Slitrk3 SLIT and NTRK-like family, member 3 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Slitrk3provided by MGI
Official Full Name: SLIT and NTRK-like family, member 3provided by MGI
Primary source: MGI:MGI:2679447
See related: Ensembl:ENSMUSG00000048304 AllianceGenome:MGI:2679447
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: ST3
Summary: Involved in regulation of presynapse assembly. Acts upstream of or within several processes, including GABAergic synaptic transmission; positive regulation of synapse assembly; and synapse organization. Located in cell surface. Is active in GABA-ergic synapse and postsynaptic membrane. Is expressed in alimentary system; bladder; central nervous system; neural retina; and peripheral nervous system. Orthologous to human SLITRK3 (SLIT and NTRK like family member 3). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in frontal lobe adult (RPKM 4.8), cortex adult (RPKM 4.0) and 8 other tissues See more
Orthologs: human all
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Genomic context

Location:: 3 E3; 3 32.59 cM

Exon count:: 4

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	3	NC_000069.7 (72954399..72965298, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	3	NC_000069.6 (73047066..73057953, complement)

Chromosome 3 - NC_000069.7 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: Mouse ENCODE transcriptome data Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

findings reveal how unique postsynaptic Cell Adhesion Molecules neuroligin 2 and slitrk3 work in concert to control synaptogenesis and establish a general framework for GABAergic synapse development.
Title: Molecular Dissection of Neuroligin 2 and Slitrk3 Reveals an Essential Framework for GABAergic Synapse Development.
These results identify Slitrk3-PTPdelta as an inhibitory-specific trans-synaptic organizing complex that is required for normal functional GABAergic synapse development.
Title: Selective control of inhibitory synapse development by Slitrk3-PTPδ trans-synaptic interaction.

Submit: New GeneRIF Correction

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (2) 1 citation
Targeted (1) 1 citation

General gene information

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Gene Ontology Provided by MGI

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
acts_upstream_of_or_within axonogenesis	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within gephyrin clustering involved in postsynaptic density assembly	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within gephyrin clustering involved in postsynaptic density assembly	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within neurotransmitter-gated ion channel clustering	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within neurotransmitter-gated ion channel clustering	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within neurotransmitter-gated ion channel clustering	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of synapse assembly	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within positive regulation of synapse assembly	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within postsynaptic density assembly	IMP Inferred from Mutant Phenotype 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 regulation of presynapse assembly	ISO Inferred from Sequence Orthology more info
involved_in synaptic membrane adhesion	IEA Inferred from Electronic Annotation more info
involved_in synaptic membrane adhesion	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within synaptic transmission, GABAergic	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within synaptic transmission, GABAergic	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within synaptic transmission, GABAergic	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within terminal button organization	IMP Inferred from Mutant Phenotype more info	PubMed

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
located_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
is_active_in GABA-ergic synapse	ISO Inferred from Sequence Orthology more info
located_in cell surface	IDA Inferred from Direct Assay more info	PubMed
located_in membrane	ISS Inferred from Sequence or Structural Similarity more info	PubMed
is_active_in postsynaptic density membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in postsynaptic density membrane	IEA Inferred from Electronic Annotation more info
is_active_in postsynaptic density membrane	ISO Inferred from Sequence Orthology more info
is_active_in postsynaptic membrane	IDA Inferred from Direct Assay more info	PubMed
is_active_in postsynaptic membrane	IMP Inferred from Mutant Phenotype more info	PubMed
is_active_in postsynaptic specialization membrane	ISO Inferred from Sequence Orthology more info

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_001357851.1 → NP_001344780.1 SLIT and NTRK-like protein 3 precursor

Status: VALIDATED

Source sequence(s)

AC102396, AK139438

Consensus CDS

CCDS17410.1

UniProtKB/Swiss-Prot

Q6NZM5, Q810B9

Related

ENSMUSP00000088561.5, ENSMUST00000059407.9

Conserved Domains (3) summary

smart00082
Location:563 → 598

LRRCT; Leucine rich repeat C-terminal domain

sd00033
Location:82 → 103

LRR_RI; leucine-rich repeat [structural motif]

pfam13855
Location:106 → 162

LRR_8; Leucine rich repeat
NM_198864.3 → NP_942564.2 SLIT and NTRK-like protein 3 precursor

See identical proteins and their annotated locations for NP_942564.2

Status: VALIDATED

Source sequence(s)

AC102396, AK139378, BC066059, BE945544

Consensus CDS

CCDS17410.1

UniProtKB/Swiss-Prot

Q6NZM5, Q810B9

Related

ENSMUSP00000141236.2, ENSMUST00000192477.2

Conserved Domains (3) summary

smart00082
Location:563 → 598

LRRCT; Leucine rich repeat C-terminal domain

sd00033
Location:82 → 103

LRR_RI; leucine-rich repeat [structural motif]

pfam13855
Location:106 → 162

LRR_8; Leucine rich repeat

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000069.7 Reference GRCm39 C57BL/6J

Range

72954399..72965298 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006501638.3 → XP_006501701.1 SLIT and NTRK-like protein 3 isoform X1

See identical proteins and their annotated locations for XP_006501701.1

UniProtKB/Swiss-Prot

Q6NZM5, Q810B9

Conserved Domains (3) summary

smart00082
Location:563 → 598

LRRCT; Leucine rich repeat C-terminal domain

sd00033
Location:82 → 103

LRR_RI; leucine-rich repeat [structural motif]

pfam13855
Location:106 → 162

LRR_8; Leucine rich repeat
XM_006501641.3 → XP_006501704.1 SLIT and NTRK-like protein 3 isoform X1

See identical proteins and their annotated locations for XP_006501704.1

UniProtKB/Swiss-Prot

Q6NZM5, Q810B9

Conserved Domains (3) summary

smart00082
Location:563 → 598

LRRCT; Leucine rich repeat C-terminal domain

sd00033
Location:82 → 103

LRR_RI; leucine-rich repeat [structural motif]

pfam13855
Location:106 → 162

LRR_8; Leucine rich repeat
XM_006501640.3 → XP_006501703.1 SLIT and NTRK-like protein 3 isoform X1

See identical proteins and their annotated locations for XP_006501703.1

UniProtKB/Swiss-Prot

Q6NZM5, Q810B9

Conserved Domains (3) summary

smart00082
Location:563 → 598

LRRCT; Leucine rich repeat C-terminal domain

sd00033
Location:82 → 103

LRR_RI; leucine-rich repeat [structural motif]

pfam13855
Location:106 → 162

LRR_8; Leucine rich repeat
XM_006501639.3 → XP_006501702.1 SLIT and NTRK-like protein 3 isoform X1

See identical proteins and their annotated locations for XP_006501702.1

UniProtKB/Swiss-Prot

Q6NZM5, Q810B9

Conserved Domains (3) summary

smart00082
Location:563 → 598

LRRCT; Leucine rich repeat C-terminal domain

sd00033
Location:82 → 103

LRR_RI; leucine-rich repeat [structural motif]

pfam13855
Location:106 → 162

LRR_8; Leucine rich repeat