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Aliases for LSAMP Gene

Aliases for LSAMP Gene

  • Limbic System-Associated Membrane Protein 2 3 5
  • IgLON Family Member 3 2 3 4
  • IGLON3 3 4
  • LAMP 3 4

External Ids for LSAMP Gene

Previous GeneCards Identifiers for LSAMP Gene

  • GC03M112358
  • GC03M115111
  • GC03M116810
  • GC03M116850
  • GC03M117012
  • GC03M115528
  • GC03M112897

Summaries for LSAMP Gene

Entrez Gene Summary for LSAMP Gene

  • This gene encodes a member of the immunoglobulin LAMP, OBCAM and neurotrimin (IgLON) family of proteins. The encoded preproprotein is proteolytically processed to generate a neuronal surface glycoprotein. This protein may act as a selective homophilic adhesion molecule during axon guidance and neuronal growth in the developing limbic system. The encoded protein may also function as a tumor suppressor and may play a role in neuropsychiatric disorders. Alternative splicing results in multiple transcript variants, at least one of which encodes a preproprotein that is proteolytically processed. [provided by RefSeq, Jan 2016]

GeneCards Summary for LSAMP Gene

LSAMP (Limbic System-Associated Membrane Protein) is a Protein Coding gene. Among its related pathways are Post-translational modification- synthesis of GPI-anchored proteins and Metabolism of proteins. An important paralog of this gene is OPCML.

UniProtKB/Swiss-Prot for LSAMP Gene

  • Mediates selective neuronal growth and axon targeting. Contributes to the guidance of developing axons and remodeling of mature circuits in the limbic system. Essential for normal growth of the hyppocampal mossy fiber projection (By similarity).

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

Genomics for LSAMP Gene

Regulatory Elements for LSAMP Gene

Enhancers for LSAMP 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
GH03G117872 0.7 ENCODE 23.3 -734.2 -734189 1.7 ZNF426 FEZF1 REST RAD21 ZNF781 ZEB1 ZNF697 BCL11A ZNF34 KLF16 LSAMP ENSG00000239268 GC03P117874 GC03P117859
GH03G117996 0.8 ENCODE 10.6 -858.1 -858064 1.5 CTCF MXI1 ZSCAN4 RBBP5 RAD21 ZNF366 POLR2A ZBTB48 ZNF143 SMC3 LSAMP ENSG00000239268 PIR43441
GH03G116144 0.5 FANTOM5 8.8 +995.0 994994 0.4 PKNOX1 PBX2 EP300 LSAMP LOC105374052 GC03P116028
GH03G117763 0.4 FANTOM5 9.9 -624.3 -624301 0.2 EP300 LOC101926953 ENSG00000239268 LSAMP LOC100421670 GC03P117727 GC03P117859
GH03G116273 0.3 FANTOM5 7.7 +865.8 865757 0.4 LSAMP GC03P116299 GC03P116196
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around LSAMP on UCSC Golden Path with GeneCards custom track

Genomic Location for LSAMP Gene

Chromosome:
3
Start:
115,802,363 bp from pter
End:
117,139,389 bp from pter
Size:
1,337,027 bases
Orientation:
Minus strand

Genomic View for LSAMP Gene

Genes around LSAMP on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for LSAMP Gene

Proteins for LSAMP Gene

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

    Protein Symbol:
    Q13449-LSAMP_HUMAN
    Recommended name:
    Limbic system-associated membrane protein
    Protein Accession:
    Q13449
    Secondary Accessions:
    • Q8IV49

    Protein attributes for LSAMP Gene

    Size:
    338 amino acids
    Molecular mass:
    37393 Da
    Quaternary structure:
    No Data Available

neXtProt entry for LSAMP Gene

Post-translational modifications for LSAMP Gene

  • Glycosylation at posLast=4040, posLast=6666, Asn136, posLast=148148, Asn279, posLast=287287, Asn300, and Asn315
  • Modification sites at PhosphoSitePlus

Other Protein References for LSAMP Gene

No data available for DME Specific Peptides for LSAMP Gene

Domains & Families for LSAMP Gene

Protein Domains for LSAMP Gene

Suggested Antigen Peptide Sequences for LSAMP Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q13449

UniProtKB/Swiss-Prot:

LSAMP_HUMAN :
  • Belongs to the immunoglobulin superfamily. IgLON family.
Family:
  • Belongs to the immunoglobulin superfamily. IgLON family.
genes like me logo Genes that share domains with LSAMP: view

Function for LSAMP Gene

Molecular function for LSAMP Gene

GENATLAS Biochemistry:
limbic system-associated membrane protein,mediating selective neuronal growth and exon targetting,expressed on the surface of somata and proximal dendrites,immunoglobulin superfamily
UniProtKB/Swiss-Prot Function:
Mediates selective neuronal growth and axon targeting. Contributes to the guidance of developing axons and remodeling of mature circuits in the limbic system. Essential for normal growth of the hyppocampal mossy fiber projection (By similarity).

Gene Ontology (GO) - Molecular Function for LSAMP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 21982860
genes like me logo Genes that share ontologies with LSAMP: view
genes like me logo Genes that share phenotypes with LSAMP: view

Animal Models for LSAMP Gene

MGI Knock Outs for LSAMP:

Animal Model Products

  • Taconic Biosciences Mouse Models for LSAMP

CRISPR Products

miRNA for LSAMP Gene

miRTarBase miRNAs that target LSAMP

Inhibitory RNA Products

Clone Products

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

Localization for LSAMP Gene

Subcellular locations from UniProtKB/Swiss-Prot for LSAMP Gene

Cell membrane; Lipid-anchor, GPI-anchor.

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 LSAMP gene
Compartment Confidence
plasma membrane 5
extracellular 5
nucleus 1
lysosome 1

Gene Ontology (GO) - Cellular Components for LSAMP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region TAS --
GO:0005886 plasma membrane TAS --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0031225 anchored component of membrane IEA --
genes like me logo Genes that share ontologies with LSAMP: view

Pathways & Interactions for LSAMP Gene

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

Gene Ontology (GO) - Biological Process for LSAMP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006501 C-terminal protein lipidation TAS --
GO:0007155 cell adhesion IEA --
GO:0007399 nervous system development TAS 8666243
GO:0035641 locomotory exploration behavior IEA --
genes like me logo Genes that share ontologies with LSAMP: view

No data available for SIGNOR curated interactions for LSAMP Gene

Drugs & Compounds for LSAMP Gene

(2) Drugs for LSAMP Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
genes like me logo Genes that share compounds with LSAMP: view

Transcripts for LSAMP Gene

CRISPR Products

Inhibitory RNA Products

Clone Products

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

No ASD Table

Relevant External Links for LSAMP Gene

GeneLoc Exon Structure for
LSAMP
ECgene alternative splicing isoforms for
LSAMP

Expression for LSAMP Gene

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

Protein differential expression in normal tissues from HIPED for LSAMP Gene

This gene is overexpressed in Frontal cortex (11.1), Serum (10.2), Cerebrospinal fluid (9.8), Nasal epithelium (8.4), and Brain (7.8).

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



NURSA nuclear receptor signaling pathways regulating expression of LSAMP Gene:

LSAMP

SOURCE GeneReport for Unigene cluster for LSAMP Gene:

Hs.26409

mRNA Expression by UniProt/SwissProt for LSAMP Gene:

Q13449-LSAMP_HUMAN
Tissue specificity: Expressed on limbic neurons and fiber tracts as well as in single layers of the superior colliculus, spinal chord and cerebellum.

Evidence on tissue expression from TISSUES for LSAMP Gene

  • Nervous system(4.5)
  • Intestine(4.2)
genes like me logo Genes that share expression patterns with LSAMP: view

Primer Products

No data available for mRNA differential expression in normal tissues , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for LSAMP Gene

Orthologs for LSAMP Gene

This gene was present in the common ancestor of animals.

Orthologs for LSAMP Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia LSAMP 34 35
  • 99.8 (n)
cow
(Bos Taurus)
Mammalia LSAMP 34
  • 94.58 (n)
mouse
(Mus musculus)
Mammalia Lsamp 34 16 35
  • 94.23 (n)
rat
(Rattus norvegicus)
Mammalia Lsamp 34
  • 94.18 (n)
dog
(Canis familiaris)
Mammalia LSAMP 34 35
  • 93 (n)
oppossum
(Monodelphis domestica)
Mammalia LSAMP 35
  • 89 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia LSAMP 35
  • 89 (a)
OneToOne
chicken
(Gallus gallus)
Aves LSAMP 34 35
  • 85.11 (n)
lizard
(Anolis carolinensis)
Reptilia LSAMP 35
  • 84 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia lsamp 34
  • 76.08 (n)
zebrafish
(Danio rerio)
Actinopterygii lsamp 34
  • 64.26 (n)
LSAMP 35
  • 48 (a)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP002628 34
  • 45.8 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG34353 34 35
  • 43.44 (n)
CG11320 35
  • 25 (a)
ManyToMany
Lac 35
  • 24 (a)
ManyToMany
Ama 35
  • 23 (a)
ManyToMany
CG14010 35
  • 22 (a)
ManyToMany
CG14521 35
  • 21 (a)
ManyToMany
CG40378 35
  • 21 (a)
ManyToMany
CG42368 35
  • 20 (a)
ManyToMany
CG34391 35
  • 19 (a)
ManyToMany
CG31708 35
  • 18 (a)
ManyToMany
CG7166 35
  • 17 (a)
ManyToMany
CG31646 35
  • 16 (a)
ManyToMany
CG42343 35
  • 16 (a)
ManyToMany
klg 35
  • 16 (a)
ManyToMany
wrapper 35
  • 16 (a)
ManyToMany
CG32791 35
  • 15 (a)
ManyToMany
CG31814 35
  • 14 (a)
ManyToMany
worm
(Caenorhabditis elegans)
Secernentea rig-5 35
  • 17 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 28 (a)
OneToMany
Species where no ortholog for LSAMP was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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 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)

Evolution for LSAMP Gene

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

Paralogs for LSAMP Gene

Paralogs for LSAMP Gene

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

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

Variants for LSAMP Gene

Sequence variations from dbSNP and Humsavar for LSAMP Gene

SNP ID Clin Chr 03 pos Sequence Context AA Info Type
rs1000008790 -- 115,941,653(+) CAACA(C/T)GGGTG intron-variant
rs1000010352 -- 116,359,527(+) ACTCA(C/T)ATTAC intron-variant, upstream-variant-2KB
rs1000017130 -- 116,118,246(+) CACTC(C/T)TAAAT intron-variant
rs1000020803 -- 115,825,371(+) CTCCT(C/G)CTATG intron-variant
rs1000023525 -- 116,202,454(+) CTTCT(A/C)TTTTT intron-variant

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

Variant ID Type Subtype PubMed ID
dgv4842n100 CNV loss 25217958
dgv922e214 CNV loss 21293372
dgv923e214 CNV loss 21293372
esv2536613 CNV deletion 19546169
esv2666380 CNV deletion 23128226
esv2670807 CNV deletion 23128226
esv2725799 CNV deletion 23290073
esv2725800 CNV deletion 23290073
esv2725801 CNV deletion 23290073
esv2725802 CNV deletion 23290073
esv274993 CNV gain+loss 21479260
esv2751975 CNV loss 17911159
esv2751976 CNV loss 17911159
esv2759170 CNV loss 17122850
esv2759171 CNV loss 17122850
esv2760762 CNV gain+loss 21179565
esv28824 CNV loss 19812545
esv3597483 CNV loss 21293372
esv3597484 CNV loss 21293372
esv3597489 CNV loss 21293372
esv3597490 CNV loss 21293372
esv3893770 CNV gain 25118596
nsv1001538 CNV loss 25217958
nsv1011135 CNV gain 25217958
nsv1011591 CNV loss 25217958
nsv1073672 CNV deletion 25765185
nsv1125233 CNV insertion 24896259
nsv1130920 CNV deletion 24896259
nsv1131717 CNV deletion 24896259
nsv1136765 CNV deletion 24896259
nsv1139149 CNV deletion 24896259
nsv1146109 CNV deletion 26484159
nsv3956 CNV insertion 18451855
nsv3957 CNV deletion 18451855
nsv437338 CNV loss 16327808
nsv472891 CNV novel sequence insertion 20440878
nsv473326 CNV novel sequence insertion 20440878
nsv477803 CNV novel sequence insertion 20440878
nsv509847 OTHER sequence alteration 20534489
nsv516570 CNV loss 19592680
nsv591344 CNV loss 21841781
nsv591345 CNV loss 21841781
nsv829685 CNV gain 17160897

Variation tolerance for LSAMP Gene

Residual Variation Intolerance Score: 35.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.76; 16.09% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for LSAMP Gene

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

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

Disorders for LSAMP Gene

Relevant External Links for LSAMP

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

No disorders were found for LSAMP Gene.

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

Publications for LSAMP Gene

  1. Polymorphisms of the tumor suppressor gene LSAMP are associated with left main coronary artery disease. (PMID: 18318786) Wang L. … Vance J.M. (Ann. Hum. Genet. 2008) 3 22 46 64
  2. Association of limbic system-associated membrane protein (LSAMP) to male completed suicide. (PMID: 18433483) Must A. … VAoli M. (BMC Med. Genet. 2008) 3 22 46 64
  3. Assignment of the gene encoding the limbic system-associated membrane protein (LAMP) to mouse chromosome 16B5 and human chromosome 3q13.2-q21. (PMID: 9615236) Pimenta A.F. … Levitt P. (Genomics 1998) 2 3 22 64
  4. cDNA cloning and structural analysis of the human limbic-system- associated membrane protein (LAMP). (PMID: 8666243) Pimenta A.F. … Levitt P. (Gene 1996) 3 4 22 64
  5. 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

Products for LSAMP Gene

Sources for LSAMP Gene

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