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Aliases for SLITRK3 Gene

Aliases for SLITRK3 Gene

  • SLIT And NTRK Like Family Member 3 2 3 5
  • SLIT And NTRK-Like Family, Member 3 2
  • KIAA0848 4

External Ids for SLITRK3 Gene

Previous GeneCards Identifiers for SLITRK3 Gene

  • GC03M166225
  • GC03M166387
  • GC03M164904
  • GC03M162274

Summaries for SLITRK3 Gene

Entrez Gene Summary for SLITRK3 Gene

  • This gene encodes a member of the Slitrk family of structurally related transmembrane proteins that are involved in controlling neurite outgrowth. The encoded protein contains two leucine-rich repeat (LRR) domains and a C-terminal domain that is partially similar to Trk neurotrophin receptor protein. Enhanced expression of this gene was found in tissue from several different types of tumors. Alternative splicing results in multiple transcript variants, all encoding the same protein. [provided by RefSeq, Jan 2016]

GeneCards Summary for SLITRK3 Gene

SLITRK3 (SLIT And NTRK Like Family Member 3) is a Protein Coding gene. Diseases associated with SLITRK3 include Gastrointestinal Stromal Tumor. An important paralog of this gene is SLITRK5.

UniProtKB/Swiss-Prot for SLITRK3 Gene

  • Suppresses neurite outgrowth.

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SLITRK3 Gene

Genomics for SLITRK3 Gene

Regulatory Elements for SLITRK3 Gene

Enhancers for SLITRK3 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
GH03G164332 0.5 ENCODE 4.1 +864.1 864082 1.6 CTCF ATF2 NR2F2 SLITRK3 PIR60025 GC03M164322
GH03G164453 0.4 VISTA 3.9 +742.3 742318 3.4 CEBPG EP300 SLITRK3 LOC105374191 LINC01323
GH03G165192 0.6 ENCODE 0.7 +4.1 4117 1.6 PKNOX1 RNF2 CBX2 ZNF384 RBBP5 CBX8 POLR2A CTBP2 ZBTB20 EZH2 SLITRK3 LINC02023
GH03G165195 0.6 Ensembl 0.7 +1.2 1209 0.2 PKNOX1 MXI1 L3MBTL2 SUZ12 RBBP5 EZH2 SLITRK3 LINC02023
GH03G165384 0.3 FANTOM5 1.3 -187.2 -187223 0.2 SLITRK3 LINC01322 GC03P165675
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SLITRK3 on UCSC Golden Path with GeneCards custom track

Genomic Location for SLITRK3 Gene

Chromosome:
3
Start:
165,186,720 bp from pter
End:
165,197,109 bp from pter
Size:
10,390 bases
Orientation:
Minus strand

Genomic View for SLITRK3 Gene

Genes around SLITRK3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SLITRK3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SLITRK3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SLITRK3 Gene

Proteins for SLITRK3 Gene

  • Protein details for SLITRK3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O94933-SLIK3_HUMAN
    Recommended name:
    SLIT and NTRK-like protein 3
    Protein Accession:
    O94933
    Secondary Accessions:
    • Q1RMY6

    Protein attributes for SLITRK3 Gene

    Size:
    977 amino acids
    Molecular mass:
    108934 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=BAA74871.2; Type=Erroneous initiation; Evidence={ECO:0000305};

neXtProt entry for SLITRK3 Gene

Post-translational modifications for SLITRK3 Gene

  • Glycosylation at isoforms=68 and Asn596
  • Modification sites at PhosphoSitePlus

Other Protein References for SLITRK3 Gene

No data available for DME Specific Peptides for SLITRK3 Gene

Domains & Families for SLITRK3 Gene

Suggested Antigen Peptide Sequences for SLITRK3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

O94933

UniProtKB/Swiss-Prot:

SLIK3_HUMAN :
  • Belongs to the SLITRK family.
Family:
  • Belongs to the SLITRK family.
genes like me logo Genes that share domains with SLITRK3: view

No data available for Gene Families for SLITRK3 Gene

Function for SLITRK3 Gene

Molecular function for SLITRK3 Gene

UniProtKB/Swiss-Prot Function:
Suppresses neurite outgrowth.
genes like me logo Genes that share phenotypes with SLITRK3: view

Animal Models for SLITRK3 Gene

MGI Knock Outs for SLITRK3:

Animal Model Products

CRISPR Products

miRNA for SLITRK3 Gene

Inhibitory RNA Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SLITRK3 Gene

Localization for SLITRK3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SLITRK3 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 SLITRK3 gene
Compartment Confidence
plasma membrane 3
mitochondrion 3
extracellular 1
peroxisome 1
endoplasmic reticulum 1

Gene Ontology (GO) - Cellular Components for SLITRK3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane TAS --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with SLITRK3: view

Pathways & Interactions for SLITRK3 Gene

SuperPathways for SLITRK3 Gene

No Data Available

Interacting Proteins for SLITRK3 Gene

STRING Interaction Network Preview (showing 1 interactants - click image to see details)
http://version10.5.string-db.org/api/image/networkList?limit=0&targetmode=proteins&caller_identity=gene_cards&network_flavor=evidence&identifiers=9606.ENSP00000241274%0d%0a9606.ENSP00000356234%0d%0a
Selected Interacting proteins: O94933-SLIK3_HUMAN ENSP00000241274 for SLITRK3 Gene via IID STRING

Gene Ontology (GO) - Biological Process for SLITRK3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007409 axonogenesis IBA --
GO:0051965 positive regulation of synapse assembly IEA --
genes like me logo Genes that share ontologies with SLITRK3: view

No data available for Pathways by source and SIGNOR curated interactions for SLITRK3 Gene

Drugs & Compounds for SLITRK3 Gene

No Compound Related Data Available

Transcripts for SLITRK3 Gene

mRNA/cDNA for SLITRK3 Gene

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

Unigene Clusters for SLITRK3 Gene

SLIT and NTRK-like family, member 3:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SLITRK3 Gene

No ASD Table

Relevant External Links for SLITRK3 Gene

GeneLoc Exon Structure for
SLITRK3
ECgene alternative splicing isoforms for
SLITRK3

Expression for SLITRK3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SLITRK3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SLITRK3 Gene

This gene is overexpressed in Fallopian Tube (x5.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for SLITRK3 Gene



NURSA nuclear receptor signaling pathways regulating expression of SLITRK3 Gene:

SLITRK3

SOURCE GeneReport for Unigene cluster for SLITRK3 Gene:

Hs.101745

mRNA Expression by UniProt/SwissProt for SLITRK3 Gene:

O94933-SLIK3_HUMAN
Tissue specificity: Expressed in the occipital lobe of the cerebral cortex of the brain. Expressed at higher levels in some astrocytic brain tumors such as astrocytomas, oligodendrogliomas, glioblastomas, gangliogliomas and primitive neuroectodermal tumors.

Evidence on tissue expression from TISSUES for SLITRK3 Gene

  • Nervous system(4.6)
genes like me logo Genes that share expression patterns with SLITRK3: view

Primer Products

No data available for Protein differential expression in normal tissues , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for SLITRK3 Gene

Orthologs for SLITRK3 Gene

This gene was present in the common ancestor of chordates.

Orthologs for SLITRK3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SLITRK3 34 35
  • 99.66 (n)
oppossum
(Monodelphis domestica)
Mammalia SLITRK3 35
  • 94 (a)
OneToOne
dog
(Canis familiaris)
Mammalia SLITRK3 34 35
  • 93.42 (n)
cow
(Bos Taurus)
Mammalia SLITRK3 34 35
  • 92.94 (n)
rat
(Rattus norvegicus)
Mammalia Slitrk3 34
  • 89.08 (n)
mouse
(Mus musculus)
Mammalia Slitrk3 34 16 35
  • 88.95 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia SLITRK3 35
  • 88 (a)
OneToOne
chicken
(Gallus gallus)
Aves SLITRK3 34 35
  • 78.8 (n)
lizard
(Anolis carolinensis)
Reptilia SLITRK3 35
  • 87 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia slitrk3 34
  • 75.74 (n)
Str.16425 34
zebrafish
(Danio rerio)
Actinopterygii SLITRK3 (2 of 2) 35
  • 78 (a)
OneToMany
LOC100334261 34
  • 71.31 (n)
slitrk3b 35
  • 67 (a)
OneToMany
Species where no ortholog for SLITRK3 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)
  • fruit fly (Drosophila melanogaster)
  • 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 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)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for SLITRK3 Gene

ENSEMBL:
Gene Tree for SLITRK3 (if available)
TreeFam:
Gene Tree for SLITRK3 (if available)

Paralogs for SLITRK3 Gene

Paralogs for SLITRK3 Gene

(7) SIMAP similar genes for SLITRK3 Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with SLITRK3: view

Variants for SLITRK3 Gene

Sequence variations from dbSNP and Humsavar for SLITRK3 Gene

SNP ID Clin Chr 03 pos Sequence Context AA Info Type
rs1000180315 -- 165,198,040(+) TTTTT(G/T)GGGAT upstream-variant-2KB
rs1000283363 -- 165,192,235(+) TATAA(A/T)GTTCA intron-variant
rs1000592840 -- 165,186,225(+) GCCTT(G/T)GATAT downstream-variant-500B
rs1000752452 -- 165,192,607(+) AAGGA(G/T)TCTCT intron-variant
rs1001206038 -- 165,192,333(+) AAAAA(C/G)AGGGA intron-variant

Structural Variations from Database of Genomic Variants (DGV) for SLITRK3 Gene

Variant ID Type Subtype PubMed ID
nsv428426 CNV loss 18775914
nsv592446 CNV loss 21841781

Variation tolerance for SLITRK3 Gene

Residual Variation Intolerance Score: 6.22% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.69; 32.19% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SLITRK3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SLITRK3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SLITRK3 Gene

Disorders for SLITRK3 Gene

MalaCards: The human disease database

(1) MalaCards diseases for SLITRK3 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
gastrointestinal stromal tumor
  • paraganglioma and gastric stromal sarcoma
- elite association - COSMIC cancer census association via MalaCards

Relevant External Links for SLITRK3

Genetic Association Database (GAD)
SLITRK3
Human Genome Epidemiology (HuGE) Navigator
SLITRK3
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SLITRK3
genes like me logo Genes that share disorders with SLITRK3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SLITRK3 Gene

Publications for SLITRK3 Gene

  1. Human SLITRK family genes: genomic organization and expression profiling in normal brain and brain tumor tissue. (PMID: 14557068) Aruga J. … Mikoshiba K. (Gene 2003) 2 3 4 22 64
  2. Prediction of the coding sequences of unidentified human genes. XII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PMID: 10048485) Nagase T. … Ohara O. (DNA Res. 1998) 2 3 4 64
  3. SLITRK3 expression correlation to gastrointestinal stromal tumor risk rating and prognosis. (PMID: 26217092) Wang C.J. … Zhang Z.G. (World J. Gastroenterol. 2015) 3 64
  4. New genetic associations detected in a host response study to hepatitis B vaccine. (PMID: 20237496) Davila S. … Seielstad M. (Genes Immun. 2010) 3 64
  5. Association of genome-wide variation with the risk of incident heart failure in adults of European and African ancestry: a prospective meta-analysis from the cohorts for heart and aging research in genomic epidemiology (CHARGE) consortium. (PMID: 20445134) Smith N.L. … Vasan R.S. (Circ Cardiovasc Genet 2010) 46 64

Products for SLITRK3 Gene

Sources for SLITRK3 Gene

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