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] See more...

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 Homolog 3 Protein 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 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 Vesicoureteral Reflux 1. Among its related pathways are Signaling by Slit and Netrin-1 signaling. 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 Summary 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 , Rfam classification and piRNA Summary for SLIT3 Gene

Genomics for SLIT3 Gene

GeneHancer (GH) Regulatory Elements for SLIT3 Gene

Promoters and enhancers for SLIT3 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SLIT3 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SLIT3

Top Transcription factor binding sites by QIAGEN in the SLIT3 gene promoter:
  • AML1a
  • AREB6
  • ATF6
  • COMP1
  • CUTL1
  • IRF-2
  • Nkx5-1
  • Pbx1a
  • POU2F1
  • POU2F1a

Genomic Locations for SLIT3 Gene

Genomic Locations for SLIT3 Gene
chr5:168,661,733-169,301,129
(GRCh38/hg38)
Size:
639,397 bases
Orientation:
Minus strand
chr5:168,088,745-168,728,133
(GRCh37/hg19)
Size:
639,389 bases
Orientation:
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:
    O75094-SLIT3_HUMAN
    Recommended name:
    Slit homolog 3 protein
    Protein Accession:
    O75094
    Secondary Accessions:
    • A6H8U9
    • J3KNP3
    • O95804
    • Q9UFH5

    Protein attributes for SLIT3 Gene

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

    Alternative splice isoforms for SLIT3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SLIT3 Gene

Post-translational modifications for SLIT3 Gene

  • Glycosylation at Asn72, Asn192, Asn563, Asn622, Asn784, Asn792, Asn797, Asn928, Asn1008, Asn1025, Asn1247, Asn1181, Thr1295, and Asn1406
  • Modification sites at PhosphoSitePlus
  • Glycosylation from GlyConnect
    • SLIT3_HUMAN (1750)

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

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

Protein Domains for SLIT3 Gene

Blocks:
  • Cysteine-rich flanking region, C-terminal
  • Aspartic acid and asparagine hydroxylation site
  • Leucine-rich repeat signature
  • EGF-like calcium-binding
  • Laminin G
  • Cystine knot, C-terminal
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for SLIT3 Gene

GenScript: Design optimal peptide antigens:
  • Multiple epidermal growth factor-like domains protein 5 (SLIT3_HUMAN)
genes like me logo Genes that share domains with SLIT3: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for SLIT3 Gene

Function for SLIT3 Gene

Molecular function for SLIT3 Gene

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

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 IEA,NAS 9813312
GO:0005515 protein binding IEA --
GO:0008201 heparin binding IBA 21873635
GO:0048495 Roundabout binding IBA,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

Secreted.

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 SLIT3 gene
Compartment Confidence
extracellular 5
mitochondrion 5
plasma membrane 4
cytoskeleton 2
nucleus 2
endoplasmic reticulum 1
endosome 1
cytosol 1
lysosome 1
golgi apparatus 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 IEA,IDA 19741192
GO:0005739 mitochondrion NAS 11443047
genes like me logo Genes that share ontologies with SLIT3: view

Pathways & Interactions for SLIT3 Gene

PathCards logo

SuperPathways for SLIT3 Gene

SuperPathway Contained pathways
1 Developmental Biology
2 Axon guidance
3 Guidance Cues and Growth Cone Motility
-
4 Signaling by Slit
-
5 Netrin-1 signaling
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
  • Development Slit-Robo signaling
2 Qiagen pathways for SLIT3 Gene
  • Guidance Cues and Growth Cone Motility
  • Signaling by Slit

Gene Ontology (GO) - Biological Process for SLIT3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003180 aortic valve morphogenesis ISS --
GO:0003181 atrioventricular valve morphogenesis IEA,ISS --
GO:0007275 multicellular organism development IEA --
GO:0007399 nervous system development IEA --
GO:0007411 axon guidance IEA,IDA 11748139
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

mRNA/cDNA for SLIT3 Gene

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

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: -
SP3:
SP4: -
SP5:
SP6:

ExUns: 21 ^ 22 ^ 23 ^ 24 ^ 25 ^ 26 ^ 27 ^ 28 ^ 29 ^ 30 ^ 31 ^ 32a · 32b · 32c ^ 33a · 33b ^ 34 ^ 35 ^ 36 ^ 37a · 37b
SP1:
SP2: - - -
SP3:
SP4:
SP5:
SP6: -

Relevant External Links for SLIT3 Gene

GeneLoc Exon Structure for
SLIT3

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, MaxQB, and MOPED for SLIT3 Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SLIT3

SOURCE GeneReport for Unigene cluster for SLIT3 Gene:

Hs.552087

mRNA Expression by UniProt/SwissProt for SLIT3 Gene:

O75094-SLIT3_HUMAN
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(2.1)
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
chimpanzee
(Pan troglodytes)
Mammalia SLIT3 31 30
  • 93.94 (n)
OneToOne
dog
(Canis familiaris)
Mammalia SLIT3 31 30
  • 91.46 (n)
OneToOne
cow
(Bos Taurus)
Mammalia SLIT3 31 30
  • 90.44 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SLIT3 31
  • 89 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Slit3 17 31 30
  • 88.84 (n)
rat
(Rattus norvegicus)
Mammalia Slit3 30
  • 88.71 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia SLIT3 31
  • 82 (a)
OneToOne
chicken
(Gallus gallus)
Aves SLIT3 31 30
  • 75.46 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SLIT3 31
  • 82 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia slit3 30
  • 73.09 (n)
Str.13269 30
zebrafish
(Danio rerio)
Actinopterygii slit3 31 30
  • 68.77 (n)
OneToOne
-- 30
fruit fly
(Drosophila melanogaster)
Insecta sli 31 32
  • 43 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea slt-1 31
  • 38 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 43 (a)
ManyToMany
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

ENSEMBL:
Gene Tree for SLIT3 (if available)
TreeFam:
Gene Tree for SLIT3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SLIT3: view image

Paralogs for SLIT3 Gene

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

  • SLIT3_HUMAN
  • J3KNP3_HUMAN
  • L8E8Y7_HUMAN
genes like me logo Genes that share paralogs with SLIT3: view

Variants for SLIT3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SLIT3 Gene

SNP ID Clinical significance and condition Chr 05 pos Variation AA Info Type
710326 Benign: not provided 168,671,245(-) G/A SYNONYMOUS_VARIANT
711944 Likely Benign: not provided 168,685,737(-) C/G MISSENSE_VARIANT
723995 Benign: not provided 168,710,886(-) G/A INTRON_VARIANT
726060 Likely Benign: not provided 168,748,403(-) C/T SYNONYMOUS_VARIANT
736167 Benign: not provided 168,671,326(-) C/T SYNONYMOUS_VARIANT

Additional dbSNP identifiers (rs#s) for SLIT3 Gene

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)
SLIT3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SLIT3

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

(4) MalaCards diseases for SLIT3 Gene - From: DISEASES

Disorder Aliases PubMed IDs
diaphragm disease
  • abnormality of the diaphragm
vesicoureteral reflux 1
  • vur1
cakut
  • renal hypodysplasia, nonsyndromic, 1
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
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
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 23 54
  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 54
  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 41 54
  4. Hundreds of variants clustered in genomic loci and biological pathways affect human height. (PMID: 20881960) Lango Allen H … Hirschhorn JN (Nature 2010) 3 41 54
  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 41 54

Products for SLIT3 Gene

Sources for SLIT3 Gene