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Aliases for DLL3 Gene

Aliases for DLL3 Gene

  • Delta Like Canonical Notch Ligand 3 2 3 5
  • Drosophila Delta Homolog 3 3 4
  • Delta3 3 4
  • Delta (Drosophila)-Like 3 2
  • Delta-Like 3 (Drosophila) 2
  • Delta-Like Protein 3 3
  • Delta-Like 3 3
  • SCDO1 3

External Ids for DLL3 Gene

Previous GeneCards Identifiers for DLL3 Gene

  • GC19P040630
  • GC19P040380
  • GC19P044665
  • GC19P044682
  • GC19P044683
  • GC19P044684
  • GC19P039989
  • GC19P036435

Summaries for DLL3 Gene

Entrez Gene Summary for DLL3 Gene

  • This gene encodes a member of the delta protein ligand family. This family functions as Notch ligands that are characterized by a DSL domain, EGF repeats, and a transmembrane domain. Mutations in this gene cause autosomal recessive spondylocostal dysostosis 1. Two transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]

CIViC summary for DLL3 Gene

GeneCards Summary for DLL3 Gene

DLL3 (Delta Like Canonical Notch Ligand 3) is a Protein Coding gene. Diseases associated with DLL3 include Spondylocostal Dysostosis 1, Autosomal Recessive and Spondylocostal Dysostosis, Autosomal Recessive. Among its related pathways are Notch signaling pathway (KEGG) and Canonical and Non-canonical Notch signaling. Gene Ontology (GO) annotations related to this gene include calcium ion binding and Notch binding. An important paralog of this gene is CRB2.

UniProtKB/Swiss-Prot for DLL3 Gene

  • Inhibits primary neurogenesis. May be required to divert neurons along a specific differentiation pathway. Plays a role in the formation of somite boundaries during segmentation of the paraxial mesoderm (By similarity).

Gene Wiki entry for DLL3 Gene

Additional gene information for DLL3 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for DLL3 Gene

Genomics for DLL3 Gene

GeneHancer (GH) Regulatory Elements for DLL3 Gene

Promoters and enhancers for DLL3 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
GH19J039497 Promoter/Enhancer 1.7 EPDnew Ensembl ENCODE 650.7 -0.2 -194 2.2 HDGF PKNOX1 SIN3A ZNF2 ZNF143 KLF13 SP3 REST ZSCAN16 GLIS1 DLL3 HNRNPL ZNF780B EID2B MED29 ENSG00000269792 LOC105372399 LGALS14 ENSG00000269172 ENSG00000267375
GH19J039397 Promoter/Enhancer 2.8 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 10.2 -91.8 -91820 20 CLOCK MLX ZFP64 FEZF1 DMAP1 YBX1 IRF4 YY1 SLC30A9 ZNF213 ZFP36 PAF1 HNRNPL FBL ZNF780B SUPT5H RN7SL566P ZNF780A ENSG00000269688 AKT2
GH19J038673 Enhancer 1.9 FANTOM5 Ensembl ENCODE dbSUPER 10.1 -804.0 -804009 42 CLOCK MLX FEZF1 DMAP1 YY1 SLC30A9 ZNF213 E2F8 ZNF548 SP3 ENSG00000267375 HNRNPL ZNF573 ZNF607 ACTN4 SUPT5H CATSPERG ENSG00000269688 PAF1 ENSG00000266963
GH19J038919 Enhancer 1.2 FANTOM5 ENCODE 10.1 -578.8 -578754 1.5 SIN3A ZNF48 YY2 ZNF662 GMEB1 ZNF184 ZSCAN16 NBN ZNF300 ZNF785 SUPT5H FBL HNRNPL SARS2 PAF1 RPS16 ERVK9-11 ENSG00000266963 ENSG00000269688 RN7SL566P
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around DLL3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the DLL3 gene promoter:
  • c-Ets-1
  • RORalpha1
  • E2F
  • E2F-1
  • E2F-2
  • E2F-3a
  • E2F-4
  • Pax-5
  • deltaCREB
  • CREB

Genomic Locations for DLL3 Gene

Genomic Locations for DLL3 Gene
9,587 bases
Plus strand
9,587 bases
Plus strand

Genomic View for DLL3 Gene

Genes around DLL3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
DLL3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for DLL3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for DLL3 Gene

Proteins for DLL3 Gene

  • Protein details for DLL3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Delta-like protein 3
    Protein Accession:
    Secondary Accessions:
    • E9PFG2
    • Q8NBS4

    Protein attributes for DLL3 Gene

    618 amino acids
    Molecular mass:
    64618 Da
    Quaternary structure:
    • Can bind and activate Notch-1 or another Notch receptor.

    Alternative splice isoforms for DLL3 Gene


neXtProt entry for DLL3 Gene

Post-translational modifications for DLL3 Gene

  • Ubiquitinated by MIB (MIB1 or MIB2), leading to its endocytosis and subsequent degradation.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for DLL3 Gene

No data available for DME Specific Peptides for DLL3 Gene

Domains & Families for DLL3 Gene

Gene Families for DLL3 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Plasma proteins
  • Predicted membrane proteins
  • Predicted secreted proteins

Suggested Antigen Peptide Sequences for DLL3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • The DSL domain is required for binding to the Notch receptor.
  • The DSL domain is required for binding to the Notch receptor.
genes like me logo Genes that share domains with DLL3: view

Function for DLL3 Gene

Molecular function for DLL3 Gene

UniProtKB/Swiss-Prot Function:
Inhibits primary neurogenesis. May be required to divert neurons along a specific differentiation pathway. Plays a role in the formation of somite boundaries during segmentation of the paraxial mesoderm (By similarity).

Phenotypes From GWAS Catalog for DLL3 Gene

Gene Ontology (GO) - Molecular Function for DLL3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005112 Notch binding NAS 10742114
GO:0005509 calcium ion binding IEA --
genes like me logo Genes that share ontologies with DLL3: view
genes like me logo Genes that share phenotypes with DLL3: view

Human Phenotype Ontology for DLL3 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for DLL3 Gene

MGI Knock Outs for DLL3:

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for DLL3 Gene

Localization for DLL3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for DLL3 Gene

Membrane; Single-pass type I membrane protein.

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 DLL3 gene
Compartment Confidence
plasma membrane 4
extracellular 1
nucleus 1
cytosol 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for DLL3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane NAS 10742114
genes like me logo Genes that share ontologies with DLL3: view

Pathways & Interactions for DLL3 Gene

genes like me logo Genes that share pathways with DLL3: view

Pathways by source for DLL3 Gene

SIGNOR curated interactions for DLL3 Gene

Is activated by:

Gene Ontology (GO) - Biological Process for DLL3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001501 skeletal system development IMP 10742114
GO:0001756 somitogenesis IEA --
GO:0007219 Notch signaling pathway IEA --
GO:0007275 multicellular organism development IEA --
GO:0007386 compartment pattern specification IEA --
genes like me logo Genes that share ontologies with DLL3: view

Drugs & Compounds for DLL3 Gene

(2) Drugs for DLL3 Gene - From: ClinicalTrials

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Antibodies Pharma 7224
Immunoglobulins Pharma 7224
genes like me logo Genes that share compounds with DLL3: view

Transcripts for DLL3 Gene

mRNA/cDNA for DLL3 Gene

(2) REFSEQ mRNAs :
(3) Additional mRNA sequences :
(197) Selected AceView cDNA sequences:
(5) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for DLL3 Gene

Delta-like 3 (Drosophila):
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for DLL3 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7a · 7b ^ 8 ^ 9
SP1: -
SP2: -
SP3: - - - -

Relevant External Links for DLL3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for DLL3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for DLL3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for DLL3 Gene

This gene is overexpressed in Brain - Nucleus accumbens (basal ganglia) (x6.3), Brain - Amygdala (x5.6), Brain - Putamen (basal ganglia) (x4.9), Brain - Hypothalamus (x4.6), Brain - Hippocampus (x4.5), and Brain - Caudate (basal ganglia) (x4.2).

NURSA nuclear receptor signaling pathways regulating expression of DLL3 Gene:


SOURCE GeneReport for Unigene cluster for DLL3 Gene:


Evidence on tissue expression from TISSUES for DLL3 Gene

  • Nervous system(4.9)
  • Skin(2.4)

Phenotype-based relationships between genes and organs from Gene ORGANizer for DLL3 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • cardiovascular
  • immune
  • integumentary
  • lymphatic
  • nervous
  • respiratory
  • skeleton
Head and neck:
  • brain
  • head
  • jaw
  • mandible
  • maxilla
  • meninges
  • mouth
  • neck
  • skull
  • tooth
  • chest wall
  • lung
  • rib
  • rib cage
  • sternum
  • pelvis
  • digit
  • finger
  • hand
  • upper limb
  • blood vessel
  • skin
  • spinal column
  • spinal cord
  • vertebrae
genes like me logo Genes that share expression patterns with DLL3: view

No data available for Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners and mRNA Expression by UniProt/SwissProt for DLL3 Gene

Orthologs for DLL3 Gene

This gene was present in the common ancestor of animals.

Orthologs for DLL3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia DLL3 34 33
  • 98.24 (n)
(Bos Taurus)
Mammalia DLL3 34 33
  • 86.94 (n)
(Canis familiaris)
Mammalia DLL3 34 33
  • 83.6 (n)
(Mus musculus)
Mammalia Dll3 16 34 33
  • 81.65 (n)
(Rattus norvegicus)
Mammalia Dll3 33
  • 81.14 (n)
(Monodelphis domestica)
Mammalia DLL3 34
  • 49 (a)
fruit fly
(Drosophila melanogaster)
Insecta wry 34
  • 10 (a)
Species where no ortholog for DLL3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • chicken (Gallus gallus)
  • 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)
  • lizard (Anolis carolinensis)
  • 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 squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for DLL3 Gene

Gene Tree for DLL3 (if available)
Gene Tree for DLL3 (if available)
Evolutionary constrained regions (ECRs) for DLL3: view image

Paralogs for DLL3 Gene

Paralogs for DLL3 Gene

(4) SIMAP similar genes for DLL3 Gene using alignment to 2 proteins:

  • M0R177_HUMAN
genes like me logo Genes that share paralogs with DLL3: view

Variants for DLL3 Gene

Sequence variations from dbSNP and Humsavar for DLL3 Gene

SNP ID Clin Chr 19 pos Variation AA Info Type
rs1005689624 uncertain-significance, Syndactyly, Jarcho-Levin syndrome 39,508,090(+) A/G 3_prime_UTR_variant, intron_variant
rs104894674 pathogenic, Spondylocostal dysostosis 1, autosomal recessive, Spondylocostal dysostosis 1, autosomal recessive (SCDO1) [MIM:277300] 39,507,099(+) G/A coding_sequence_variant, missense_variant
rs104894675 pathogenic, Spondylocostal dysostosis 1, autosomal recessive 39,504,130(+) C/T coding_sequence_variant, stop_gained
rs104894676 pathogenic, Spondylocostal dysostosis 1, autosomal recessive 39,507,456(+) G/A coding_sequence_variant, missense_variant
rs1110627 benign, Spondylocostal dysostosis 1, autosomal recessive, not specified, Jarcho-Levin syndrome, Syndactyly 39,504,071(+) T/C coding_sequence_variant, missense_variant

Structural Variations from Database of Genomic Variants (DGV) for DLL3 Gene

Variant ID Type Subtype PubMed ID
nsv1114009 CNV deletion 24896259
nsv1127684 CNV deletion 24896259
nsv523856 CNV loss 19592680
nsv953573 CNV deletion 24416366

Variation tolerance for DLL3 Gene

Gene Damage Index Score: 7.30; 81.39% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for DLL3 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 DLL3 Gene

Disorders for DLL3 Gene

MalaCards: The human disease database

(11) MalaCards diseases for DLL3 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
spondylocostal dysostosis 1, autosomal recessive
  • spondylothoracic dysostosis
spondylocostal dysostosis, autosomal recessive
  • spondylocostal dysplasia
  • dysostoses
spondylocostal dysostosis 1
  • scdo1
cascade stomach
  • hourglass stricture or stenosis of stomach
- elite association - COSMIC cancer census association via MalaCards
Search DLL3 in MalaCards View complete list of genes associated with diseases


  • Spondylocostal dysostosis 1, autosomal recessive (SCDO1) [MIM:277300]: A condition of variable severity associated with vertebral and rib segmentation defects. The main skeletal malformations include fusion of vertebrae, hemivertebrae, fusion of certain ribs, and other rib malformations. Deformity of the chest and spine (severe scoliosis, kyphoscoliosis and lordosis) is a natural consequence of the malformation and leads to a dwarf-like appearance. As the thorax is small, infants frequently have respiratory insufficiency and repeated respiratory infections resulting in life-threatening complications in the first year of life. {ECO:0000269 PubMed:10742114}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for DLL3

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 DLL3: view

No data available for Genatlas for DLL3 Gene

Publications for DLL3 Gene

  1. Mutations in the human delta homologue, DLL3, cause axial skeletal defects in spondylocostal dysostosis. (PMID: 10742114) Bulman MP … Turnpenny PD (Nature genetics 2000) 2 3 4 22 58
  2. Axial skeletal defects caused by mutation in the spondylocostal dysplasia/pudgy gene Dll3 are associated with disruption of the segmentation clock within the presomitic mesoderm. (PMID: 11923214) Dunwoodie SL … Beddington RS (Development (Cambridge, England) 2002) 3 22 44 58
  3. High-density association study of 383 candidate genes for volumetric BMD at the femoral neck and lumbar spine among older men. (PMID: 19453261) Yerges LM … MrOS Research Group (Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research 2009) 3 44 58
  4. Signal sequence and keyword trap in silico for selection of full-length human cDNAs encoding secretion or membrane proteins from oligo-capped cDNA libraries. (PMID: 16303743) Otsuki T … Isogai T (DNA research : an international journal for rapid publication of reports on genes and genomes 2005) 3 4 58
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58

Products for DLL3 Gene

Sources for DLL3 Gene

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