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    LSAMP limbic system associated membrane protein [ Homo sapiens (human) ]

    Gene ID: 4045, updated on 1-Jun-2019

    Summary

    Official Symbol
    LSAMPprovided by HGNC
    Official Full Name
    limbic system associated membrane proteinprovided by HGNC
    Primary source
    HGNC:HGNC:6705
    See related
    Ensembl:ENSG00000185565 MIM:603241
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    LAMP; IGLON3
    Summary
    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]
    Expression
    Biased expression in brain (RPKM 19.9), prostate (RPKM 5.4) and 9 other tissues See more
    Orthologs

    Genomic context

    See LSAMP in Genome Data Viewer
    Location:
    3q13.31
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    109 current GRCh38.p12 (GCF_000001405.38) 3 NC_000003.12 (115802363..116445538, complement)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (115521210..116164385, complement)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene growth associated protein 43 Neighboring gene 3q13.2-q13.31 distal HERV-H recombination region Neighboring gene uncharacterized LOC105374053 Neighboring gene RNA, 7SL, cytoplasmic 815, pseudogene Neighboring gene small nucleolar RNA, C/D box 155 Neighboring gene uncharacterized LOC107986116 Neighboring gene uncharacterized LOC105374052 Neighboring gene LSAMP antisense RNA 1 Neighboring gene long intergenic non-protein coding RNA 903 Neighboring gene RNA, 7SL, cytoplasmic 582, pseudogene

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Phenotypes

    NHGRI GWAS Catalog

    Description
    Cross-Disorder Genome-Wide Analyses Suggest a Complex Genetic Relationship Between Tourette's Syndrome and OCD.
    NHGRI GWA Catalog
    Genome-wide survival analysis of age at onset of alcohol dependence in extended high-risk COGA families.
    NHGRI GWA Catalog

    Pathways from BioSystems

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • FLJ34254, FLJ35396, FLJ37216, FLJ54658

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    cell adhesion IEA
    Inferred from Electronic Annotation
    more info
     
    nervous system development TAS
    Traceable Author Statement
    more info
    PubMed 
    Component Evidence Code Pubs
    anchored component of membrane IEA
    Inferred from Electronic Annotation
    more info
     
    cytosol IDA
    Inferred from Direct Assay
    more info
     
    extracellular region TAS
    Traceable Author Statement
    more info
     
    plasma membrane TAS
    Traceable Author Statement
    more info
     

    General protein information

    Preferred Names
    limbic system-associated membrane protein
    Names
    IgLON family member 3

    NCBI Reference Sequences (RefSeq)

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001318915.2NP_001305844.1  limbic system-associated membrane protein isoform 2 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) includes two alternate in-frame exons in the 3' coding region compared to variant 1. The encoded isoform (2) is longer than isoform 1. The encoded isoform (2) may undergo proteolytic processing similar to isoform 1.
      Source sequence(s)
      AA702209, AC012598, AK091573, AK092715, AK299851, BC033803
      UniProtKB/Swiss-Prot
      Q13449
      UniProtKB/TrEMBL
      B7Z661
      Related
      ENSP00000328455.4, ENST00000333617.8
      Conserved Domains (3) summary
      pfam13927
      Location:131201
      Ig_3; Immunoglobulin domain
      cd00096
      Location:235302
      Ig; Immunoglobulin domain
      cl11960
      Location:38128
      Ig; Immunoglobulin domain
    2. NM_002338.5NP_002329.2  limbic system-associated membrane protein isoform 1 preproprotein

      See identical proteins and their annotated locations for NP_002329.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the shorter transcript and encodes the shorter isoform (1).
      Source sequence(s)
      AA702209, AC012598, AK091573, AK092715, AK299851, BC033803
      Consensus CDS
      CCDS2982.1
      UniProtKB/Swiss-Prot
      Q13449
      UniProtKB/TrEMBL
      B7Z661
      Related
      ENSP00000419000.1, ENST00000490035.7
      Conserved Domains (2) summary
      pfam13927
      Location:218294
      Ig_3; Immunoglobulin domain
      cl11960
      Location:38128
      Ig; Immunoglobulin domain

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p12 Primary Assembly

    Genomic

    1. NC_000003.12 Reference GRCh38.p12 Primary Assembly

      Range
      115802363..116445538 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017006383.2XP_016861872.1  limbic system-associated membrane protein isoform X1

      Conserved Domains (4) summary
      smart00408
      Location:232297
      IGc2; Immunoglobulin C-2 Type
      smart00410
      Location:40128
      IG_like; Immunoglobulin like
      pfam07679
      Location:218305
      I-set; Immunoglobulin I-set domain
      cl11960
      Location:38128
      Ig; Immunoglobulin domain
    2. XM_024453520.1XP_024309288.1  limbic system-associated membrane protein isoform X3

      Conserved Domains (2) summary
      pfam13927
      Location:34104
      Ig_3; Immunoglobulin domain
      cd00096
      Location:138205
      Ig; Immunoglobulin domain
    3. XM_024453521.1XP_024309289.1  limbic system-associated membrane protein isoform X4

      Conserved Domains (2) summary
      pfam13927
      Location:34104
      Ig_3; Immunoglobulin domain
      cd00096
      Location:138205
      Ig; Immunoglobulin domain
    4. XM_024453522.1XP_024309290.1  limbic system-associated membrane protein isoform X5

      Conserved Domains (1) summary
      cd00096
      Location:71138
      Ig; Immunoglobulin domain
    5. XM_017006384.2XP_016861873.1  limbic system-associated membrane protein isoform X5

      Conserved Domains (1) summary
      cd00096
      Location:71138
      Ig; Immunoglobulin domain
    6. XM_011512840.3XP_011511142.1  limbic system-associated membrane protein isoform X2

      Conserved Domains (4) summary
      smart00408
      Location:232297
      IGc2; Immunoglobulin C-2 Type
      smart00410
      Location:40128
      IG_like; Immunoglobulin like
      pfam07679
      Location:218305
      I-set; Immunoglobulin I-set domain
      cl11960
      Location:38128
      Ig; Immunoglobulin domain
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