Human Gene LAMP2 (uc011mtz.2)
  Description: Homo sapiens lysosomal-associated membrane protein 2 (LAMP2), transcript variant C, mRNA.
RefSeq Summary (NM_001122606): The protein encoded by this gene is a member of a family of membrane glycoproteins. This glycoprotein provides selectins with carbohydrate ligands. It may play a role in tumor cell metastasis. It may also function in the protection, maintenance, and adhesion of the lysosome. Alternative splicing of this gene results in multiple transcript variants encoding distinct proteins. [provided by RefSeq, Jul 2008].
Transcript (Including UTRs)
   Position: hg19 chrX:119,560,003-119,603,204 Size: 43,202 Total Exon Count: 7 Strand: -
Coding Region
   Position: hg19 chrX:119,562,339-119,603,024 Size: 40,686 Coding Exon Count: 7 

Page IndexSequence and LinksPrimersGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesGeneReviewsModel Information
Methods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chrX:119,560,003-119,603,204)mRNA (may differ from genome)Protein (300 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCLynxMalacardsMGI
OMIMPubMedUniProtKBWikipediaBioGrid CRISPR DB

-  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): LAMP2
CDC HuGE Published Literature: LAMP2

-  MalaCards Disease Associations
  MalaCards Gene Search: LAMP2
Diseases sorted by gene-association score: danon disease* (1711), cardiomyopathy* (150), atrial standstill, digenic* (126), glycogen storage disease ii (18), lysosomal acid phosphatase deficiency (14), salla disease (12), myopathy, x-linked, with excessive autophagy (12), fabry disease (9), cholesterol ester storage disease (6), myopathy (5), dilated cardiomyopathy (2), cardiomyopathy, familial hypertrophic (1)
* = Manually curated disease association

-  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: 59.78 RPKM in Brain - Spinal cord (cervical c-1)
Total median expression: 1126.55 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 -69.00180-0.383 Picture PostScript Text
3' UTR -549.912336-0.235 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)

ModBase Predicted Comparative 3D Structure on B7Z2R9
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
  Cellular Component:
GO:0005764 lysosome
GO:0005765 lysosomal membrane
GO:0016020 membrane
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  BC040653 - Homo sapiens cDNA clone IMAGE:4797120.
LF385316 - JP 2014500723-A/192819: Polycomb-Associated Non-Coding RNAs.
AK226066 - Homo sapiens mRNA for lysosomal-associated membrane protein 2 precursor variant, clone: fj10535.
AK295038 - Homo sapiens cDNA FLJ52540 complete cds, highly similar to Lysosome-associated membrane glycoprotein 2 precursor.
AY561849 - Homo sapiens lysosomal-associated membrane protein 2C (LAMP2) mRNA, complete cds.
AB528277 - Synthetic construct DNA, clone: pF1KB9376, Homo sapiens LAMP2 gene for lysosomal-associated membrane protein 2, without stop codon, in Flexi system.
LF379868 - JP 2014500723-A/187371: Polycomb-Associated Non-Coding RNAs.
X77196 - H.sapiens mRNA for lysosome-associated membrane protein-2.
AK291090 - Homo sapiens cDNA FLJ77117 complete cds, highly similar to Homo sapiens lysosomal-associated membrane protein 2 (LAMP2), transcript variant LAMP2A, mRNA.
J04183 - Homo sapiens lysosomal membrane glycoprotein-2 (LAMP2), complete cds.
S79873 - h-lamp-2=lysosome-associated membrane protein-2 {alternatively spliced} [human, liver, mRNA, 4006 nt].
U36336 - Human lysosome-associated membrane protein-2b (LAMP2) mRNA, alternatively spliced form h-lamp-2b, complete cds.
BC002965 - Homo sapiens lysosomal-associated membrane protein 2, mRNA (cDNA clone MGC:1710 IMAGE:3543019), complete cds.
AK293931 - Homo sapiens cDNA FLJ52535 complete cds, highly similar to Homo sapiens lysosomal-associated membrane protein 2 (LAMP2), transcript variant LAMP2B, mRNA.
AK304405 - Homo sapiens cDNA FLJ58780 complete cds, highly similar to Homo sapiens lysosomal-associated membrane protein 2 (LAMP2), transcript variant LAMP2B, mRNA.
KJ897118 - Synthetic construct Homo sapiens clone ccsbBroadEn_06512 LAMP2 gene, encodes complete protein.
KR709861 - Synthetic construct Homo sapiens clone CCSBHm_00006896 LAMP2 (LAMP2) mRNA, encodes complete protein.
KR709862 - Synthetic construct Homo sapiens clone CCSBHm_00006897 LAMP2 (LAMP2) mRNA, encodes complete protein.
DQ892095 - Synthetic construct clone IMAGE:100004725; FLH186841.01X; RZPDo839B0172D lysosomal-associated membrane protein 2 (LAMP2) gene, encodes complete protein.
DQ895288 - Synthetic construct Homo sapiens clone IMAGE:100009748; FLH186837.01L; RZPDo839B0162D lysosomal-associated membrane protein 2 (LAMP2) gene, encodes complete protein.
LF379882 - JP 2014500723-A/187385: Polycomb-Associated Non-Coding RNAs.
LF379883 - JP 2014500723-A/187386: Polycomb-Associated Non-Coding RNAs.
LF379887 - JP 2014500723-A/187390: Polycomb-Associated Non-Coding RNAs.
LF379888 - JP 2014500723-A/187391: Polycomb-Associated Non-Coding RNAs.
CU678318 - Synthetic construct Homo sapiens gateway clone IMAGE:100019273 5' read LAMP2 mRNA.
LF379889 - JP 2014500723-A/187392: Polycomb-Associated Non-Coding RNAs.
LF211457 - JP 2014500723-A/18960: Polycomb-Associated Non-Coding RNAs.
JD071608 - Sequence 52632 from Patent EP1572962.
MA620893 - JP 2018138019-A/192819: Polycomb-Associated Non-Coding RNAs.
MA615445 - JP 2018138019-A/187371: Polycomb-Associated Non-Coding RNAs.
MA615459 - JP 2018138019-A/187385: Polycomb-Associated Non-Coding RNAs.
MA615460 - JP 2018138019-A/187386: Polycomb-Associated Non-Coding RNAs.
MA615464 - JP 2018138019-A/187390: Polycomb-Associated Non-Coding RNAs.
MA615465 - JP 2018138019-A/187391: Polycomb-Associated Non-Coding RNAs.
MA615466 - JP 2018138019-A/187392: Polycomb-Associated Non-Coding RNAs.
MA447034 - JP 2018138019-A/18960: Polycomb-Associated Non-Coding RNAs.

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

-  Other Names for This Gene
  Alternate Gene Symbols: AK295038, B7Z2R9, B7Z2R9_HUMAN, NM_001122606, NP_001116078
UCSC ID: uc011mtz.2
RefSeq Accession: NM_001122606
Protein: B7Z2R9

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene LAMP2:
danon (Danon Disease)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: AK295038.1
exon count: 7CDS single in 3' UTR: no RNA size: 1433
ORF size: 903CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1971.50frame shift in genome: no % Coverage: 99.93
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.