Human Gene LRRTM4 (ENST00000409884.6_9) from GENCODE V47lift37
  Description: leucine rich repeat transmembrane neuronal 4, transcript variant 3 (from RefSeq NM_001282924.3)
Gencode Transcript: ENST00000409884.6_9
Gencode Gene: ENSG00000176204.14_14
Transcript (Including UTRs)
   Position: hg19 chr2:76,974,811-77,749,502 Size: 774,692 Total Exon Count: 4 Strand: -
Coding Region
   Position: hg19 chr2:76,975,821-77,748,797 Size: 772,977 Coding Exon Count: 3 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:76,974,811-77,749,502)mRNA (may differ from genome)Protein (590 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsHGNC
MGIOMIMPubMedReactomeUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: LRRT4_HUMAN
DESCRIPTION: RecName: Full=Leucine-rich repeat transmembrane neuronal protein 4; Flags: Precursor;
FUNCTION: May play a role in the development and maintenance of the vertebrate nervous system. Exhibits strong synaptogenic activity, restricted to excitatory presynaptic differentiation (By similarity).
SUBCELLULAR LOCATION: Cell membrane; Single-pass type I membrane protein (By similarity). Cell junction, synapse, postsynaptic cell membrane; Single-pass type I membrane protein (By similarity).
TISSUE SPECIFICITY: Expressed in neuronal tissues.
SIMILARITY: Belongs to the LRRTM family.
SIMILARITY: Contains 10 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


-  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: 3.40 RPKM in Brain - Frontal Cortex (BA9)
Total median expression: 20.21 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 -104.40415-0.252 Picture PostScript Text
3' UTR -255.301010-0.253 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
IPR001611 - Leu-rich_rpt
IPR003591 - Leu-rich_rpt_typical-subtyp
IPR000372 - LRR-contain_N

Pfam Domains:
PF00560 - Leucine Rich Repeat
PF12799 - Leucine Rich repeats (2 copies)
PF13306 - BspA type Leucine rich repeat region (6 copies)
PF13855 - Leucine rich repeat

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

ModBase Predicted Comparative 3D Structure on Q86VH4
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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    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004860 protein kinase inhibitor activity

Biological Process:
GO:0006469 negative regulation of protein kinase activity
GO:0019221 cytokine-mediated signaling pathway
GO:0046426 negative regulation of JAK-STAT cascade

Cellular Component:
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
  AK122612 - Homo sapiens cDNA FLJ16022 fis, clone BRAMY2019300, highly similar to Leucine-rich repeat transmembrane neuronalprotein 4 precursor.
AY358324 - Homo sapiens clone DNA142392 GFHL3075 (UNQ3075) mRNA, complete cds.
AK126961 - Homo sapiens cDNA FLJ45014 fis, clone BRAWH3014609.
AK022630 - Homo sapiens cDNA FLJ12568 fis, clone NT2RM4000857, weakly similar to LEUCINE-RICH ALPHA-2-GLYCOPROTEIN.
BC017769 - Homo sapiens leucine rich repeat transmembrane neuronal 4, mRNA (cDNA clone IMAGE:4283863), complete cds.
BC098267 - Homo sapiens leucine rich repeat transmembrane neuronal 4, mRNA (cDNA clone MGC:120634 IMAGE:40026833), complete cds.
BC098301 - Homo sapiens leucine rich repeat transmembrane neuronal 4, mRNA (cDNA clone MGC:120635 IMAGE:40026836), complete cds.
BC099738 - Homo sapiens leucine rich repeat transmembrane neuronal 4, mRNA (cDNA clone MGC:120636 IMAGE:40026837), complete cds.
BC110058 - Homo sapiens leucine rich repeat transmembrane neuronal 4, mRNA (cDNA clone MGC:120633 IMAGE:40026832), complete cds.
AY182030 - Homo sapiens leucine-rich repeat transmembrane neuronal 4 protein mRNA, complete cds.
CU676050 - Synthetic construct Homo sapiens gateway clone IMAGE:100022107 5' read LRRTM4 mRNA.
KJ903273 - Synthetic construct Homo sapiens clone ccsbBroadEn_12667 LRRTM4 gene, encodes complete protein.
KJ901074 - Synthetic construct Homo sapiens clone ccsbBroadEn_10468 LRRTM4 gene, encodes complete protein.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q86VH4 (Reactome details) participates in the following event(s):

R-HSA-6797974 LRRTMs bind NRXNs
R-HSA-6794361 Neurexins and neuroligins
R-HSA-6794362 Protein-protein interactions at synapses
R-HSA-112316 Neuronal System

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000409884.1, ENST00000409884.2, ENST00000409884.3, ENST00000409884.4, ENST00000409884.5, LRRT4_HUMAN, NM_001282924, Q4FZ98, Q6UXJ7, Q86VH4, uc319ghk.1, uc319ghk.2, UNQ3075/PRO9907
UCSC ID: ENST00000409884.6_9
RefSeq Accession: NM_001134745.3
Protein: Q86VH4 (aka LRRT4_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.