Free for academic non-profit institutions. Other users need a Commercial license

Aliases for SLITRK1 Gene

Aliases for SLITRK1 Gene

  • SLIT And NTRK Like Family Member 1 2 3 5
  • Leucine-Rich Repeat-Containing Protein 12 3 4
  • LRRC12 3 4
  • SLIT And NTRK-Like Family, Member 1 2
  • Leucine Rich Repeat Containing 12 2
  • SLIT And NTRK-Like Protein 1 3
  • Slit And Trk Like Gene 1 3
  • KIAA1910 4
  • TTM 3

External Ids for SLITRK1 Gene

Previous HGNC Symbols for SLITRK1 Gene

  • LRRC12

Previous GeneCards Identifiers for SLITRK1 Gene

  • GC13M082251
  • GC13M082249
  • GC13M083349
  • GC13M084451
  • GC13M065151

Summaries for SLITRK1 Gene

Entrez Gene Summary for SLITRK1 Gene

  • This gene encodes a member of the SLITRK protein family. Members of this family are integral membrane proteins that are characterized by two N-terminal leucine-rich repeat (LRR) domains and a C-terminal region that shares homology with trk neurotrophin receptors. However, the protein encoded by this gene lacks the region of homology to neurotrophin receptors. This protein is thought to be involved in neurite outgrowth. Mutations in this gene may be associated with Tourette syndrome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]

GeneCards Summary for SLITRK1 Gene

SLITRK1 (SLIT And NTRK Like Family Member 1) is a Protein Coding gene. Diseases associated with SLITRK1 include Trichotillomania and Gilles De La Tourette Syndrome. An important paralog of this gene is SLITRK2.

UniProtKB/Swiss-Prot for SLITRK1 Gene

  • It is involved in synaptogenesis and promotes excitatory synapse differentiation (PubMed:27273464, PubMed:27812321). Enhances neuronal dendrite outgrowth (PubMed:16224024, PubMed:19640509).

Gene Wiki entry for SLITRK1 Gene

Additional gene information for SLITRK1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SLITRK1 Gene

Genomics for SLITRK1 Gene

GeneHancer (GH) Regulatory Elements for SLITRK1 Gene

Promoters and enhancers for SLITRK1 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
GH13J083881 Promoter/Enhancer 1.1 Ensembl ENCODE 650.7 +0.3 293 1.1 MXI1 BACH1 SIN3A MIER2 REST ZNF512B POLR2A CTBP2 ZNF143 EHMT2 SLITRK1 LOC105370286
GH13J083883 Enhancer 0.4 ENCODE 650.7 -0.7 -708 0.1 CTBP1 PKNOX1 L3MBTL2 SLITRK1 VENTXP2
GH13J083100 Enhancer 0.8 ENCODE 8.9 +780.7 780653 1.9 ATF1 TAF9B ARNT NFRKB CHAMP1 POLR2B CREM SMARCA5 SMAD5 ZNF148 SLITRK1 GC13M083079 ENSG00000270400
GH13J083221 Enhancer 0.5 ENCODE 5.9 +660.4 660364 1.6 JUND POLR2A NFE2 MAFK SLITRK1 GC13P083229 GC13P083166
GH13J083906 Enhancer 0.3 FANTOM5 0.3 -24.2 -24175 0.1 VENTXP2 SLITRK1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SLITRK1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SLITRK1 gene promoter:
  • CUTL1
  • STAT1beta
  • STAT1alpha
  • STAT1
  • SRY
  • Nkx2-5
  • POU2F1
  • POU2F1c
  • POU2F1a

Genomic Locations for SLITRK1 Gene

Genomic Locations for SLITRK1 Gene
chr13:83,877,205-83,882,393
(GRCh38/hg38)
Size:
5,189 bases
Orientation:
Minus strand
chr13:84,451,343-84,456,528
(GRCh37/hg19)
Size:
5,186 bases
Orientation:
Minus strand

Genomic View for SLITRK1 Gene

Genes around SLITRK1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SLITRK1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SLITRK1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SLITRK1 Gene

Proteins for SLITRK1 Gene

  • Protein details for SLITRK1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96PX8-SLIK1_HUMAN
    Recommended name:
    SLIT and NTRK-like protein 1
    Protein Accession:
    Q96PX8
    Secondary Accessions:
    • Q5U5I6
    • Q96SF9

    Protein attributes for SLITRK1 Gene

    Size:
    696 amino acids
    Molecular mass:
    77735 Da
    Quaternary structure:
    • Can form homodimers; homodimerization requires repeat LRR 2 (PubMed:27273464). Interacts with YWHAB, YWHAE, YWHAG, YWHAH, SFN, YWHAQ and YWHAZ (PubMed:19640509).
    SequenceCaution:
    • Sequence=BAB67803.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for SLITRK1 Gene

neXtProt entry for SLITRK1 Gene

Post-translational modifications for SLITRK1 Gene

  • Undergoes proteolytic cleavage that results in shedding of the ectodomain and cleavage of the C-terminal cytoplasmic tail. Glycosylated. Phosphorylation at Ser-695 is necessary for proper function in promoting neurite outgrowth.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SLITRK1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for SLITRK1 Gene

Domains & Families for SLITRK1 Gene

Gene Families for SLITRK1 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Plasma proteins
  • Predicted membrane proteins

Suggested Antigen Peptide Sequences for SLITRK1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q96PX8

UniProtKB/Swiss-Prot:

SLIK1_HUMAN :
  • Belongs to the SLITRK family.
Family:
  • Belongs to the SLITRK family.
genes like me logo Genes that share domains with SLITRK1: view

Function for SLITRK1 Gene

Molecular function for SLITRK1 Gene

UniProtKB/Swiss-Prot Function:
It is involved in synaptogenesis and promotes excitatory synapse differentiation (PubMed:27273464, PubMed:27812321). Enhances neuronal dendrite outgrowth (PubMed:16224024, PubMed:19640509).

Phenotypes From GWAS Catalog for SLITRK1 Gene

Gene Ontology (GO) - Molecular Function for SLITRK1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 19640509
genes like me logo Genes that share ontologies with SLITRK1: view
genes like me logo Genes that share phenotypes with SLITRK1: view

Human Phenotype Ontology for SLITRK1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for SLITRK1 Gene

MGI Knock Outs for SLITRK1:

Animal Model Products

  • Taconic Biosciences Mouse Models for SLITRK1

CRISPR Products

miRNA for SLITRK1 Gene

miRTarBase miRNAs that target SLITRK1

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SLITRK1

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for SLITRK1 Gene

Localization for SLITRK1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SLITRK1 Gene

Membrane; Single-pass type I membrane protein. Secreted. Cell junction, synapse.

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 SLITRK1 gene
Compartment Confidence
plasma membrane 5
extracellular 4
endoplasmic reticulum 1

Gene Ontology (GO) - Cellular Components for SLITRK1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA --
GO:0005615 extracellular space IBA --
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 SLITRK1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for SLITRK1 Gene

Pathways & Interactions for SLITRK1 Gene

SuperPathways for SLITRK1 Gene

No Data Available

Interacting Proteins for SLITRK1 Gene

Gene Ontology (GO) - Biological Process for SLITRK1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007399 nervous system development IEA --
GO:0007409 axonogenesis IEA --
GO:0007416 synapse assembly IMP 27273464
GO:0030534 adult behavior IEA --
GO:0035264 multicellular organism growth IEA --
genes like me logo Genes that share ontologies with SLITRK1: view

No data available for Pathways by source and SIGNOR curated interactions for SLITRK1 Gene

Drugs & Compounds for SLITRK1 Gene

No Compound Related Data Available

Transcripts for SLITRK1 Gene

mRNA/cDNA for SLITRK1 Gene

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

Unigene Clusters for SLITRK1 Gene

SLIT and NTRK-like family, member 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SLITRK1

Alternative Splicing Database (ASD) splice patterns (SP) for SLITRK1 Gene

No ASD Table

Relevant External Links for SLITRK1 Gene

GeneLoc Exon Structure for
SLITRK1
ECgene alternative splicing isoforms for
SLITRK1

Expression for SLITRK1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SLITRK1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SLITRK1 Gene

This gene is overexpressed in Brain - Frontal Cortex (BA9) (x8.8), Brain - Anterior cingulate cortex (BA24) (x7.8), Brain - Cortex (x7.5), Brain - Hippocampus (x5.0), and Brain - Amygdala (x4.9).

Protein differential expression in normal tissues from HIPED for SLITRK1 Gene

This gene is overexpressed in Cerebrospinal fluid (32.2), Serum (12.7), Lung (11.9), and Kidney (8.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for SLITRK1 Gene



NURSA nuclear receptor signaling pathways regulating expression of SLITRK1 Gene:

SLITRK1

SOURCE GeneReport for Unigene cluster for SLITRK1 Gene:

Hs.415478

mRNA Expression by UniProt/SwissProt for SLITRK1 Gene:

Q96PX8-SLIK1_HUMAN
Tissue specificity: Expressed predominantly in the frontal lobe of the cerebral cortex of the brain. Also expressed in some astrocytic brain tumors such as astrocytomas, oligodendrogliomas, glioblastomas, gangliogliomas and primitive neuroectodermal tumors.

Evidence on tissue expression from TISSUES for SLITRK1 Gene

  • Nervous system(4.7)

Phenotype-based relationships between genes and organs from Gene ORGANizer for SLITRK1 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • integumentary
  • nervous
  • respiratory
  • skeletal muscle
Regions:
Head and neck:
  • brain
  • cerebellum
  • cranial nerve
  • ear
  • head
  • larynx
  • mouth
  • neck
  • nose
  • pharynx
  • scalp
  • vocal cord
Thorax:
  • heart
General:
  • blood vessel
  • hair
  • peripheral nervous system
  • skin
genes like me logo Genes that share expression patterns with SLITRK1: view

No data available for Protein tissue co-expression partners for SLITRK1 Gene

Orthologs for SLITRK1 Gene

This gene was present in the common ancestor of animals.

Orthologs for SLITRK1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SLITRK1 34 33
  • 99.81 (n)
OneToOne
cow
(Bos Taurus)
Mammalia SLITRK1 34 33
  • 95.45 (n)
OneToOne
dog
(Canis familiaris)
Mammalia SLITRK1 34 33
  • 94.92 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Slitrk1 16 34 33
  • 92.91 (n)
rat
(Rattus norvegicus)
Mammalia Slitrk1 33
  • 92.53 (n)
oppossum
(Monodelphis domestica)
Mammalia SLITRK1 34
  • 92 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 2 (a)
ManyToMany
-- 34
  • 1 (a)
ManyToMany
chicken
(Gallus gallus)
Aves SLITRK1 34 33
  • 81.36 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SLITRK1 34
  • 85 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia slitrk1 33
  • 74.92 (n)
zebrafish
(Danio rerio)
Actinopterygii SLITRK1 34
  • 71 (a)
OneToOne
LOC558743 33
  • 69 (n)
fruit fly
(Drosophila melanogaster)
Insecta sli 34
  • 10 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea slt-1 34
  • 10 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 16 (a)
OneToMany
Species where no ortholog for SLITRK1 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 SLITRK1 Gene

ENSEMBL:
Gene Tree for SLITRK1 (if available)
TreeFam:
Gene Tree for SLITRK1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SLITRK1: view image

Paralogs for SLITRK1 Gene

Paralogs for SLITRK1 Gene

(6) SIMAP similar genes for SLITRK1 Gene using alignment to 1 proteins:

  • SLIK1_HUMAN
genes like me logo Genes that share paralogs with SLITRK1: view

Variants for SLITRK1 Gene

Sequence variations from dbSNP and Humsavar for SLITRK1 Gene

SNP ID Clin Chr 13 pos Variation AA Info Type
rs1035448844 (TTM) [MIM:613229] 83,879,757(-) C/T coding_sequence_variant, missense_variant
rs1037756552 uncertain-significance, Tourette Syndrome 83,879,187(-) A/C 3_prime_UTR_variant
rs1046202 likely-benign, Tourette Syndrome 83,877,375(-) A/T 3_prime_UTR_variant
rs140472390 uncertain-significance, Tourette Syndrome 83,878,104(-) G/C 3_prime_UTR_variant
rs140875495 uncertain-significance, Tourette Syndrome 83,881,577(-) C/G 5_prime_UTR_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for SLITRK1 Gene

Variant ID Type Subtype PubMed ID
nsv1040716 CNV gain 25217958
nsv562552 CNV loss 21841781

Variation tolerance for SLITRK1 Gene

Residual Variation Intolerance Score: 15.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.22; 24.41% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SLITRK1 Gene

Human Gene Mutation Database (HGMD)
SLITRK1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SLITRK1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SLITRK1 Gene

Disorders for SLITRK1 Gene

MalaCards: The human disease database

(10) MalaCards diseases for SLITRK1 Gene - From: HGMD, OMIM, ClinVar, GTR, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

SLIK1_HUMAN
  • Trichotillomania (TTM) [MIM:613229]: A neuropsychiatric disorder characterized by chronic, repetitive, or compulsive hair pulling resulting in noticeable hair loss. Affected individuals may develop physical complications and often have overlapping psychological disorders, such as Gilles de la Tourette syndrome or obsessive-compulsive disorder. {ECO:0000269 PubMed:16224024, ECO:0000269 PubMed:17003809, ECO:0000269 PubMed:27812321}. Note=The disease may be caused by mutations affecting the gene represented in this entry.

Additional Disease Information for SLITRK1

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 SLITRK1: view

No data available for Genatlas for SLITRK1 Gene

Publications for SLITRK1 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 58
  2. Sequence variants in SLITRK1 are associated with Tourette's syndrome. (PMID: 16224024) Abelson JF … State MW (Science (New York, N.Y.) 2005) 3 4 44 58
  3. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PMID: 12975309) Clark HF … Gray A (Genome research 2003) 2 3 4 58
  4. Slitrk1 is localized to excitatory synapses and promotes their development. (PMID: 27273464) Beaubien F … Cloutier JF (Scientific reports 2016) 3 4 58
  5. Characterization of SLITRK1 variation in obsessive-compulsive disorder. (PMID: 23990902) Ozomaro U … Grice DE (PloS one 2013) 3 4 58

Products for SLITRK1 Gene

Sources for SLITRK1 Gene

Content
Loading form....