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

    Gene ID: 288665, updated on 13-Apr-2024

    Summary

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    Official Symbol
    Cux2provided by RGD
    Official Full Name
    cut-like homeobox 2provided by RGD
    Primary source
    RGD:1305967
    See related
    Ensembl: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 cellular response to organic substance and negative regulation of transcription, DNA-templated. 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, Apr 2022]
    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

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    See Cux2 in Genome Data Viewer
    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_086030.1Genomic Context describing neighboring genes Neighboring gene myosin light chain 2 Neighboring gene uncharacterized LOC120095979 Neighboring gene uncharacterized LOC120095978 Neighboring gene uncharacterized LOC134481298 Neighboring gene PH domain containing endocytic trafficking adaptor 1 Neighboring gene SH2B adaptor protein 3 Neighboring gene ataxin 2

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. Linkage disequilibrium mapping of bipolar affective disorder at 12q23-q24 provides evidence for association at CUX2 and FLJ32356. Glaser B, et al. Am J Med Genet B Neuropsychiatr Genet, 2005 Jan 5. PMID 15389760
    2. CUX2 protein functions as an accessory factor in the repair of oxidative DNA damage. Pal R, et al. J Biol Chem, 2015 Sep 11. PMID 26221032, Free PMC Article
    3. Cux1 and Cux2 regulate dendritic branching, spine morphology, and synapses of the upper layer neurons of the cortex. Cubelos B, et al. Neuron, 2010 May 27. PMID 20510857, Free PMC Article
    4. Characterization of three growth hormone-responsive transcription factors preferentially expressed in adult female liver. Laz EV, et al. Endocrinology, 2007 Jul. PMID 17412818, Free PMC Article
    5. Biochemical characterization of the mammalian Cux2 protein. Gingras H, et al. Gene, 2005 Jan 3. PMID 15656993

    See all (8) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    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
    acts_upstream_of_or_within cellular response to organic substance ISO
    Inferred from Sequence Orthology
    more info
    		  
    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)

    1. NM_001271380.1 → NP_001258309.1  homeobox protein cut-like 2 isoform 1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000012
      UniProtKB/TrEMBL
      F1M048
      Related
      ENSRNOP00000001697.7, ENSRNOT00000001697.8
      Conserved Domains (2) summary
      pfam00046
      Location:1116 → 1169
      Homeobox; Homeobox domain
      pfam02376
      Location:988 → 1064
      CUT; CUT domain

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

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000012

    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

    1. NC_086030.1 Reference GRCr8

      Range
      40168402..40368303
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. 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

    2. 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

    3. 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

    4. 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

    5. 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

    6. 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

    7. 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

    8. 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

    9. 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

    10. 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

    11. 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

    12. 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

    13. 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

    14. 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

    15. 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

    16. 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

    1. 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.
    Nucleotide Protein Strain
    Heading Accession and Version

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