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LRRC4C leucine rich repeat containing 4C [ Homo sapiens (human) ]

Gene ID: 57689, updated on 10-Oct-2019

Summary

Official Symbol
LRRC4Cprovided by HGNC
Official Full Name
leucine rich repeat containing 4Cprovided by HGNC
Primary source
HGNC:HGNC:29317
See related
Ensembl:ENSG00000148948 MIM:608817
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
NGL1; NGL-1
Summary
NGL1 is a specific binding partner for netrin G1 (NTNG1; MIM 608818), which is a member of the netrin family of axon guidance molecules (Lin et al., 2003 [PubMed 14595443]).[supplied by OMIM, Mar 2008]
Expression
Biased expression in brain (RPKM 5.3), adrenal (RPKM 0.7) and 1 other tissue See more
Orthologs

Genomic context

See LRRC4C in Genome Data Viewer
Location:
11p12
Exon count:
14
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) 11 NC_000011.10 (40107066..41460419, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (40135524..41481186, complement)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene adaptor related protein complex 5 mu 1 subunit pseudogene Neighboring gene zinc finger CCHC-type containing 9 pseudogene Neighboring gene zinc finger protein 12 pseudogene Neighboring gene RNA, U6 small nuclear 365, pseudogene Neighboring gene ribosomal protein L9 pseudogene 23 Neighboring gene long intergenic non-protein coding RNA 1499

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
An integration of genome-wide association study and gene expression profiling to prioritize the discovery of novel susceptibility Loci for osteoporosis-related traits.
NHGRI GWA Catalog
Genome wide association study (GWAS) of Chagas cardiomyopathy in Trypanosoma cruzi seropositive subjects.
NHGRI GWA Catalog
Genome-wide association study of temperament in bipolar disorder reveals significant associations with three novel Loci.
NHGRI GWA Catalog
Genome-wide pharmacogenomic study of neurocognition as an indicator of antipsychotic treatment response in schizophrenia.
NHGRI GWA Catalog
Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers.
NHGRI GWA Catalog

Pathways from BioSystems

  • Axon guidance, organism-specific biosystem (from KEGG)
    Axon guidance, organism-specific biosystemAxon guidance represents a key stage in the formation of neuronal network. Axons are guided by a variety of guidance factors, such as netrins, ephrins, Slits, and semaphorins. These guidance cues are...
  • Axon guidance, conserved biosystem (from KEGG)
    Axon guidance, conserved biosystemAxon guidance represents a key stage in the formation of neuronal network. Axons are guided by a variety of guidance factors, such as netrins, ephrins, Slits, and semaphorins. These guidance cues are...
  • Cell adhesion molecules (CAMs), organism-specific biosystem (from KEGG)
    Cell adhesion molecules (CAMs), organism-specific biosystemCell adhesion molecules are (glyco)proteins expressed on the cell surface and play a critical role in a wide array of biologic processes that include hemostasis, the immune response, inflammation, em...
  • Cell adhesion molecules (CAMs), conserved biosystem (from KEGG)
    Cell adhesion molecules (CAMs), conserved biosystemCell adhesion molecules are (glyco)proteins expressed on the cell surface and play a critical role in a wide array of biologic processes that include hemostasis, the immune response, inflammation, em...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • KIAA1580

Gene Ontology Provided by GOA

Function Evidence Code Pubs
cell adhesion molecule binding IPI
Inferred from Physical Interaction
more info
PubMed 
cell-cell adhesion mediator activity IGI
Inferred from Genetic Interaction
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
modulation of chemical synaptic transmission IEA
Inferred from Electronic Annotation
more info
 
regulation of axonogenesis IDA
Inferred from Direct Assay
more info
PubMed 
synaptic membrane adhesion IGI
Inferred from Genetic Interaction
more info
PubMed 
Component Evidence Code Pubs
Schaffer collateral - CA1 synapse IEA
Inferred from Electronic Annotation
more info
 
cell junction IEA
Inferred from Electronic Annotation
more info
 
extracellular space HDA PubMed 
glutamatergic synapse IEA
Inferred from Electronic Annotation
more info
 
integral component of membrane NAS
Non-traceable Author Statement
more info
PubMed 
integral component of postsynaptic density membrane IEA
Inferred from Electronic Annotation
more info
 
membrane IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
leucine-rich repeat-containing protein 4C
Names
netrin-G1 ligand

NCBI Reference Sequences (RefSeq)

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_001258419.2NP_001245348.1  leucine-rich repeat-containing protein 4C precursor

    See identical proteins and their annotated locations for NP_001245348.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 encode the same protein.
    Source sequence(s)
    AB046800, AC090138, BX951676, DQ084201, DQ084202
    Consensus CDS
    CCDS31464.1
    UniProtKB/Swiss-Prot
    Q9HCJ2
    UniProtKB/TrEMBL
    Q4JIV9, Q4JIW0
    Related
    ENSP00000437132.1, ENST00000528697.6
    Conserved Domains (5) summary
    smart00013
    Location:4780
    LRRNT; Leucine rich repeat N-terminal domain
    smart00082
    Location:301339
    LRRCT; Leucine rich repeat C-terminal domain
    smart00410
    Location:360443
    IG_like; Immunoglobulin like
    COG4886
    Location:77287
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    sd00033
    Location:78101
    LRR_RI; leucine-rich repeat [structural motif]
  2. NM_020929.2NP_065980.1  leucine-rich repeat-containing protein 4C precursor

    See identical proteins and their annotated locations for NP_065980.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the shortest transcript. Variants 1 and 2 encode the same protein.
    Source sequence(s)
    AB046800, AI806109, DA387604, DQ084201, DQ084202
    Consensus CDS
    CCDS31464.1
    UniProtKB/Swiss-Prot
    Q9HCJ2
    UniProtKB/TrEMBL
    Q4JIV9, Q4JIW0
    Related
    ENSP00000434761.1, ENST00000530763.5
    Conserved Domains (5) summary
    smart00013
    Location:4780
    LRRNT; Leucine rich repeat N-terminal domain
    smart00082
    Location:301339
    LRRCT; Leucine rich repeat C-terminal domain
    smart00410
    Location:360443
    IG_like; Immunoglobulin like
    COG4886
    Location:77287
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    sd00033
    Location:78101
    LRR_RI; leucine-rich repeat [structural motif]

RNA

  1. NR_047673.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) uses an alternate 5'-most exon compared to variant 1. This variant is represented as non-coding due to the presence of an upstream ORF that is predicted to interfere with translation of the longest ORF; translation of the upstream ORF renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AB046800, AI806109, AK289646, BC041374
  2. NR_047674.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) uses an alternate 5'-most exon compared to variant 1. This variant is represented as non-coding due to the presence of an upstream ORF that is predicted to interfere with translation of the longest ORF; translation of the upstream ORF renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AB046800, AI806109, AY358293, BC041374

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109.20190905

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p13 Primary Assembly

    Range
    40107066..41460419 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017018075.2XP_016873564.1  leucine-rich repeat-containing protein 4C isoform X1

    UniProtKB/Swiss-Prot
    Q9HCJ2
    Conserved Domains (5) summary
    smart00013
    Location:4780
    LRRNT; Leucine rich repeat N-terminal domain
    smart00082
    Location:301339
    LRRCT; Leucine rich repeat C-terminal domain
    smart00410
    Location:360443
    IG_like; Immunoglobulin like
    COG4886
    Location:77287
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    sd00033
    Location:78101
    LRR_RI; leucine-rich repeat [structural motif]
  2. XM_017018073.2XP_016873562.1  leucine-rich repeat-containing protein 4C isoform X1

    UniProtKB/Swiss-Prot
    Q9HCJ2
    Conserved Domains (5) summary
    smart00013
    Location:4780
    LRRNT; Leucine rich repeat N-terminal domain
    smart00082
    Location:301339
    LRRCT; Leucine rich repeat C-terminal domain
    smart00410
    Location:360443
    IG_like; Immunoglobulin like
    COG4886
    Location:77287
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    sd00033
    Location:78101
    LRR_RI; leucine-rich repeat [structural motif]
  3. XM_017018077.2XP_016873566.1  leucine-rich repeat-containing protein 4C isoform X1

    UniProtKB/Swiss-Prot
    Q9HCJ2
    Conserved Domains (5) summary
    smart00013
    Location:4780
    LRRNT; Leucine rich repeat N-terminal domain
    smart00082
    Location:301339
    LRRCT; Leucine rich repeat C-terminal domain
    smart00410
    Location:360443
    IG_like; Immunoglobulin like
    COG4886
    Location:77287
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    sd00033
    Location:78101
    LRR_RI; leucine-rich repeat [structural motif]
  4. XM_017018072.2XP_016873561.1  leucine-rich repeat-containing protein 4C isoform X1

    UniProtKB/Swiss-Prot
    Q9HCJ2
    Conserved Domains (5) summary
    smart00013
    Location:4780
    LRRNT; Leucine rich repeat N-terminal domain
    smart00082
    Location:301339
    LRRCT; Leucine rich repeat C-terminal domain
    smart00410
    Location:360443
    IG_like; Immunoglobulin like
    COG4886
    Location:77287
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    sd00033
    Location:78101
    LRR_RI; leucine-rich repeat [structural motif]
  5. XM_017018079.2XP_016873568.1  leucine-rich repeat-containing protein 4C isoform X1

    UniProtKB/Swiss-Prot
    Q9HCJ2
    Conserved Domains (5) summary
    smart00013
    Location:4780
    LRRNT; Leucine rich repeat N-terminal domain
    smart00082
    Location:301339
    LRRCT; Leucine rich repeat C-terminal domain
    smart00410
    Location:360443
    IG_like; Immunoglobulin like
    COG4886
    Location:77287
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    sd00033
    Location:78101
    LRR_RI; leucine-rich repeat [structural motif]
  6. XM_017018070.2XP_016873559.1  leucine-rich repeat-containing protein 4C isoform X1

    UniProtKB/Swiss-Prot
    Q9HCJ2
    Conserved Domains (5) summary
    smart00013
    Location:4780
    LRRNT; Leucine rich repeat N-terminal domain
    smart00082
    Location:301339
    LRRCT; Leucine rich repeat C-terminal domain
    smart00410
    Location:360443
    IG_like; Immunoglobulin like
    COG4886
    Location:77287
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    sd00033
    Location:78101
    LRR_RI; leucine-rich repeat [structural motif]
  7. XM_011520244.3XP_011518546.1  leucine-rich repeat-containing protein 4C isoform X1

    See identical proteins and their annotated locations for XP_011518546.1

    UniProtKB/Swiss-Prot
    Q9HCJ2
    Conserved Domains (5) summary
    smart00013
    Location:4780
    LRRNT; Leucine rich repeat N-terminal domain
    smart00082
    Location:301339
    LRRCT; Leucine rich repeat C-terminal domain
    smart00410
    Location:360443
    IG_like; Immunoglobulin like
    COG4886
    Location:77287
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    sd00033
    Location:78101
    LRR_RI; leucine-rich repeat [structural motif]
  8. XM_011520240.3XP_011518542.1  leucine-rich repeat-containing protein 4C isoform X1

    See identical proteins and their annotated locations for XP_011518542.1

    UniProtKB/Swiss-Prot
    Q9HCJ2
    Conserved Domains (5) summary
    smart00013
    Location:4780
    LRRNT; Leucine rich repeat N-terminal domain
    smart00082
    Location:301339
    LRRCT; Leucine rich repeat C-terminal domain
    smart00410
    Location:360443
    IG_like; Immunoglobulin like
    COG4886
    Location:77287
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    sd00033
    Location:78101
    LRR_RI; leucine-rich repeat [structural motif]
  9. XM_017018071.2XP_016873560.1  leucine-rich repeat-containing protein 4C isoform X1

    UniProtKB/Swiss-Prot
    Q9HCJ2
    Conserved Domains (5) summary
    smart00013
    Location:4780
    LRRNT; Leucine rich repeat N-terminal domain
    smart00082
    Location:301339
    LRRCT; Leucine rich repeat C-terminal domain
    smart00410
    Location:360443
    IG_like; Immunoglobulin like
    COG4886
    Location:77287
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    sd00033
    Location:78101
    LRR_RI; leucine-rich repeat [structural motif]
  10. XM_011520243.3XP_011518545.1  leucine-rich repeat-containing protein 4C isoform X1

    See identical proteins and their annotated locations for XP_011518545.1

    UniProtKB/Swiss-Prot
    Q9HCJ2
    Conserved Domains (5) summary
    smart00013
    Location:4780
    LRRNT; Leucine rich repeat N-terminal domain
    smart00082
    Location:301339
    LRRCT; Leucine rich repeat C-terminal domain
    smart00410
    Location:360443
    IG_like; Immunoglobulin like
    COG4886
    Location:77287
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    sd00033
    Location:78101
    LRR_RI; leucine-rich repeat [structural motif]
  11. XM_011520238.3XP_011518540.1  leucine-rich repeat-containing protein 4C isoform X1

    See identical proteins and their annotated locations for XP_011518540.1

    UniProtKB/Swiss-Prot
    Q9HCJ2
    Conserved Domains (5) summary
    smart00013
    Location:4780
    LRRNT; Leucine rich repeat N-terminal domain
    smart00082
    Location:301339
    LRRCT; Leucine rich repeat C-terminal domain
    smart00410
    Location:360443
    IG_like; Immunoglobulin like
    COG4886
    Location:77287
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    sd00033
    Location:78101
    LRR_RI; leucine-rich repeat [structural motif]
  12. XM_011520239.3XP_011518541.1  leucine-rich repeat-containing protein 4C isoform X1

    See identical proteins and their annotated locations for XP_011518541.1

    UniProtKB/Swiss-Prot
    Q9HCJ2
    Conserved Domains (5) summary
    smart00013
    Location:4780
    LRRNT; Leucine rich repeat N-terminal domain
    smart00082
    Location:301339
    LRRCT; Leucine rich repeat C-terminal domain
    smart00410
    Location:360443
    IG_like; Immunoglobulin like
    COG4886
    Location:77287
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    sd00033
    Location:78101
    LRR_RI; leucine-rich repeat [structural motif]
  13. XM_024448626.1XP_024304394.1  leucine-rich repeat-containing protein 4C isoform X1

    Conserved Domains (5) summary
    smart00013
    Location:4780
    LRRNT; Leucine rich repeat N-terminal domain
    smart00082
    Location:301339
    LRRCT; Leucine rich repeat C-terminal domain
    smart00410
    Location:360443
    IG_like; Immunoglobulin like
    COG4886
    Location:77287
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    sd00033
    Location:78101
    LRR_RI; leucine-rich repeat [structural motif]
  14. XM_024448627.1XP_024304395.1  leucine-rich repeat-containing protein 4C isoform X1

    Conserved Domains (5) summary
    smart00013
    Location:4780
    LRRNT; Leucine rich repeat N-terminal domain
    smart00082
    Location:301339
    LRRCT; Leucine rich repeat C-terminal domain
    smart00410
    Location:360443
    IG_like; Immunoglobulin like
    COG4886
    Location:77287
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    sd00033
    Location:78101
    LRR_RI; leucine-rich repeat [structural motif]
  15. XM_024448628.1XP_024304396.1  leucine-rich repeat-containing protein 4C isoform X1

    Conserved Domains (5) summary
    smart00013
    Location:4780
    LRRNT; Leucine rich repeat N-terminal domain
    smart00082
    Location:301339
    LRRCT; Leucine rich repeat C-terminal domain
    smart00410
    Location:360443
    IG_like; Immunoglobulin like
    COG4886
    Location:77287
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    sd00033
    Location:78101
    LRR_RI; leucine-rich repeat [structural motif]
  16. XM_011520242.3XP_011518544.1  leucine-rich repeat-containing protein 4C isoform X1

    See identical proteins and their annotated locations for XP_011518544.1

    UniProtKB/Swiss-Prot
    Q9HCJ2
    Conserved Domains (5) summary
    smart00013
    Location:4780
    LRRNT; Leucine rich repeat N-terminal domain
    smart00082
    Location:301339
    LRRCT; Leucine rich repeat C-terminal domain
    smart00410
    Location:360443
    IG_like; Immunoglobulin like
    COG4886
    Location:77287
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    sd00033
    Location:78101
    LRR_RI; leucine-rich repeat [structural motif]
  17. XM_017018076.2XP_016873565.1  leucine-rich repeat-containing protein 4C isoform X1

    UniProtKB/Swiss-Prot
    Q9HCJ2
    Related
    ENSP00000278198.1, ENST00000278198.2
    Conserved Domains (5) summary
    smart00013
    Location:4780
    LRRNT; Leucine rich repeat N-terminal domain
    smart00082
    Location:301339
    LRRCT; Leucine rich repeat C-terminal domain
    smart00410
    Location:360443
    IG_like; Immunoglobulin like
    COG4886
    Location:77287
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    sd00033
    Location:78101
    LRR_RI; leucine-rich repeat [structural motif]
  18. XM_011520241.3XP_011518543.1  leucine-rich repeat-containing protein 4C isoform X1

    See identical proteins and their annotated locations for XP_011518543.1

    UniProtKB/Swiss-Prot
    Q9HCJ2
    Conserved Domains (5) summary
    smart00013
    Location:4780
    LRRNT; Leucine rich repeat N-terminal domain
    smart00082
    Location:301339
    LRRCT; Leucine rich repeat C-terminal domain
    smart00410
    Location:360443
    IG_like; Immunoglobulin like
    COG4886
    Location:77287
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    sd00033
    Location:78101
    LRR_RI; leucine-rich repeat [structural motif]
  19. XM_017018078.2XP_016873567.1  leucine-rich repeat-containing protein 4C isoform X1

    UniProtKB/Swiss-Prot
    Q9HCJ2
    Conserved Domains (5) summary
    smart00013
    Location:4780
    LRRNT; Leucine rich repeat N-terminal domain
    smart00082
    Location:301339
    LRRCT; Leucine rich repeat C-terminal domain
    smart00410
    Location:360443
    IG_like; Immunoglobulin like
    COG4886
    Location:77287
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    sd00033
    Location:78101
    LRR_RI; leucine-rich repeat [structural motif]
  20. XM_017018074.2XP_016873563.1  leucine-rich repeat-containing protein 4C isoform X1

    UniProtKB/Swiss-Prot
    Q9HCJ2
    Related
    ENSP00000436976.1, ENST00000527150.5
    Conserved Domains (5) summary
    smart00013
    Location:4780
    LRRNT; Leucine rich repeat N-terminal domain
    smart00082
    Location:301339
    LRRCT; Leucine rich repeat C-terminal domain
    smart00410
    Location:360443
    IG_like; Immunoglobulin like
    COG4886
    Location:77287
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    sd00033
    Location:78101
    LRR_RI; leucine-rich repeat [structural motif]
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