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

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: mouse all
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Genomic context

Location:: 3q26.1

Exon count:: 4

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (165186720..165197109, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	3	NC_060927.1 (167969610..167980005, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	3	NC_000003.11 (164904508..164914897, complement)

Chromosome 3 - NC_000003.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

SLITRK2, an X-linked modifier of the age at onset in C9orf72 frontotemporal lobar degeneration.
Title: SLITRK2, an X-linked modifier of the age at onset in C9orf72 frontotemporal lobar degeneration.
SLITRK3 expression is a highly significant predictor of gastrointestinal stromal tumor recurrence and metastasis.
Title: SLITRK3 expression correlation to gastrointestinal stromal tumor risk rating and prognosis.
Observational study of gene-disease association. (HuGE Navigator)
Title: New genetic associations detected in a host response study to hepatitis B vaccine.

Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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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
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
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
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
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

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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)

NM_001318810.2 → NP_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:562 → 597

LRRCT; Leucine rich repeat C-terminal domain

sd00033
Location:81 → 102

LRR_RI; leucine-rich repeat [structural motif]

pfam13855
Location:105 → 161

LRR_8; Leucine rich repeat
NM_001318811.2 → NP_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:562 → 597

LRRCT; Leucine rich repeat C-terminal domain

sd00033
Location:81 → 102

LRR_RI; leucine-rich repeat [structural motif]

pfam13855
Location:105 → 161

LRR_8; Leucine rich repeat
NM_014926.4 → NP_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:562 → 597

LRRCT; Leucine rich repeat C-terminal domain

sd00033
Location:81 → 102

LRR_RI; leucine-rich repeat [structural motif]

pfam13855
Location:105 → 161

LRR_8; Leucine rich repeat