 → 310

SMC_prok_B; chromosome segregation protein SMC, common bacterial type

pfam00046
Location:1134 → 1188

Homeobox; Homeobox domain

pfam02376
Location:1006 → 1082

CUT; CUT domain
XM_039089261.2 → XP_038945189.1 homeobox protein cut-like 2 isoform X6

Conserved Domains (3) summary

TIGR02168
Location:107 → 310

SMC_prok_B; chromosome segregation protein SMC, common bacterial type

pfam00046
Location:1134 → 1188

Homeobox; Homeobox domain

pfam02376
Location:1006 → 1082

CUT; CUT domain
XM_039089253.2 → XP_038945181.1 homeobox protein cut-like 2 isoform X6

Conserved Domains (3) summary

TIGR02168
Location:107 → 310

SMC_prok_B; chromosome segregation protein SMC, common bacterial type

pfam00046
Location:1134 → 1188

Homeobox; Homeobox domain

pfam02376
Location:1006 → 1082

CUT; CUT domain
XM_039089260.2 → XP_038945188.1 homeobox protein cut-like 2 isoform X6

Conserved Domains (3) summary

TIGR02168
Location:107 → 310

SMC_prok_B; chromosome segregation protein SMC, common bacterial type

pfam00046
Location:1134 → 1188

Homeobox; Homeobox domain

pfam02376
Location:1006 → 1082

CUT; CUT domain
XM_039089263.2 → XP_038945191.1 homeobox protein cut-like 2 isoform X6

Conserved Domains (3) summary

TIGR02168
Location:107 → 310

SMC_prok_B; chromosome segregation protein SMC, common bacterial type

pfam00046
Location:1134 → 1188

Homeobox; Homeobox domain

pfam02376
Location:1006 → 1082

CUT; CUT domain
XM_039089262.2 → XP_038945190.1 homeobox protein cut-like 2 isoform X6

Conserved Domains (3) summary

TIGR02168
Location:107 → 310

SMC_prok_B; chromosome segregation protein SMC, common bacterial type

pfam00046
Location:1134 → 1188

Homeobox; Homeobox domain

pfam02376
Location:1006 → 1082

CUT; CUT domain
XM_039089259.2 → XP_038945187.1 homeobox protein cut-like 2 isoform X6

Conserved Domains (3) summary

TIGR02168
Location:107 → 310

SMC_prok_B; chromosome segregation protein SMC, common bacterial type

pfam00046
Location:1134 → 1188

Homeobox; Homeobox domain

pfam02376
Location:1006 → 1082

CUT; CUT domain
XM_039089251.2 → XP_038945179.1 homeobox protein cut-like 2 isoform X5

Conserved Domains (3) summary

TIGR02168
Location:164 → 367

SMC_prok_B; chromosome segregation protein SMC, common bacterial type

pfam00046
Location:1191 → 1245

Homeobox; Homeobox domain

pfam02376
Location:1063 → 1139

CUT; CUT domain

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_001105931.1: Suppressed sequence

Description

NM_001105931.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.