Human Gene LAMA3 (ENST00000313654.14_6) from GENCODE V47lift37
  Description: laminin subunit alpha 3, transcript variant 1 (from RefSeq NM_198129.4)
Gencode Transcript: ENST00000313654.14_6
Gencode Gene: ENSG00000053747.17_10
Transcript (Including UTRs)
   Position: hg19 chr18:21,269,417-21,535,030 Size: 265,614 Total Exon Count: 75 Strand: +
Coding Region
   Position: hg19 chr18:21,269,648-21,534,612 Size: 264,965 Coding Exon Count: 75 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesGeneReviewsModel Information
Methods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr18:21,269,417-21,535,030)mRNA (may differ from genome)Protein (3333 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: LAMA3_HUMAN
DESCRIPTION: RecName: Full=Laminin subunit alpha-3; AltName: Full=Epiligrin 170 kDa subunit; Short=E170; AltName: Full=Epiligrin subunit alpha; AltName: Full=Kalinin subunit alpha; AltName: Full=Laminin-5 subunit alpha; AltName: Full=Laminin-6 subunit alpha; AltName: Full=Laminin-7 subunit alpha; AltName: Full=Nicein subunit alpha; 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.
FUNCTION: Laminin-5 is thought to be involved in (1) cell adhesion via integrin alpha-3/beta-1 in focal adhesion and integrin alpha- 6/beta-4 in hemidesmosomes, (2) signal transduction via tyrosine phosphorylation of pp125-FAK and p80, (3) differentiation of keratinocytes.
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. Alpha-3 is a subunit of laminin-5 (laminin-332 or epiligrin/kalinin/nicein), laminin-6 (laminin-311 or K-laminin) and laminin-7 (laminin-321 or KS-laminin).
SUBCELLULAR LOCATION: Secreted, extracellular space, extracellular matrix, basement membrane. Note=Major component.
TISSUE SPECIFICITY: Skin; respiratory, urinary, and digestive epithelia and in other specialized tissues with prominent secretory or protective functions. Epithelial basement membrane, and epithelial cell tongue that migrates into a wound bed. A differential and focal expression of the subunit alpha-3 is observed in the CNS.
INDUCTION: Laminin-5 is up-regulated in wound sites of human skin.
DOMAIN: The alpha-helical domains I and II are thought to interact with other laminin chains to form a coiled coil structure.
DOMAIN: Domain G is globular.
DISEASE: Defects in LAMA3 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 LAMA3 are the cause of laryngoonychocutaneous syndrome (LOCS) [MIM:245660]. LOCS is an autosomal recessive epithelial disorder confined to the Punjabi Muslim population. The condition is characterized by cutaneous erosions, nail dystrophy and exuberant vascular granulation tissue in certain epithelia, especially conjunctiva and larynx.
SIMILARITY: Contains 15 laminin EGF-like domains.
SIMILARITY: Contains 5 laminin G-like domains.
SIMILARITY: Contains 1 laminin IV type A domain.
SIMILARITY: Contains 1 laminin N-terminal domain.
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/LAMA3";

-  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


-  MalaCards Disease Associations
  MalaCards Gene Search: LAMA3
Diseases sorted by gene-association score: laryngoonychocutaneous syndrome* (1379), epidermolysis bullosa, junctional, herlitz type* (733), epidermolysis bullosa, junctional, non-herlitz type* (566), lama3-related junctional epidermolysis bullosa* (100), junctional epidermolysis bullosa (35), cicatricial pemphigoid (26), epidermolysis bullosa acquisita (24), epidermolysis bullosa (19), maternal uniparental disomy of chromosome 1 (18), bullous pemphigoid (8), nuclear senile cataract (8), vitreous detachment (6), bullous skin disease (6), vesiculobullous skin disease (5), autoimmune disease of skin and connective tissue (5), lens disease (5)
* = 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: 11.29 RPKM in Lung
Total median expression: 171.82 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 -131.10231-0.568 Picture PostScript Text
3' UTR -63.70418-0.152 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
IPR008985 - ConA-like_lec_gl_sf
IPR013320 - ConA-like_subgrp
IPR013032 - EGF-like_CS
IPR002049 - EGF_laminin
IPR009030 - Growth_fac_rcpt
IPR018031 - Laminin_B_subgr
IPR000034 - Laminin_B_type_IV
IPR001791 - Laminin_G
IPR009254 - Laminin_I
IPR010307 - Laminin_II
IPR008211 - Laminin_N

Pfam Domains:
PF00052 - Laminin B (Domain IV)
PF00053 - Laminin EGF domain
PF00054 - Laminin G domain
PF00055 - Laminin N-terminal (Domain VI)
PF02210 - Laminin G domain
PF06008 - Laminin Domain I
PF06009 - Laminin Domain II
PF13385 - Concanavalin A-like lectin/glucanases superfamily

SCOP Domains:
49785 - Galactose-binding domain-like
49899 - Concanavalin A-like lectins/glucanases
57196 - EGF/Laminin
57184 - Growth factor receptor domain
57997 - Tropomyosin
58104 - Methyl-accepting chemotaxis protein (MCP) signaling domain

ModBase Predicted Comparative 3D Structure on Q16787
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 DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005102 receptor binding
GO:0005198 structural molecule activity

Biological Process:
GO:0007155 cell adhesion
GO:0008544 epidermis development
GO:0030155 regulation of cell adhesion
GO:0030198 extracellular matrix organization
GO:0030334 regulation of cell migration
GO:0031581 hemidesmosome assembly
GO:0035987 endodermal cell differentiation
GO:0045995 regulation of embryonic development

Cellular Component:
GO:0005576 extracellular region
GO:0005604 basement membrane
GO:0005610 laminin-5 complex
GO:0005783 endoplasmic reticulum
GO:0031012 extracellular matrix
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  AK096422 - Homo sapiens cDNA FLJ39103 fis, clone NTONG2002970, highly similar to Homo sapiens laminin alpha 3b chain mRNA.
BC093406 - Homo sapiens laminin, alpha 3, mRNA (cDNA clone IMAGE:30347985), partial cds.
BC172580 - Synthetic construct Homo sapiens clone IMAGE:100069274, MGC:199285 laminin, alpha 3 (LAMA3) mRNA, encodes complete protein.
AB107369 - Homo sapiens LAMA3 mRNA for laminin alpha 3b chain, complete cds.
AY327115 - Homo sapiens laminin alpha 3 splice variant b1 (LAMA3) mRNA, complete cds; alternatively spliced.
AY327116 - Homo sapiens laminin alpha 3 splice variant b2 (LAMA3) mRNA, complete cds; alternatively spliced.
AF005258 - Homo sapiens laminin alpha 3b chain mRNA, partial cds.
BC033663 - Homo sapiens laminin, alpha 3, mRNA (cDNA clone IMAGE:4449486), partial cds.
X85108 - H.sapiens mRNA for laminin alpha 3b chain.
X84900 - H.sapiens mRNA for laminin-5, alpha3b chain.
X85107 - H.sapiens mRNA for laminin alpha 3a chain.
BC172402 - Synthetic construct Homo sapiens clone IMAGE:100069096, MGC:199107 laminin, alpha 3 (LAMA3) mRNA, encodes complete protein.
AY327114 - Homo sapiens laminin alpha 3 splice variant a (LAMA3) mRNA, complete cds; alternatively spliced.
L34155 - Homo sapiens laminin-related protein (LamA3) mRNA, complete cds.
X77598 - H.sapiens LAM A3 mRNA for laminin alpha 3 chain.
BC043618 - Homo sapiens, Similar to laminin, alpha 3, clone IMAGE:6154551, mRNA.
AB208853 - Homo sapiens mRNA for Laminin alpha 3b chain variant protein.
JD390056 - Sequence 371080 from Patent EP1572962.
JD255599 - Sequence 236623 from Patent EP1572962.
JD138570 - Sequence 119594 from Patent EP1572962.
JD107447 - Sequence 88471 from Patent EP1572962.
JD483967 - Sequence 464991 from Patent EP1572962.
L34156 - Homo sapiens epiligrin alpha 3 (LamA3) mRNA, partial cds.
X84392 - H.sapiens mRNA for laminin-5.
AK024889 - Homo sapiens cDNA: FLJ21236 fis, clone COL01111.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_agrPathway - Agrin in Postsynaptic Differentiation

Reactome (by CSHL, EBI, and GO)

Protein Q16787 (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-2327803 Laminins bind Nidogens 1, 2
R-HSA-2426355 NTN4 binds laminins with gamma-1, gamma-3
R-HSA-2396124 AGRN binds Laminins with gamma-1 subunit
R-HSA-446083 CD151 interacts with BP180 and the integrin alpha 6 subunit
R-HSA-2426450 Laminins:Nidogens binds collagen type IV networks
R-HSA-2426530 Laminins:Nidogens binds HSPG2
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-3000178 ECM proteoglycans
R-HSA-1474290 Collagen formation
R-HSA-1500931 Cell-Cell communication

-  Other Names for This Gene
  Alternate Gene Symbols: B0YJ33, ENST00000313654.1, ENST00000313654.10, ENST00000313654.11, ENST00000313654.12, ENST00000313654.13, ENST00000313654.2, ENST00000313654.3, ENST00000313654.4, ENST00000313654.5, ENST00000313654.6, ENST00000313654.7, ENST00000313654.8, ENST00000313654.9, LAMA3_HUMAN, LAMNA, NM_198129, Q13679, Q13680, Q16787, Q6VU67, Q6VU68, Q6VU69, Q76E14, Q96TG0, uc317plr.1, uc317plr.2
UCSC ID: ENST00000313654.14_6
RefSeq Accession: NM_198129.4
Protein: Q16787 (aka LAMA3_HUMAN or LMA3_HUMAN)

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene LAMA3:
ebj (Junctional Epidermolysis Bullosa)

-  Gene Model Information
  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.