Human Gene SLITRK1 (ENST00000377084.3) from GENCODE V44
  Description: Homo sapiens SLIT and NTRK like family member 1 (SLITRK1), transcript variant 1, mRNA. (from RefSeq NM_052910)
RefSeq Summary (NM_052910): 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].
Gencode Transcript: ENST00000377084.3
Gencode Gene: ENSG00000178235.8
Transcript (Including UTRs)
   Position: hg38 chr13:83,877,205-83,882,393 Size: 5,189 Total Exon Count: 1 Strand: -
Coding Region
   Position: hg38 chr13:83,879,417-83,881,507 Size: 2,091 Coding Exon Count: 1 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr13:83,877,205-83,882,393)mRNA (may differ from genome)Protein (696 aa)
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HGNCHPRDLynxMalacardsMGIneXtProt
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-  Comments and Description Text from UniProtKB
  ID: SLIK1_HUMAN
DESCRIPTION: RecName: Full=SLIT and NTRK-like protein 1; AltName: Full=Leucine-rich repeat-containing protein 12; Flags: Precursor;
FUNCTION: Enhances neuronal dendrite outgrowth.
SUBCELLULAR LOCATION: Membrane; Single-pass type I membrane protein (Potential).
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.
DEVELOPMENTAL STAGE: At 20 weeks of gestation, expressed in multiple brain regions, including the developing neo-cortical plate, subplate zone, striatum, globus pallidus, thalamus and subthalamus.
DISEASE: Defects in SLITRK1 may be a cause of Gilles de la Tourette syndrome (GTS) [MIM:137580]. GTS is a neurologic disorder manifested particularly by motor and vocal tics and associated with behavioral abnormalities.
DISEASE: Defects in SLITRK1 may be a cause of trichotillomania (TTM) [MIM:613229]. It is 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 psychologic disorders, such as Gilles de la Tourette syndrome or obsessive-compulsive disorder.
SIMILARITY: Belongs to the SLITRK family.
SIMILARITY: Contains 12 LRR (leucine-rich) repeats.
SIMILARITY: Contains 2 LRRCT domains.
SIMILARITY: Contains 2 LRRNT domains.
SEQUENCE CAUTION: Sequence=BAB67803.1; Type=Erroneous initiation;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: SLITRK1
Diseases sorted by gene-association score: gilles de la tourette syndrome* (1038), trichotillomania* (998), obsessive-compulsive disorder (18), body dysmorphic disorder (17), neurotic excoriation (16), impulse control disorder (14), stereotypic movement disorder (12), kleptomania (11), tic disorder (10), follicular mucinosis (6)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 7.26 RPKM in Brain - Frontal Cortex (BA9)
Total median expression: 41.05 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -286.90886-0.324 Picture PostScript Text
3' UTR -600.202212-0.271 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR000483 - Cys-rich_flank_reg_C
IPR001611 - Leu-rich_rpt
IPR003591 - Leu-rich_rpt_typical-subtyp
IPR000372 - LRR-contain_N

Pfam Domains:
PF00560 - Leucine Rich Repeat

ModBase Predicted Comparative 3D Structure on Q96PX8
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-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding

Biological Process:
GO:0007399 nervous system development
GO:0007409 axonogenesis
GO:0007416 synapse assembly
GO:0030534 adult behavior
GO:0035264 multicellular organism growth
GO:0042592 homeostatic process
GO:0050772 positive regulation of axonogenesis
GO:0051965 positive regulation of synapse assembly

Cellular Component:
GO:0005576 extracellular region
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0030054 cell junction
GO:0045202 synapse


-  Descriptions from all associated GenBank mRNAs
  AB067497 - Homo sapiens mRNA for KIAA1910 protein.
BC051738 - Homo sapiens SLIT and NTRK-like family, member 1, mRNA (cDNA clone MGC:51091 IMAGE:4816570), complete cds.
JD248235 - Sequence 229259 from Patent EP1572962.
JD269118 - Sequence 250142 from Patent EP1572962.
JD493894 - Sequence 474918 from Patent EP1572962.
JD091919 - Sequence 72943 from Patent EP1572962.
JD244873 - Sequence 225897 from Patent EP1572962.
JD097331 - Sequence 78355 from Patent EP1572962.
JD512185 - Sequence 493209 from Patent EP1572962.
JD280035 - Sequence 261059 from Patent EP1572962.
JD306158 - Sequence 287182 from Patent EP1572962.
JD242344 - Sequence 223368 from Patent EP1572962.
JD285118 - Sequence 266142 from Patent EP1572962.
JD244369 - Sequence 225393 from Patent EP1572962.
JD060313 - Sequence 41337 from Patent EP1572962.
JD300003 - Sequence 281027 from Patent EP1572962.
JD115837 - Sequence 96861 from Patent EP1572962.
JD299406 - Sequence 280430 from Patent EP1572962.
JD479328 - Sequence 460352 from Patent EP1572962.
JD444080 - Sequence 425104 from Patent EP1572962.
JD394057 - Sequence 375081 from Patent EP1572962.
JD131154 - Sequence 112178 from Patent EP1572962.
JD376695 - Sequence 357719 from Patent EP1572962.
AY358289 - Homo sapiens clone DNA37150 LLWI233 (UNQ233) mRNA, complete cds.
JD508318 - Sequence 489342 from Patent EP1572962.
JD038490 - Sequence 19514 from Patent EP1572962.
AK299479 - Homo sapiens cDNA FLJ54428 complete cds, highly similar to SLIT and NTRK-like protein 1 precursor.
JD496588 - Sequence 477612 from Patent EP1572962.
JD167883 - Sequence 148907 from Patent EP1572962.
JD379863 - Sequence 360887 from Patent EP1572962.
JD074520 - Sequence 55544 from Patent EP1572962.
JD123014 - Sequence 104038 from Patent EP1572962.
JD414081 - Sequence 395105 from Patent EP1572962.
JD054268 - Sequence 35292 from Patent EP1572962.
AB385515 - Synthetic construct DNA, clone: pF1KA1910, Homo sapiens SLITRK1 gene for SLIT and NTRK-like protein 1 precursor, complete cds, without stop codon, in Flexi system.
JD403806 - Sequence 384830 from Patent EP1572962.
JD273661 - Sequence 254685 from Patent EP1572962.
JD055013 - Sequence 36037 from Patent EP1572962.
JD402605 - Sequence 383629 from Patent EP1572962.
JD113899 - Sequence 94923 from Patent EP1572962.
JD113898 - Sequence 94922 from Patent EP1572962.
JD045603 - Sequence 26627 from Patent EP1572962.
JD439925 - Sequence 420949 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q96PX8 (Reactome details) participates in the following event(s):

R-HSA-6797803 PTPRD binds SLITRK1-6
R-HSA-388844 Receptor-type tyrosine-protein phosphatases
R-HSA-6794362 Protein-protein interactions at synapses
R-HSA-112316 Neuronal System

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000377084.1, ENST00000377084.2, KIAA1910, LRRC12, NM_052910, Q5U5I6, Q96PX8, Q96SF9, SLIK1_HUMAN, uc001vlk.1, uc001vlk.2, uc001vlk.3, uc001vlk.4, UNQ233/PRO266
UCSC ID: ENST00000377084.3
RefSeq Accession: NM_052910
Protein: Q96PX8 (aka SLIK1_HUMAN or SLK1_HUMAN)
CCDS: CCDS9464.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.