Lrrtm4 leucine rich repeat transmembrane neuronal 4 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Lrrtm4provided by MGI
Official Full Name: leucine rich repeat transmembrane neuronal 4provided by MGI
Primary source: MGI:MGI:2389180
See related: Ensembl:ENSMUSG00000052581 AllianceGenome:MGI:2389180
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: A230052N11; 7530419J18Rik
Summary: Enables heparan sulfate proteoglycan binding activity. Involved in regulation of synapse assembly. Acts upstream of or within AMPA glutamate receptor clustering; positive regulation of synapse assembly; and regulation of presynaptic membrane organization. Located in glutamatergic synapse and postsynaptic membrane. Part of AMPA glutamate receptor complex. Is expressed in several structures, including central nervous system; embryo mesenchyme; and future midbrain. Orthologous to human LRRTM4 (leucine rich repeat transmembrane neuronal 4). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in cortex adult (RPKM 3.0), frontal lobe adult (RPKM 2.8) and 6 other tissues See more
Orthologs: human all
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Genomic context

Location:: 6; 6 C3

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
109	current	GRCm39 (GCF_000001635.27)	6	NC_000072.7 (79995828..80787143)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	6	NC_000072.6 (80018858..80810162)

Chromosome 6 - NC_000072.7 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
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?

LRRTM4 is a member of the transsynaptic complex between rod photoreceptors and bipolar cells.
Title: LRRTM4 is a member of the transsynaptic complex between rod photoreceptors and bipolar cells.
LRRTMs engage the protein domains of Nrx but require its heparan sulfate (HS) modification to induce presynaptic differentiation. Binding to HS of Nrx is sufficient for LRRTM3 and LRRTM4 to induce synaptogenesis. Nrx1gamma is a potent synapse organizer and LRRTM4 is its postsynaptic ligand. Mice expressing a mutant form of LRRTM4 that can't bind HS show structural and functional deficits at dentate gyrus excitatory syn...
Title: LRRTMs Organize Synapses through Differential Engagement of Neurexin and PTPσ.
LRRTM4 is a key synapse organizing molecule at rod bipolar cell (RBC) terminals, where it regulates function of GABAergic synapse and assembly of RBC synaptic dyads.
Title: LRRTM4: A Novel Regulator of Presynaptic Inhibition and Ribbon Synapse Arrangements of Retinal Bipolar Cells.
This study demonistrated that LRRTM4-HSPG complex mediates excitatory synapse development on dentate gyrus granule cells.
Title: An LRRTM4-HSPG complex mediates excitatory synapse development on dentate gyrus granule cells.

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Variation

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Alleles

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

Targeted (2) 1 citation

General gene information

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Homology

Homologs of the Lrrtm4 gene: The Lrrtm4 gene is conserved in human, chimpanzee, Rhesus monkey, dog, cow, rat, chicken, zebrafish, and frog.
Orthologs from Annotation Pipeline: 459 organisms have orthologs with human gene Lrrtm4
Orthologs

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables heparan sulfate proteoglycan binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
acts_upstream_of_or_within AMPA glutamate receptor clustering	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 positive regulation of synapse assembly	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within regulation of presynaptic membrane organization	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of synapse assembly	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of synapse assembly	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within synapse organization	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
part_of AMPA glutamate receptor complex	IDA Inferred from Direct Assay more info	PubMed
is_active_in GABA-ergic synapse	IDA Inferred from Direct Assay more info	PubMed
is_active_in extracellular matrix	IBA Inferred from Biological aspect of Ancestor more info	PubMed
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info	PubMed
is_active_in glutamatergic synapse	IDA Inferred from Direct Assay more info	PubMed
is_active_in glutamatergic synapse	IMP Inferred from Mutant Phenotype more info	PubMed
is_active_in glutamatergic synapse	ISO Inferred from Sequence Orthology more info
located_in membrane	ISS Inferred from Sequence or Structural Similarity more info	PubMed
is_active_in photoreceptor ribbon synapse	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	IEA Inferred from Electronic Annotation more info
is_active_in postsynaptic density membrane	ISO Inferred from Sequence Orthology more info
located_in postsynaptic membrane	IDA Inferred from Direct Assay more info	PubMed
is_active_in synapse	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: leucine-rich repeat transmembrane neuronal protein 4

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_001134743.1 → NP_001128215.1 leucine-rich repeat transmembrane neuronal protein 4 isoform 3 precursor

See identical proteins and their annotated locations for NP_001128215.1

Status: VALIDATED

Description

Transcript Variant: This variant (3) differs in both UTR's and has multiple differences in the coding region, compared to variant 1. The encoded isoform (3) has distinct N- and C-termini and is longer than isoform 1.

Source sequence(s)

BC037216, BY130176

Consensus CDS

CCDS71778.1

UniProtKB/Swiss-Prot

Q80XG9

UniProtKB/TrEMBL

A0A0R4J1T4, A0A6P5PYF1

Related

ENSMUSP00000117263.2, ENSMUST00000147663.8

Conserved Domains (3) summary

sd00031
Location:304 → 316

LRR_1; leucine-rich repeat [structural motif]

sd00033
Location:65 → 87

LRR_RI; leucine-rich repeat [structural motif]

pfam13855
Location:134 → 194

LRR_8; Leucine rich repeat
NM_001282102.1 → NP_001269031.1 leucine-rich repeat transmembrane neuronal protein 4 isoform 2 precursor

See identical proteins and their annotated locations for NP_001269031.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) uses an alternate 5' terminal exon, and thus differs in the 5' UTR and 5' coding region, compared to variant 1. These differences result in translation initiation at an alternate AUG and result in an isoform (2) with a longer and distinct N-terminus, compared to isoform 1.

Source sequence(s)

AK038656, BY130176

Consensus CDS

CCDS71779.1

UniProtKB/TrEMBL

A0A8C6HTX7, E9Q8Y9, Q8BYQ8

Related

ENSMUSP00000121621.2, ENSMUST00000136421.2

Conserved Domains (4) summary

COG4886
Location:55 → 315

LRR; Leucine-rich repeat (LRR) protein [Transcription]

sd00031
Location:304 → 316

LRR_1; leucine-rich repeat [structural motif]

sd00033
Location:65 → 87

LRR_RI; leucine-rich repeat [structural motif]

pfam13855
Location:135 → 194

LRR_8; Leucine rich repeat
NM_001347261.1 → NP_001334190.1 leucine-rich repeat transmembrane neuronal protein 4 isoform 4 precursor

Status: VALIDATED

Description

Transcript Variant: This variant (4) differs in the 3' UTR and has multiple differences in the coding region, compared to variant 1. The encoded isoform (4) has distinct N- and C-termini and is longer than isoform 1.

Source sequence(s)

AC153827, AC156282

Consensus CDS

CCDS90065.1

UniProtKB/Swiss-Prot

Q80XG9, Q8JZS8

UniProtKB/TrEMBL

A0A6P7R4C7

Conserved Domains (4) summary

COG4886
Location:54 → 314

LRR; Leucine-rich repeat (LRR) protein [Transcription]

sd00031
Location:303 → 315

LRR_1; leucine-rich repeat [structural motif]

sd00033
Location:64 → 86

LRR_RI; leucine-rich repeat [structural motif]

pfam13855
Location:134 → 193

LRR_8; Leucine rich repeat
NM_178731.5 → NP_848846.3 leucine-rich repeat transmembrane neuronal protein 4 isoform 1 precursor

See identical proteins and their annotated locations for NP_848846.3

Status: VALIDATED

Description

Transcript Variant: This variant (1) encodes the shortest isoform (1).

Source sequence(s)

AK038656, CJ059997

Consensus CDS

CCDS20259.2

UniProtKB/Swiss-Prot

Q80XG9

UniProtKB/TrEMBL

A0A8C6HTY8, Q8BYQ8

Related

ENSMUSP00000074232.5, ENSMUST00000074662.5

Conserved Domains (4) summary

cd00116
Location:84 → 295

LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...

sd00031
Location:303 → 315

LRR_1; leucine-rich repeat [structural motif]

sd00033
Location:64 → 86

LRR_RI; leucine-rich repeat [structural motif]

pfam13855
Location:133 → 193

LRR_8; Leucine rich repeat

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 109 details...

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

Reference GRCm39 C57BL/6J

Genomic

NC_000072.7 Reference GRCm39 C57BL/6J

Range

79995828..80787143

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006506089.4 → XP_006506152.1 leucine-rich repeat transmembrane neuronal protein 4 isoform X4

See identical proteins and their annotated locations for XP_006506152.1

UniProtKB/TrEMBL

A0A8C6HTX7, E9Q8Y9

Conserved Domains (4) summary

COG4886
Location:55 → 315

LRR; Leucine-rich repeat (LRR) protein [Transcription]

sd00031
Location:304 → 316

LRR_1; leucine-rich repeat [structural motif]

sd00033
Location:65 → 87

LRR_RI; leucine-rich repeat [structural motif]

pfam13855
Location:135 → 194

LRR_8; Leucine rich repeat
XM_006506088.4 → XP_006506151.1 leucine-rich repeat transmembrane neuronal protein 4 isoform X3

Conserved Domains (4) summary

COG4886
Location:55 → 315

LRR; Leucine-rich repeat (LRR) protein [Transcription]

sd00031
Location:304 → 316

LRR_1; leucine-rich repeat [structural motif]

sd00033
Location:65 → 87

LRR_RI; leucine-rich repeat [structural motif]

pfam13855
Location:135 → 194

LRR_8; Leucine rich repeat
XM_011241336.4 → XP_011239638.1 leucine-rich repeat transmembrane neuronal protein 4 isoform X5

Conserved Domains (4) summary

COG4886
Location:55 → 315

LRR; Leucine-rich repeat (LRR) protein [Transcription]

sd00031
Location:304 → 316

LRR_1; leucine-rich repeat [structural motif]

sd00033
Location:65 → 87

LRR_RI; leucine-rich repeat [structural motif]

pfam13855
Location:135 → 194

LRR_8; Leucine rich repeat
XM_036166111.1 → XP_036022004.1 leucine-rich repeat transmembrane neuronal protein 4 isoform X2

Conserved Domains (3) summary

sd00031
Location:304 → 316

LRR_1; leucine-rich repeat [structural motif]

sd00033
Location:65 → 87

LRR_RI; leucine-rich repeat [structural motif]

cd21340
Location:91 → 312

PPP1R42; protein phosphatase 1 regulatory subunit 42
XM_006506087.2 → XP_006506150.1 leucine-rich repeat transmembrane neuronal protein 4 isoform X1

See identical proteins and their annotated locations for XP_006506150.1

UniProtKB/Swiss-Prot

Q80XG9, Q8JZS8

UniProtKB/TrEMBL

A0A6P7R4C7

Conserved Domains (4) summary

COG4886
Location:54 → 314

LRR; Leucine-rich repeat (LRR) protein [Transcription]

sd00031
Location:303 → 315

LRR_1; leucine-rich repeat [structural motif]

sd00033
Location:64 → 86

LRR_RI; leucine-rich repeat [structural motif]

pfam13855
Location:134 → 193

LRR_8; Leucine rich repeat
XM_006506085.3 → XP_006506148.1 leucine-rich repeat transmembrane neuronal protein 4 isoform X1

See identical proteins and their annotated locations for XP_006506148.1

UniProtKB/Swiss-Prot

Q80XG9, Q8JZS8

UniProtKB/TrEMBL

A0A6P7R4C7

Related

ENSMUSP00000121124.2, ENSMUST00000126399.2

Conserved Domains (4) summary

COG4886
Location:54 → 314

LRR; Leucine-rich repeat (LRR) protein [Transcription]

sd00031
Location:303 → 315

LRR_1; leucine-rich repeat [structural motif]

sd00033
Location:64 → 86

LRR_RI; leucine-rich repeat [structural motif]

pfam13855
Location:134 → 193

LRR_8; Leucine rich repeat
XM_006506086.3 → XP_006506149.1 leucine-rich repeat transmembrane neuronal protein 4 isoform X1

See identical proteins and their annotated locations for XP_006506149.1

UniProtKB/Swiss-Prot

Q80XG9, Q8JZS8

UniProtKB/TrEMBL

A0A6P7R4C7

Related

ENSMUSP00000115016.2, ENSMUST00000133918.8

Conserved Domains (4) summary

COG4886
Location:54 → 314

LRR; Leucine-rich repeat (LRR) protein [Transcription]

sd00031
Location:303 → 315

LRR_1; leucine-rich repeat [structural motif]

sd00033
Location:64 → 86

LRR_RI; leucine-rich repeat [structural motif]

pfam13855
Location:134 → 193

LRR_8; Leucine rich repeat