Human Gene LRRC4 (ENST00000249363.4_7) from GENCODE V47lift37
  Description: leucine rich repeat containing 4 (from RefSeq NM_022143.5)
Gencode Transcript: ENST00000249363.4_7
Gencode Gene: ENSG00000128594.8_13
Transcript (Including UTRs)
   Position: hg19 chr7:127,667,124-127,671,490 Size: 4,367 Total Exon Count: 2 Strand: -
Coding Region
   Position: hg19 chr7:127,668,732-127,670,693 Size: 1,962 Coding Exon Count: 1 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr7:127,667,124-127,671,490)mRNA (may differ from genome)Protein (653 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: LRRC4_HUMAN
DESCRIPTION: RecName: Full=Leucine-rich repeat-containing protein 4; AltName: Full=Brain tumor-associated protein BAG; AltName: Full=Nasopharyngeal carcinoma-associated gene 14 protein; AltName: Full=Netrin-G2 ligand; Short=NGL-2; Flags: Precursor;
FUNCTION: Synaptic adhesion protein. Regulates the formation of exitatory synapses through the recruitment of pre-and-postsynaptic proteins. Organize the lamina/pathway-specific differentiation of dendrites. Plays a important role for auditory synaptic responses. Involved in the suppression of glioma (By similarity).
SUBUNIT: Interacts with NTNG2 (By similarity). Interacts with DLG4 (By similarity). Forms a complex with DLG4 and with NMDA receptors.
SUBCELLULAR LOCATION: Membrane; Single-pass type I membrane protein. Cell junction, synapse, postsynaptic cell membrane (By similarity). Note=LRRC4 and DLG4 are interdependent for synaptic localization (By similarity).
TISSUE SPECIFICITY: Specifically expressed in brain.
DOMAIN: The last 4 C-terminal residues bind to the first 2 PDZ domains of DLG4 (By similarity).
PTM: N-glycosylated (By similarity).
SIMILARITY: Contains 1 Ig-like (immunoglobulin-like) domain.
SIMILARITY: Contains 9 LRR (leucine-rich) repeats.
SIMILARITY: Contains 1 LRRCT domain.
SIMILARITY: Contains 1 LRRNT domain.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: LRRC4
Diseases sorted by gene-association score: nasopharyngitis (6), nasopharyngeal disease (5)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  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: 23.13 RPKM in Brain - Cortex
Total median expression: 186.79 RPKM



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

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -283.30625-0.453 Picture PostScript Text
3' UTR -464.701608-0.289 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:
PF00560 - Leucine Rich Repeat
PF07679 - Immunoglobulin I-set domain
PF13306 - BspA type Leucine rich repeat region (6 copies)
PF13855 - Leucine rich repeat
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
2DL9 - NMR MuPIT 3ZYI - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q9HBW1
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 DetailsGene Details    
Gene SorterGene Sorter    
 RGDEnsembl   
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004860 protein kinase inhibitor activity
GO:0005515 protein binding

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:0050807 regulation of synapse organization
GO:0050808 synapse organization
GO:0097119 postsynaptic density protein 95 clustering

Cellular Component:
GO:0005737 cytoplasm
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0030054 cell junction
GO:0043197 dendritic spine
GO:0044309 neuron spine
GO:0045202 synapse
GO:0045211 postsynaptic membrane
GO:0060076 excitatory synapse


-  Descriptions from all associated GenBank mRNAs
  LF207054 - JP 2014500723-A/14557: Polycomb-Associated Non-Coding RNAs.
AF196976 - Homo sapiens brain tumor associated protein LRRC4 (LRRC4) mRNA, complete cds.
BC036685 - Homo sapiens leucine rich repeat containing 4, mRNA (cDNA clone IMAGE:5259284).
JD485884 - Sequence 466908 from Patent EP1572962.
JD328564 - Sequence 309588 from Patent EP1572962.
JD372874 - Sequence 353898 from Patent EP1572962.
BC111561 - Homo sapiens leucine rich repeat containing 4, mRNA (cDNA clone MGC:133342 IMAGE:40068142), complete cds.
BC111745 - Homo sapiens leucine rich repeat containing 4, mRNA (cDNA clone MGC:133343 IMAGE:40068146), complete cds.
JD210332 - Sequence 191356 from Patent EP1572962.
JD155281 - Sequence 136305 from Patent EP1572962.
JD176726 - Sequence 157750 from Patent EP1572962.
JD495255 - Sequence 476279 from Patent EP1572962.
JD332074 - Sequence 313098 from Patent EP1572962.
JD434006 - Sequence 415030 from Patent EP1572962.
LF360795 - JP 2014500723-A/168298: Polycomb-Associated Non-Coding RNAs.
JD311094 - Sequence 292118 from Patent EP1572962.
JD045997 - Sequence 27021 from Patent EP1572962.
JD236305 - Sequence 217329 from Patent EP1572962.
JD174309 - Sequence 155333 from Patent EP1572962.
JD516490 - Sequence 497514 from Patent EP1572962.
JD230246 - Sequence 211270 from Patent EP1572962.
JD223314 - Sequence 204338 from Patent EP1572962.
JD490215 - Sequence 471239 from Patent EP1572962.
JD316692 - Sequence 297716 from Patent EP1572962.
JD536944 - Sequence 517968 from Patent EP1572962.
JD293822 - Sequence 274846 from Patent EP1572962.
JD050709 - Sequence 31733 from Patent EP1572962.
AK172751 - Homo sapiens cDNA FLJ23912 fis, clone CAE04210, highly similar to Homo sapiens leucine rich repeat containing 4 (LRRC4).
JD307667 - Sequence 288691 from Patent EP1572962.
AJ297858 - Homo sapiens mRNA for hypothetical protein (BAG gene).
AY358307 - Homo sapiens clone DNA58721 NAG14 (UNQ554) mRNA, complete cds.
JD483948 - Sequence 464972 from Patent EP1572962.
AK314047 - Homo sapiens cDNA, FLJ94710, Homo sapiens NAG14 protein (NAG14), mRNA.
KJ894529 - Synthetic construct Homo sapiens clone ccsbBroadEn_03923 LRRC4 gene, encodes complete protein.
AB587377 - Synthetic construct DNA, clone: pF1KB5045, Homo sapiens LRRC4 gene for leucine rich repeat containing 4, without stop codon, in Flexi system.
LF212009 - JP 2014500723-A/19512: Polycomb-Associated Non-Coding RNAs.
DQ575484 - Homo sapiens piRNA piR-43596, complete sequence.
DQ583425 - Homo sapiens piRNA piR-50537, complete sequence.
JD139483 - Sequence 120507 from Patent EP1572962.
JD469879 - Sequence 450903 from Patent EP1572962.
MA442631 - JP 2018138019-A/14557: Polycomb-Associated Non-Coding RNAs.
MA596372 - JP 2018138019-A/168298: Polycomb-Associated Non-Coding RNAs.
MA447586 - JP 2018138019-A/19512: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: A4D0Y9, BAG, ENST00000249363.1, ENST00000249363.2, ENST00000249363.3, LRRC4_HUMAN, NAG14, NM_022143, Q14DU9, Q6ZMI8, Q96A85, Q9HBW1, uc317ezk.1, uc317ezk.2, UNQ554/PRO1111
UCSC ID: ENST00000249363.4_7
RefSeq Accession: NM_022143.5
Protein: Q9HBW1 (aka LRRC4_HUMAN or LRR4_HUMAN)

-  Gene Model Information
  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.