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Aliases for SLIT3 Gene

Aliases for SLIT3 Gene

  • Slit Guidance Ligand 3 2 3 5
  • Multiple Epidermal Growth Factor-Like Domains Protein 5 3 4
  • Multiple EGF-Like Domains Protein 5 3 4
  • Slit-3 3 4
  • SLIL2 3 4
  • MEGF5 3 4
  • Slit (Drosophila) Homolog 3 2
  • Slit Homolog 3 (Drosophila) 2
  • Slit Homolog 3 Protein 3
  • Slit Homolog 3 3
  • KIAA0814 4
  • SLIT1 3
  • Slit2 3

External Ids for SLIT3 Gene

Previous HGNC Symbols for SLIT3 Gene

  • SLIL2

Previous GeneCards Identifiers for SLIT3 Gene

  • GC05M168328
  • GC05M168797
  • GC05M168024
  • GC05M168069
  • GC05M168074
  • GC05M168021
  • GC05M163191
  • GC05M168088

Summaries for SLIT3 Gene

Entrez Gene Summary for SLIT3 Gene

  • The protein encoded by this gene is secreted, likely interacting with roundabout homolog receptors to effect cell migration. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2012]

GeneCards Summary for SLIT3 Gene

SLIT3 (Slit Guidance Ligand 3) is a Protein Coding gene. Diseases associated with SLIT3 include Diaphragm Disease and Diaphragmatic Hernia, Congenital. Among its related pathways are Developmental Biology and Spinal Cord Injury. Gene Ontology (GO) annotations related to this gene include calcium ion binding and Roundabout binding. An important paralog of this gene is SLIT2.

UniProtKB/Swiss-Prot for SLIT3 Gene

  • May act as molecular guidance cue in cellular migration, and function may be mediated by interaction with roundabout homolog receptors.

Gene Wiki entry for SLIT3 Gene

Additional gene information for SLIT3 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SLIT3 Gene

Genomics for SLIT3 Gene

GeneHancer (GH) Regulatory Elements for SLIT3 Gene

Promoters and enhancers for SLIT3 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
GH05I169299 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE 550.8 -0.4 -351 3.1 PKNOX1 ZSCAN4 KLF17 SIN3A ZNF2 RAD21 ZNF335 GLIS2 ZNF366 ZSCAN5C SLIT3 MIR585 LOC105377715
GH05I168624 Enhancer 1.1 FANTOM5 ENCODE 21.1 +676.1 676081 1.5 FOXA2 MLX ARID4B ZNF48 YY1 ATF7 RXRA MIER2 REST KAT8 SLIT3 ENSG00000254192 PANK3 LOC101927969 FBLL1 RPL10P9
GH05I170273 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 12.6 -980.9 -980890 17.7 HDGF PKNOX1 IRF4 ZNF280A TCF12 ZNF207 ZNF143 ATF7 RUNX3 REST KCNMB1 SLIT3 CTD-2270F17.1 LCP2 C5orf58 GC05M170247
GH05I168529 Promoter 1 Ensembl 10.1 +771.6 771628 0.6 MXI1 ZNF76 CEBPG ZNF335 ZFHX2 POLR2A ZBTB48 ZBTB20 EGR2 EZH2 FBLL1 RARS PANK3 LOC101927969 SLIT3 SLC2A3P1 GC05M168548
GH05I168600 Enhancer 0.9 ENCODE 10 +700.5 700454 0.9 FOXA2 MLX ARNT FEZF1 ZNF48 YY1 RXRA NFYC REST KAT8 PANK3 ENSG00000254192 LOC101927969 SLIT3 FBLL1 RPL10P9
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SLIT3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SLIT3 gene promoter:

Genomic Locations for SLIT3 Gene

Genomic Locations for SLIT3 Gene
639,397 bases
Minus strand

Genomic View for SLIT3 Gene

Genes around SLIT3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SLIT3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SLIT3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SLIT3 Gene

Proteins for SLIT3 Gene

  • Protein details for SLIT3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Slit homolog 3 protein
    Protein Accession:
    Secondary Accessions:
    • A6H8U9
    • J3KNP3
    • O95804
    • Q9UFH5

    Protein attributes for SLIT3 Gene

    1523 amino acids
    Molecular mass:
    167713 Da
    Quaternary structure:
    No Data Available
    • Sequence=BAA32466.2; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305}; Sequence=CAB59249.1; Type=Miscellaneous discrepancy; Note=Intron retention.; Evidence={ECO:0000305};

    Alternative splice isoforms for SLIT3 Gene


neXtProt entry for SLIT3 Gene

Post-translational modifications for SLIT3 Gene

  • Glycosylation at posLast=7272, isoforms=2, 3, 4192, isoforms=2, 3, 4563, isoforms=2, 3, 4622, isoforms=2, 3, 4784, posLast=792792, isoforms=2, 3, 4797, isoforms=2, 3, 4928, posLast=10081008, posLast=10251025, posLast=11811181, isoforms=2, 3, 41247, posLast=12951295, and posLast=14061406
  • Modification sites at PhosphoSitePlus

Other Protein References for SLIT3 Gene

No data available for DME Specific Peptides for SLIT3 Gene

Domains & Families for SLIT3 Gene

Gene Families for SLIT3 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted secreted proteins

Suggested Antigen Peptide Sequences for SLIT3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with SLIT3: view

No data available for UniProtKB/Swiss-Prot for SLIT3 Gene

Function for SLIT3 Gene

Molecular function for SLIT3 Gene

GENATLAS Biochemistry:
SLIT Drosophila homolog 3,expressed in the cerebellum and chyroid,ligand of GPC1,involved in histogenesis of central nervous system
UniProtKB/Swiss-Prot Function:
May act as molecular guidance cue in cellular migration, and function may be mediated by interaction with roundabout homolog receptors.

Phenotypes From GWAS Catalog for SLIT3 Gene

Gene Ontology (GO) - Molecular Function for SLIT3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding NAS 9813312
GO:0048495 Roundabout binding IPI 15207848
genes like me logo Genes that share ontologies with SLIT3: view
genes like me logo Genes that share phenotypes with SLIT3: view

Animal Models for SLIT3 Gene

MGI Knock Outs for SLIT3:

Animal Model Products

  • Taconic Biosciences Mouse Models for SLIT3

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SLIT3 Gene

Localization for SLIT3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SLIT3 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 SLIT3 gene
Compartment Confidence
extracellular 5
mitochondrion 5
plasma membrane 3
cytoskeleton 2
nucleus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cell Junctions (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SLIT3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA --
GO:0005615 extracellular space IDA,IEA 19741192
GO:0005739 mitochondrion NAS 11443047
genes like me logo Genes that share ontologies with SLIT3: view

Pathways & Interactions for SLIT3 Gene

genes like me logo Genes that share pathways with SLIT3: view

Pathways by source for SLIT3 Gene

1 BioSystems pathway for SLIT3 Gene
3 Reactome pathways for SLIT3 Gene
1 KEGG pathway for SLIT3 Gene
1 GeneGo (Thomson Reuters) pathway for SLIT3 Gene

Gene Ontology (GO) - Biological Process for SLIT3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007275 multicellular organism development IEA --
GO:0007399 nervous system development IEA --
GO:0007411 axon guidance IEA,IDA 11748139
GO:0008285 negative regulation of cell proliferation IEA --
GO:0009887 animal organ morphogenesis IEA --
genes like me logo Genes that share ontologies with SLIT3: view

No data available for SIGNOR curated interactions for SLIT3 Gene

Drugs & Compounds for SLIT3 Gene

No Compound Related Data Available

Transcripts for SLIT3 Gene

Unigene Clusters for SLIT3 Gene

Slit homolog 3 (Drosophila):
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SLIT3 Gene

ExUns: 1 ^ 2a · 2b ^ 3 ^ 4 ^ 5 ^ 6 ^ 7a · 7b ^ 8 ^ 9 ^ 10 ^ 11 ^ 12a · 12b ^ 13a · 13b ^ 14 ^ 15 ^ 16 ^ 17 ^ 18a · 18b ^ 19a · 19b ^ 20 ^
SP1: - - - -
SP2: -
SP4: -

ExUns: 21 ^ 22 ^ 23 ^ 24 ^ 25 ^ 26 ^ 27 ^ 28 ^ 29 ^ 30 ^ 31 ^ 32a · 32b · 32c ^ 33a · 33b ^ 34 ^ 35 ^ 36 ^ 37a · 37b
SP2: - - -
SP6: -

Relevant External Links for SLIT3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for SLIT3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SLIT3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SLIT3 Gene

This gene is overexpressed in Artery - Tibial (x4.3).

Protein differential expression in normal tissues from HIPED for SLIT3 Gene

This gene is overexpressed in Liver, secretome (32.0), Gallbladder (12.6), and Fetal ovary (10.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for SLIT3 Gene

NURSA nuclear receptor signaling pathways regulating expression of SLIT3 Gene:


SOURCE GeneReport for Unigene cluster for SLIT3 Gene:


mRNA Expression by UniProt/SwissProt for SLIT3 Gene:

Tissue specificity: Predominantly expressed in thyroid.

Evidence on tissue expression from TISSUES for SLIT3 Gene

  • Nervous system(4.8)
  • Heart(2.5)
  • Lung(2.2)
  • Muscle(2.2)
  • Kidney(2)
genes like me logo Genes that share expression patterns with SLIT3: view

No data available for Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for SLIT3 Gene

Orthologs for SLIT3 Gene

This gene was present in the common ancestor of animals.

Orthologs for SLIT3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia SLIT3 33 34
  • 93.94 (n)
(Canis familiaris)
Mammalia SLIT3 33 34
  • 91.46 (n)
(Bos Taurus)
Mammalia SLIT3 33 34
  • 90.44 (n)
(Monodelphis domestica)
Mammalia SLIT3 34
  • 89 (a)
(Mus musculus)
Mammalia Slit3 33 16 34
  • 88.84 (n)
(Rattus norvegicus)
Mammalia Slit3 33
  • 88.71 (n)
(Ornithorhynchus anatinus)
Mammalia SLIT3 34
  • 82 (a)
(Gallus gallus)
Aves SLIT3 33 34
  • 75.46 (n)
(Anolis carolinensis)
Reptilia SLIT3 34
  • 82 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia slit3 33
  • 73.09 (n)
Str.13269 33
(Danio rerio)
Actinopterygii slit3 33 34
  • 68.77 (n)
-- 33
fruit fly
(Drosophila melanogaster)
Insecta sli 35 34
  • 41 (a)
(Caenorhabditis elegans)
Secernentea slt-1 34
  • 38 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 43 (a)
Species where no ortholog for SLIT3 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)
  • 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)
  • 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 SLIT3 Gene

Gene Tree for SLIT3 (if available)
Gene Tree for SLIT3 (if available)

Paralogs for SLIT3 Gene

Paralogs for SLIT3 Gene

(17) SIMAP similar genes for SLIT3 Gene using alignment to 3 proteins:

genes like me logo Genes that share paralogs with SLIT3: view

Variants for SLIT3 Gene

Sequence variations from dbSNP and Humsavar for SLIT3 Gene

SNP ID Clin Chr 05 pos Variation AA Info Type
rs1000001766 -- 168,814,187(-) G/A intron_variant
rs1000013424 -- 169,163,606(-) T/G intron_variant
rs1000018307 -- 168,691,343(-) A/T intron_variant
rs1000023682 -- 169,022,503(-) AAAA/AA intron_variant
rs1000024201 -- 168,828,040(-) A/C intron_variant

Structural Variations from Database of Genomic Variants (DGV) for SLIT3 Gene

Variant ID Type Subtype PubMed ID
dgv1666e212 CNV loss 25503493
dgv360n21 CNV loss 19592680
esv2391131 CNV deletion 18987734
esv2516692 CNV insertion 19546169
esv2658777 CNV deletion 23128226
esv2731044 CNV deletion 23290073
esv2731045 CNV deletion 23290073
esv2731046 CNV deletion 23290073
esv2731047 CNV deletion 23290073
esv2731048 CNV deletion 23290073
esv2731049 CNV deletion 23290073
esv2731050 CNV deletion 23290073
esv2731052 CNV deletion 23290073
esv2731053 CNV deletion 23290073
esv275039 CNV loss 21479260
esv275423 CNV loss 21479260
esv28158 CNV loss 19812545
esv3305463 CNV mobile element insertion 20981092
esv3308939 CNV mobile element insertion 20981092
esv3309307 CNV mobile element insertion 20981092
esv3350246 CNV duplication 20981092
esv3354715 CNV insertion 20981092
esv3390212 CNV insertion 20981092
esv3396598 CNV insertion 20981092
esv3435779 CNV insertion 20981092
esv3566984 CNV deletion 23714750
esv3570543 CNV loss 25503493
esv3570544 CNV loss 25503493
esv3570545 CNV loss 25503493
esv3607537 CNV loss 21293372
esv3607540 CNV loss 21293372
esv3607542 CNV gain 21293372
esv6957 OTHER inversion 19470904
esv989985 CNV deletion 20482838
nsv1016765 CNV gain 25217958
nsv1017688 CNV gain 25217958
nsv1028080 CNV gain 25217958
nsv1031257 CNV gain 25217958
nsv1034127 CNV gain 25217958
nsv1073932 CNV deletion 25765185
nsv1074886 CNV deletion 25765185
nsv1121732 CNV deletion 24896259
nsv1124006 CNV deletion 24896259
nsv1126729 CNV deletion 24896259
nsv1137046 CNV deletion 24896259
nsv1140366 OTHER inversion 24896259
nsv1145075 CNV deletion 24896259
nsv1151667 CNV deletion 26484159
nsv1153731 CNV deletion 26484159
nsv328526 CNV deletion 16902084
nsv462513 CNV loss 19166990
nsv472304 CNV novel sequence insertion 20440878
nsv472488 CNV novel sequence insertion 20440878
nsv5122 CNV deletion 18451855
nsv512862 CNV insertion 21212237
nsv600258 CNV loss 21841781

Variation tolerance for SLIT3 Gene

Residual Variation Intolerance Score: 18.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.53; 71.98% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SLIT3 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 SLIT3 Gene

Disorders for SLIT3 Gene

MalaCards: The human disease database

(2) MalaCards diseases for SLIT3 Gene - From: HGMD and DISEASES

Disorder Aliases PubMed IDs
diaphragm disease
  • abnormality of the diaphragm
diaphragmatic hernia, congenital
  • dih
- elite association - COSMIC cancer census association via MalaCards
Search SLIT3 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for SLIT3

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 SLIT3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SLIT3 Gene

Publications for SLIT3 Gene

  1. Cloning and expressions of three mammalian homologues of Drosophila slit suggest possible roles for Slit in the formation and maintenance of the nervous system. (PMID: 9813312) Itoh A … Sakano S (Brain research. Molecular brain research 1998) 2 3 4 22 58
  2. Identification of high-molecular-weight proteins with multiple EGF-like motifs by motif-trap screening. (PMID: 9693030) Nakayama M … Ohara O (Genomics 1998) 2 3 4 58
  3. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 44 58
  4. Hundreds of variants clustered in genomic loci and biological pathways affect human height. (PMID: 20881960) Lango Allen H … Hirschhorn JN (Nature 2010) 3 44 58
  5. Polymorphisms involved in the miR-218-LAMB3 pathway and susceptibility of cervical cancer, a case-control study in Chinese women. (PMID: 20163849) Zhou X … Hu Z (Gynecologic oncology 2010) 3 44 58

Products for SLIT3 Gene

Sources for SLIT3 Gene

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