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    Cux1 cut-like homeobox 1 [ Mus musculus (house mouse) ]

    Gene ID: 13047, updated on 19-Nov-2024

    Summary

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    Official Symbol
    Cux1provided by MGI
    Official Full Name
    cut-like homeobox 1provided by MGI
    Primary source
    MGI:MGI:88568
    See related
    Ensembl:ENSMUSG00000029705 AllianceGenome:MGI:88568
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    CDP; Cux; Cutl1; Cux-1
    Summary
    Enables RNA polymerase II cis-regulatory region sequence-specific DNA binding activity and chromatin binding activity. Involved in positive regulation of dendrite morphogenesis. Acts upstream of or within several processes, including inner ear auditory receptor cell differentiation; lung development; and negative regulation of transcription by RNA polymerase II. Located in cytoplasm; neuron projection; and nucleus. Is expressed in several structures, including alimentary system; genitourinary system; nervous system; respiratory system; and sensory organ. Orthologous to human CUX1 (cut like homeobox 1). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in thymus adult (RPKM 14.0), kidney adult (RPKM 8.1) and 28 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Cux1 in Genome Data Viewer
    Location:
    5 G2; 5 75.96 cM
    Exon count:
    34
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 5 NC_000071.7 (136276989..136596429, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 5 NC_000071.6 (136248135..136567590, complement)

    Chromosome 5 - NC_000071.7Genomic Context describing neighboring genes Neighboring gene ribosomal protein L7A pseudogene Neighboring gene SH2B adaptor protein 2 Neighboring gene predicted gene, 30408 Neighboring gene predicted gene, 16599 Neighboring gene CapStarr-seq enhancer MGSCv37_chr5:136886527-136886728 Neighboring gene microRNA 721 Neighboring gene STARR-seq mESC enhancer starr_14619 Neighboring gene STARR-seq mESC enhancer starr_14620 Neighboring gene predicted gene, 54307 Neighboring gene CapStarr-seq enhancer MGSCv37_chr5:137026660-137026843 Neighboring gene STARR-seq mESC enhancer starr_14621 Neighboring gene STARR-positive B cell enhancer ABC_E4794 Neighboring gene CapStarr-seq enhancer MGSCv37_chr5:137093643-137093839 Neighboring gene CapStarr-seq enhancer MGSCv37_chr5:137093950-137094103 Neighboring gene CapStarr-seq enhancer MGSCv37_chr5:137099197-137099306 Neighboring gene predicted gene, 38722 Neighboring gene myosin, light chain 10, regulatory

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. The N-terminal region of the CCAAT displacement protein (CDP)/Cux transcription factor functions as an autoinhibitory domain that modulates DNA binding. Truscott M, et al. J Biol Chem, 2004 Nov 26. PMID 15377665
    2. A novel colonic repressor element regulates intestinal gene expression by interacting with Cux/CDP. Boudreau F, et al. Mol Cell Biol, 2002 Aug. PMID 12101240, Free PMC Article
    3. Differentiation-induced cleavage of Cutl1/CDP generates a novel dominant-negative isoform that regulates mammary gene expression. Maitra U, et al. Mol Cell Biol, 2006 Oct. PMID 17015474, Free PMC Article
    4. The function of CUX1 in oxidative DNA damage repair is needed to prevent premature senescence of mouse embryo fibroblasts. Ramdzan ZM, et al. Oncotarget, 2015 Feb 28. PMID 25682875, Free PMC Article
    5. Cux-1 transgenic mice develop glomerulosclerosis and interstitial fibrosis. Brantley JG, et al. Kidney Int, 2003 Apr. PMID 12631340

    See all (563) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. CUX1-related neurodevelopmental disorder: deep insights into phenotype-genotype spectrum and underlying pathology.
      Title: CUX1-related neurodevelopmental disorder: deep insights into phenotype-genotype spectrum and underlying pathology.
    2. CUX1 promotes epithelial-mesenchymal transition (EMT) in renal fibrosis of UUO model by targeting MMP7.
      Title: CUX1 promotes epithelial-mesenchymal transition (EMT) in renal fibrosis of UUO model by targeting MMP7.
    3. Loss of a 7q gene, CUX1, disrupts epigenetically driven DNA repair and drives therapy-related myeloid neoplasms.
      Title: Loss of a 7q gene, CUX1, disrupts epigenetically driven DNA repair and drives therapy-related myeloid neoplasms.
    4. To determine the role for CUX1 in hematopoiesis, this study generated 2 short hairpin RNA-based mouse models with approximately 54% (Cux1(mid)) or approximately 12% (Cux1(low)) residual CUX1 protein. Cux1(mid) mice develop myelodysplastic syndrome (MDS) with anemia and trilineage dysplasia, whereas CUX1(low) mice developed MDS/myeloproliferative neoplasms and anemia.
      Title: Gene dosage effect of CUX1 in a murine model disrupts HSC homeostasis and controls the severity and mortality of MDS.
    5. reduction of VAV2 in absence of CUX1 was associated with a significant decrease of RAC1 activity in response to epithelial wounding. Our results identify a novel pathway by which CUX1 regulates normal intestinal epithelial cell restitution
      Title: Transcription factor CUX1 is required for intestinal epithelial wound healing and targets the VAV2-RAC1 Signalling complex.
    6. Cux1 expression in polycystic kidney disease is not directly involved in cystogenesis but promotes cell proliferation required for expansion of existing cysts, primarily by repression of p27.
      Title: Cux1 promotes cell proliferation and polycystic kidney disease progression in an ADPKD mouse model.
    7. Cux1 is essential for the developmental modulation of intrinsic excitability and the switch to a Kv1-dependent firing mode necessary for interhemispheric innervation.
      Title: Cux1 Enables Interhemispheric Connections of Layer II/III Neurons by Regulating Kv1-Dependent Firing.
    8. Findings reinforce the link between oxidative DNA damage and cellular senescence and suggest that the role of CUX1 as an accessory factor in DNA repair will be critical in physiological situations that generate higher levels of reactive oxygen species.
      Title: The function of CUX1 in oxidative DNA damage repair is needed to prevent premature senescence of mouse embryo fibroblasts.
    9. Results suggest that by their differential effects on basal and apical dendrites, Cux1 and Cux2 can promote the integration of layer II-III neurons in the intracortical networks in highly specific ways
      Title: Cux1 and Cux2 selectively target basal and apical dendritic compartments of layer II-III cortical neurons.
    10. Results show that Cux1 is expressed in cerebellar granule cell precursors and downregulated as they terminally differentiate; suggests some limitations of established medulloblastoma cell lines and mouse models
      Title: The transcription factor Cux1 in cerebellar granule cell development and medulloblastoma pathogenesis.
    Submit: New GeneRIF Correction See all GeneRIFs (42)

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA4047, MGC102214, mKIAA4047

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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 IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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 IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables chromatin binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein-macromolecule adaptor activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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 inner ear auditory receptor cell differentiation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within kidney development IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within lung development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of dendrite morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in retrograde transport, vesicle recycling within Golgi ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in Golgi apparatus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in Golgi membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in neuron projection IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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 IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    protein CASP; homeobox protein cut-like 1
    Names
    CCAAT displacement protein
    Cux/CDP homeoprotein
    cut-like 1
    homeobox protein cux-1

    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_001291233.2 → NP_001278162.1  homeobox protein cut-like 1 isoform c

      Status: VALIDATED

      Source sequence(s)
      AC080158, AC083890, AC087329
      UniProtKB/TrEMBL
      H3BJQ9
      Related
      ENSMUSP00000135086.2, ENSMUST00000176172.8
      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

    2. NM_001291234.2 → NP_001278163.1  homeobox protein cut-like 1 isoform d

      Status: VALIDATED

      Source sequence(s)
      AC080158, AC083890, AC087329
      Consensus CDS
      CCDS71684.1
      UniProtKB/Swiss-Prot
      O08994, P53564, P70301, Q571L6, Q91ZD2
      UniProtKB/TrEMBL
      H3BK24
      Related
      ENSMUSP00000135223.3, ENSMUST00000175975.9
      Conserved Domains (5) summary
      pfam00046
      Location:1231 → 1284
      Homeobox; Homeobox domain
      pfam02376
      Location:1106 → 1183
      CUT; CUT domain
      pfam13851
      Location:131 → 350
      GAS; Growth-arrest specific micro-tubule binding
      cl23720
      Location:290 → 372
      RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)
      cl23765
      Location:108 → 248
      iSH2_PI3K_IA_R; Inter-Src homology 2 (iSH2) helical domain of Class IA Phosphoinositide 3-kinase Regulatory subunits

    3. NM_001291238.2 → NP_001278167.1  protein CASP isoform e

      Status: VALIDATED

      Source sequence(s)
      AC080158, AC083890, AC087329
      Consensus CDS
      CCDS71685.1
      UniProtKB/Swiss-Prot
      P70403, Q7TQJ4, Q91WN6
      UniProtKB/TrEMBL
      H3BJN3
      Related
      ENSMUSP00000135054.2, ENSMUST00000176216.9
      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

    4. NM_001291239.2 → NP_001278168.1  protein CASP isoform f

      Status: VALIDATED

      Source sequence(s)
      AC080158, AC083890, AC087329
      UniProtKB/TrEMBL
      Q9JJB6
      Conserved Domains (4) summary
      pfam07851
      Location:390 → 494
      TMPIT; TMPIT-like protein
      pfam08172
      Location:506 → 721
      CASP_C; CASP C terminal
      pfam13851
      Location:216 → 435
      GAS; Growth-arrest specific micro-tubule binding
      pfam15290
      Location:231 → 374
      Syntaphilin; Golgi-localized syntaxin-1-binding clamp

    5. NM_001291240.2 → NP_001278169.1  protein CASP isoform g

      Status: VALIDATED

      Source sequence(s)
      AC080158, AC083890, AC087329
      UniProtKB/TrEMBL
      Q9JJB6
      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

    6. NM_001405079.1 → NP_001392008.1  homeobox protein cut-like 1 isoform h

      Status: VALIDATED

      Source sequence(s)
      AC080158, AC083890, AC087329

    7. NM_001405081.1 → NP_001392010.1  homeobox protein cut-like 1 isoform i

      Status: VALIDATED

      Source sequence(s)
      AC080158, AC083890, AC087329

    8. NM_001405082.1 → NP_001392011.1  homeobox protein cut-like 1 isoform j

      Status: VALIDATED

      Source sequence(s)
      AC080158, AC083890, AC087329
      Related
      ENSMUSP00000135370.3, ENSMUST00000176486.9

    9. NM_001405083.1 → NP_001392012.1  homeobox protein cut-like 1 isoform k

      Status: VALIDATED

      Source sequence(s)
      AC080158, AC083890, AC087329

    10. NM_001405084.1 → NP_001392013.1  homeobox protein cut-like 1 isoform l

      Status: VALIDATED

      Source sequence(s)
      AC080158, AC083890, AC087329

    11. NM_001405085.1 → NP_001392014.1  protein CASP isoform m

      Status: VALIDATED

      Source sequence(s)
      AC080158, AC083890, AC087329

    12. NM_001405086.1 → NP_001392015.1  protein CASP isoform n

      Status: VALIDATED

      Source sequence(s)
      AC080158, AC083890, AC087329

    13. NM_009986.5 → NP_034116.3  homeobox protein cut-like 1 isoform a

      Status: VALIDATED

      Source sequence(s)
      AC080158, AC083890, AC087329
      Consensus CDS
      CCDS39328.1
      UniProtKB/TrEMBL
      E9QKE9, Q5BL05
      Related
      ENSMUSP00000004097.9, ENSMUST00000004097.16
      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

    14. NM_198602.4 → NP_941004.2  protein CASP isoform b

      Status: VALIDATED

      Source sequence(s)
      AC080158, AC083890, AC087329
      Consensus CDS
      CCDS57391.1
      UniProtKB/Swiss-Prot
      P70403, Q7TQJ4, Q91WN6
      UniProtKB/TrEMBL
      H3BKT0
      Related
      ENSMUSP00000135512.2, ENSMUST00000176745.8
      Conserved Domains (3) summary
      pfam07851
      Location:305 → 409
      TMPIT; TMPIT-like protein
      pfam08172
      Location:421 → 636
      CASP_C; CASP C terminal
      pfam15290
      Location:146 → 289
      Syntaphilin; Golgi-localized syntaxin-1-binding clamp

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000071.7 Reference GRCm39 C57BL/6J

      Range
      136276989..136596429 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_030254113.2 → XP_030109973.1  homeobox protein cut-like 1 isoform X12

      UniProtKB/TrEMBL
      Q5BL05
      Conserved Domains (4) summary
      PHA03247
      Location:634 → 817
      PHA03247; large tegument protein UL36; Provisional
      TIGR02169
      Location:18 → 368
      SMC_prok_A; chromosome segregation protein SMC, primarily archaeal type
      pfam00046
      Location:1131 → 1185
      Homeobox; Homeobox domain
      pfam02376
      Location:1006 → 1079
      CUT; CUT domain

    2. XM_036164773.1 → XP_036020666.1  homeobox protein cut-like 1 isoform X9

      UniProtKB/TrEMBL
      H3BJQ9
      Conserved Domains (4) summary
      PHA03247
      Location:736 → 919
      PHA03247; large tegument protein UL36; Provisional
      COG1196
      Location:16 → 377
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      pfam00046
      Location:1233 → 1287
      Homeobox; Homeobox domain
      pfam02376
      Location:1108 → 1185
      CUT; CUT domain

    3. XM_030254110.2 → XP_030109970.1  homeobox protein cut-like 1 isoform X10

      UniProtKB/TrEMBL
      Q5BL05
      Conserved Domains (4) summary
      PHA03247
      Location:680 → 863
      PHA03247; large tegument protein UL36; Provisional
      COG0419
      Location:17 → 430
      SbcC; DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]
      pfam00046
      Location:1177 → 1231
      Homeobox; Homeobox domain
      pfam02376
      Location:1052 → 1125
      CUT; CUT domain

    4. XM_030254108.2 → XP_030109968.1  homeobox protein cut-like 1 isoform X5

      UniProtKB/TrEMBL
      H3BJQ9
      Conserved Domains (4) summary
      PHA03247
      Location:760 → 943
      PHA03247; large tegument protein UL36; Provisional
      TIGR04523
      Location:17 → 399
      Mplasa_alph_rch; helix-rich Mycoplasma protein
      pfam00046
      Location:1257 → 1311
      Homeobox; Homeobox domain
      pfam02376
      Location:1132 → 1205
      CUT; CUT domain

    5. XM_030254106.2 → XP_030109966.1  homeobox protein cut-like 1 isoform X2

      UniProtKB/TrEMBL
      H3BJQ9
      Conserved Domains (4) summary
      PHA03247
      Location:845 → 1028
      PHA03247; large tegument protein UL36; Provisional
      COG0419
      Location:103 → 482
      SbcC; DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]
      pfam00046
      Location:1342 → 1396
      Homeobox; Homeobox domain
      pfam02376
      Location:1217 → 1290
      CUT; CUT domain

    6. XM_017320654.3 → XP_017176143.1  homeobox protein cut-like 1 isoform X1

      UniProtKB/TrEMBL
      H3BJQ9
      Conserved Domains (4) summary
      PHA03247
      Location:867 → 1050
      PHA03247; large tegument protein UL36; Provisional
      COG0419
      Location:103 → 482
      SbcC; DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]
      pfam00046
      Location:1364 → 1418
      Homeobox; Homeobox domain
      pfam02376
      Location:1239 → 1312
      CUT; CUT domain

    7. XM_006504354.4 → XP_006504417.1  homeobox protein cut-like 1 isoform X8

      UniProtKB/TrEMBL
      H3BLS0, Q5BL05
      Related
      ENSMUSP00000135892.2, ENSMUST00000176778.8
      Conserved Domains (5) summary
      PHA03247
      Location:739 → 922
      PHA03247; large tegument protein UL36; Provisional
      TIGR02168
      Location:196 → 447
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type
      TIGR04211
      Location:400 → 502
      SH3_and_anchor; SH3 domain protein
      pfam00046
      Location:1236 → 1290
      Homeobox; Homeobox domain
      pfam02376
      Location:1111 → 1184
      CUT; CUT domain

    8. XM_030254107.2 → XP_030109967.1  homeobox protein cut-like 1 isoform X4

      UniProtKB/Swiss-Prot
      O08994, P53564, P70301, Q571L6, Q91ZD2
      Conserved Domains (4) summary
      PHA03247
      Location:819 → 1002
      PHA03247; large tegument protein UL36; Provisional
      TIGR02168
      Location:196 → 447
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type
      pfam00046
      Location:1316 → 1370
      Homeobox; Homeobox domain
      pfam02376
      Location:1191 → 1264
      CUT; CUT domain
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P53564.3 GenPept UniProtKB/Swiss-Prot:P53564
    P70403.2 GenPept UniProtKB/Swiss-Prot:P70403

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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