Human Gene PPHLN1 (uc001rng.1) Description and Page Index
  Description: Homo sapiens periphilin 1 (PPHLN1), transcript variant 1, mRNA.
RefSeq Summary (NM_016488): The protein encoded by this gene is one of the several proteins that become sequentially incorporated into the cornified cell envelope during the terminal differentiation of keratinocyte at the outer layers of epidermis. This protein interacts with periplakin, which is known as a precursor of the cornified cell envelope. The cellular localization pattern and insolubility of this protein suggest that it may play a role in epithelial differentiation and contribute to epidermal integrity and barrier formation. Multiple alternatively spliced transcript variants encoding distinct isoforms have been observed. [provided by RefSeq, Jul 2008].
Transcript (Including UTRs)
   Position: hg19 chr12:42,719,947-42,842,422 Size: 122,476 Total Exon Count: 13 Strand: +
Coding Region
   Position: hg19 chr12:42,729,705-42,840,420 Size: 110,716 Coding Exon Count: 12 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr12:42,719,947-42,842,422)mRNA (may differ from genome)Protein (458 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedStanford SOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: PPHLN_HUMAN
DESCRIPTION: RecName: Full=Periphilin-1; AltName: Full=Gastric cancer antigen Ga50;
FUNCTION: Involved in epithelial differentiation and contributes to epidermal integrity and barrier formation.
SUBUNIT: Homodimer. Interacts with PPL.
SUBCELLULAR LOCATION: Nucleus. Cytoplasm. Note=In undifferentiated keratinocytes expressed in speckle-type nuclear granules and at the nuclear membrane, but in the differentiated keratinocytes colocalized with periplakin at the cell periphery and at cell-cell junctions.
TISSUE SPECIFICITY: Ubiquitous.
PTM: Substrate of transglutaminase (in vitro).
SEQUENCE CAUTION: Sequence=AAH25306.1; Type=Erroneous initiation;

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): PPHLN1
CDC HuGE Published Literature: PPHLN1
Positive Disease Associations: Respiratory Function Tests
Related Studies:
  1. Respiratory Function Tests
    Jemma B Wilk et al. BMC medical genetics 2007, Framingham Heart Study genome-wide association: results for pulmonary function measures., BMC medical genetics. [PubMed 17903307]
    GSTO2 and IL6R are credible candidate genes for association to pulmonary function identified by GWA. These and other observed associations warrant replication studies. This resource of GWA results for pulmonary function measures is publicly available at http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?id=phs000007 webcite.

-  MalaCards Disease Associations
  MalaCards Gene Search: PPHLN1
Diseases sorted by gene-association score: intrahepatic cholangiocarcinoma (2)

-  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: 14.27 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 346.28 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 -35.80105-0.341 Picture PostScript Text
3' UTR -510.602002-0.255 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
  Pfam Domains:
PF11488 - Transcriptional regulatory protein LGE1

ModBase Predicted Comparative 3D Structure on Q8NEY8
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:0003723 RNA binding
GO:0005515 protein binding

Biological Process:
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0031424 keratinization
GO:0045892 negative regulation of transcription, DNA-templated

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005694 chromosome
GO:0005737 cytoplasm
GO:0005794 Golgi apparatus
GO:0005829 cytosol


-  Descriptions from all associated GenBank mRNAs
  AK129910 - Homo sapiens cDNA FLJ26400 fis, clone HRT08950.
AK303612 - Homo sapiens cDNA FLJ52823 complete cds, highly similar to Periphilin-1.
LF385073 - JP 2014500723-A/192576: Polycomb-Associated Non-Coding RNAs.
AY157850 - Homo sapiens periphilin 1 (PPHLN1) mRNA, complete cds.
AK055690 - Homo sapiens cDNA FLJ31128 fis, clone IMR322000863.
AK299951 - Homo sapiens cDNA FLJ52742 complete cds, highly similar to Periphilin-1.
AK056622 - Homo sapiens cDNA FLJ32060 fis, clone OCBBF1000016.
AY039238 - Homo sapiens gastric cancer antigen Ga50 (HSPC232) mRNA, complete cds.
AK303680 - Homo sapiens cDNA FLJ58824 complete cds, highly similar to Periphilin-1.
AK308022 - Homo sapiens cDNA, FLJ97970.
AF151066 - Homo sapiens HSPC232 mRNA, complete cds.
AK299682 - Homo sapiens cDNA FLJ54524 complete cds, highly similar to Homo sapiens periphilin 1 (PPHLN1), transcript variant 4, mRNA.
BC015322 - Homo sapiens cDNA clone IMAGE:4424280, containing frame-shift errors.
BC039832 - Homo sapiens periphilin 1, mRNA (cDNA clone MGC:48786 IMAGE:6051282), complete cds.
BC040449 - Homo sapiens periphilin 1, mRNA (cDNA clone IMAGE:6043945).
BC025306 - Homo sapiens, clone IMAGE:4893383, mRNA, partial cds.
AF151040 - Homo sapiens HSPC206 mRNA, complete cds.
BC033753 - Homo sapiens mRNA similar to hypothetical protein (cDNA clone IMAGE:5211696).
MA620650 - JP 2018138019-A/192576: Polycomb-Associated Non-Coding RNAs.
CU691776 - Synthetic construct Homo sapiens gateway clone IMAGE:100021071 5' read PPHLN1 mRNA.
HQ448511 - Synthetic construct Homo sapiens clone IMAGE:100071945; CCSB011260_01 periphilin 1 (PPHLN1) gene, encodes complete protein.
AB590797 - Synthetic construct DNA, clone: pFN21AE1922, Homo sapiens PPHLN1 gene for periphilin 1, without stop codon, in Flexi system.
AK000186 - Homo sapiens cDNA FLJ20179 fis, clone COL10178.
LF337706 - JP 2014500723-A/145209: Polycomb-Associated Non-Coding RNAs.
BX647697 - Homo sapiens mRNA; cDNA DKFZp686M24126 (from clone DKFZp686M24126).
AK124921 - Homo sapiens cDNA FLJ42931 fis, clone BRSSN2011262.
JD301943 - Sequence 282967 from Patent EP1572962.
JD037546 - Sequence 18570 from Patent EP1572962.
JD205335 - Sequence 186359 from Patent EP1572962.
JD082001 - Sequence 63025 from Patent EP1572962.
JD477857 - Sequence 458881 from Patent EP1572962.
JD084674 - Sequence 65698 from Patent EP1572962.
JD514809 - Sequence 495833 from Patent EP1572962.
JD372814 - Sequence 353838 from Patent EP1572962.
JD069462 - Sequence 50486 from Patent EP1572962.
JD232362 - Sequence 213386 from Patent EP1572962.
JD524152 - Sequence 505176 from Patent EP1572962.
LF337707 - JP 2014500723-A/145210: Polycomb-Associated Non-Coding RNAs.
MA573283 - JP 2018138019-A/145209: Polycomb-Associated Non-Coding RNAs.
MA573284 - JP 2018138019-A/145210: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: HSPC206, HSPC232, NM_016488, NP_057572, PPHLN_HUMAN, Q86YT2, Q8IXN3, Q8NEY8, Q8TB09, Q96NB9, Q9NXL4, Q9P0P6, Q9P0R9
UCSC ID: uc001rng.1
RefSeq Accession: NM_016488
Protein: Q8NEY8 (aka PPHLN_HUMAN or PPHL_HUMAN)
CCDS: CCDS31777.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_016488.6
exon count: 13CDS single in 3' UTR: no RNA size: 3484
ORF size: 1377CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2579.00frame 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.