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Aliases for LRRTM2 Gene

Aliases for LRRTM2 Gene

  • Leucine Rich Repeat Transmembrane Neuronal 2 2 3 5
  • Leucine-Rich Repeat Neuronal 2 Protein 4
  • KIAA0416 4
  • LRRN2 4

External Ids for LRRTM2 Gene

Previous GeneCards Identifiers for LRRTM2 Gene

  • GC05M138235
  • GC05M138281
  • GC05U900490
  • GC05M133394
  • GC05M138205

Summaries for LRRTM2 Gene

GeneCards Summary for LRRTM2 Gene

LRRTM2 (Leucine Rich Repeat Transmembrane Neuronal 2) is a Protein Coding gene. Among its related pathways are Transmission across Chemical Synapses and Protein-protein interactions at synapses. Gene Ontology (GO) annotations related to this gene include neurexin family protein binding. An important paralog of this gene is LRRTM1.

UniProtKB/Swiss-Prot for LRRTM2 Gene

  • Involved in the development and maintenance of excitatory synapse in the vertebrate nervous system. Regulates surface expression of AMPA receptors and instructs the development of functional glutamate release sites. Acts as a ligand for the presynaptic receptors NRXN1-A and NRXN1-B (By similarity).

Additional gene information for LRRTM2 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LRRTM2 Gene

Genomics for LRRTM2 Gene

GeneHancer (GH) Regulatory Elements for LRRTM2 Gene

Promoters and enhancers for LRRTM2 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH05I138873 Promoter/Enhancer 1.4 EPDnew Ensembl ENCODE 550.8 +0.5 505 2.7 MXI1 ATF1 ZBTB21 JUN ZSCAN4 ZNF2 ZNF324 ZNF335 GATA3 POLR2A LRRTM2 LOC105379194 GC05P138821 CTNNA1
GH05I138752 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 10.7 +121.3 121258 3.4 SMAD1 FOXA2 ARNT ARID4B NEUROD1 SIN3A DMAP1 ZNF2 ZBTB7B IRF4 LOC105379194 CTNNA1 MATR3 REEP2 DNAJC18 LRRTM2 HSPA9 GC05P138766
GH05I138335 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 10.6 +537.8 537828 5 CLOCK ZFP64 FEZF1 DMAP1 YBX1 IRF4 YY1 ZNF213 E2F8 ZNF143 CDC25C FAM53C HNRNPA0 KDM3B RPL7P19 CDC23 REEP2 MATR3 NME5 SPOCK1
GH05I138463 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 5 +410.1 410119 4.1 CLOCK IRF4 YY1 E2F8 ZNF143 SP3 SSRP1 ZNF610 ZNF585B GLIS1 EGR1 HNRNPA0 CDC23 KDM3B BRD8 RPL7P19 ETF1 FAM13B FAM53C REEP2
GH05I138449 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 7.3 +425.3 425308 1 HDGF ATF1 ARID4B SIN3A ZNF2 ZNF48 GLIS2 ZNF213 E2F8 ARID2 REEP2 LRRTM2 NME5 WNT8A ENSG00000271196 GC05P138442 GC05M138244
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around LRRTM2 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the LRRTM2 gene promoter:

Genomic Locations for LRRTM2 Gene

Genomic Locations for LRRTM2 Gene
chr5:138,868,923-138,875,368
(GRCh38/hg38)
Size:
6,446 bases
Orientation:
Minus strand
chr5:138,204,612-138,211,057
(GRCh37/hg19)

Genomic View for LRRTM2 Gene

Genes around LRRTM2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LRRTM2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LRRTM2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LRRTM2 Gene

Proteins for LRRTM2 Gene

  • Protein details for LRRTM2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O43300-LRRT2_HUMAN
    Recommended name:
    Leucine-rich repeat transmembrane neuronal protein 2
    Protein Accession:
    O43300
    Secondary Accessions:
    • A0AVL3
    • A8K4U9
    • B7ZLN8
    • Q7L770

    Protein attributes for LRRTM2 Gene

    Size:
    516 amino acids
    Molecular mass:
    59076 Da
    Quaternary structure:
    • Interacts with DLG4 and NRXN1.
    SequenceCaution:
    • Sequence=BAA24846.2; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

neXtProt entry for LRRTM2 Gene

Post-translational modifications for LRRTM2 Gene

  • Glycosylation at posLast=5757, isoforms=126, posLast=243243, and posLast=362362

Other Protein References for LRRTM2 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for LRRTM2 Gene

Domains & Families for LRRTM2 Gene

Gene Families for LRRTM2 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted membrane proteins
  • Predicted secreted proteins

Suggested Antigen Peptide Sequences for LRRTM2 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

O43300

UniProtKB/Swiss-Prot:

LRRT2_HUMAN :
  • Synaptogenic effects are mediated by the extracellular LRR region.
  • Belongs to the LRRTM family.
Domain:
  • Synaptogenic effects are mediated by the extracellular LRR region.
Family:
  • Belongs to the LRRTM family.
genes like me logo Genes that share domains with LRRTM2: view

Function for LRRTM2 Gene

Molecular function for LRRTM2 Gene

UniProtKB/Swiss-Prot Function:
Involved in the development and maintenance of excitatory synapse in the vertebrate nervous system. Regulates surface expression of AMPA receptors and instructs the development of functional glutamate release sites. Acts as a ligand for the presynaptic receptors NRXN1-A and NRXN1-B (By similarity).

Phenotypes From GWAS Catalog for LRRTM2 Gene

Gene Ontology (GO) - Molecular Function for LRRTM2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0042043 neurexin family protein binding IEA --
genes like me logo Genes that share ontologies with LRRTM2: view
genes like me logo Genes that share phenotypes with LRRTM2: view

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for LRRTM2 Gene

Localization for LRRTM2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LRRTM2 Gene

Cell membrane; Single-pass type I membrane protein. Cell junction, synapse, postsynaptic cell membrane; Single-pass type I membrane protein. Note=Localized to excitatory synapses. {ECO:0000250}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for LRRTM2 gene
Compartment Confidence
plasma membrane 4
peroxisome 2
extracellular 1
mitochondrion 1
endoplasmic reticulum 1
cytosol 1

Gene Ontology (GO) - Cellular Components for LRRTM2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0030054 cell junction IEA --
GO:0045202 synapse IEA --
genes like me logo Genes that share ontologies with LRRTM2: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for LRRTM2 Gene

Pathways & Interactions for LRRTM2 Gene

genes like me logo Genes that share pathways with LRRTM2: view

Pathways by source for LRRTM2 Gene

Gene Ontology (GO) - Biological Process for LRRTM2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002091 negative regulation of receptor internalization IEA --
GO:0050808 synapse organization IEA --
GO:0051965 positive regulation of synapse assembly IEA --
GO:0060291 long-term synaptic potentiation IEA --
genes like me logo Genes that share ontologies with LRRTM2: view

No data available for SIGNOR curated interactions for LRRTM2 Gene

Drugs & Compounds for LRRTM2 Gene

No Compound Related Data Available

Transcripts for LRRTM2 Gene

mRNA/cDNA for LRRTM2 Gene

(1) REFSEQ mRNAs :
(4) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for LRRTM2 Gene

No ASD Table

Relevant External Links for LRRTM2 Gene

GeneLoc Exon Structure for
LRRTM2
ECgene alternative splicing isoforms for
LRRTM2

Expression for LRRTM2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for LRRTM2 Gene

Protein differential expression in normal tissues from HIPED for LRRTM2 Gene

This gene is overexpressed in Platelet (57.7) and Frontal cortex (8.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for LRRTM2 Gene



Protein tissue co-expression partners for LRRTM2 Gene

NURSA nuclear receptor signaling pathways regulating expression of LRRTM2 Gene:

LRRTM2

mRNA Expression by UniProt/SwissProt for LRRTM2 Gene:

O43300-LRRT2_HUMAN
Tissue specificity: Expressed in neuronal tissues.

Evidence on tissue expression from TISSUES for LRRTM2 Gene

  • Nervous system(4.5)
  • Lung(4.1)
genes like me logo Genes that share expression patterns with LRRTM2: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for LRRTM2 Gene

Orthologs for LRRTM2 Gene

This gene was present in the common ancestor of animals.

Orthologs for LRRTM2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia LRRTM2 33 34
  • 99.94 (n)
dog
(Canis familiaris)
Mammalia LRRTM2 33 34
  • 97.29 (n)
cow
(Bos Taurus)
Mammalia LRRTM2 33 34
  • 96.71 (n)
oppossum
(Monodelphis domestica)
Mammalia LRRTM2 34
  • 96 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Lrrtm2 33
  • 95.53 (n)
mouse
(Mus musculus)
Mammalia Lrrtm2 33 16 34
  • 95.28 (n)
chicken
(Gallus gallus)
Aves LRRTM2 33 34
  • 85.7 (n)
lizard
(Anolis carolinensis)
Reptilia LRRTM2 34
  • 86 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii LOC101884631 33
  • 63.31 (n)
lrrtm2 34 34
  • 62 (a)
OneToMany
fruit fly
(Drosophila melanogaster)
Insecta haf 34
  • 9 (a)
OneToMany
Species where no ortholog for LRRTM2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for LRRTM2 Gene

ENSEMBL:
Gene Tree for LRRTM2 (if available)
TreeFam:
Gene Tree for LRRTM2 (if available)

Paralogs for LRRTM2 Gene

(4) SIMAP similar genes for LRRTM2 Gene using alignment to 3 proteins:

genes like me logo Genes that share paralogs with LRRTM2: view

Variants for LRRTM2 Gene

Sequence variations from dbSNP and Humsavar for LRRTM2 Gene

SNP ID Clin Chr 05 pos Variation AA Info Type
rs188837597 likely-benign, Hereditary cancer-predisposing syndrome 138,869,248(-) T/C downstream_transcript_variant
rs199741027 likely-benign, Hereditary cancer-predisposing syndrome 138,874,890(-) A/C/T intron_variant
rs555861358 likely-benign, Hereditary cancer-predisposing syndrome 138,875,388(-) C/T upstream_transcript_variant
rs1000132696 -- 138,870,732(-) A/G 3_prime_UTR_variant
rs1000140136 -- 138,873,394(-) A/G coding_sequence_variant, synonymous_variant

Variation tolerance for LRRTM2 Gene

Residual Variation Intolerance Score: 20.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.49; 10.70% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LRRTM2 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
LRRTM2

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Structural Variations from Database of Genomic Variants (DGV) for LRRTM2 Gene

Disorders for LRRTM2 Gene

Additional Disease Information for LRRTM2

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for LRRTM2 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for LRRTM2 Gene

Publications for LRRTM2 Gene

  1. A novel gene family encoding leucine-rich repeat transmembrane proteins differentially expressed in the nervous system. (PMID: 12676565) Laurén J … Timmusk T (Genomics 2003) 2 3 4 58
  2. Integrated genomic analysis implicates haploinsufficiency of multiple chromosome 5q31.2 genes in de novo myelodysplastic syndromes pathogenesis. (PMID: 19240791) Graubert TA … Walter MJ (PloS one 2009) 3 44 58
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  4. Prediction of the coding sequences of unidentified human genes. VIII. 78 new cDNA clones from brain which code for large proteins in vitro. (PMID: 9455477) Ishikawa K … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 1997) 3 4 58
  5. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58

Products for LRRTM2 Gene

Sources for LRRTM2 Gene

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