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

Gene ID: 4045, updated on 3-Dec-2023

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; AllianceGenome:HGNC:6705
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
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Genomic context

See LSAMP in Genome Data Viewer
Location:
3q13.31
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (115802374..116445487, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (118522573..119165711, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (115521221..116164334, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14618 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:115376638-115377510 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:115377511-115378382 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:115417888-115418741 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:115431872-115432372 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:115432373-115432873 Neighboring gene growth associated protein 43 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:115502891-115503391 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr3:115503423-115504101 Neighboring gene uncharacterized LOC124909412 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:115511955-115512480 Neighboring gene uncharacterized LOC124906269 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:115512481-115513006 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr3:115513007-115513531 Neighboring gene NANOG hESC enhancer GRCh37_chr3:115513693-115514194 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:115514334-115515272 Neighboring gene 3q13.2-q13.31 distal HERV-H recombination region Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:115515273-115516210 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:115517565-115518070 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20285 Neighboring gene uncharacterized LOC124909413 Neighboring gene uncharacterized LOC105374053 Neighboring gene RNA, 7SL, cytoplasmic 815, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20286 Neighboring gene small nucleolar RNA, C/D box 155 Neighboring gene uncharacterized LOC107986116 Neighboring gene uncharacterized LOC124909414 Neighboring gene NANOG hESC enhancer GRCh37_chr3:115709155-115709940 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20287 Neighboring gene NANOG hESC enhancer GRCh37_chr3:115809463-115809964 Neighboring gene uncharacterized LOC105374052 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:115917016-115917516 Neighboring gene NANOG hESC enhancer GRCh37_chr3:115975635-115976191 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:115978423-115979314 Neighboring gene MPRA-validated peak4776 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr3:116065268-116065439 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:116079173-116079763 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:116110286-116110815 Neighboring gene LSAMP antisense RNA 1 Neighboring gene NANOG hESC enhancer GRCh37_chr3:116238426-116238927 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 Functions

What's a GeneRIF?

Phenotypes

EBI GWAS Catalog

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • FLJ34254, FLJ35396, FLJ37216, FLJ54658

Gene Ontology Provided by GOA

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

General protein information

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

NCBI Reference Sequences (RefSeq)

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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/TrEMBL
    H3BLU2
    Related
    ENSP00000328455.4, ENST00000333617.8
    Conserved Domains (2) summary
    pfam13927
    Location:219294
    Ig_3; 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, Q8IV49
    UniProtKB/TrEMBL
    H3BLU2
    Related
    ENSP00000419000.1, ENST00000490035.7
    Conserved Domains (3) summary
    pfam13927
    Location:218294
    Ig_3; Immunoglobulin domain
    cd00096
    Location:235239
    Ig; Ig strand B [structural motif]
    cl11960
    Location:38128
    Ig; Immunoglobulin domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    115802374..116445487 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017006383.3XP_016861872.1  limbic system-associated membrane protein isoform X1

    UniProtKB/TrEMBL
    H3BLU2
    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_024453520.2XP_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_024453522.2XP_024309290.1  limbic system-associated membrane protein isoform X4

    Conserved Domains (1) summary
    cd00096
    Location:71138
    Ig; Immunoglobulin domain
  4. XM_017006384.3XP_016861873.1  limbic system-associated membrane protein isoform X4

    Conserved Domains (1) summary
    cd00096
    Location:71138
    Ig; Immunoglobulin domain
  5. XM_011512840.4XP_011511142.1  limbic system-associated membrane protein isoform X2

    UniProtKB/TrEMBL
    H3BLU2
    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

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    118522573..119165711 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054346509.1XP_054202484.1  limbic system-associated membrane protein isoform X1

    UniProtKB/TrEMBL
    H3BLU2
  2. XM_054346511.1XP_054202486.1  limbic system-associated membrane protein isoform X3

  3. XM_054346512.1XP_054202487.1  limbic system-associated membrane protein isoform X4

  4. XM_054346513.1XP_054202488.1  limbic system-associated membrane protein isoform X4

  5. XM_054346510.1XP_054202485.1  limbic system-associated membrane protein isoform X2

    UniProtKB/TrEMBL
    H3BLU2