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Aliases for DLX3 Gene

Aliases for DLX3 Gene

  • Distal-Less Homeobox 3 2 3 5
  • Distal-Less Homeo Box 3 2
  • Homeobox Protein DLX-3 3
  • AI4 3
  • TDO 3

External Ids for DLX3 Gene

Previous GeneCards Identifiers for DLX3 Gene

  • GC17M047778
  • GC17M050547
  • GC17M048409
  • GC17M048543
  • GC17M048542
  • GC17M045423
  • GC17M048067
  • GC17M043432

Summaries for DLX3 Gene

Entrez Gene Summary for DLX3 Gene

  • Many vertebrate homeo box-containing genes have been identified on the basis of their sequence similarity with Drosophila developmental genes. Members of the Dlx gene family contain a homeobox that is related to that of Distal-less (Dll), a gene expressed in the head and limbs of the developing fruit fly. The Distal-less (Dlx) family of genes comprises at least 6 different members, DLX1-DLX6. Trichodentoosseous syndrome (TDO), an autosomal dominant condition, has been correlated with DLX3 gene mutation. This gene is located in a tail-to-tail configuration with another member of the gene family on the long arm of chromosome 17. Mutations in this gene have been associated with the autosomal dominant conditions trichodentoosseous syndrome and amelogenesis imperfecta with taurodontism. [provided by RefSeq, Jul 2008]

GeneCards Summary for DLX3 Gene

DLX3 (Distal-Less Homeobox 3) is a Protein Coding gene. Diseases associated with DLX3 include Trichodentoosseous Syndrome and Amelogenesis Imperfecta, Type Iv. Gene Ontology (GO) annotations related to this gene include DNA binding transcription factor activity and chromatin binding. An important paralog of this gene is DLX5.

UniProtKB/Swiss-Prot for DLX3 Gene

  • Likely to play a regulatory role in the development of the ventral forebrain. May play a role in craniofacial patterning and morphogenesis.

Gene Wiki entry for DLX3 Gene

Additional gene information for DLX3 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for DLX3 Gene

Genomics for DLX3 Gene

GeneHancer (GH) Regulatory Elements for DLX3 Gene

Promoters and enhancers for DLX3 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH17J049994 Promoter/Enhancer 1.5 EPDnew Ensembl ENCODE 656.2 +0.3 253 1.5 ZSCAN4 KLF17 SIN3A KLF14 ZNF2 RFX5 ZNF335 ZNF366 EGR2 ZNF398 DLX3 ENSG00000248172 DLX4
GH17J049996 Promoter/Enhancer 1.4 Ensembl ENCODE 650.7 -1.9 -1851 0.8 ARID4B SIN3A ZNF48 GLIS2 ARID2 ZNF143 SP3 RXRA SP5 REST ENSG00000248172 DLX3 PICART1
GH17J049993 Promoter 0.9 Ensembl 650.7 +1.4 1423 0.4 TFAP4 RNF2 SIN3A ERF ETV5 RBPJ ETS1 ZNF512B ZBTB33 EZH2 DLX3 SPATA20 DLX4
GH17J050046 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 11 -61.7 -61690 21.3 HDGF PKNOX1 CLOCK SMAD1 FOXA2 SIN3A FEZF1 ZBTB7B YY1 ZNF213 ITGA3 PICART1 ENSG00000262837 LUC7L3 FAM117A FLJ45513 PDK2 ENSG00000250282 LOC105371824 COL1A1
GH17J049850 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 11.6 +143.7 143690 1.9 HDGF ATF1 ARID4B SIN3A DMAP1 GLI4 ZNF2 ZNF48 YY1 GTF3C2 ENSG00000262837 UBE2Z ENSG00000248172 DLX3 FLJ45513 SLC35B1 ENSG00000250310 NXPH3 LOC100288866 SPOP
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around DLX3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the DLX3 gene promoter:
  • C/EBPalpha
  • MyoD
  • Lmo2
  • COMP1
  • RORalpha2
  • RFX1
  • AREB6
  • YY1

Genomic Locations for DLX3 Gene

Genomic Locations for DLX3 Gene
18,146 bases
Minus strand
5,220 bases
Minus strand

Genomic View for DLX3 Gene

Genes around DLX3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
DLX3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for DLX3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for DLX3 Gene

Proteins for DLX3 Gene

  • Protein details for DLX3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Homeobox protein DLX-3
    Protein Accession:
    Secondary Accessions:
    • B3KQL6

    Protein attributes for DLX3 Gene

    287 amino acids
    Molecular mass:
    31738 Da
    Quaternary structure:
    • Heterodimer with MEIS1.

    Three dimensional structures from OCA and Proteopedia for DLX3 Gene

neXtProt entry for DLX3 Gene

Post-translational modifications for DLX3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for DLX3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for DLX3 Gene

Domains & Families for DLX3 Gene

Gene Families for DLX3 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins
  • Transcription factors

Suggested Antigen Peptide Sequences for DLX3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the distal-less homeobox family.
  • Belongs to the distal-less homeobox family.
genes like me logo Genes that share domains with DLX3: view

Function for DLX3 Gene

Molecular function for DLX3 Gene

UniProtKB/Swiss-Prot Function:
Likely to play a regulatory role in the development of the ventral forebrain. May play a role in craniofacial patterning and morphogenesis.
GENATLAS Biochemistry:
Drosophila distal less homolog Dlx3,homeo domain encoding gene

Phenotypes From GWAS Catalog for DLX3 Gene

Gene Ontology (GO) - Molecular Function for DLX3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding NAS 19274049
GO:0001077 transcriptional activator activity, RNA polymerase II proximal promoter sequence-specific DNA binding IEA --
GO:0003677 DNA binding IEA --
GO:0003682 chromatin binding IEA --
GO:0003700 DNA binding transcription factor activity TAS 9467018
genes like me logo Genes that share ontologies with DLX3: view
genes like me logo Genes that share phenotypes with DLX3: view

Human Phenotype Ontology for DLX3 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for DLX3 Gene

MGI Knock Outs for DLX3:

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for DLX3 Gene

Localization for DLX3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for DLX3 Gene

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for DLX3 gene
Compartment Confidence
nucleus 5

Gene Ontology (GO) - Cellular Components for DLX3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
genes like me logo Genes that share ontologies with DLX3: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for DLX3 Gene

Pathways & Interactions for DLX3 Gene

No Data Available

SIGNOR curated interactions for DLX3 Gene


Gene Ontology (GO) - Biological Process for DLX3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001568 blood vessel development IEA --
GO:0001890 placenta development IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006357 regulation of transcription by RNA polymerase II IEA --
GO:0006366 transcription by RNA polymerase II IEA --
genes like me logo Genes that share ontologies with DLX3: view

No data available for Pathways by source for DLX3 Gene

Drugs & Compounds for DLX3 Gene

No Compound Related Data Available

Transcripts for DLX3 Gene

mRNA/cDNA for DLX3 Gene

(1) REFSEQ mRNAs :
(4) Additional mRNA sequences :
(47) Selected AceView cDNA sequences:
(2) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for DLX3 Gene

Distal-less homeobox 3:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for DLX3 Gene

No ASD Table

Relevant External Links for DLX3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for DLX3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for DLX3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for DLX3 Gene

This gene is overexpressed in Skin - Sun Exposed (Lower leg) (x22.8) and Skin - Not Sun Exposed (Suprapubic) (x20.3).

Protein differential expression in normal tissues from HIPED for DLX3 Gene

This gene is overexpressed in Placenta (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for DLX3 Gene

Protein tissue co-expression partners for DLX3 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of DLX3 Gene:


SOURCE GeneReport for Unigene cluster for DLX3 Gene:


Evidence on tissue expression from TISSUES for DLX3 Gene

  • Eye(4)
  • Skin(2.2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for DLX3 Gene

Germ Layers:
  • ectoderm
  • mesoderm
  • digestive
  • integumentary
  • skeletal muscle
  • skeleton
Head and neck:
  • brain
  • cheek
  • chin
  • face
  • forehead
  • head
  • jaw
  • mandible
  • maxilla
  • mouth
  • neck
  • sinus
  • skull
  • tooth
  • chest wall
  • clavicle
  • rib
  • rib cage
  • scapula
  • sternum
  • pelvis
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • nail
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
  • hair
  • skin
  • spinal column
  • vertebrae
genes like me logo Genes that share expression patterns with DLX3: view

No data available for mRNA Expression by UniProt/SwissProt for DLX3 Gene

Orthologs for DLX3 Gene

This gene was present in the common ancestor of animals.

Orthologs for DLX3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia DLX3 34 33
  • 100 (n)
(Monodelphis domestica)
Mammalia DLX3 34
  • 97 (a)
(Bos Taurus)
Mammalia DLX3 34 33
  • 93.96 (n)
(Canis familiaris)
Mammalia DLX3 34 33
  • 93.5 (n)
(Rattus norvegicus)
Mammalia Dlx3 33
  • 91.64 (n)
(Mus musculus)
Mammalia Dlx3 16 34 33
  • 91.17 (n)
(Gallus gallus)
Aves DLX3 34 33
  • 78.54 (n)
(Anolis carolinensis)
Reptilia DLX3 34
  • 77 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia dlx3 33
  • 65.22 (n)
Str.1302 33
African clawed frog
(Xenopus laevis)
Amphibia dlx3-A-prov 33
(Danio rerio)
Actinopterygii dlx3b 34 33 33
  • 69.92 (n)
fruit fly
(Drosophila melanogaster)
Insecta Dll 34
  • 27 (a)
(Caenorhabditis elegans)
Secernentea ceh-43 34
  • 29 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 21 (a)
CSA.6494 34
  • 14 (a)
Species where no ortholog for DLX3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for DLX3 Gene

Gene Tree for DLX3 (if available)
Gene Tree for DLX3 (if available)
Evolutionary constrained regions (ECRs) for DLX3: view image

Paralogs for DLX3 Gene

Paralogs for DLX3 Gene

(13) SIMAP similar genes for DLX3 Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with DLX3: view

Variants for DLX3 Gene

Sequence variations from dbSNP and Humsavar for DLX3 Gene

SNP ID Clin Chr 17 pos Variation AA Info Type
rs10459948 likely-benign, Amelogenesis Imperfecta, Dominant 49,995,132(-) G/T 5_prime_UTR_variant
rs1057518764 likely-pathogenic, Amelogenesis imperfecta, Peripheral pulmonary artery stenosis 49,991,807(-) CCCC/CCCCC coding_sequence_variant, frameshift
rs11868203 uncertain-significance, Amelogenesis Imperfecta, Dominant 49,991,799(-) C/A/T coding_sequence_variant, synonymous_variant
rs12452477 benign, Amelogenesis Imperfecta, Dominant 49,990,589(-) T/C 3_prime_UTR_variant
rs139226711 uncertain-significance, Amelogenesis Imperfecta, Dominant 49,994,747(-) C/T coding_sequence_variant, synonymous_variant

Structural Variations from Database of Genomic Variants (DGV) for DLX3 Gene

Variant ID Type Subtype PubMed ID
nsv833474 CNV loss 17160897

Variation tolerance for DLX3 Gene

Residual Variation Intolerance Score: 48.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.26; 25.26% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for DLX3 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for DLX3 Gene

Disorders for DLX3 Gene

MalaCards: The human disease database

(10) MalaCards diseases for DLX3 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, DISEASES, Novoseek, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search DLX3 in MalaCards View complete list of genes associated with diseases


  • Trichodentoosseous syndrome (TDO) [MIM:190320]: An autosomal dominant disease characterized by curly kinky hair at birth, enamel hypoplasia, taurodontism, thickening of cortical bones and variable expression of craniofacial morphology. {ECO:0000269 PubMed:9467018}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Amelogenesis imperfecta 4 (AI4) [MIM:104510]: An autosomal dominant defect of enamel formation associated with enlarged pulp chambers. Enamel is thin, teeth are small and widely spaced. {ECO:0000269 PubMed:15666299}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for DLX3

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with DLX3: view

No data available for Genatlas for DLX3 Gene

Publications for DLX3 Gene

  1. Increased bone density associated with DLX3 mutation in the tricho-dento-osseous syndrome. (PMID: 15454107) Haldeman RJ … Wright JT (Bone 2004) 3 22 44 58
  2. Genomic structure and functional control of the Dlx3-7 bigene cluster. (PMID: 11792834) Sumiyama K … Ruddle FH (Proceedings of the National Academy of Sciences of the United States of America 2002) 3 4 22 58
  3. DNA-dependent formation of transcription factor pairs alters their binding specificity. (PMID: 26550823) Jolma A … Taipale J (Nature 2015) 3 4 58
  4. Uncombable hair and atopic dermatitis in a case of trichodento-osseous syndrome. (PMID: 20151948) Mayer DE … Jarisch R (Journal der Deutschen Dermatologischen Gesellschaft = Journal of the German Society of Dermatology : JDDG 2010) 3 22 58
  5. Homeodomain protein Dlx3 induces phosphorylation-dependent p63 degradation. (PMID: 19282665) Di Costanzo A … Calabrò V (Cell cycle (Georgetown, Tex.) 2009) 3 22 58

Products for DLX3 Gene

Sources for DLX3 Gene

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