Human Gene LCE2D (uc001fag.4) Description and Page Index
  Description: Homo sapiens late cornified envelope 2D (LCE2D), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr1:152,635,887-152,637,135 Size: 1,249 Total Exon Count: 2 Strand: +
Coding Region
   Position: hg19 chr1:152,636,582-152,636,914 Size: 333 Coding Exon Count: 1 

Page IndexSequence and LinksUniProtKB CommentsCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:152,635,887-152,637,135)mRNA (may differ from genome)Protein (110 aa)
Gene SorterGenome BrowserOther Species FASTATable SchemaBioGPSCGAP
EnsemblEntrez GeneExonPrimerGeneCardsGeneNetworkHGNC
HPRDLynxMGIneXtProtOMIMPubMed
ReactomeStanford SOURCEUniProtKB

-  Comments and Description Text from UniProtKB
  ID: LCE2D_HUMAN
DESCRIPTION: RecName: Full=Late cornified envelope protein 2D; AltName: Full=Late envelope protein 12; AltName: Full=Small proline-rich-like epidermal differentiation complex protein 1A;
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.
INDUCTION: By calcium and UVB.
MISCELLANEOUS: Belongs to the LCE cluster present on 1q21.
SIMILARITY: Belongs to the LCE family.

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

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 64.76 RPKM in Skin - Sun Exposed (Lower leg)
Total median expression: 98.59 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 -8.1040-0.203 Picture PostScript Text
3' UTR -55.04221-0.249 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 Q5TA82
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
GO:0005515 protein binding

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
  BC130603 - Homo sapiens late cornified envelope 2D, mRNA (cDNA clone MGC:163475 IMAGE:40146634), complete cds.
BC130605 - Homo sapiens late cornified envelope 2D, mRNA (cDNA clone MGC:163477 IMAGE:40146636), complete cds.
JD265083 - Sequence 246107 from Patent EP1572962.
KJ905661 - Synthetic construct Homo sapiens clone ccsbBroadEn_15312 LCE2D gene, encodes complete protein.

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

Protein Q5TA82 (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: A1L4M8, LCE2D_HUMAN, LEP12, NM_178430, NP_848517, Q5TA82, SPRL1A, uc001fag.3
UCSC ID: uc001fag.4
RefSeq Accession: NM_178430
Protein: Q5TA82 (aka LCE2D_HUMAN)
CCDS: CCDS1018.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_178430.3
exon count: 2CDS single in 3' UTR: no RNA size: 594
ORF size: 333CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 863.00frame 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.