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Aliases for LRRTM4 Gene

Aliases for LRRTM4 Gene

  • Leucine Rich Repeat Transmembrane Neuronal 4 2 3 5

External Ids for LRRTM4 Gene

Previous GeneCards Identifiers for LRRTM4 Gene

  • GC02M077701
  • GC02M077719
  • GC02M077718
  • GC02M077655
  • GC02M076830
  • GC02M076974

Summaries for LRRTM4 Gene

GeneCards Summary for LRRTM4 Gene

LRRTM4 (Leucine Rich Repeat Transmembrane Neuronal 4) is a Protein Coding gene. Among its related pathways are Protein-protein interactions at synapses and Transmission across Chemical Synapses. GO annotations related to this gene include heparan sulfate proteoglycan binding. An important paralog of this gene is LRRTM3.

UniProtKB/Swiss-Prot for LRRTM4 Gene

  • 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).

No data available for Entrez Gene Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LRRTM4 Gene

Genomics for LRRTM4 Gene

Regulatory Elements for LRRTM4 Gene

Enhancers for LRRTM4 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
GH02F077261 0.7 FANTOM5 6 +331.9 331928 0.4 LRRTM4 GC02M077297 GC02M077190
GH02F077150 0.3 FANTOM5 5.6 +442.7 442682 0.2 LRRTM4 GC02M077040 GC02M077190
GH02F077604 0.6 ENCODE 5.5 -12.2 -12234 1.6 SOX13 ELF3 CEBPG YY1 GATA4 RERE NR2F6 CREM MIXL1 SOX5 LRRTM4 ENSG00000227088
GH02F077466 0.3 FANTOM5 4.7 +126.7 126654 0.1 LRRTM4 GC02P077430 GC02M077564
GH02F077205 0.3 FANTOM5 4.4 +387.4 387377 0.3 MAFK LRRTM4 GC02M077190 GC02M077297
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around LRRTM4 on UCSC Golden Path with GeneCards custom track

Genomic Location for LRRTM4 Gene

Chromosome:
2
Start:
76,747,457 bp from pter
End:
77,593,319 bp from pter
Size:
845,863 bases
Orientation:
Minus strand

Genomic View for LRRTM4 Gene

Genes around LRRTM4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LRRTM4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LRRTM4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LRRTM4 Gene

Proteins for LRRTM4 Gene

  • Protein details for LRRTM4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q86VH4-LRRT4_HUMAN
    Recommended name:
    Leucine-rich repeat transmembrane neuronal protein 4
    Protein Accession:
    Q86VH4
    Secondary Accessions:
    • Q4FZ98
    • Q6UXJ7

    Protein attributes for LRRTM4 Gene

    Size:
    590 amino acids
    Molecular mass:
    67217 Da
    Quaternary structure:
    • Peripherally associated with AMPAR complex. AMPAR complex consists of an inner core made of 4 pore-forming GluA/GRIA proteins (GRIA1, GRIA2, GRIA3 and GRIA4) and 4 major auxiliary subunits arranged in a twofold symmetry. One of the two pairs of distinct binding sites is occupied either by CNIH2, CNIH3 or CACNG2, CACNG3. The other harbors CACNG2, CACNG3, CACNG4, CACNG8 or GSG1L. This inner core of AMPAR complex is complemented by outer core constituents binding directly to the GluA/GRIA proteins at sites distinct from the interaction sites of the inner core constituents. Outer core constituents include at least PRRT1, PRRT2, CKAMP44/SHISA9, FRRS1L and NRN1. The proteins of the inner and outer core serve as a platform for other, more peripherally associated AMPAR constituents, including LRRTM4. Alone or in combination, these auxiliary subunits control the gating and pharmacology of the AMPAR complex and profoundly impact their biogenesis and protein processing (By similarity).

    Alternative splice isoforms for LRRTM4 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for LRRTM4 Gene

Post-translational modifications for LRRTM4 Gene

  • Glycosylation at Asn 58, Asn 126, and Asn 291
  • Modification sites at PhosphoSitePlus

Antibody Products

No data available for DME Specific Peptides for LRRTM4 Gene

Domains & Families for LRRTM4 Gene

Graphical View of Domain Structure for InterPro Entry

Q86VH4

UniProtKB/Swiss-Prot:

LRRT4_HUMAN :
  • Contains 1 LRRCT domain.
  • Belongs to the LRRTM family.
  • Contains 10 LRR (leucine-rich) repeats.
Domain:
  • Contains 1 LRRCT domain.
  • Contains 1 LRRNT domain.
Family:
  • Belongs to the LRRTM family.
Similarity:
  • Contains 10 LRR (leucine-rich) repeats.
genes like me logo Genes that share domains with LRRTM4: view

No data available for Gene Families for LRRTM4 Gene

Function for LRRTM4 Gene

Molecular function for LRRTM4 Gene

UniProtKB/Swiss-Prot 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).

Gene Ontology (GO) - Molecular Function for LRRTM4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004860 protein kinase inhibitor activity IBA --
genes like me logo Genes that share ontologies with LRRTM4: view
genes like me logo Genes that share phenotypes with LRRTM4: view

Animal Models for LRRTM4 Gene

MGI Knock Outs for LRRTM4:

Animal Model Products

  • Taconic Biosciences Mouse Models for LRRTM4

Inhibitory RNA Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for LRRTM4 Gene

Localization for LRRTM4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LRRTM4 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
Jensen Localization Image for LRRTM4 Gene COMPARTMENTS Subcellular localization image for LRRTM4 gene
Compartment Confidence
plasma membrane 4
golgi apparatus 2
endoplasmic reticulum 1
extracellular 1

Gene Ontology (GO) - Cellular Components for LRRTM4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IBA --
GO:0005886 plasma membrane IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0030054 cell junction IEA --
genes like me logo Genes that share ontologies with LRRTM4: view

Pathways & Interactions for LRRTM4 Gene

genes like me logo Genes that share pathways with LRRTM4: view

Pathways by source for LRRTM4 Gene

Interacting Proteins for LRRTM4 Gene

Gene Ontology (GO) - Biological Process for LRRTM4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006469 negative regulation of protein kinase activity IBA --
GO:0019221 cytokine-mediated signaling pathway IBA --
GO:0046426 negative regulation of JAK-STAT cascade IBA --
GO:0050808 synapse organization IEA --
genes like me logo Genes that share ontologies with LRRTM4: view

No data available for SIGNOR curated interactions for LRRTM4 Gene

Transcripts for LRRTM4 Gene

Unigene Clusters for LRRTM4 Gene

Leucine rich repeat transmembrane neuronal 4:
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for LRRTM4 Gene

No ASD Table

Relevant External Links for LRRTM4 Gene

GeneLoc Exon Structure for
LRRTM4
ECgene alternative splicing isoforms for
LRRTM4

Expression for LRRTM4 Gene

mRNA expression in normal human tissues for LRRTM4 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for LRRTM4 Gene

This gene is overexpressed in Brain - Frontal Cortex (BA9) (x8.1), Brain - Cortex (x7.5), and Brain - Anterior cingulate cortex (BA24) (x7.0).

Protein differential expression in normal tissues from HIPED for LRRTM4 Gene

This gene is overexpressed in Heart (59.4) and Fetal Brain (9.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for LRRTM4 Gene



Protein tissue co-expression partners for LRRTM4 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of LRRTM4 Gene:

LRRTM4

SOURCE GeneReport for Unigene cluster for LRRTM4 Gene:

Hs.285782

mRNA Expression by UniProt/SwissProt for LRRTM4 Gene:

Q86VH4-LRRT4_HUMAN
Tissue specificity: Expressed in neuronal tissues.
genes like me logo Genes that share expression patterns with LRRTM4: view

Primer Products

Orthologs for LRRTM4 Gene

This gene was present in the common ancestor of animals.

Orthologs for LRRTM4 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia LRRTM4 34 35
  • 99.66 (n)
dog
(Canis familiaris)
Mammalia LRRTM4 34 35
  • 94.35 (n)
cow
(Bos Taurus)
Mammalia LRRTM4 34 35
  • 93.84 (n)
oppossum
(Monodelphis domestica)
Mammalia LRRTM4 35
  • 92 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Lrrtm4 34
  • 87.91 (n)
mouse
(Mus musculus)
Mammalia Lrrtm4 34 16 35
  • 87.72 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia LRRTM4 35
  • 81 (a)
OneToOne
chicken
(Gallus gallus)
Aves LRRTM4 34 35
  • 81.98 (n)
lizard
(Anolis carolinensis)
Reptilia LRRTM4 35
  • 88 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia lrrtm4 34
  • 74.86 (n)
zebrafish
(Danio rerio)
Actinopterygii LRRTM4 (1 of 4) 35
  • 67 (a)
OneToMany
LOC100333709 34
  • 66.32 (n)
lrrtm4l2 35
  • 58 (a)
OneToMany
LRRTM4 (3 of 4) 35
  • 57 (a)
OneToMany
lrrtm4l1 35
  • 51 (a)
OneToMany
fruit fly
(Drosophila melanogaster)
Insecta haf 35
  • 9 (a)
OneToMany
Species where no ortholog for LRRTM4 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 LRRTM4 Gene

ENSEMBL:
Gene Tree for LRRTM4 (if available)
TreeFam:
Gene Tree for LRRTM4 (if available)

Paralogs for LRRTM4 Gene

(5) SIMAP similar genes for LRRTM4 Gene using alignment to 5 proteins:

genes like me logo Genes that share paralogs with LRRTM4: view

Variants for LRRTM4 Gene

Sequence variations from dbSNP and Humsavar for LRRTM4 Gene

SNP ID Clin Chr 02 pos Sequence Context AA Info Type
rs10048661 -- 77,026,778(+) GCTGC(A/G)TATTT intron-variant
rs10062751 -- 77,139,872(+) ATTCA(C/T)AATTG intron-variant
rs10084200 -- 76,924,651(+) TGAGC(A/G)TAATA intron-variant
rs10084401 -- 76,926,384(+) ATTAC(A/G)TAATA intron-variant
rs1016347 -- 77,357,771(+) ATGAG(C/T)GTAGC intron-variant

Structural Variations from Database of Genomic Variants (DGV) for LRRTM4 Gene

Variant ID Type Subtype PubMed ID
dgv1131e212 CNV loss 25503493
dgv244e215 CNV deletion 23714750
dgv3878n100 CNV loss 25217958
dgv707e214 CNV loss 21293372
dgv709e199 CNV deletion 23128226
esv2090944 CNV deletion 18987734
esv2609871 CNV deletion 19546169
esv2658076 CNV deletion 23128226
esv2659916 CNV deletion 23128226
esv2672350 CNV deletion 23128226
esv2676549 CNV deletion 23128226
esv2720234 CNV deletion 23290073
esv2720235 CNV deletion 23290073
esv2720236 CNV deletion 23290073
esv2720237 CNV deletion 23290073
esv2759066 CNV loss 17122850
esv27593 CNV loss 19812545
esv2762264 CNV loss 21179565
esv2762680 CNV loss 21179565
esv27982 CNV loss 19812545
esv3381001 CNV insertion 20981092
esv3558877 CNV deletion 23714750
esv3583875 CNV loss 25503493
esv3591331 CNV gain 21293372
esv3591334 CNV gain 21293372
esv3591335 CNV loss 21293372
esv3591336 CNV gain 21293372
esv3591337 CNV gain 21293372
esv3591338 CNV gain 21293372
esv3591340 CNV loss 21293372
esv3591341 CNV loss 21293372
esv3591343 CNV loss 21293372
esv3591344 CNV loss 21293372
esv3591345 CNV loss 21293372
esv3591348 CNV gain 21293372
esv3591349 CNV loss 21293372
esv3591350 CNV loss 21293372
esv3591352 CNV loss 21293372
esv3591353 CNV gain 21293372
esv3591354 CNV loss 21293372
esv3591355 CNV loss 21293372
esv3892703 CNV gain 25118596
esv3892714 CNV gain 25118596
esv8705 CNV gain 19470904
nsv10046 CNV loss 18304495
nsv1005001 CNV loss 25217958
nsv1005392 CNV gain 25217958
nsv1007408 CNV gain 25217958
nsv1008307 CNV loss 25217958
nsv1011401 CNV gain 25217958
nsv1014895 CNV loss 25217958
nsv1110743 CNV insertion 24896259
nsv1115562 CNV duplication 24896259
nsv1149693 CNV duplication 26484159
nsv214053 CNV insertion 16902084
nsv2789 CNV deletion 18451855
nsv2790 CNV insertion 18451855
nsv2791 CNV insertion 18451855
nsv458263 CNV loss 19166990
nsv458274 CNV loss 19166990
nsv458285 CNV loss 19166990
nsv458296 CNV loss 19166990
nsv470473 CNV loss 18288195
nsv508094 OTHER sequence alteration 20534489
nsv508095 OTHER sequence alteration 20534489
nsv518504 CNV loss 19592680
nsv519950 CNV gain 19592680
nsv520560 CNV loss 19592680
nsv520715 CNV gain 19592680
nsv523873 CNV loss 19592680
nsv523910 CNV loss 19592680
nsv524535 CNV gain 19592680
nsv525625 CNV loss 19592680
nsv526121 CNV loss 19592680
nsv582235 CNV gain 21841781
nsv582250 CNV loss 21841781
nsv582251 CNV loss 21841781
nsv582252 CNV loss 21841781
nsv582253 CNV loss 21841781
nsv582254 CNV loss 21841781
nsv582255 CNV loss 21841781
nsv582256 CNV loss 21841781
nsv582257 CNV loss 21841781
nsv818054 CNV loss 17921354
nsv818055 CNV loss 17921354
nsv829468 CNV loss 20364138
nsv834266 CNV gain 17160897
nsv834267 CNV loss 17160897
nsv961421 CNV duplication 23825009
nsv997284 CNV loss 25217958
nsv999822 CNV gain 25217958

Variation tolerance for LRRTM4 Gene

Residual Variation Intolerance Score: 11% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.13; 22.97% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for LRRTM4 Gene

Human Gene Mutation Database (HGMD)
LRRTM4
SNPedia medical, phenotypic, and genealogical associations of SNPs for
LRRTM4

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LRRTM4 Gene

Disorders for LRRTM4 Gene

Relevant External Links for LRRTM4

Genetic Association Database (GAD)
LRRTM4
Human Genome Epidemiology (HuGE) Navigator
LRRTM4
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
LRRTM4

No disorders were found for LRRTM4 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for LRRTM4 Gene

Publications for LRRTM4 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 22 64
  2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose J.E. … Uhl G.R. (Mol. Med. 2010) 3 46 64
  3. 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
  4. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PMID: 12975309) Clark H.F. … Gray A.M. (Genome Res. 2003) 3 4 64
  5. The BioPlex Network: A Systematic Exploration of the Human Interactome. (PMID: 26186194) Huttlin E.L. … Gygi S.P. (Cell 2015) 3 64

Products for LRRTM4 Gene

Sources for LRRTM4 Gene

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