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SLITRK1 SLIT and NTRK like family member 1 [ Homo sapiens (human) ]

Gene ID: 114798, updated on 21-Dec-2019

Summary

Official Symbol
SLITRK1provided by HGNC
Official Full Name
SLIT and NTRK like family member 1provided by HGNC
Primary source
HGNC:HGNC:20297
See related
Ensembl:ENSG00000178235 MIM:609678
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
TTM; LRRC12
Summary
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]
Expression
Restricted expression toward brain (RPKM 10.6) See more
Orthologs

Genomic context

See SLITRK1 in Genome Data Viewer
Location:
13q31.1
Exon count:
2
Annotation release Status Assembly Chr Location
109.20191205 current GRCh38.p13 (GCF_000001405.39) 13 NC_000013.11 (83877205..83882474, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (84451340..84456528, complement)

Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene RNA, U6 small nuclear 67, pseudogene Neighboring gene uncharacterized LOC105370286 Neighboring gene VENT homeobox pseudogene 2 Neighboring gene ubiquitin conjugating enzyme E2 D3 pseudogene 4

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Hair-pulling
MedGen: C0040953 OMIM: 613229 GeneReviews: Not available
Compare labs
Tourette Syndrome
MedGen: C0040517 OMIM: 137580 GeneReviews: Not available
Compare labs

NHGRI GWAS Catalog

Description
A genome-wide search for quantitative trait loci affecting the cortical surface area and thickness of Heschl's gyrus.
NHGRI GWA Catalog
Genome-wide association study combining pathway analysis for typical sporadic amyotrophic lateral sclerosis in Chinese Han populations.
NHGRI GWA Catalog
Genome-wide association study of irritable vs. elated mania suggests genetic differences between clinical subtypes of bipolar disorder.
NHGRI GWA Catalog
Genome-wide association study of temperament in bipolar disorder reveals significant associations with three novel Loci.
NHGRI GWA Catalog

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ54428, KIAA0918, KIAA1910, RP11-395N17.1

Gene Ontology Provided by GOA

Function Evidence Code Pubs
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
adult behavior IEA
Inferred from Electronic Annotation
more info
 
axonogenesis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
homeostatic process IEA
Inferred from Electronic Annotation
more info
 
multicellular organism growth IEA
Inferred from Electronic Annotation
more info
 
positive regulation of axonogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of synapse assembly IEA
Inferred from Electronic Annotation
more info
 
regulation of presynapse assembly IDA
Inferred from Direct Assay
more info
PubMed 
regulation of presynapse assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
synapse assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
synaptic membrane adhesion IDA
Inferred from Direct Assay
more info
PubMed 
synaptic membrane adhesion IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
GABA-ergic synapse IDA
Inferred from Direct Assay
more info
PubMed 
GABA-ergic synapse IMP
Inferred from Mutant Phenotype
more info
PubMed 
cell junction IEA
Inferred from Electronic Annotation
more info
 
extracellular region IEA
Inferred from Electronic Annotation
more info
 
glutamatergic synapse IDA
Inferred from Direct Assay
more info
PubMed 
glutamatergic synapse IMP
Inferred from Mutant Phenotype
more info
PubMed 
integral component of postsynaptic density membrane IEA
Inferred from Electronic Annotation
more info
 
plasma membrane TAS
Traceable Author Statement
more info
 
synapse ISS
Inferred from Sequence or Structural Similarity
more info
 

General protein information

Preferred Names
SLIT and NTRK-like protein 1
Names
leucine-rich repeat-containing protein 12
slit and trk like gene 1

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_016748.1 RefSeqGene

    Range
    5001..10189
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001281503.2NP_001268432.1  SLIT and NTRK-like protein 1 precursor

    See identical proteins and their annotated locations for NP_001268432.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an internal segment compared to variant 1. Both variants 1 and 2 encode the same protein.
    Source sequence(s)
    AB067497, AI500170, AL355481, DC334447, HY157227
    Consensus CDS
    CCDS9464.1
    UniProtKB/Swiss-Prot
    Q96PX8
    Conserved Domains (3) summary
    sd00033
    Location:377400
    LRR_RI; leucine-rich repeat [structural motif]
    pfam13855
    Location:375435
    LRR_8; Leucine rich repeat
    cl15307
    Location:212250
    TPKR_C2; Tyrosine-protein kinase receptor C2 Ig-like domain
  2. NM_052910.2NP_443142.1  SLIT and NTRK-like protein 1 precursor

    See identical proteins and their annotated locations for NP_443142.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript. Both variants 1 and 2 encode the same protein.
    Source sequence(s)
    AA677641, AB067497, AI500170, DA240278
    Consensus CDS
    CCDS9464.1
    UniProtKB/Swiss-Prot
    Q96PX8
    Related
    ENSP00000366288.2, ENST00000377084.3
    Conserved Domains (3) summary
    sd00033
    Location:377400
    LRR_RI; leucine-rich repeat [structural motif]
    pfam13855
    Location:375435
    LRR_8; Leucine rich repeat
    cl15307
    Location:212250
    TPKR_C2; Tyrosine-protein kinase receptor C2 Ig-like domain

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20191205

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000013.11 Reference GRCh38.p13 Primary Assembly

    Range
    83877205..83882474 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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