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Aliases for LRRTM1 Gene

Aliases for LRRTM1 Gene

  • Leucine Rich Repeat Transmembrane Neuronal 1 2 3 5

External Ids for LRRTM1 Gene

Previous GeneCards Identifiers for LRRTM1 Gene

  • GC02U900202
  • GC02M080490
  • GC02M080499
  • GC02M080427
  • GC02M080382

Summaries for LRRTM1 Gene

GeneCards Summary for LRRTM1 Gene

LRRTM1 (Leucine Rich Repeat Transmembrane Neuronal 1) is a Protein Coding gene. Diseases associated with LRRTM1 include Schizophrenia and Autism Spectrum Disorder. Among its related pathways are Protein-protein interactions at synapses and Transmission across Chemical Synapses. An important paralog of this gene is LRRTM2.

UniProtKB/Swiss-Prot for LRRTM1 Gene

  • Exhibits strong synaptogenic activity, restricted to excitatory presynaptic differentiation, acting at both pre- and postsynaptic level.

Gene Wiki entry for LRRTM1 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LRRTM1 Gene

Genomics for LRRTM1 Gene

Regulatory Elements for LRRTM1 Gene

Enhancers for LRRTM1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH02G080301 0.4 FANTOM5 2.1 +3.3 3340 0.4 HDGF EZH2 LRRTM1 LOC100420108
GH02G080303 0.8 ENCODE 0.7 +1.3 1269 0.1 USF1 PKNOX1 SUZ12 BMI1 ARID3A POLR2A EED RELB IKZF2 CREM LRRTM1 LOC100420108
GH02G080361 0.7 ENCODE 0.2 -57.3 -57312 0.1 SMARCE1 TAL1 CEBPB DPF2 BRCA1 ARID1B TCF12 NFIC GATA2 NCOR1 LOC105374824 LRRTM1
GH02G080284 0.3 FANTOM5 0.3 +20.2 20213 0.2 LRRTM1 LOC100420108
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around LRRTM1 on UCSC Golden Path with GeneCards custom track

Genomic Location for LRRTM1 Gene

Chromosome:
2
Start:
80,288,280 bp from pter
End:
80,304,749 bp from pter
Size:
16,470 bases
Orientation:
Minus strand

Genomic View for LRRTM1 Gene

Genes around LRRTM1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LRRTM1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LRRTM1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LRRTM1 Gene

Proteins for LRRTM1 Gene

  • Protein details for LRRTM1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q86UE6-LRRT1_HUMAN
    Recommended name:
    Leucine-rich repeat transmembrane neuronal protein 1
    Protein Accession:
    Q86UE6
    Secondary Accessions:
    • A8K397
    • D6W5K1
    • Q96DN1

    Protein attributes for LRRTM1 Gene

    Size:
    522 amino acids
    Molecular mass:
    58641 Da
    Quaternary structure:
    No Data Available
    Miscellaneous:
    • This gene is imprinted, being predominantly expressed from the paternal allele and showing a variable pattern of maternal down-regulation. May be associated paternally with handedness and schizophrenia.

neXtProt entry for LRRTM1 Gene

Post-translational modifications for LRRTM1 Gene

  • Glycosylation at posLast=5656, Asn63, posLast=130130, and Asn380
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for LRRTM1 Gene

Domains & Families for LRRTM1 Gene

Suggested Antigen Peptide Sequences for LRRTM1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q86UE6

UniProtKB/Swiss-Prot:

LRRT1_HUMAN :
  • Belongs to the LRRTM family.
Family:
  • Belongs to the LRRTM family.
genes like me logo Genes that share domains with LRRTM1: view

No data available for Gene Families for LRRTM1 Gene

Function for LRRTM1 Gene

Molecular function for LRRTM1 Gene

UniProtKB/Swiss-Prot Function:
Exhibits strong synaptogenic activity, restricted to excitatory presynaptic differentiation, acting at both pre- and postsynaptic level.

Gene Ontology (GO) - Molecular Function for LRRTM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003674 molecular_function ND --
GO:0004860 protein kinase inhibitor activity IBA --
genes like me logo Genes that share ontologies with LRRTM1: view
genes like me logo Genes that share phenotypes with LRRTM1: view

Animal Models for LRRTM1 Gene

MGI Knock Outs for LRRTM1:

Animal Model Products

  • Taconic Biosciences Mouse Models for LRRTM1

CRISPR Products

miRNA for LRRTM1 Gene

miRTarBase miRNAs that target LRRTM1

Inhibitory RNA Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for LRRTM1 Gene

Localization for LRRTM1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LRRTM1 Gene

Cell membrane; Single-pass type I membrane protein. Cell junction, synapse, postsynaptic cell membrane; Single-pass type I membrane protein.

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 LRRTM1 gene
Compartment Confidence
endoplasmic reticulum 5
plasma membrane 4
extracellular 1
peroxisome 1
lysosome 1

Gene Ontology (GO) - Cellular Components for LRRTM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005783 endoplasmic reticulum IDA 17667961
GO:0005886 plasma membrane IEA --
GO:0009986 NOT cell surface IDA 17667961
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with LRRTM1: view

Pathways & Interactions for LRRTM1 Gene

genes like me logo Genes that share pathways with LRRTM1: view

Pathways by source for LRRTM1 Gene

Interacting Proteins for LRRTM1 Gene

Gene Ontology (GO) - Biological Process for LRRTM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002091 negative regulation of receptor internalization IEA --
GO:0006469 negative regulation of protein kinase activity IBA --
GO:0007626 locomotory behavior IEA --
GO:0008150 biological_process ND --
GO:0019221 cytokine-mediated signaling pathway IBA --
genes like me logo Genes that share ontologies with LRRTM1: view

No data available for SIGNOR curated interactions for LRRTM1 Gene

Drugs & Compounds for LRRTM1 Gene

No Compound Related Data Available

Transcripts for LRRTM1 Gene

Unigene Clusters for LRRTM1 Gene

Leucine rich repeat transmembrane neuronal 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for LRRTM1 Gene

ExUns: 1a · 1b ^ 2a · 2b
SP1:
SP2:

Relevant External Links for LRRTM1 Gene

GeneLoc Exon Structure for
LRRTM1
ECgene alternative splicing isoforms for
LRRTM1

Expression for LRRTM1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for LRRTM1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for LRRTM1 Gene

This gene is overexpressed in Brain - Nucleus accumbens (basal ganglia) (x7.8), Brain - Putamen (basal ganglia) (x6.1), Brain - Caudate (basal ganglia) (x5.6), Brain - Hippocampus (x4.9), Brain - Cortex (x4.9), Brain - Anterior cingulate cortex (BA24) (x4.3), and Brain - Frontal Cortex (BA9) (x4.1).

Protein differential expression in normal tissues from HIPED for LRRTM1 Gene

This gene is overexpressed in Platelet (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for LRRTM1 Gene



Protein tissue co-expression partners for LRRTM1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of LRRTM1 Gene:

LRRTM1

SOURCE GeneReport for Unigene cluster for LRRTM1 Gene:

Hs.591580

mRNA Expression by UniProt/SwissProt for LRRTM1 Gene:

Q86UE6-LRRT1_HUMAN
Tissue specificity: Predominantly expressed in forebrain regions including thalamus and cerebral cortex.

Evidence on tissue expression from TISSUES for LRRTM1 Gene

  • Nervous system(4.7)
genes like me logo Genes that share expression patterns with LRRTM1: view

Primer Products

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for LRRTM1 Gene

Orthologs for LRRTM1 Gene

This gene was present in the common ancestor of animals.

Orthologs for LRRTM1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia LRRTM1 35 34
  • 99.81 (n)
OneToOne
dog
(Canis familiaris)
Mammalia LRRTM1 35 34
  • 95.98 (n)
OneToOne
cow
(Bos Taurus)
Mammalia LRRTM1 34
  • 95.52 (n)
mouse
(Mus musculus)
Mammalia Lrrtm1 35 16 34
  • 92.19 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia LRRTM1 34
  • 91.76 (n)
oppossum
(Monodelphis domestica)
Mammalia LRRTM1 35
  • 87 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia LRRTM1 35
  • 85 (a)
OneToOne
chicken
(Gallus gallus)
Aves LRRTM1 35 34
  • 79.21 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia LRRTM1 35
  • 85 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia lrrtm1 34
  • 74.97 (n)
zebrafish
(Danio rerio)
Actinopterygii lrrtm1 35 34
  • 66.41 (n)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta haf 35
  • 9 (a)
OneToMany
Species where no ortholog for LRRTM1 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)
  • 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)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for LRRTM1 Gene

ENSEMBL:
Gene Tree for LRRTM1 (if available)
TreeFam:
Gene Tree for LRRTM1 (if available)

Paralogs for LRRTM1 Gene

(7) SIMAP similar genes for LRRTM1 Gene using alignment to 4 proteins:

genes like me logo Genes that share paralogs with LRRTM1: view

Variants for LRRTM1 Gene

Sequence variations from dbSNP and Humsavar for LRRTM1 Gene

SNP ID Clin Chr 02 pos Sequence Context AA Info Type
rs1001985415 -- 80,301,505(+) AAACT(A/G)TCTGG intron-variant
rs1002902617 -- 80,306,329(+) TATCC(A/T)AGGTC intron-variant, upstream-variant-2KB
rs1002974987 -- 80,305,962(+) GTAGT(C/G)GCACT intron-variant, upstream-variant-2KB
rs1003719076 -- 80,305,571(+) ACACA(A/T)CCTAA intron-variant, upstream-variant-2KB
rs1004090041 -- 80,302,044(+) GTGGG(C/G)TGGGG intron-variant, utr-variant-3-prime

Structural Variations from Database of Genomic Variants (DGV) for LRRTM1 Gene

Variant ID Type Subtype PubMed ID
esv2759069 CNV loss 17122850

Variation tolerance for LRRTM1 Gene

Residual Variation Intolerance Score: 21.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 11.25; 92.50% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for LRRTM1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
LRRTM1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LRRTM1 Gene

Disorders for LRRTM1 Gene

MalaCards: The human disease database

(2) MalaCards diseases for LRRTM1 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
schizophrenia
  • schizophrenia 12
autism spectrum disorder
  • pervasive development disorder
- elite association - COSMIC cancer census association via MalaCards

Relevant External Links for LRRTM1

Genetic Association Database (GAD)
LRRTM1
Human Genome Epidemiology (HuGE) Navigator
LRRTM1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
LRRTM1
genes like me logo Genes that share disorders with LRRTM1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for LRRTM1 Gene

Publications for LRRTM1 Gene

  1. A novel gene family encoding leucine-rich repeat transmembrane proteins differentially expressed in the nervous system. (PMID: 12676565) Lauren J. … Timmusk T.T. (Genomics 2003) 2 3 4 64
  2. Family-based analysis of genetic variation underlying psychosis-inducing effects of cannabis: sibling analysis and proband follow-up. (PMID: 21041608) van Winkel R. (Arch. Gen. Psychiatry 2011) 3 46 64
  3. LRRTM1 on chromosome 2p12 is a maternally suppressed gene that is associated paternally with handedness and schizophrenia. (PMID: 17667961) Francks C. … Monaco A.P. (Mol. Psychiatry 2007) 3 4 64
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 64
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64

Products for LRRTM1 Gene

Sources for LRRTM1 Gene

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