Human Gene LRRC4C (uc031pzu.1) Description and Page Index
  Description: Homo sapiens leucine rich repeat containing 4C (LRRC4C), transcript variant 1, mRNA.
RefSeq Summary (NM_020929): 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].
Transcript (Including UTRs)
   Position: hg19 chr11:40,135,751-41,481,186 Size: 1,345,436 Total Exon Count: 5 Strand: -
Coding Region
   Position: hg19 chr11:40,135,920-40,137,842 Size: 1,923 Coding Exon Count: 1 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr11:40,135,751-41,481,186)mRNA (may differ from genome)Protein (640 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedStanford SOURCEUniProtKB

-  Comments and Description Text from UniProtKB
  ID: LRC4C_HUMAN
DESCRIPTION: RecName: Full=Leucine-rich repeat-containing protein 4C; AltName: Full=Netrin-G1 ligand; Short=NGL-1; Flags: Precursor;
FUNCTION: May promote neurite outgrowth of developing thalamic neurons.
SUBUNIT: Interacts with NTNG1 and WHRN.
SUBCELLULAR LOCATION: Membrane; Single-pass type I membrane protein.
TISSUE SPECIFICITY: Highly expressed in the cerebral cortex, including frontal, parietal and occipital lobes. Putamen, amygdala, hippocampus and medulla oblongata show moderate expression. Caudate nucleus and thalamus express small amounts, whereas other brain regions show very weak or no expression.
DOMAIN: The LRR region is both necessary and sufficient for the interaction with NTNG1.
SIMILARITY: Contains 1 Ig-like C2-type (immunoglobulin-like) domain.
SIMILARITY: Contains 9 LRR (leucine-rich) repeats.
SIMILARITY: Contains 1 LRRCT domain.
SIMILARITY: Contains 1 LRRNT domain.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): LRRC4C
CDC HuGE Published Literature: LRRC4C
Positive Disease Associations: Albuminuria , Asthma , Body Height , Cholesterol, LDL , Fibrinogen , Hip , Insulin , Insulin Resistance , Intuition , Lipoproteins, VLDL , Magnesium , Mental Competency , Sleep , Tunica Media
Related Studies:
  1. Albuminuria
    Shih-Jen Hwang et al. BMC medical genetics 2007, A genome-wide association for kidney function and endocrine-related traits in the NHLBI's Framingham Heart Study., BMC medical genetics. [PubMed 17903292]
    Kidney function traits and TSH are associated with SNPs on the Affymetrix GeneChip Human Mapping 100K SNP set. These data will serve as a valuable resource for replication as more SNPs associated with kidney function and endocrine traits are identified.
  2. Asthma
    , , . [PubMed 0]
  3. Body Height
    , , . [PubMed 0]
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: LRRC4C
Diseases sorted by gene-association score: chief cell adenoma (16), extragonadal seminoma (16)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 6.39 RPKM in Brain - Frontal Cortex (BA9)
Total median expression: 60.60 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -126.24532-0.237 Picture PostScript Text
3' UTR -14.60169-0.086 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR000483 - Cys-rich_flank_reg_C
IPR007110 - Ig-like
IPR013783 - Ig-like_fold
IPR013098 - Ig_I-set
IPR003598 - Ig_sub2
IPR001611 - Leu-rich_rpt
IPR003591 - Leu-rich_rpt_typical-subtyp
IPR000372 - LRR-contain_N

Pfam Domains:
PF00047 - Immunoglobulin domain
PF00560 - Leucine Rich Repeat
PF07679 - Immunoglobulin I-set domain
PF07686 - Immunoglobulin V-set domain
PF12799 - Leucine Rich repeats (2 copies)
PF13306 - Leucine rich repeats (6 copies)
PF13855 - Leucine rich repeat
PF13895 - Immunoglobulin domain
PF13927 - Immunoglobulin domain

SCOP Domains:
48726 - Immunoglobulin
52047 - RNI-like
52058 - L domain-like
52075 - Outer arm dynein light chain 1

Protein Data Bank (PDB) 3-D Structure
MuPIT help

3ZYJ
- X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q9HCJ2
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
      
      
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004860 protein kinase inhibitor activity
GO:0005515 protein binding
GO:0050839 cell adhesion molecule binding
GO:0098632 protein binding involved in cell-cell adhesion

Biological Process:
GO:0006469 negative regulation of protein kinase activity
GO:0019221 cytokine-mediated signaling pathway
GO:0046426 negative regulation of JAK-STAT cascade
GO:0050770 regulation of axonogenesis
GO:0099560 synaptic membrane adhesion

Cellular Component:
GO:0005615 extracellular space
GO:0005737 cytoplasm
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0030054 cell junction
GO:0045202 synapse
GO:0045211 postsynaptic membrane


-  Descriptions from all associated GenBank mRNAs
  DQ084201 - Homo sapiens netrin-G1 ligand splice variant 3 (NGL1) mRNA, complete cds, alternatively spliced.
DQ084202 - Homo sapiens netrin-G1 ligand splice variant 4 (NGL1) mRNA, complete cds, alternatively spliced.
AY358293 - Homo sapiens clone DNA40981 LNKM292 (UNQ292) mRNA, complete cds.
AB046800 - Homo sapiens KIAA1580 mRNA for KIAA1580 protein.
BC041374 - Homo sapiens leucine rich repeat containing 4C, mRNA (cDNA clone MGC:43884 IMAGE:5274422), complete cds.
AK289646 - Homo sapiens cDNA FLJ75991 complete cds, highly similar to Homo sapiens leucine rich repeat containing 4C (LRRC4C), mRNA.
JD363460 - Sequence 344484 from Patent EP1572962.
KJ901069 - Synthetic construct Homo sapiens clone ccsbBroadEn_10463 LRRC4C gene, encodes complete protein.
AB384241 - Synthetic construct DNA, clone: pF1KSDA1580, Homo sapiens LRRC4C gene for leucine-rich repeat-containing protein 4C, complete cds, without stop codon, in Flexi system.
CU691990 - Synthetic construct Homo sapiens gateway clone IMAGE:100020985 5' read LRRC4C mRNA.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04360 - Axon guidance

-  Other Names for This Gene
  Alternate Gene Symbols: A8K0T1, KIAA1580, LRC4C_HUMAN, NGL1, NM_020929, NP_065980, Q7L0N3, Q9HCJ2, uc001mxc.1, UNQ292/PRO331
UCSC ID: uc031pzu.1
RefSeq Accession: NM_020929
Protein: Q9HCJ2 (aka LRC4C_HUMAN)
CCDS: CCDS31464.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_020929.2
exon count: 5CDS single in 3' UTR: no RNA size: 2626
ORF size: 1923CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3927.50frame shift in genome: no % Coverage: 99.92
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.