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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. Among its related pathways are Guidance Cues and Growth Cone Motility and Developmental Biology. 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

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

Genomics for SLIT3 Gene

Regulatory Elements for SLIT3 Gene

Enhancers for SLIT3 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH05F168624 1.2 FANTOM5 ENCODE 10.1 +676.1 676082 1.5 ELF3 ATF1 MLX ARID4B ZNF48 ZSCAN9 RAD21 RARA KAT2B YY1 ENSG00000254192 PANK3 LOC101927969 SLIT3 FBLL1 RPL10P9
GH05F168600 1 ENCODE 10 +700.5 700455 0.9 MLX FEZF1 ZNF48 YY1 NFYC KAT8 MIER3 GLIS1 KLF1 ZNF792 PANK3 ENSG00000254192 LOC101927969 SLIT3 FBLL1 RPL10P9
GH05F169100 1 Ensembl ENCODE 9.7 +200.4 200367 0.3 PKNOX1 INSM2 KLF17 FEZF1 ZIC2 ZBTB48 ZNF366 PRDM10 NFE2 FOS LOC728095 SLIT3 LOC105377712 GC05M169154
GH05F168653 0.8 Ensembl ENCODE 10.3 +646.8 646829 1.4 SMARCA4 SIN3A REST RAD21 LOC101927969 PANK3 SLIT3 FBLL1 ENSG00000254192 RPL10P9
GH05F168645 0.8 ENCODE 10.1 +654.0 654013 2.6 GTF2F1 KLF1 PKNOX1 JUN MAX CEBPG RAD21 RFX5 GATA3 CTBP1 FBLL1 LOC101927969 SLIT3 ENSG00000254192 RPL10P9
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SLIT3 on UCSC Golden Path with GeneCards custom track

Promoters for SLIT3 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001416372 829 2201 CTCF PKNOX1 SIN3A RAD21 GLIS2 ZNF366 POLR2A PATZ1 PRDM10 ZNF263

Genomic Location for SLIT3 Gene

168,661,733 bp from pter
169,301,129 bp from pter
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 Asn 72, Asn 192, Asn 563, Asn 622, Asn 784, Asn 792, Asn 797, Asn 928, Asn 1008, Asn 1025, Asn 1181, Asn 1247, Thr 1295, and Asn 1406
  • Modification sites at PhosphoSitePlus

Other Protein References for SLIT3 Gene

Antibody Products

  • Cloud-Clone Corp. Antibodies for SLIT3
  • Santa Cruz Biotechnology (SCBT) Antibodies for SLIT3

No data available for DME Specific Peptides for SLIT3 Gene

Domains & Families for SLIT3 Gene

Suggested Antigen Peptide Sequences for SLIT3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Contains 1 CTCK (C-terminal cystine knot-like) domain.
  • Contains 20 LRR (leucine-rich) repeats.
  • Contains 1 CTCK (C-terminal cystine knot-like) domain.
  • Contains 9 EGF-like domains.
  • Contains 1 laminin G-like domain.
  • Contains 4 LRRCT domains.
  • Contains 4 LRRNT domains.
  • Contains 20 LRR (leucine-rich) repeats.
genes like me logo Genes that share domains with SLIT3: view

No data available for Gene Families 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.

Gene Ontology (GO) - Molecular Function for SLIT3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding NAS 9813312
GO:0008201 heparin binding IBA --
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

miRNA for SLIT3 Gene

miRTarBase miRNAs that target SLIT3

Inhibitory RNA Products

Flow Cytometry 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 1
nucleus 1

Gene Ontology (GO) - Cellular Components for SLIT3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA --
GO:0005578 proteinaceous extracellular matrix IBA --
GO:0005615 extracellular space IEA,IDA 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

Transcripts for SLIT3 Gene

Unigene Clusters for SLIT3 Gene

Slit homolog 3 (Drosophila):
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry 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 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.
genes like me logo Genes that share expression patterns with SLIT3: view

Primer Products

No data available for Protein tissue co-expression partners 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 34 35
  • 93.94 (n)
(Canis familiaris)
Mammalia SLIT3 34 35
  • 91.46 (n)
(Bos Taurus)
Mammalia SLIT3 34 35
  • 90.44 (n)
(Monodelphis domestica)
Mammalia SLIT3 35
  • 89 (a)
(Mus musculus)
Mammalia Slit3 34 16 35
  • 88.84 (n)
(Rattus norvegicus)
Mammalia Slit3 34
  • 88.71 (n)
(Ornithorhynchus anatinus)
Mammalia SLIT3 35
  • 82 (a)
(Gallus gallus)
Aves SLIT3 34 35
  • 75.46 (n)
(Anolis carolinensis)
Reptilia SLIT3 35
  • 82 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia slit3 34
  • 73.09 (n)
Str.13269 34
(Danio rerio)
Actinopterygii slit3 34 35
  • 68.77 (n)
-- 34
fruit fly
(Drosophila melanogaster)
Insecta sli 36 35
  • 41 (a)
(Caenorhabditis elegans)
Secernentea slt-1 35
  • 38 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 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 Sequence Context AA Info Type
rs10035147 -- 168,750,929(+) tgtta(C/G)gacat intron-variant
rs10035339 -- 169,010,093(+) AAAAA(C/G)CATAG intron-variant
rs10035582 -- 168,880,183(+) TACAG(C/T)CTCAT intron-variant
rs10035793 -- 169,080,751(+) CTGCA(A/G)TTACG intron-variant
rs10036081 -- 169,272,768(+) GCAGG(A/T)GAGCC intron-variant, upstream-variant-2KB

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

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

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)

Relevant External Links for SLIT3 Gene

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

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SLIT3 Gene

Disorders for SLIT3 Gene

Relevant External Links for SLIT3

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:

No disorders were found for SLIT3 Gene.

No data available for MalaCards , 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 Res. Mol. Brain Res. 1998) 2 3 4 22 64
  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 64
  3. 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. (Gynecol. Oncol. 2010) 3 46 64
  4. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose J.E. … Uhl G.R. (Mol. Med. 2010) 3 46 64
  5. Hundreds of variants clustered in genomic loci and biological pathways affect human height. (PMID: 20881960) Lango Allen H. … Hirschhorn J.N. (Nature 2010) 3 46 64

Products for SLIT3 Gene

Sources for SLIT3 Gene

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