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

Gene ID: 797445, updated on 4-Jan-2025

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, Jan 2025]
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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