Human Gene LAMP1 (uc001vtm.1)
  Description: Homo sapiens lysosomal-associated membrane protein 1 (LAMP1), mRNA.
RefSeq Summary (NM_005561): The protein encoded by this gene is a member of a family of membrane glycoproteins. This glycoprotein provides selectins with carbohydrate ligands. It may also play a role in tumor cell metastasis. [provided by RefSeq, Jul 2008].
Transcript (Including UTRs)
   Position: hg19 chr13:113,951,469-113,977,741 Size: 26,273 Total Exon Count: 9 Strand: +
Coding Region
   Position: hg19 chr13:113,951,750-113,976,736 Size: 24,987 Coding Exon Count: 9 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsMalaCards
CTDGene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein Structure
Other SpeciesGO AnnotationsmRNA DescriptionsPathwaysOther NamesModel Information
Methods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr13:113,951,469-113,977,741)mRNA (may differ from genome)Protein (417 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMalacards
MGIneXtProtOMIMPubMedReactomeTreefam
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: LAMP1_HUMAN
DESCRIPTION: RecName: Full=Lysosome-associated membrane glycoprotein 1; Short=LAMP-1; Short=Lysosome-associated membrane protein 1; AltName: Full=CD107 antigen-like family member A; AltName: CD_antigen=CD107a; Flags: Precursor;
FUNCTION: Presents carbohydrate ligands to selectins. Also implicated in tumor cell metastasis.
SUBCELLULAR LOCATION: Cell membrane; Single-pass type I membrane protein. Endosome membrane; Single-pass type I membrane protein. Lysosome membrane; Single-pass type I membrane protein. Late endosome. Note=This protein shuttles between lysosomes, endosomes, and the plasma membrane. Co-localizes with OSBPL1A at the late endosome.
PTM: O- and N-glycosylated; some of the 18 N-linked glycans are polylactosaminoglycans.
SIMILARITY: Belongs to the LAMP family.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): LAMP1
CDC HuGE Published Literature: LAMP1
Positive Disease Associations: Arteries , Parkinson Disease
Related Studies:
  1. Arteries
    , , . [PubMed 0]
  2. Parkinson Disease
    , , . [PubMed 0]

-  MalaCards Disease Associations
  MalaCards Gene Search: LAMP1
Diseases sorted by gene-association score: salla disease (4), tuberculosis (4), hermansky-pudlak syndrome 2 (4), lysosomal acid phosphatase deficiency (4), hemophagocytic lymphohistiocytosis (3), retinitis pigmentosa (0)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene
  • D003300 Copper
  • D013749 Tetrachlorodibenzodioxin
  • C404910 2,2-bis(4-hydroxyphenyl)-1,1,1-trichloroethane
  • C532162 2-(1H-indazol-4-yl)-6-(4-methanesulfonylpiperazin-1-ylmethyl)-4-morpholin-4-ylthieno(3,2-d)pyrimidine
  • C030370 2-methoxy-5-(2',3',4'-trimethoxyphenyl)tropone
  • C009505 4,4'-diaminodiphenylmethane
  • C430898 AGN 194204
  • D000643 Ammonium Chloride
  • D001564 Benzo(a)pyrene
  • D001710 Biotin
          more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 156.97 RPKM in Artery - Aorta
Total median expression: 4333.97 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -144.60281-0.515 Picture PostScript Text
3' UTR -380.721005-0.379 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR018134 - LAMP_CS
IPR002000 - Lysosome-assoc_membr_glycop

Pfam Domains:
PF01299 - Lysosome-associated membrane glycoprotein (Lamp)

ModBase Predicted Comparative 3D Structure on P11279
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0001618 virus receptor activity
GO:0005515 protein binding
GO:0019899 enzyme binding
GO:0019904 protein domain specific binding

Biological Process:
GO:0008626 granzyme-mediated apoptotic signaling pathway
GO:0016032 viral process
GO:0043312 neutrophil degranulation
GO:0043323 positive regulation of natural killer cell degranulation
GO:0045954 positive regulation of natural killer cell mediated cytotoxicity
GO:0046718 viral entry into host cell
GO:0048102 autophagic cell death
GO:0050821 protein stabilization
GO:0072594 establishment of protein localization to organelle
GO:0090160 Golgi to lysosome transport
GO:1902513 regulation of organelle transport along microtubule

Cellular Component:
GO:0005737 cytoplasm
GO:0005764 lysosome
GO:0005765 lysosomal membrane
GO:0005768 endosome
GO:0005770 late endosome
GO:0005771 multivesicular body
GO:0005773 vacuole
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0005887 integral component of plasma membrane
GO:0008021 synaptic vesicle
GO:0009897 external side of plasma membrane
GO:0009986 cell surface
GO:0010008 endosome membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0030425 dendrite
GO:0031410 cytoplasmic vesicle
GO:0031982 vesicle
GO:0035577 azurophil granule membrane
GO:0042383 sarcolemma
GO:0042470 melanosome
GO:0043025 neuronal cell body
GO:0044194 cytolytic granule
GO:0044754 autolysosome
GO:0045335 phagocytic vesicle
GO:0048471 perinuclear region of cytoplasm
GO:0061474 phagolysosome membrane
GO:0070062 extracellular exosome
GO:0097208 alveolar lamellar body
GO:0101003 ficolin-1-rich granule membrane


-  Descriptions from all associated GenBank mRNAs
  E02135 - cDNA encoding human tumor necrosis factor.
E01813 - cDNA encoding human tumor cytotoxic factor.
AK092398 - Homo sapiens cDNA FLJ35079 fis, clone PLACE6005283, highly similar to Lysosome-associated membrane glycoprotein 1 precursor.
BC025335 - Homo sapiens lysosomal-associated membrane protein 1, mRNA (cDNA clone IMAGE:4583687).
BC093044 - Homo sapiens lysosomal-associated membrane protein 1, mRNA (cDNA clone MGC:111070 IMAGE:30390596), complete cds.
J04182 - Homo sapiens lysosomal membrane glycoprotein-1 (LAMP1) mRNA, complete cds.
BC021288 - Homo sapiens lysosomal-associated membrane protein 1, mRNA (cDNA clone MGC:29494 IMAGE:5019745), complete cds.
AK301584 - Homo sapiens cDNA FLJ57633 complete cds, highly similar to Lysosome-associated membrane glycoprotein 1 precursor.
AB463850 - Synthetic construct DNA, clone: pF1KB8102, Homo sapiens LAMP1 gene for lysosomal-associated membrane protein 1, without stop codon, in Flexi system.
KJ891533 - Synthetic construct Homo sapiens clone ccsbBroadEn_00927 LAMP1 gene, encodes complete protein.
DQ895854 - Synthetic construct Homo sapiens clone IMAGE:100010314; FLH188327.01L; RZPDo839B0363D lysosomal-associated membrane protein 1 (LAMP1) gene, encodes complete protein.
DQ892614 - Synthetic construct clone IMAGE:100005244; FLH188331.01X; RZPDo839B0373D lysosomal-associated membrane protein 1 (LAMP1) gene, encodes complete protein.
AB209319 - Homo sapiens mRNA for LAMP1 protein variant protein.
J03263 - Human lysosome-associated membrane glycoprotein (lamp A) mRNA, complete cds.
BC006345 - Homo sapiens lysosomal-associated membrane protein 1, mRNA (cDNA clone IMAGE:4100802), partial cds.
BC007845 - Homo sapiens lysosomal-associated membrane protein 1, mRNA (cDNA clone IMAGE:4128923), partial cds.
JD528098 - Sequence 509122 from Patent EP1572962.
JD404557 - Sequence 385581 from Patent EP1572962.
DQ599164 - Homo sapiens piRNA piR-37230, complete sequence.
JD060802 - Sequence 41826 from Patent EP1572962.
JD259369 - Sequence 240393 from Patent EP1572962.
JD544430 - Sequence 525454 from Patent EP1572962.
JD235780 - Sequence 216804 from Patent EP1572962.
JD091618 - Sequence 72642 from Patent EP1572962.
JD175242 - Sequence 156266 from Patent EP1572962.
JD181235 - Sequence 162259 from Patent EP1572962.
JD362178 - Sequence 343202 from Patent EP1572962.
JD254975 - Sequence 235999 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04142 - Lysosome

Reactome (by CSHL, EBI, and GO)

Protein P11279 (Reactome details) participates in the following event(s):

R-HSA-6798739 Exocytosis of azurophil granule membrane proteins
R-HSA-6800426 Exocytosis of ficolin-rich granule membrane proteins
R-HSA-6798695 Neutrophil degranulation
R-HSA-168249 Innate Immune System
R-HSA-168256 Immune System

-  Other Names for This Gene
  Alternate Gene Symbols: LAMP1_HUMAN, NM_005561, NP_005552, P11279, Q8WU33, Q96I40, Q9BRD2, Q9NP13
UCSC ID: uc001vtm.1
RefSeq Accession: NM_005561
Protein: P11279 (aka LAMP1_HUMAN or LMP1_HUMAN)
CCDS: CCDS41909.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_005561.3
exon count: 9CDS single in 3' UTR: no RNA size: 2560
ORF size: 1254CDS single in intron: no Alignment % ID: 99.88
txCdsPredict score: 2705.00frame shift in genome: no % Coverage: 99.22
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.