Human Gene LCE5A (uc001ezy.3)
  Description: Homo sapiens late cornified envelope 5A (LCE5A), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr1:152,483,320-152,484,653 Size: 1,334 Total Exon Count: 2 Strand: +
Coding Region
   Position: hg19 chr1:152,484,011-152,484,367 Size: 357 Coding Exon Count: 1 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:152,483,320-152,484,653)mRNA (may differ from genome)Protein (118 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
HGNCHPRDLynxMGIneXtProtOMIM
PubMedReactomeUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: LCE5A_HUMAN
DESCRIPTION: RecName: Full=Late cornified envelope protein 5A; AltName: Full=Late envelope protein 18; AltName: Full=Small proline-rich-like epidermal differentiation complex protein 5A;
FUNCTION: Precursors of the cornified envelope of the stratum corneum.
TISSUE SPECIFICITY: Skin-specific. Expression was readily detected in adult trunk skin, adult arm skin, fetal skin, penal skin, vulva, esophagus and tongue. Not expressed in the cervix, rectum, lung, colon, or placenta. Expression is observed in the heart.
MISCELLANEOUS: Belongs to the LCE cluster present on 1q21.
SIMILARITY: Belongs to the LCE 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): LCE5A
CDC HuGE Published Literature: LCE5A
Positive Disease Associations: hair morphology
Related Studies:
  1. hair morphology
    Medland ,et al. 2009, Common Variants in the Trichohyalin Gene Are Associated with Straight Hair in Europeans, American journal of human genetics 2009 85- 5 : 750-5. [PubMed 19896111]

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  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: 47.47 RPKM in Skin - Sun Exposed (Lower leg)
Total median expression: 79.06 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 -55.40176-0.315 Picture PostScript Text
3' UTR -76.71286-0.268 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
IPR026075 - SPRR/LCE

Pfam Domains:
PF14672 - Late cornified envelope

ModBase Predicted Comparative 3D Structure on Q5TCM9
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 Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005198 structural molecule activity

Biological Process:
GO:0008544 epidermis development
GO:0018149 peptide cross-linking
GO:0030216 keratinocyte differentiation
GO:0031424 keratinization

Cellular Component:
GO:0001533 cornified envelope
GO:0005737 cytoplasm


-  Descriptions from all associated GenBank mRNAs
  JD435599 - Sequence 416623 from Patent EP1572962.
JD434738 - Sequence 415762 from Patent EP1572962.
JD391114 - Sequence 372138 from Patent EP1572962.
JD456286 - Sequence 437310 from Patent EP1572962.
AB528166 - Synthetic construct DNA, clone: pF1KE0225, Homo sapiens LCE5A gene for late cornified envelope 5A, without stop codon, in Flexi system.
BC140434 - Synthetic construct Homo sapiens clone IMAGE:100014491, MGC:173172 late cornified envelope 5A (LCE5A) mRNA, encodes complete protein.
BC156866 - Synthetic construct Homo sapiens clone IMAGE:100062701, MGC:190591 late cornified envelope 5A (LCE5A) mRNA, encodes complete protein.
JD317710 - Sequence 298734 from Patent EP1572962.
JD079112 - Sequence 60136 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q5TCM9 (Reactome details) participates in the following event(s):

R-HSA-6814298 Late envelope proteins bind cornified envelope:CDSN
R-HSA-6814387 CASP14 cleaves filaggrin
R-HSA-6809371 Formation of the cornified envelope
R-HSA-6805567 Keratinization
R-HSA-1266738 Developmental Biology

-  Other Names for This Gene
  Alternate Gene Symbols: LCE5A_HUMAN, LEP18, NM_178438, NP_848525, Q5TCM9, SPRL5A
UCSC ID: uc001ezy.3
RefSeq Accession: NM_178438
Protein: Q5TCM9 (aka LCE5A_HUMAN)
CCDS: CCDS1011.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_178438.4
exon count: 2CDS single in 3' UTR: no RNA size: 819
ORF size: 357CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 860.00frame 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.