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

    Gene ID: 241568, updated on 27-Nov-2024

    Summary

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    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

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    See Lrrc4c in Genome Data Viewer
    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_000068.8Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_05189 Neighboring gene AXL receptor tyrosine kinase pseudogene Neighboring gene predicted gene 13799 Neighboring gene STARR-seq mESC enhancer starr_05191 Neighboring gene STARR-seq mESC enhancer starr_05192 Neighboring gene STARR-seq mESC enhancer starr_05193 Neighboring gene STARR-seq mESC enhancer starr_05194 Neighboring gene STARR-seq mESC enhancer starr_05196 Neighboring gene sorting nexin 25 pseudogene Neighboring gene ribosomal RNA processing 8, methyltransferase, homolog pseudogene Neighboring gene predicted gene, 22313 Neighboring gene predicted gene, 54117 Neighboring gene STARR-seq mESC enhancer starr_05199 Neighboring gene STARR-seq mESC enhancer starr_05200 Neighboring gene STARR-seq mESC enhancer starr_05202 Neighboring gene STARR-seq mESC enhancer starr_05203 Neighboring gene corepressor interacting with RBPJ, 1 pseudogene Neighboring gene STARR-seq mESC enhancer starr_05204 Neighboring gene 60S ribosomal protein L27a-like

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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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    Related articles in PubMed

    1. Editorial: Allan Guttmacher, M.D.--a life fulfilled. Sturgis SH. N Engl J Med, 1974 May 9. PMID 4595443
    2. NGL-1/LRRC4C Deletion Moderately Suppresses Hippocampal Excitatory Synapse Development and Function in an Input-Independent Manner. Choi Y, et al. Front Mol Neurosci, 2019. PMID 31156385, Free PMC Article
    3. NGL-3 in the regulation of brain development, Akt/GSK3b signaling, long-term depression, and locomotive and cognitive behaviors. Lee H, et al. PLoS Biol, 2019 Jun. PMID 31166939, Free PMC Article
    4. The maternal microbiome modulates fetal neurodevelopment in mice. Vuong HE, et al. Nature, 2020 Oct. PMID 32968276, Free PMC Article
    5. Axonal netrin-Gs transneuronally determine lamina-specific subdendritic segments. Nishimura-Akiyoshi S, et al. Proc Natl Acad Sci U S A, 2007 Sep 11. PMID 17785411, Free PMC Article

    See all (32) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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

    Homology

    Clone Names

    • KIAA1580

    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)

    1. 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

    2. 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

    3. 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

    4. 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

    5. 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

    6. 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

    7. 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

    1. NC_000068.8 Reference GRCm39 C57BL/6J

      Range
      96148514..97466871
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. 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

    2. 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
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8C031.2 GenPept UniProtKB/Swiss-Prot:Q8C031

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Other Literature Sources
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