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alx3 ALX homeobox 3 [ Danio rerio (zebrafish) ]

Gene ID: 566955, updated on 4-Jan-2025

Summary

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Official Symbol
alx3provided by ZNC
Official Full Name
ALX homeobox 3provided by ZNC
Primary source
ZFIN:ZDB-GENE-120221-3
See related
AllianceGenome:ZFIN:ZDB-GENE-120221-3
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
Summary
Predicted to enable DNA binding activity and DNA-binding transcription factor activity, RNA polymerase II-specific. Acts upstream of or within camera-type eye morphogenesis; neural crest cell migration; and skeletal system development. Predicted to be located in nucleus. Is expressed in cranial neural crest; head mesenchyme; neural crest; neurocranium; and periocular mesenchyme. Human ortholog(s) of this gene implicated in frontonasal dysplasia 1. Orthologous to human ALX3 (ALX homeobox 3). [provided by Alliance of Genome Resources, Jan 2025]
Orthologs
human mouse all
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Genomic context

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See alx3 in Genome Data Viewer
Location:
chromosome: 8
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCz11 (GCF_000002035.6) 8 NC_007119.7 (24796544..24808048, complement)
105 previous assembly GRCz10 (GCF_000002035.5) 8 NC_007119.6 (24779534..24788916, complement)

Chromosome 8 - NC_007119.7Genomic Context describing neighboring genes Neighboring gene solute carrier family 16 member 4 Neighboring gene RNA binding motif protein 15 Neighboring gene solute carrier family 6 member 17 Neighboring gene potassium voltage-gated channel, Shaw-related subfamily, member 4

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. ALX1-related frontonasal dysplasia results from defective neural crest cell development and migration. Pini J, et al. EMBO Mol Med, 2020 Oct 7. PMID 32914578, Free PMC Article
  2. Defective neural crest migration revealed by a Zebrafish model of Alx1-related frontonasal dysplasia. Dee CT, et al. Hum Mol Genet, 2013 Jan 15. PMID 23059813
  3. Evolution of the Alx homeobox gene family: parallel retention and independent loss of the vertebrate Alx3 gene. McGonnell IM, et al. Evol Dev, 2011 Jul-Aug. PMID 21740507, Free PMC Article
  4. TFAP2 paralogs regulate midfacial development in part through a conserved ALX genetic pathway. Nguyen TT, et al. Development, 2024 Jan 1. PMID 38063857, Free PMC Article
  5. Zebrafish models of alx-linked frontonasal dysplasia reveal a role for Alx1 and Alx3 in the anterior segment and vasculature of the developing eye. Yoon B, et al. Biol Open, 2022 May 15. PMID 35142342, Free PMC Article

See all (12) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The alx3 gene shapes the zebrafish neurocranium by regulating frontonasal neural crest cell differentiation timing.
    Title: The alx3 gene shapes the zebrafish neurocranium by regulating frontonasal neural crest cell differentiation timing.
Submit: New GeneRIF Correction

General gene information

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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 IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
acts_upstream_of_or_within camera-type eye morphogenesis IGI
Inferred from Genetic Interaction
more info
 PubMed 
acts_upstream_of_or_within cartilage development IGI
Inferred from Genetic Interaction
more info
 PubMed 
acts_upstream_of_or_within cartilage development IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within cranial skeletal system development IGI
Inferred from Genetic Interaction
more info
 PubMed 
acts_upstream_of_or_within cranial skeletal system development IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within embryonic neurocranium morphogenesis IGI
Inferred from Genetic Interaction
more info
 PubMed 
acts_upstream_of_or_within embryonic neurocranium morphogenesis IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within neural crest cell differentiation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within neural crest cell migration IGI
Inferred from Genetic Interaction
more info
 PubMed 
acts_upstream_of_or_within regulation of DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
homeobox protein aristaless-like 3

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_007119.7 Reference GRCz11 Primary Assembly

    Range
    24796544..24808048 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_690238.6 → XP_695330.1  homeobox protein aristaless-like 3 isoform X2

    UniProtKB/TrEMBL
    A0A8N7TDQ1
    Conserved Domains (1) summary
    pfam00046
    Location:158 → 210
    Homeobox; Homeobox domain

  2. XM_005167112.5 → XP_005167169.1  homeobox protein aristaless-like 3 isoform X3

    UniProtKB/TrEMBL
    A0A8M2BEJ5
    Conserved Domains (1) summary
    pfam00046
    Location:159 → 211
    Homeobox; Homeobox domain

  3. XM_005167111.5 → XP_005167168.1  homeobox protein aristaless-like 3 isoform X1

    UniProtKB/TrEMBL
    A0A8M2BF28
    Conserved Domains (1) summary
    pfam00046
    Location:159 → 211
    Homeobox; Homeobox domain

Reference GRCz11 ALT_DRER_TU_1

Genomic

  1. NW_018394725.1 Reference GRCz11 ALT_DRER_TU_1

    Range
    322558..334413 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_021472079.2 → XP_021327754.1  homeobox protein aristaless-like 3 isoform X2

    UniProtKB/TrEMBL
    A0A8M9PS84
    Conserved Domains (1) summary
    pfam00046
    Location:158 → 210
    Homeobox; Homeobox domain

  2. XM_021472080.2 → XP_021327755.1  homeobox protein aristaless-like 3 isoform X3

    UniProtKB/TrEMBL
    A0A8M9Q2T1
    Conserved Domains (2) summary
    pfam12561
    Location:57 → 114
    TagA; ToxR activated gene A lipoprotein
    pfam00046
    Location:159 → 211
    Homeobox; Homeobox domain

  3. XM_021472078.2 → XP_021327753.1  homeobox protein aristaless-like 3 isoform X1

    UniProtKB/TrEMBL
    A0A8M9PL59
    Conserved Domains (2) summary
    pfam12561
    Location:57 → 114
    TagA; ToxR activated gene A lipoprotein
    pfam00046
    Location:159 → 211
    Homeobox; Homeobox domain
Nucleotide Protein Strain
Heading Accession and Version

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