Human Gene LAMB3 (uc001hhh.3) Description and Page Index
  Description: Homo sapiens laminin, beta 3 (LAMB3), transcript variant 1, mRNA.
RefSeq Summary (NM_000228): The product encoded by this gene is a laminin that belongs to a family of basement membrane proteins. This protein is a beta subunit laminin, which together with an alpha and a gamma subunit, forms laminin-5. Mutations in this gene cause epidermolysis bullosa junctional Herlitz type, and generalized atrophic benign epidermolysis bullosa, diseases that are characterized by blistering of the skin. Multiple alternatively spliced transcript variants that encode the same protein have been found for this gene. [provided by RefSeq, Jul 2008].
Transcript (Including UTRs)
   Position: hg19 chr1:209,788,218-209,825,820 Size: 37,603 Total Exon Count: 23 Strand: -
Coding Region
   Position: hg19 chr1:209,788,616-209,824,289 Size: 35,674 Coding Exon Count: 22 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:209,788,218-209,825,820)mRNA (may differ from genome)Protein (1172 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkHGNCHPRDLynxMGIneXtProt
OMIMPubMedReactomeStanford SOURCETreefamUniProtKB
Wikipedia

-  Comments and Description Text from UniProtKB
  ID: LAMB3_HUMAN
DESCRIPTION: RecName: Full=Laminin subunit beta-3; AltName: Full=Epiligrin subunit bata; AltName: Full=Kalinin B1 chain; AltName: Full=Kalinin subunit beta; AltName: Full=Laminin B1k chain; AltName: Full=Laminin-5 subunit beta; AltName: Full=Nicein subunit beta; Flags: Precursor;
FUNCTION: Binding to cells via a high affinity receptor, laminin is thought to mediate the attachment, migration and organization of cells into tissues during embryonic development by interacting with other extracellular matrix components.
SUBUNIT: Laminin is a complex glycoprotein, consisting of three different polypeptide chains (alpha, beta, gamma), which are bound to each other by disulfide bonds into a cross-shaped molecule comprising one long and three short arms with globules at each end. Beta-3 is a subunit of laminin-5 (laminin-332 or epiligrin/kalinin/nicein). Interacts with ECM1.
SUBCELLULAR LOCATION: Secreted, extracellular space, extracellular matrix, basement membrane.
TISSUE SPECIFICITY: Found in the basement membranes (major component).
DOMAIN: The alpha-helical domains I and II are thought to interact with other laminin chains to form a coiled coil structure.
DOMAIN: Domain VI is globular.
DISEASE: Defects in LAMB3 are a cause of epidermolysis bullosa junctional Herlitz type (H-JEB) [MIM:226700]; also known as junctional epidermolysis bullosa Herlitz-Pearson type. JEB defines a group of blistering skin diseases characterized by tissue separation which occurs within the dermo-epidermal basement membrane. H-JEB is a severe, infantile and lethal form. Death occurs usually within the first six months of life. Occasionally, children survive to teens. H-JEB is marked by bullous lesions at birth and extensive denudation of skin and mucous membranes that may be hemorrhagic.
DISEASE: Defects in LAMB3 are a cause of generalized atrophic benign epidermolysis bullosa (GABEB) [MIM:226650]. GABEB is a non- lethal, adult form of junctional epidermolysis bullosa characterized by life-long blistering of the skin, associated with hair and tooth abnormalities.
SIMILARITY: Contains 6 laminin EGF-like domains.
SIMILARITY: Contains 1 laminin N-terminal domain.
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/LAMB3";

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): LAMB3
CDC HuGE Published Literature: LAMB3

-  MalaCards Disease Associations
  MalaCards Gene Search: LAMB3
Diseases sorted by gene-association score: epidermolysis bullosa, junctional, herlitz type* (1599), epidermolysis bullosa, junctional, non-herlitz type* (1117), amelogenesis imperfecta, type ia* (1000), hypoplastic amelogenesis imperfecta* (261), lamb3-related junctional epidermolysis bullosa* (100), epidermolysis bullosa (33), junctional epidermolysis bullosa (26), vesiculobullous skin disease (14), maternal uniparental disomy of chromosome 1 (13), cardiomyopathy, dilated, 1d (9), bullous pemphigoid (8), skin disease (3)
* = 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: 24.17 RPKM in Skin - Sun Exposed (Lower leg)
Total median expression: 261.92 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 -50.00144-0.347 Picture PostScript Text
3' UTR -124.34398-0.312 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
IPR013032 - EGF-like_CS
IPR002049 - EGF_laminin
IPR008211 - Laminin_N

Pfam Domains:
PF00053 - Laminin EGF domain
PF00055 - Laminin N-terminal (Domain VI)

SCOP Domains:
46966 - Spectrin repeat
49785 - Galactose-binding domain-like
57196 - EGF/Laminin

ModBase Predicted Comparative 3D Structure on Q13751
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
  Molecular Function:
GO:0005198 structural molecule activity
GO:0005515 protein binding
GO:0044877 macromolecular complex binding

Biological Process:
GO:0007155 cell adhesion
GO:0008544 epidermis development
GO:0030198 extracellular matrix organization
GO:0031581 hemidesmosome assembly
GO:0035987 endodermal cell differentiation
GO:0050873 brown fat cell differentiation

Cellular Component:
GO:0005576 extracellular region
GO:0005604 basement membrane
GO:0005610 laminin-5 complex


-  Descriptions from all associated GenBank mRNAs
  BC075838 - Homo sapiens laminin, beta 3, mRNA (cDNA clone MGC:88729 IMAGE:6291096), complete cds.
BC058922 - Homo sapiens cDNA clone IMAGE:5175186, containing frame-shift errors.
D37766 - Homo sapiens mRNA for Laminin-5 beta3 chain, complete cds.
JD360177 - Sequence 341201 from Patent EP1572962.
JD368056 - Sequence 349080 from Patent EP1572962.
L25541 - Human laminin S B3 chain (LAMB3) mRNA, complete cds.
JD560481 - Sequence 541505 from Patent EP1572962.
JD353792 - Sequence 334816 from Patent EP1572962.
JD166809 - Sequence 147833 from Patent EP1572962.
AY035783 - Homo sapiens laminin 5 beta 3 subunit (LAMB3) mRNA, complete cds.
EU831471 - Synthetic construct Homo sapiens clone HAIB:100066500; DKFZo008G0117 laminin, beta 3 protein (LAMB3) gene, encodes complete protein.
EU831558 - Synthetic construct Homo sapiens clone HAIB:100066587; DKFZo004G0118 laminin, beta 3 protein (LAMB3) gene, encodes complete protein.
AB384989 - Synthetic construct DNA, clone: pF1KB4802, Homo sapiens LAMB3 gene for laminin subunit beta-3 precursor, complete cds, without stop codon, in Flexi system.
KU178159 - Homo sapiens laminin beta 3 isoform 1 (LAMB3) mRNA, partial cds.
KU178160 - Homo sapiens laminin beta 3 isoform 2 (LAMB3) mRNA, complete cds, alternatively spliced.
AK296851 - Homo sapiens cDNA FLJ61309 complete cds, highly similar to Laminin beta-3 chain precursor.
JD020357 - Sequence 1381 from Patent EP1572962.
JD031290 - Sequence 12314 from Patent EP1572962.
AK309524 - Homo sapiens cDNA, FLJ99565.
JD023876 - Sequence 4900 from Patent EP1572962.
JD030717 - Sequence 11741 from Patent EP1572962.
JD021548 - Sequence 2572 from Patent EP1572962.
JD029427 - Sequence 10451 from Patent EP1572962.
JD024888 - Sequence 5912 from Patent EP1572962.
JD426138 - Sequence 407162 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04510 - Focal adhesion
hsa04512 - ECM-receptor interaction
hsa05200 - Pathways in cancer
hsa05222 - Small cell lung cancer

Reactome (by CSHL, EBI, and GO)

Protein Q13751 (Reactome details) participates in the following event(s):

R-HSA-349626 Integrin alpha2beta1 binds laminin-332
R-HSA-446089 BP180 interacts extracellularly with Laminin 332
R-HSA-1566979 Laminin-332 degradation by laminin-322 degrading extracellular proteinases
R-HSA-2396234 Collagen type VII binds laminin-322 and collagen IV
R-HSA-3787997 Laminin-332 binds collagen type VII
R-HSA-3791155 Laminin-322 degradation by MMP14
R-HSA-432956 BP230 is recruited to the hemidesmosome
R-HSA-2213192 Hemidesmosome formation
R-HSA-216048 Integrins alpha3beta1, alpha6beta4 bind laminin-332, 511, 521, (211, 221)
R-HSA-3907292 Integrin alpha6beta1 binds laminin-322, 512, 521, 211, 221, 411
R-HSA-2328129 Dystroglycan binds Laminins and Dystrophin
R-HSA-2396083 Laminins bind galactosyl sulfatide and related sulfated glycolipids
R-HSA-446083 CD151 interacts with BP180 and the integrin alpha 6 subunit
R-HSA-446077 BP230 interacts with keretin K5/K14
R-HSA-3000157 Laminin interactions
R-HSA-446107 Type I hemidesmosome assembly
R-HSA-1474228 Degradation of the extracellular matrix
R-HSA-2214320 Anchoring fibril formation
R-HSA-2022090 Assembly of collagen fibrils and other multimeric structures
R-HSA-3000171 Non-integrin membrane-ECM interactions
R-HSA-1474244 Extracellular matrix organization
R-HSA-446728 Cell junction organization
R-HSA-1474290 Collagen formation
R-HSA-1500931 Cell-Cell communication

-  Other Names for This Gene
  Alternate Gene Symbols: D3DT88, LAMB3_HUMAN, LAMNB1, NM_000228, NP_001121113, O14947, Q13751, Q14733, Q9UJK4, Q9UJL1
UCSC ID: uc001hhh.3
RefSeq Accession: NM_000228
Protein: Q13751 (aka LAMB3_HUMAN or LMB3_HUMAN)
CCDS: CCDS1487.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene LAMB3:
ebj (Junctional Epidermolysis Bullosa)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_000228.2
exon count: 23CDS single in 3' UTR: no RNA size: 4093
ORF size: 3519CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3856.00frame 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.