Human Gene LAMP3 (uc003flh.4) Description and Page Index
  Description: Homo sapiens lysosomal-associated membrane protein 3 (LAMP3), mRNA.
RefSeq Summary (NM_014398): Dendritic cells (DCs) are the most potent antigen-presenting cells. Immature DCs efficiently capture antigens and differentiate into interdigitating dendritic cells (IDCs) in lymphoid tissues that induce primary T-cell responses (summary by de Saint-Vis et al., 1998 [PubMed 9768752]).[supplied by OMIM, Dec 2010]. Sequence Note: This RefSeq record was created from transcript and genomic sequence data because no single transcript was available for the full length of the gene. The extent of this transcript is supported by transcript alignments. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: BC032940.2, AB013924.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA2144333 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000265598.8/ ENSP00000265598.3 RefSeq Select criteria :: based on conservation, expression ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr3:182,840,003-182,880,667 Size: 40,665 Total Exon Count: 6 Strand: -
Coding Region
   Position: hg19 chr3:182,841,869-182,880,443 Size: 38,575 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr3:182,840,003-182,880,667)mRNA (may differ from genome)Protein (416 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCHPRDLynxMGIneXtProt
OMIMPubMedStanford SOURCETreefamUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: LAMP3_HUMAN
DESCRIPTION: RecName: Full=Lysosome-associated membrane glycoprotein 3; Short=LAMP-3; Short=Lysosomal-associated membrane protein 3; AltName: Full=DC-lysosome-associated membrane glycoprotein; Short=DC LAMP; AltName: Full=Protein TSC403; AltName: CD_antigen=CD208; Flags: Precursor;
FUNCTION: Might change the lysosome function after the transfer of peptide-MHC class II molecules to the surface of dendritic cells.
SUBCELLULAR LOCATION: Lysosome membrane; Single-pass type I membrane protein.
TISSUE SPECIFICITY: Expressed in lymphoid organs and dendritic cells. Expressed in lung. Up-regulated in carcinomas of the esophagus, colon, rectum, ureter, stomach, breast, fallopian tube, thyroid and parotid tissues.
SIMILARITY: Belongs to the LAMP family.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): LAMP3
CDC HuGE Published Literature: LAMP3
Positive Disease Associations: Bipolar Disorder
Related Studies:
  1. Bipolar Disorder
    Paul R Burton et al. Nature 2007, Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls., Nature. [PubMed 17554300]
  2. Bipolar Disorder
    Yuan Jiang et al. Genetic epidemiology 2011, Propensity score-based nonparametric test revealing genetic variants underlying bipolar disorder., Genetic epidemiology. [PubMed 21254220]

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           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: 49.56 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 121.12 RPKM



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

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -109.90224-0.491 Picture PostScript Text
3' UTR -495.331866-0.265 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
IPR002000 - Lysosome-assoc_membr_glycop

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

Protein Data Bank (PDB) 3-D Structure
MuPIT help

4AKM
- X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q9UQV4
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 orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Biological Process:
GO:0002250 adaptive immune response
GO:0002376 immune system process
GO:0010506 regulation of autophagy
GO:0010628 positive regulation of gene expression
GO:0035455 response to interferon-alpha
GO:0043154 negative regulation of cysteine-type endopeptidase activity involved in apoptotic process
GO:1901799 negative regulation of proteasomal protein catabolic process
GO:1903900 regulation of viral life cycle
GO:0046718 viral entry into host cell

Cellular Component:
GO:0005764 lysosome
GO:0005765 lysosomal membrane
GO:0005769 early endosome
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0030659 cytoplasmic vesicle membrane
GO:0031410 cytoplasmic vesicle
GO:0031982 vesicle
GO:0043231 intracellular membrane-bounded organelle
GO:0048471 perinuclear region of cytoplasm
GO:0097233 alveolar lamellar body membrane


-  Descriptions from all associated GenBank mRNAs
  BC032940 - Homo sapiens lysosomal-associated membrane protein 3, mRNA (cDNA clone MGC:26448 IMAGE:4829125), complete cds.
AJ005766 - Homo sapiens mRNA for lysosome-associated membrane protein.
AB013924 - Homo sapiens mRNA for TSC403 protein, complete cds.
LQ878897 - Sequence 12 from Patent WO2018154075.
AK302894 - Homo sapiens cDNA FLJ51411 complete cds, highly similar to Lysosome-associated membrane glycoprotein 3 precursor.
AK313172 - Homo sapiens cDNA, FLJ93669, highly similar to Homo sapiens lysosomal-associated membrane protein 3 (LAMP3), mRNA.
KJ898657 - Synthetic construct Homo sapiens clone ccsbBroadEn_08051 LAMP3 gene, encodes complete protein.
DQ892118 - Synthetic construct clone IMAGE:100004748; FLH183197.01X; RZPDo839H02140D lysosomal-associated membrane protein 3 (LAMP3) gene, encodes complete protein.
JD358533 - Sequence 339557 from Patent EP1572962.
JD327080 - Sequence 308104 from Patent EP1572962.
JD429485 - Sequence 410509 from Patent EP1572962.
JD467803 - Sequence 448827 from Patent EP1572962.
JD273386 - Sequence 254410 from Patent EP1572962.
JD360216 - Sequence 341240 from Patent EP1572962.
JD065407 - Sequence 46431 from Patent EP1572962.
JD137254 - Sequence 118278 from Patent EP1572962.
JD239544 - Sequence 220568 from Patent EP1572962.
JD364172 - Sequence 345196 from Patent EP1572962.
JD168622 - Sequence 149646 from Patent EP1572962.
JD504362 - Sequence 485386 from Patent EP1572962.
JD236995 - Sequence 218019 from Patent EP1572962.
JD524887 - Sequence 505911 from Patent EP1572962.
JD052158 - Sequence 33182 from Patent EP1572962.
JD094871 - Sequence 75895 from Patent EP1572962.
JD359859 - Sequence 340883 from Patent EP1572962.
JD330332 - Sequence 311356 from Patent EP1572962.
JD112959 - Sequence 93983 from Patent EP1572962.
JD285400 - Sequence 266424 from Patent EP1572962.
JD285399 - Sequence 266423 from Patent EP1572962.
JD072188 - Sequence 53212 from Patent EP1572962.
JD213571 - Sequence 194595 from Patent EP1572962.
JD407927 - Sequence 388951 from Patent EP1572962.
JD256911 - Sequence 237935 from Patent EP1572962.
JD258888 - Sequence 239912 from Patent EP1572962.
JD353184 - Sequence 334208 from Patent EP1572962.
JD213570 - Sequence 194594 from Patent EP1572962.
JD353183 - Sequence 334207 from Patent EP1572962.
JD274870 - Sequence 255894 from Patent EP1572962.
JD428888 - Sequence 409912 from Patent EP1572962.
JD436605 - Sequence 417629 from Patent EP1572962.
JD053991 - Sequence 35015 from Patent EP1572962.
JD519328 - Sequence 500352 from Patent EP1572962.
JD365033 - Sequence 346057 from Patent EP1572962.

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

-  Other Names for This Gene
  Alternate Gene Symbols: D3DNS4, DCLAMP, LAMP3_HUMAN, NM_014398, NP_055213, O94781, Q8NEC8, Q9UQV4, TSC403
UCSC ID: uc003flh.4
RefSeq Accession: NM_014398
Protein: Q9UQV4 (aka LAMP3_HUMAN)
CCDS: CCDS3242.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_014398.3
exon count: 6CDS single in 3' UTR: no RNA size: 3341
ORF size: 1251CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2702.00frame shift in genome: no % Coverage: 100.00
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.