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

    Gene ID: 116639, updated on 2-Nov-2024

    Summary

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    Official Symbol
    Cux1provided by RGD
    Official Full Name
    cut-like homeobox 1provided by RGD
    Primary source
    RGD:620618
    See related
    EnsemblRapid: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, Nov 2024]
    Expression
    Biased expression in Thymus (RPKM 235.8), Kidney (RPKM 177.0) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Cux1 in Genome Data Viewer
    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_086030.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC120095912 Neighboring gene uncharacterized LOC134481274 Neighboring gene uncharacterized LOC134481273 Neighboring gene uncharacterized LOC134481275 Neighboring gene uncharacterized LOC134481276 Neighboring gene SH2B adaptor protein 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 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?
    1. 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.
    2. 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.
    3. 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.
    4. 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

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    Markers

    Homology

    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

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    Preferred Names
    homeobox protein cut-like 1
    Names
    CCAAT displacement protein
    cut-like 1
    homeobox protein cux-1

    NCBI Reference Sequences (RefSeq)

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    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)

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

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000012

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

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000012

    3. 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
      ENSRNOP00000089950.1, ENSRNOT00000097976.2
      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

    1. NC_086030.1 Reference GRCr8

      Range
      25728393..26062497
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063270998.1 → XP_063127068.1  homeobox protein cut-like 1 isoform X8

    2. XM_063270996.1 → XP_063127066.1  homeobox protein cut-like 1 isoform X5

    3. XM_063271001.1 → XP_063127071.1  homeobox protein cut-like 1 isoform X12

      Related
      ENSRNOP00000056243.4, ENSRNOT00000059486.7

    4. XM_063271003.1 → XP_063127073.1  homeobox protein cut-like 1 isoform X14

    5. 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
      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

    6. 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

    7. XM_063270997.1 → XP_063127067.1  homeobox protein cut-like 1 isoform X7

    8. XM_063271005.1 → XP_063127075.1  homeobox protein cut-like 1 isoform X17

    9. XM_063271006.1 → XP_063127076.1  homeobox protein cut-like 1 isoform X18

    10. XM_063271000.1 → XP_063127070.1  homeobox protein cut-like 1 isoform X9

    11. XM_063271002.1 → XP_063127072.1  homeobox protein cut-like 1 isoform X13

    12. XM_063271011.1 → XP_063127081.1  homeobox protein cut-like 1 isoform X24

      Related
      ENSRNOP00000103400.1, ENSRNOT00000149512.1

    13. XM_063271010.1 → XP_063127080.1  homeobox protein cut-like 1 isoform X23

    14. XM_063271009.1 → XP_063127079.1  homeobox protein cut-like 1 isoform X22

    15. 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

    16. XM_063270995.1 → XP_063127065.1  homeobox protein cut-like 1 isoform X4

    17. 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)

    18. 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
      Related
      ENSRNOP00000080302.2, ENSRNOT00000112152.2
      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

    19. XM_063271004.1 → XP_063127074.1  homeobox protein cut-like 1 isoform X15

    20. 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

    21. XM_063270994.1 → XP_063127064.1  homeobox protein cut-like 1 isoform X3

      Related
      ENSRNOP00000104247.1, ENSRNOT00000156078.1

    22. 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

    23. 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, ENSRNOT00000044841.8
      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

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

    RNA

    1. XR_010056362.1 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P53565.2 GenPept UniProtKB/Swiss-Prot:P53565

    Gene LinkOut

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