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    cux1a cut-like homeobox 1a [ Danio rerio (zebrafish) ]

    Gene ID: 797445, updated on 9-Dec-2024

    Summary

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    Official Symbol
    cux1aprovided by ZNC
    Official Full Name
    cut-like homeobox 1aprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-030131-5868
    See related
    Ensembl:ENSDARG00000078459 AllianceGenome:ZFIN:ZDB-GENE-030131-5868
    Gene type
    protein coding
    RefSeq status
    MODEL
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    fi22b07; wu:fi22b07; wu:fk35a11; si:ch211-251d10.5
    Summary
    Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to act upstream of or within regulation of DNA-templated transcription. Predicted to be active in nucleus. Is expressed in brain. Orthologous to human CUX1 (cut like homeobox 1). [provided by Alliance of Genome Resources, Dec 2024]
    Orthologs
    all
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    Genomic context

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    See cux1a in Genome Data Viewer
    Location:
    chromosome: 10
    Exon count:
    26
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 10 NC_007121.7 (32900629..33156812, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 10 NC_007121.6 (32958657..33213111, complement)

    Chromosome 10 - NC_007121.7Genomic Context describing neighboring genes Neighboring gene dnaJ homolog subfamily C member 30, mitochondrial Neighboring gene potassium channel tetramerization domain containing 7 Neighboring gene uncharacterized LOC137496525 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: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • BioProject: PRJEB1986
    • Analysis date: Fri Dec 8 19:48:10 2017

    Bibliography

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    Related articles in PubMed

    1. Homozygous Mutations in CSF1R Cause a Pediatric-Onset Leukoencephalopathy and Can Result in Congenital Absence of Microglia. Oosterhof N, et al. Am J Hum Genet, 2019 May 2. PMID 30982608, Free PMC Article
    2. The evolutionary fate of alternatively spliced homologous exons after gene duplication. Abascal F, et al. Genome Biol Evol, 2015 Apr 29. PMID 25931610, Free PMC Article
    3. Prematurely terminated intron-retaining mRNAs invade axons in SFPQ null-driven neurodegeneration and are a hallmark of ALS. Taylor R, et al. Nat Commun, 2022 Nov 22. PMID 36414621, Free PMC Article
    4. The Golgi matrix protein giantin is required for normal cilia function in zebrafish. Bergen DJM, et al. Biol Open, 2017 Aug 15. PMID 28546340, Free PMC Article
    5. 15000 unique zebrafish EST clusters and their future use in microarray for profiling gene expression patterns during embryogenesis. Lo J, et al. Genome Res, 2003 Mar. PMID 12618376, Free PMC Article

    See all (7) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    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 transcription regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within regulation of DNA-templated transcription IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    cut-like homeobox 1; homeobox protein cut-like 1

    NCBI Reference Sequences (RefSeq)

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    RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

    Reference GRCz11 Primary Assembly

    Genomic

    1. NC_007121.7 Reference GRCz11 Primary Assembly

      Range
      32900629..33156812 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_021479404.2 → XP_021335079.1  homeobox protein cut-like 1 isoform X8

      UniProtKB/TrEMBL
      A0A8M9QCL4
      Conserved Domains (3) summary
      pfam00046
      Location:1228 → 1281
      Homeobox; Homeobox domain
      pfam02376
      Location:1088 → 1165
      CUT; CUT domain
      cl25732
      Location:18 → 370
      SMC_N; RecF/RecN/SMC N terminal domain

    2. XM_021479403.2 → XP_021335078.1  homeobox protein cut-like 1 isoform X7

      UniProtKB/TrEMBL
      A0A8M9Q6L3
      Conserved Domains (3) summary
      pfam00046
      Location:1243 → 1296
      Homeobox; Homeobox domain
      pfam02376
      Location:1103 → 1180
      CUT; CUT domain
      cl25732
      Location:18 → 370
      SMC_N; RecF/RecN/SMC N terminal domain

    3. XM_005172720.5 → XP_005172777.1  homeobox protein cut-like 1 isoform X4

      UniProtKB/TrEMBL
      A0A2R8QFA5, A0A8M2BK19
      Related
      ENSDARP00000150637.1, ENSDART00000182065.1
      Conserved Domains (5) summary
      pfam00046
      Location:1272 → 1325
      Homeobox; Homeobox domain
      pfam00261
      Location:127 → 371
      Tropomyosin; Tropomyosin
      pfam02376
      Location:1132 → 1209
      CUT; CUT domain
      pfam11593
      Location:325 → 574
      Med3; Mediator complex subunit 3 fungal
      cl23720
      Location:290 → 359
      RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)

    4. XM_003199366.6 → XP_003199414.2  homeobox protein cut-like 1 isoform X6

      UniProtKB/TrEMBL
      A0A8M1RNM7
      Conserved Domains (5) summary
      pfam00046
      Location:1255 → 1308
      Homeobox; Homeobox domain
      pfam00261
      Location:127 → 371
      Tropomyosin; Tropomyosin
      pfam02376
      Location:1115 → 1192
      CUT; CUT domain
      pfam11593
      Location:325 → 574
      Med3; Mediator complex subunit 3 fungal
      cl23720
      Location:290 → 359
      RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)

    5. XM_005172721.5 → XP_005172778.1  homeobox protein cut-like 1 isoform X5

      UniProtKB/TrEMBL
      A0A2R8Q0A5, A0A8M2BJW5
      Related
      ENSDARP00000147023.1, ENSDART00000192268.1
      Conserved Domains (5) summary
      pfam00046
      Location:1270 → 1323
      Homeobox; Homeobox domain
      pfam00261
      Location:127 → 371
      Tropomyosin; Tropomyosin
      pfam02376
      Location:1130 → 1207
      CUT; CUT domain
      pfam11593
      Location:325 → 574
      Med3; Mediator complex subunit 3 fungal
      cl23720
      Location:290 → 359
      RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)

    6. XM_005172719.5 → XP_005172776.1  homeobox protein cut-like 1 isoform X3

      UniProtKB/TrEMBL
      A0A8M2BJZ7
      Conserved Domains (5) summary
      pfam00046
      Location:1284 → 1337
      Homeobox; Homeobox domain
      pfam00261
      Location:127 → 371
      Tropomyosin; Tropomyosin
      pfam02376
      Location:1144 → 1221
      CUT; CUT domain
      pfam11593
      Location:325 → 574
      Med3; Mediator complex subunit 3 fungal
      cl23720
      Location:290 → 359
      RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)

    7. XM_068223832.1 → XP_068079933.1  homeobox protein cut-like 1 isoform X2

    8. XM_005172718.5 → XP_005172775.1  homeobox protein cut-like 1 isoform X1

      UniProtKB/TrEMBL
      A0A8M2BJX8, E7F4J9
      Related
      ENSDARP00000075613.4, ENSDART00000081170.6
      Conserved Domains (5) summary
      pfam00046
      Location:1299 → 1352
      Homeobox; Homeobox domain
      pfam00261
      Location:127 → 371
      Tropomyosin; Tropomyosin
      pfam02376
      Location:1159 → 1236
      CUT; CUT domain
      pfam11593
      Location:325 → 574
      Med3; Mediator complex subunit 3 fungal
      cl23720
      Location:290 → 359
      RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)
    Nucleotide Protein Strain
    Heading Accession and Version

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