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 th... See more...

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
  • SLIT And NTRK-Like Protein 1 3 4
  • KIAA1910 2 4
  • LRRC12 3 4
  • SLIT And NTRK-Like Family, Member 1 2
  • Leucine Rich Repeat Containing 12 2
  • Slit And Trk Like Gene 1 3
  • SLITRK1 5
  • 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 Summary 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

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SLITRK1 Gene

Genomics for SLITRK1 Gene

GeneHancer (GH) Regulatory Elements Pubs

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 1.3 Ensembl ENCODE CraniofacialAtlas 600.7 +0.3 273 2.8 REST KDM1A ZNF143 POLR2A EZH2 ZNF512B RAD21 RUNX3 YY1 MIER1 SLITRK1 ENSG00000285680
GH13J083100 Enhancer 0.8 ENCODE 8.9 +780.7 780734 1.9 BRD9 SOX6 HMBOX1 POLR2A TAF9B CHD2 NFRKB MYC EP400 NCOR1 SLITRK1 ENSG00000270400 lnc-NDFIP2-28 piR-35398-009 ENSG00000286385
GH13J083838 Enhancer 0.3 Ensembl 11.6 +43.1 43073 1.6 TRIM28 SMARCA4 SLITRK1 piR-41245-080 piR-30197-003
GH13J083221 Enhancer 0.6 Ensembl ENCODE 5.9 +660.4 660445 1.6 JUND NFE2 MAFK YY1 NFE2L2 POLR2A SLITRK1 piR-32023-070 RF00994-285 ENSG00000286385
GH13J083215 Enhancer 0.5 Ensembl ENCODE 6.1 +666.0 665973 2.6 JUND FOS SLITRK1 RF00994-285 piR-32023-070 ENSG00000286385
- 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 the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SLITRK1

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

Genomic Locations for SLITRK1 Gene

Genomic Locations for SLITRK1 Gene
chr13:83,877,205-83,882,474
(GRCh38/hg38)
Size:
5,270 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:

Assay Products

  • Boster Bio ELISA Kits for SLITRK1

No data available for DME Specific Peptides for SLITRK1 Gene

Domains & Families for SLITRK1 Gene

Gene Families for SLITRK1 Gene

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

Protein Domains for SLITRK1 Gene

InterPro:
Blocks:
  • Leucine-rich repeat signature
ProtoNet:

Suggested Antigen Peptide Sequences for SLITRK1 Gene

GenScript: Design optimal peptide antigens:
  • Leucine-rich repeat-containing protein 12 (SLIK1_HUMAN)

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
nucleus 2
cytosol 2
cytoskeleton 1
mitochondrion 1
endoplasmic reticulum 1
endosome 1
lysosome 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for SLITRK1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA --
GO:0005886 plasma membrane TAS --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0030054 cell junction 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

PathCards logo

SuperPathways for SLITRK1 Gene

No Data Available

Interacting Proteins for SLITRK1 Gene

STRING Interaction Network Preview (showing top 5 STRING interactants - click image to see top 25)
STRING Interaction Network
Selected Interacting proteins: Q96PX8-SLIK1_HUMAN ENSP00000366288 for SLITRK1 Gene via UniProtKB MINT STRING IID

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 IBA 21873635
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 :
9 NCBI additional mRNA sequence :
2 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

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

Expression for SLITRK1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and 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



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for 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)
  • Skin(2.4)
  • Blood(2.2)
  • Kidney(2.1)
  • Muscle(2.1)

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 30 31
  • 99.81 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia SLITRK1 30 31
  • 95.45 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia SLITRK1 30 31
  • 94.92 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Slitrk1 30 17 31
  • 92.91 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Slitrk1 30
  • 92.53 (n)
Oppossum
(Monodelphis domestica)
Mammalia SLITRK1 31
  • 92 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia -- 31
  • 2 (a)
ManyToMany
-- 31
  • 1 (a)
ManyToMany
Chicken
(Gallus gallus)
Aves SLITRK1 30 31
  • 81.36 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia SLITRK1 31
  • 85 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia slitrk1 30
  • 74.92 (n)
Zebrafish
(Danio rerio)
Actinopterygii SLITRK1 31
  • 71 (a)
OneToOne
LOC558743 30
  • 69 (n)
Fruit Fly
(Drosophila melanogaster)
Insecta sli 31
  • 10 (a)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea slt-1 31
  • 10 (a)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 16 (a)
OneToMany
Species where no ortholog for SLITRK1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (Ciona intestinalis)
  • 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

(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, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SLITRK1 Gene

SNP ID Clinical significance and condition Chr 13 pos Variation AA Info Type
707905 Benign: not provided 83,880,652(-) G/A SYNONYMOUS_VARIANT
720611 Benign/Likely Benign: Tourette Syndrome; not provided 83,880,520(-) A/C MISSENSE_VARIANT
739922 Conflicting Interpretations: Tourette Syndrome; not provided 83,881,070(-) G/T MISSENSE_VARIANT
786242 Conflicting Interpretations: Tourette Syndrome; not provided 83,879,537(-) G/C SYNONYMOUS_VARIANT
880920 Uncertain Significance: Tourette Syndrome 83,877,210(-) G/T THREE_PRIME_UTR_VARIANT

Additional dbSNP identifiers (rs#s) for SLITRK1 Gene

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

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

Disorder Aliases PubMed IDs
trichotillomania
  • ttm
gilles de la tourette syndrome
  • gts
obsessive-compulsive disorder
  • ocd
body dysmorphic disorder
  • body dysmorphia
kleptomania
  • pathological stealing
- 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
Open Targets Platform
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 23
  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 41
  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
  4. Slitrk1 is localized to excitatory synapses and promotes their development. (PMID: 27273464) Beaubien F … Cloutier JF (Scientific reports 2016) 3 4
  5. Characterization of SLITRK1 variation in obsessive-compulsive disorder. (PMID: 23990902) Ozomaro U … Grice DE (PloS one 2013) 3 4

Products for SLITRK1 Gene

  • Boster Bio Antibodies for SLITRK1
  • Boster Bio ELISA Kits for SLITRK1

Sources for SLITRK1 Gene