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SLITRK3 SLIT and NTRK like family member 3 [ Homo sapiens (human) ]

Gene ID: 22865, updated on 22-Sep-2022

Summary

Official Symbol
SLITRK3provided by HGNC
Official Full Name
SLIT and NTRK like family member 3provided by HGNC
Primary source
HGNC:HGNC:23501
See related
Ensembl:ENSG00000121871 MIM:609679; AllianceGenome:HGNC:23501
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
Summary
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]
Expression
Biased expression in brain (RPKM 6.5), esophagus (RPKM 2.6) and 6 other tissues See more
Orthologs
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Genomic context

See SLITRK3 in Genome Data Viewer
Location:
3q26.1
Exon count:
4
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (165186720..165197109, complement)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (167969610..167980005, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (164904508..164914897, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107986050 Neighboring gene uncharacterized LOC105374192 Neighboring gene sucrase-isomaltase Neighboring gene long intergenic non-protein coding RNA 1322 Neighboring gene Sharpr-MPRA regulatory region 7963 Neighboring gene butyrylcholinesterase

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?

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Homology

Clone Names

  • KIAA0848, MGC138681

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
involved_in axonogenesis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in gephyrin clustering involved in postsynaptic density assembly IEA
Inferred from Electronic Annotation
more info
 
involved_in neurotransmitter-gated ion channel clustering IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of synapse assembly IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in regulation of presynapse assembly IDA
Inferred from Direct Assay
more info
PubMed 
involved_in regulation of presynapse assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in synaptic membrane adhesion IDA
Inferred from Direct Assay
more info
PubMed 
involved_in synaptic membrane adhesion IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in synaptic transmission, GABAergic IEA
Inferred from Electronic Annotation
more info
 
involved_in terminal button organization IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
is_active_in GABA-ergic synapse IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
is_active_in GABA-ergic synapse IDA
Inferred from Direct Assay
more info
PubMed 
is_active_in GABA-ergic synapse IMP
Inferred from Mutant Phenotype
more info
PubMed 
located_in cell surface IEA
Inferred from Electronic Annotation
more info
 
located_in plasma membrane TAS
Traceable Author Statement
more info
 
is_active_in postsynaptic density membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
is_active_in postsynaptic specialization membrane IDA
Inferred from Direct Assay
more info
PubMed 
is_active_in postsynaptic specialization membrane IMP
Inferred from Mutant Phenotype
more info
PubMed 

General protein information

Preferred Names
SLIT and NTRK-like protein 3
Names
slit and trk like gene 3

NCBI Reference Sequences (RefSeq)

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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.

mRNA and Protein(s)

  1. NM_001318810.2NP_001305739.1  SLIT and NTRK-like protein 3 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript. Variants 1 - 3 encode the same protein.
    Source sequence(s)
    AB020655, AC013458, AK290024, BC040491
    Consensus CDS
    CCDS3197.1
    UniProtKB/Swiss-Prot
    O94933, Q1RMY6
    Related
    ENSP00000420091.1, ENST00000475390.2
    Conserved Domains (3) summary
    smart00082
    Location:562597
    LRRCT; Leucine rich repeat C-terminal domain
    sd00033
    Location:81102
    LRR_RI; leucine-rich repeat [structural motif]
    pfam13855
    Location:105161
    LRR_8; Leucine rich repeat
  2. NM_001318811.2NP_001305740.1  SLIT and NTRK-like protein 3 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1 - 3 encode the same protein.
    Source sequence(s)
    AB020655, AC013458, BC040491, DA233757
    Consensus CDS
    CCDS3197.1
    UniProtKB/Swiss-Prot
    O94933, Q1RMY6
    Conserved Domains (3) summary
    smart00082
    Location:562597
    LRRCT; Leucine rich repeat C-terminal domain
    sd00033
    Location:81102
    LRR_RI; leucine-rich repeat [structural motif]
    pfam13855
    Location:105161
    LRR_8; Leucine rich repeat
  3. NM_014926.4NP_055741.2  SLIT and NTRK-like protein 3 precursor

    See identical proteins and their annotated locations for NP_055741.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 - 3 encode the same protein.
    Source sequence(s)
    AB020655, AC013458, BC040491, DA123399
    Consensus CDS
    CCDS3197.1
    UniProtKB/Swiss-Prot
    O94933, Q1RMY6
    Related
    ENSP00000241274.3, ENST00000241274.3
    Conserved Domains (3) summary
    smart00082
    Location:562597
    LRRCT; Leucine rich repeat C-terminal domain
    sd00033
    Location:81102
    LRR_RI; leucine-rich repeat [structural motif]
    pfam13855
    Location:105161
    LRR_8; Leucine rich repeat

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    165186720..165197109 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    167969610..167980005 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)