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] See more...

Aliases for DLL3 Gene

Aliases for DLL3 Gene

  • Delta Like Canonical Notch Ligand 3 2 3 5
  • Drosophila Delta Homolog 3 3 4
  • Delta-Like Protein 3 3 4
  • Delta3 3 4
  • Delta (Drosophila)-Like 3 2
  • Delta-Like 3 (Drosophila) 2
  • 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 NOTCH1 regulation of human endothelial cell calcification and Notch Signaling Pathway (WikiPathways). Gene Ontology (GO) annotations related to this gene include calcium ion binding and Notch binding. An important paralog of this gene is CD93.

UniProtKB/Swiss-Prot Summary 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 , Rfam classification 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
Score
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 500.7 -0.5 -494 2 CTCF ZSCAN5C RBAK ZNF639 ZNF10 ZBTB5 ZIC2 ZBTB10 ZNF423 ZBTB26 DLL3 ZNF780B RPS16 HNRNPL EID2B MED29 PAK4 SPTBN4 ENSG00000267892 SUPT5H
GH19J039499 Promoter 0.7 Ensembl 500.7 +0.8 805 0.2 ZIC2 ZBTB26 EZH2 ZNF335 ZBTB48 IKZF1 GLIS1 TBP HDAC6 RBM39 DLL3 SUPT5H ZNF780B ZNF780A TIMM50 piR-57134-056
GH19J039397 Promoter/Enhancer 3 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 10.2 -91.8 -91820 20 RXRA EP300 FOXK2 HNRNPK ZBTB40 ZNF217 CTCF ZSCAN5C SIN3A NRF1 ZFP36 PAF1 5EW4_A-031 MG828566 HNRNPL ZNF780B FBL SUPT5H RPS16 EID2B
GH19J038673 Promoter/Enhancer 2.1 FANTOM5 Ensembl ENCODE dbSUPER 10.1 -803.3 -803347 43.3 EP300 ZNF217 CTCF ZSCAN5C TCF12 POLR2G USF1 SP1 NCOR1 RBAK ENSG00000267375 ZNF573 ZNF607 ACTN4 CAPN12 SUPT5H PAK4 ENSG00000267152 PAF1 CATSPERG
GH19J038919 Enhancer 1.2 FANTOM5 Ensembl ENCODE 10.1 -578.8 -578754 1.5 ZNF300 ZBTB10 TSC22D4 ZNF662 TRIM25 ZNF148 ZNF195 ZBTB17 ZSCAN18 POLR2A lnc-CCER2-4 SUPT5H FBL SARS2 PAF1 HNRNPL ERVK9-11 PAK4 RPS16 SAMD4B
- 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

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for DLL3

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

Genomic Locations for DLL3 Gene

Genomic Locations for DLL3 Gene
chr19:39,498,895-39,508,481
(GRCh38/hg38)
Size:
9,587 bases
Orientation:
Plus strand
chr19:39,989,535-39,999,121
(GRCh37/hg19)
Size:
9,587 bases
Orientation:
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:
    Q9NYJ7-DLL3_HUMAN
    Recommended name:
    Delta-like protein 3
    Protein Accession:
    Q9NYJ7
    Secondary Accessions:
    • E9PFG2
    • Q8NBS4

    Protein attributes for DLL3 Gene

    Size:
    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

    UniProtKB/Swiss-Prot:

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 intracellular proteins
  • Predicted membrane proteins

Protein Domains for DLL3 Gene

Blocks:
  • Type I EGF
  • EGF-like calcium-binding
  • Type II EGF-like signature
  • Delta/Serrate/lag-2 (DSL) protein
  • Notch ligand, N-terminal
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for DLL3 Gene

GenScript: Design optimal peptide antigens:
  • Drosophila Delta homolog 3 (DLL3_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9NYJ7

UniProtKB/Swiss-Prot:

DLL3_HUMAN :
  • The DSL domain is required for binding to the Notch receptor.
Domain:
  • 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:

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

COMPARTMENTS
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 5
nucleus 3
extracellular 2
cytoskeleton 2
cytosol 2
lysosome 2
mitochondrion 1
endoplasmic reticulum 1
endosome 1
golgi apparatus 1

Subcellular locations from the

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

Gene Ontology (GO) - Cellular Components for DLL3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IBA 21873635
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

Activates:
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 IBA 21873635
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

No Compound Related Data Available

Transcripts for DLL3 Gene

mRNA/cDNA for DLL3 Gene

2 REFSEQ mRNAs :
6 NCBI additional mRNA sequence :
5 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

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: - - - -
SP4:

Relevant External Links for DLL3 Gene

GeneLoc Exon Structure for
DLL3

Expression for DLL3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and 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).

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for DLL3

SOURCE GeneReport for Unigene cluster for DLL3 Gene:

Hs.127792

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
Systems:
  • cardiovascular
  • immune
  • integumentary
  • lymphatic
  • nervous
  • respiratory
  • skeleton
Regions:
Head and neck:
  • brain
  • head
  • jaw
  • mandible
  • maxilla
  • meninges
  • mouth
  • neck
  • skull
  • tooth
Thorax:
  • chest wall
  • lung
  • rib
  • rib cage
  • sternum
Pelvis:
  • pelvis
Limb:
  • digit
  • finger
  • hand
  • upper limb
General:
  • 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
chimpanzee
(Pan troglodytes)
Mammalia DLL3 31 30
  • 98.24 (n)
OneToOne
cow
(Bos Taurus)
Mammalia DLL3 31 30
  • 86.94 (n)
OneToOne
dog
(Canis familiaris)
Mammalia DLL3 31 30
  • 83.6 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Dll3 17 31 30
  • 81.65 (n)
rat
(Rattus norvegicus)
Mammalia Dll3 30
  • 81.14 (n)
oppossum
(Monodelphis domestica)
Mammalia DLL3 31
  • 49 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta wry 31
  • 10 (a)
OneToMany
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

ENSEMBL:
Gene Tree for DLL3 (if available)
TreeFam:
Gene Tree for DLL3 (if available)
Aminode:
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:

  • DLL3_HUMAN
  • M0R177_HUMAN
genes like me logo Genes that share paralogs with DLL3: view

Variants for DLL3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for DLL3 Gene

SNP ID Clinical significance and condition Chr 19 pos Variation AA Info Type
650393 Uncertain Significance: not provided 39,507,337(+) T/G MISSENSE_VARIANT
665177 Uncertain Significance: not provided 39,505,374(+) G/T MISSENSE_VARIANT
668476 Likely Benign: not provided 39,505,336(+) G/A SYNONYMOUS_VARIANT
672988 Benign: not provided 39,498,780(+) C/A
672989 Likely Benign: not provided 39,500,635(+) C/T SYNONYMOUS_VARIANT

Additional dbSNP identifiers (rs#s) for DLL3 Gene

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)
DLL3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
DLL3

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

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

Disorder Aliases PubMed IDs
spondylocostal dysostosis 1, autosomal recessive
  • spondylothoracic dysostosis
spondylocostal dysostosis, autosomal recessive
  • spondylocostal dysplasia
dysostosis
  • dysostoses
cascade stomach
  • hourglass stricture or stenosis of stomach
leukodystrophy and acquired microcephaly with or without dystonia
  • ldamd
- elite association - COSMIC cancer census association via MalaCards
Search DLL3 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

DLL3_HUMAN
  • 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
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
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 23 54
  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 23 41 54
  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 41 54
  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 54
  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 54

Products for DLL3 Gene

Sources for DLL3 Gene