Nlgn3 neuroligin 3 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Nlgn3provided by RGD
Official Full Name: neuroligin 3provided by RGD
Primary source: RGD:621119
See related: EnsemblRapid:ENSRNOG00000003812 AllianceGenome:RGD:621119
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Enables cell adhesion molecule binding activity; neurexin family protein binding activity; and signaling receptor activity. Involved in several processes, including inhibitory postsynaptic potential; neuron cell-cell adhesion; and synapse assembly. Acts upstream of or within synapse organization. Located in several cellular components, including excitatory synapse; inhibitory synapse; and postsynaptic membrane. Is active in GABA-ergic synapse; glutamatergic synapse; and postsynaptic specialization membrane. Used to study autism spectrum disorder. Biomarker of sciatic neuropathy. Human ortholog(s) of this gene implicated in autistic disorder. Orthologous to human NLGN3 (neuroligin 3). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Brain (RPKM 118.9), Heart (RPKM 8.6) and 2 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: Xq22

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	X	NC_086039.1 (70469251..70497380)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	X	NC_051356.1 (66427926..66457378)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	X	NC_005120.4 (71199390..71227460)

Chromosome X - NC_086039.1 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: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Results showed that in pyramidal and interneurons, neuroligin 1 and neuroligin 3 were involved in excitatory synapse formation, and neuroligin 2 in GABAergic synapse formation.
Title: Neuroligins Differentially Mediate Subtype-Specific Synapse Formation in Pyramidal Neurons and Interneurons.
e found that NLGN3 function at inhibitory synapses in rat CA1 depends on the presence of NLGN2 and identified a domain in the extracellular region that accounted for this functional difference between NLGN2 and 3 specifically at inhibitory synapses.
Title: Distinct roles for extracellular and intracellular domains in neuroligin function at inhibitory synapses.
show that up-regulation of BiP (immunoglobulin heavy-chain-binding protein) and CHOP [C/EBP (CCAAT/enhancer-binding protein)-homologous protein] was induced by both mutant proteins but not by wild-type neuroligin3
Title: Autism-associated R451C mutation in neuroligin3 leads to activation of the unfolded protein response in a PC12 Tet-On inducible system.
Studied the effect of clonal overexpression of NL3 and NL2 in neurons of the rat cerebral cortex in vivo after in utero electroporation, found that overexpression of NL3 has strong effects on GABAergic synapses and neuronal radial migration
Title: In vivo clonal overexpression of neuroligin 3 and neuroligin 2 in neurons of the rat cerebral cortex: Differential effects on GABAergic synapses and neuronal migration.
Data from studies using cross-linking reagents suggest that neuroligins in neurons cultured from embryonic hippocampus, striatum, or cerebellum form constitutive dimers, including homodimers and, most notably, neuroligin 1/3 heteromers.
Title: Homodimerization and isoform-specific heterodimerization of neuroligins.
On a wild-type background, overexpression of a full-length version of NLGN3 yielded an increase in AMPA receptor (AMPAR)-evoked currents.
Title: Functional dependence of neuroligin on a new non-PDZ intracellular domain.
Neuroligin 3 trafficking deficiencies arising from mutations in the alpha/beta-hydrolase fold protein family.
Title: Neuroligin trafficking deficiencies arising from mutations in the alpha/beta-hydrolase fold protein family.
these data suggest that intracellular mechanisms are involved in the targeting of different neuroligin family members such as Nlgn2 and Nlgn3 to synapses
Title: Postsynaptic scaffolding molecules modulate the localization of neuroligins.
Data show beta-cell expression of the neuroligin 3, and show that neuroligin expression affects insulin secretion in INS-1 beta-cells and rat islet cells.
Title: Expression of neurexin, neuroligin, and their cytoplasmic binding partners in the pancreatic beta-cells and the involvement of neuroligin in insulin secretion.
Rat NL3 is a synaptic adhesion molecule that is a shared component of glutamatergic and GABAergic synapses.
Title: Neuroligin-3 is a neuronal adhesion protein at GABAergic and glutamatergic synapses.

Submit: New GeneRIF Correction See all GeneRIFs (12)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

MARC_10371-10372:999098922:1 (e-PCR)
- UniSTS:267121

RH79662 (e-PCR)
- UniSTS:83609

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables cell adhesion molecule binding	IPI Inferred from Physical Interaction more info	PubMed
enables neurexin family protein binding	IBA Inferred from Biological aspect of Ancestor more info
enables neurexin family protein binding	IEA Inferred from Electronic Annotation more info
enables neurexin family protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables scaffold protein binding	IEA Inferred from Electronic Annotation more info
enables scaffold protein binding	ISO Inferred from Sequence Orthology more info
enables signaling receptor activity	IBA Inferred from Biological aspect of Ancestor more info
enables signaling receptor activity	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in adult behavior	IEA Inferred from Electronic Annotation more info
involved_in adult behavior	ISO Inferred from Sequence Orthology more info
involved_in axon extension	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cell adhesion	IEA Inferred from Electronic Annotation more info
involved_in chemical synaptic transmission	IBA Inferred from Biological aspect of Ancestor more info
involved_in circadian sleep/wake cycle	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in excitatory postsynaptic potential	ISO Inferred from Sequence Orthology more info
involved_in excitatory postsynaptic potential	ISS Inferred from Sequence or Structural Similarity more info
involved_in inhibitory postsynaptic potential	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within inhibitory postsynaptic potential	ISO Inferred from Sequence Orthology more info
involved_in inhibitory postsynaptic potential	ISO Inferred from Sequence Orthology more info
involved_in learning	IEA Inferred from Electronic Annotation more info
involved_in learning	ISO Inferred from Sequence Orthology more info
involved_in long-term synaptic potentiation	ISO Inferred from Sequence Orthology more info
involved_in membrane assembly	IEA Inferred from Electronic Annotation more info
involved_in modulation of chemical synaptic transmission	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within modulation of chemical synaptic transmission	ISO Inferred from Sequence Orthology more info
involved_in modulation of chemical synaptic transmission	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of dendritic spine morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of excitatory postsynaptic potential	ISO Inferred from Sequence Orthology more info
involved_in neuron cell-cell adhesion	IBA Inferred from Biological aspect of Ancestor more info
involved_in neuron cell-cell adhesion	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within oligodendrocyte differentiation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of AMPA receptor activity	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of dendritic spine development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of excitatory postsynaptic potential	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of excitatory postsynaptic potential	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of glutamate receptor signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of glutamate receptor signaling pathway	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of inhibitory postsynaptic potential	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of multicellular organismal process	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of protein localization to synapse	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of synapse assembly	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of synapse assembly	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of synaptic transmission, glutamatergic	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of synaptic transmission, glutamatergic	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of synaptic vesicle clustering	ISO Inferred from Sequence Orthology more info
involved_in postsynaptic membrane assembly	IBA Inferred from Biological aspect of Ancestor more info
involved_in postsynaptic membrane assembly	ISO Inferred from Sequence Orthology more info
involved_in postsynaptic membrane assembly	ISS Inferred from Sequence or Structural Similarity more info
involved_in postsynaptic specialization assembly	IDA Inferred from Direct Assay more info	PubMed
involved_in prepulse inhibition	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in presynaptic membrane assembly	IBA Inferred from Biological aspect of Ancestor more info
involved_in presynaptic membrane assembly	IDA Inferred from Direct Assay more info	PubMed
involved_in receptor-mediated endocytosis	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of AMPA receptor activity	ISO Inferred from Sequence Orthology more info
involved_in regulation of AMPA receptor activity	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of NMDA receptor activity	ISO Inferred from Sequence Orthology more info
involved_in regulation of NMDA receptor activity	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in regulation of dendritic spine morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in regulation of dendritic spine morphogenesis	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in regulation of long-term synaptic potentiation	ISO Inferred from Sequence Orthology more info
involved_in regulation of long-term synaptic potentiation	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in regulation of membrane potential	IEA Inferred from Electronic Annotation more info
involved_in regulation of nervous system process	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of respiratory gaseous exchange by nervous system process	ISO Inferred from Sequence Orthology more info
involved_in regulation of respiratory gaseous exchange by nervous system process	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of signal transduction	IEA Inferred from Electronic Annotation more info
involved_in regulation of synaptic transmission, glutamatergic	ISO Inferred from Sequence Orthology more info
involved_in regulation of synaptic transmission, glutamatergic	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of terminal button organization	ISO Inferred from Sequence Orthology more info
involved_in regulation of terminal button organization	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in rhythmic synaptic transmission	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in social behavior	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within social behavior	ISO Inferred from Sequence Orthology more info
involved_in social behavior	ISO Inferred from Sequence Orthology more info
involved_in social behavior	ISS Inferred from Sequence or Structural Similarity more info
involved_in synapse assembly	IDA Inferred from Direct Assay more info	PubMed
involved_in synapse assembly	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within synapse organization	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within synapse organization	ISO Inferred from Sequence Orthology more info
involved_in synapse organization	ISO Inferred from Sequence Orthology more info
involved_in synaptic vesicle endocytosis	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within visual learning	ISO Inferred from Sequence Orthology more info
involved_in vocalization behavior	IEA Inferred from Electronic Annotation more info
involved_in vocalization behavior	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
is_active_in GABA-ergic synapse	IDA Inferred from Direct Assay more info	PubMed
is_active_in cell surface	IBA Inferred from Biological aspect of Ancestor more info
located_in cell surface	IDA Inferred from Direct Assay more info	PubMed
located_in cell surface	IEA Inferred from Electronic Annotation more info
located_in cell surface	ISO Inferred from Sequence Orthology more info
located_in dendrite	IDA Inferred from Direct Assay more info	PubMed
located_in endocytic vesicle	IDA Inferred from Direct Assay more info	PubMed
located_in excitatory synapse	IDA Inferred from Direct Assay more info	PubMed
located_in excitatory synapse	IEA Inferred from Electronic Annotation more info
located_in excitatory synapse	ISO Inferred from Sequence Orthology more info
is_active_in glutamatergic synapse	IDA Inferred from Direct Assay more info	PubMed
located_in inhibitory synapse	IC Inferred by Curator more info	PubMed
located_in inhibitory synapse	IDA Inferred from Direct Assay more info	PubMed
located_in neuronal cell body	IDA Inferred from Direct Assay more info	PubMed
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	IEA Inferred from Electronic Annotation more info
located_in postsynaptic membrane	IDA Inferred from Direct Assay more info	PubMed
is_active_in postsynaptic specialization membrane	IDA Inferred from Direct Assay more info	PubMed
located_in presynapse	IEA Inferred from Electronic Annotation more info
is_active_in synapse	IBA Inferred from Biological aspect of Ancestor more info
located_in synapse	IDA Inferred from Direct Assay more info	PubMed
located_in synapse	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: neuroligin-3

Names: gliotactin homolog

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_001431657.1 → NP_001418586.1 neuroligin-3 isoform 1 precursor

Status: VALIDATED

Source sequence(s)

JAXUCZ010000021

UniProtKB/TrEMBL

A0A8I5ZNW2, D3ZDC0
NM_001431658.1 → NP_001418587.1 neuroligin-3 isoform 3 precursor

Status: VALIDATED

Source sequence(s)

JAXUCZ010000021

UniProtKB/TrEMBL

A0A096MK63, A0A8I5ZNW2
NM_134336.3 → NP_599163.2 neuroligin-3 isoform 2 precursor

See identical proteins and their annotated locations for NP_599163.2

Status: VALIDATED

Source sequence(s)

JAXUCZ010000021

UniProtKB/Swiss-Prot

Q62889

UniProtKB/TrEMBL

A6IQB3, F1LPZ8

Related

ENSRNOP00000005077.3, ENSRNOT00000005077.7

Conserved Domains (1) summary

pfam00135
Location:40 → 624

COesterase; Carboxylesterase family

RNA

NR_197237.1 RNA Sequence

Status: VALIDATED

Source sequence(s)

JAXUCZ010000021
NR_197238.1 RNA Sequence

Status: VALIDATED

Source sequence(s)

JAXUCZ010000021
NR_197239.1 RNA Sequence

Status: VALIDATED

Source sequence(s)

JAXUCZ010000021