Lrrc4c leucine rich repeat containing 4C [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Lrrc4cprovided by MGI
Official Full Name: leucine rich repeat containing 4Cprovided by MGI
Primary source: MGI:MGI:2442636
See related: Ensembl:ENSMUSG00000050587 AllianceGenome:MGI:2442636
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: NGL-1; 6430556C10Rik
Summary: Predicted to enable cell-cell adhesion mediator activity. Involved in modulation of chemical synaptic transmission and synaptic membrane adhesion. Is active in Schaffer collateral - CA1 synapse; glutamatergic synapse; and postsynaptic density membrane. Is expressed in central nervous system and eye. Orthologous to human LRRC4C (leucine rich repeat containing 4C). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in cortex adult (RPKM 4.7), frontal lobe adult (RPKM 3.8) and 8 other tissues See more
Orthologs: human all
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Genomic context

Location:: 2 E1; 2 52.3 cM

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	2	NC_000068.8 (96148514..97466871)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	2	NC_000068.7 (96318169..97631672)

Chromosome 2 - NC_000068.8 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?

Axonal NGL-1 transneuronally determines lamina-specific subdendritic segments.
Title: Axonal netrin-Gs transneuronally determine lamina-specific subdendritic segments.
NGL-1 is most abundant in the striatum and the cerebral cortex--the intermediate and final targets, of thalamocortical axons; surface-bound NGL-1 stimulates, but soluble NGL-1 disrupts, the growth of embryonic thalamic axons.
Title: Editorial: Allan Guttmacher, M.D.--a life fulfilled.

Submit: New GeneRIF Correction

Variation

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Alleles

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

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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

48.MMHAP64FLH6.seq (e-PCR)
- UniSTS:158987

D2Mit130 (e-PCR), detects polymorphism
- UniSTS:128990

Lrrc4c (e-PCR), detects polymorphism
- UniSTS:525559

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables cell adhesion molecule binding	ISO Inferred from Sequence Orthology more info
enables cell-cell adhesion mediator activity	IBA Inferred from Biological aspect of Ancestor more info
enables cell-cell adhesion mediator activity	IEA Inferred from Electronic Annotation more info
enables cell-cell adhesion mediator activity	ISO Inferred from Sequence Orthology more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in modulation of chemical synaptic transmission	IBA Inferred from Biological aspect of Ancestor more info
involved_in modulation of chemical synaptic transmission	IDA Inferred from Direct Assay more info	PubMed
involved_in modulation of chemical synaptic transmission	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of axonogenesis	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of axonogenesis	ISO Inferred from Sequence Orthology more info
involved_in regulation of axonogenesis	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in synaptic membrane adhesion	IBA Inferred from Biological aspect of Ancestor more info
involved_in synaptic membrane adhesion	IDA Inferred from Direct Assay more info	PubMed
involved_in synaptic membrane adhesion	IEP Inferred from Expression Pattern more info	PubMed
involved_in synaptic membrane adhesion	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in synaptic membrane adhesion	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
is_active_in Schaffer collateral - CA1 synapse	IDA Inferred from Direct Assay more info	PubMed
is_active_in glutamatergic synapse	IBA Inferred from Biological aspect of Ancestor more info
is_active_in glutamatergic synapse	IDA Inferred from Direct Assay more info	PubMed
is_active_in glutamatergic synapse	IEP Inferred from Expression Pattern more info	PubMed
is_active_in glutamatergic synapse	IMP Inferred from Mutant Phenotype more info	PubMed
located_in membrane	ISO Inferred from Sequence Orthology more info
located_in membrane	ISS Inferred from Sequence or Structural Similarity more info	PubMed
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
is_active_in postsynaptic density membrane	IBA Inferred from Biological aspect of Ancestor more info
is_active_in postsynaptic density membrane	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: leucine-rich repeat-containing protein 4C

Names: netrin-G1 ligand

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_001289742.1 → NP_001276671.1 leucine-rich repeat-containing protein 4C precursor

See identical proteins and their annotated locations for NP_001276671.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) differs in the 5' UTR compared to variant 5. All seven variants encode the same protein.

Source sequence(s)

AK034276, AK048322, AV345568, BY626397

Consensus CDS

CCDS16460.1

UniProtKB/Swiss-Prot

Q505E5, Q8BGH8, Q8C031

Related

ENSMUSP00000125218.3, ENSMUST00000162807.9

Conserved Domains (6) summary

smart00013
Location:47 → 80

LRRNT; Leucine rich repeat N-terminal domain

smart00082
Location:301 → 339

LRRCT; Leucine rich repeat C-terminal domain

smart00409
Location:360 → 443

IG; Immunoglobulin

sd00033
Location:78 → 101

LRR_RI; leucine-rich repeat [structural motif]

pfam13855
Location:220 → 279

LRR_8; Leucine rich repeat

cd21340
Location:65 → 235

PPP1R42; protein phosphatase 1 regulatory subunit 42
NM_001289743.1 → NP_001276672.1 leucine-rich repeat-containing protein 4C precursor

See identical proteins and their annotated locations for NP_001276672.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 5. All seven variants encode the same protein.

Source sequence(s)

AK034276, AV345568

Consensus CDS

CCDS16460.1

UniProtKB/Swiss-Prot

Q505E5, Q8BGH8, Q8C031

Related

ENSMUSP00000130984.2, ENSMUST00000135431.8

Conserved Domains (6) summary

smart00013
Location:47 → 80

LRRNT; Leucine rich repeat N-terminal domain

smart00082
Location:301 → 339

LRRCT; Leucine rich repeat C-terminal domain

smart00409
Location:360 → 443

IG; Immunoglobulin

sd00033
Location:78 → 101

LRR_RI; leucine-rich repeat [structural motif]

pfam13855
Location:220 → 279

LRR_8; Leucine rich repeat

cd21340
Location:65 → 235

PPP1R42; protein phosphatase 1 regulatory subunit 42
NM_001289744.1 → NP_001276673.1 leucine-rich repeat-containing protein 4C precursor

See identical proteins and their annotated locations for NP_001276673.1

Status: VALIDATED

Description

Transcript Variant: This variant (4) differs in the 5' UTR compared to variant 5. All seven variants encode the same protein.

Source sequence(s)

AK032467, AK034276, AV345568, BC094588, BY286924

Consensus CDS

CCDS16460.1

UniProtKB/Swiss-Prot

Q505E5, Q8BGH8, Q8C031

Conserved Domains (6) summary

smart00013
Location:47 → 80

LRRNT; Leucine rich repeat N-terminal domain

smart00082
Location:301 → 339

LRRCT; Leucine rich repeat C-terminal domain

smart00409
Location:360 → 443

IG; Immunoglobulin

sd00033
Location:78 → 101

LRR_RI; leucine-rich repeat [structural motif]

pfam13855
Location:220 → 279

LRR_8; Leucine rich repeat

cd21340
Location:65 → 235

PPP1R42; protein phosphatase 1 regulatory subunit 42
NM_001363047.1 → NP_001349976.1 leucine-rich repeat-containing protein 4C precursor

Status: VALIDATED

Description

Transcript Variant: This variant (5) represents the longest transcript. All seven variants encode the same protein.

Source sequence(s)

AL672273, AL672307, AL732507, AL844145, AL845319, BX813336

Consensus CDS

CCDS16460.1

UniProtKB/Swiss-Prot

Q505E5, Q8BGH8, Q8C031

Conserved Domains (6) summary

smart00013
Location:47 → 80

LRRNT; Leucine rich repeat N-terminal domain

smart00082
Location:301 → 339

LRRCT; Leucine rich repeat C-terminal domain

smart00409
Location:360 → 443

IG; Immunoglobulin

sd00033
Location:78 → 101

LRR_RI; leucine-rich repeat [structural motif]

pfam13855
Location:220 → 279

LRR_8; Leucine rich repeat

cd21340
Location:65 → 235

PPP1R42; protein phosphatase 1 regulatory subunit 42
NM_001363048.1 → NP_001349977.1 leucine-rich repeat-containing protein 4C precursor

Status: VALIDATED

Description

Transcript Variant: This variant (6) differs in the 5' UTR compared to variant 5. All seven variants encode the same protein.

Source sequence(s)

AL672273, AL672307, AL732507, AL844145, AL845319, BX813336

Consensus CDS

CCDS16460.1

UniProtKB/Swiss-Prot

Q505E5, Q8BGH8, Q8C031

Conserved Domains (6) summary

smart00013
Location:47 → 80

LRRNT; Leucine rich repeat N-terminal domain

smart00082
Location:301 → 339

LRRCT; Leucine rich repeat C-terminal domain

smart00409
Location:360 → 443

IG; Immunoglobulin

sd00033
Location:78 → 101

LRR_RI; leucine-rich repeat [structural motif]

pfam13855
Location:220 → 279

LRR_8; Leucine rich repeat

cd21340
Location:65 → 235

PPP1R42; protein phosphatase 1 regulatory subunit 42
NM_001363049.1 → NP_001349978.1 leucine-rich repeat-containing protein 4C precursor

Status: VALIDATED

Description

Transcript Variant: This variant (7) differs in the 5' UTR compared to variant 5. All seven variants encode the same protein.

Source sequence(s)

AL844145, BX813336

Consensus CDS

CCDS16460.1

UniProtKB/Swiss-Prot

Q505E5, Q8BGH8, Q8C031

Conserved Domains (6) summary

smart00013
Location:47 → 80

LRRNT; Leucine rich repeat N-terminal domain

smart00082
Location:301 → 339

LRRCT; Leucine rich repeat C-terminal domain

smart00409
Location:360 → 443

IG; Immunoglobulin

sd00033
Location:78 → 101

LRR_RI; leucine-rich repeat [structural motif]

pfam13855
Location:220 → 279

LRR_8; Leucine rich repeat

cd21340
Location:65 → 235

PPP1R42; protein phosphatase 1 regulatory subunit 42
NM_178725.6 → NP_848840.3 leucine-rich repeat-containing protein 4C precursor

See identical proteins and their annotated locations for NP_848840.3

Status: VALIDATED

Description

Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 5. All seven variants encode the same protein.

Source sequence(s)

AK032467, AV345568, BC094588, BY626397

Consensus CDS

CCDS16460.1

UniProtKB/Swiss-Prot

Q505E5, Q8BGH8, Q8C031

Related

ENSMUSP00000131795.2, ENSMUST00000059049.8

Conserved Domains (6) summary

smart00013
Location:47 → 80

LRRNT; Leucine rich repeat N-terminal domain

smart00082
Location:301 → 339

LRRCT; Leucine rich repeat C-terminal domain

smart00409
Location:360 → 443

IG; Immunoglobulin

sd00033
Location:78 → 101

LRR_RI; leucine-rich repeat [structural motif]

pfam13855
Location:220 → 279

LRR_8; Leucine rich repeat

cd21340
Location:65 → 235

PPP1R42; protein phosphatase 1 regulatory subunit 42

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_000068.8 Reference GRCm39 C57BL/6J

Range

96148514..97466871

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_036161910.1 → XP_036017803.1 leucine-rich repeat-containing protein 4C isoform X1

UniProtKB/Swiss-Prot

Q505E5, Q8BGH8, Q8C031

Conserved Domains (6) summary

smart00013
Location:47 → 80

LRRNT; Leucine rich repeat N-terminal domain

smart00082
Location:301 → 339

LRRCT; Leucine rich repeat C-terminal domain

smart00409
Location:360 → 443

IG; Immunoglobulin

sd00033
Location:78 → 101

LRR_RI; leucine-rich repeat [structural motif]

pfam13855
Location:220 → 279

LRR_8; Leucine rich repeat

cd21340
Location:65 → 235

PPP1R42; protein phosphatase 1 regulatory subunit 42
XM_036161912.1 → XP_036017805.1 leucine-rich repeat-containing protein 4C isoform X1

UniProtKB/Swiss-Prot

Q505E5, Q8BGH8, Q8C031

Conserved Domains (6) summary

smart00013
Location:47 → 80

LRRNT; Leucine rich repeat N-terminal domain

smart00082
Location:301 → 339

LRRCT; Leucine rich repeat C-terminal domain

smart00409
Location:360 → 443

IG; Immunoglobulin

sd00033
Location:78 → 101

LRR_RI; leucine-rich repeat [structural motif]

pfam13855
Location:220 → 279

LRR_8; Leucine rich repeat

cd21340
Location:65 → 235

PPP1R42; protein phosphatase 1 regulatory subunit 42