Human Gene PNN (ENST00000216832.9_4) from GENCODE V47lift37
  Description: pinin, desmosome associated protein (from RefSeq NM_002687.4)
Gencode Transcript: ENST00000216832.9_4
Gencode Gene: ENSG00000100941.9_7
Transcript (Including UTRs)
   Position: hg19 chr14:39,644,458-39,652,424 Size: 7,967 Total Exon Count: 9 Strand: +
Coding Region
   Position: hg19 chr14:39,644,484-39,651,067 Size: 6,584 Coding Exon Count: 9 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr14:39,644,458-39,652,424)mRNA (may differ from genome)Protein (717 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PININ_HUMAN
DESCRIPTION: RecName: Full=Pinin; AltName: Full=140 kDa nuclear and cell adhesion-related phosphoprotein; AltName: Full=Desmosome-associated protein; AltName: Full=Domain-rich serine protein; Short=DRS protein; Short=DRSP; AltName: Full=Melanoma metastasis clone A protein; AltName: Full=Nuclear protein SDK3; AltName: Full=SR-like protein;
FUNCTION: Transcriptional activator binding to the E-box 1 core sequence of the E-cadherin promoter gene; the core-binding sequence is 5'CAGGTG-3'. Capable of reversing CTBP1-mediated transcription repression. Component of a splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junction on mRNAs. The EJC is a dynamic structure consisting of a few core proteins and several more peripheral nuclear and cytoplasmic associated factors that join the complex only transiently either during EJC assembly or during subsequent mRNA metabolism. Participates in the regulation of alternative pre-mRNA splicing. Associates to spliced mRNA within 60 nt upstream of the 5'-splice sites. Involved in the establishment and maintenance of epithelia cell-cell adhesion. Potential tumor suppressor for renal cell carcinoma.
SUBUNIT: Found in a mRNA splicing-dependent exon junction complex (EJC), at least composed of ACIN1, CASC3, EIF4A3, MAGOH, PNN, RBM8A, RNPS1, SAP18 and ALYREF/THOC4. Found in a complex with SR proteins. Found in a mRNP complex with RNPS1. Interacts with C6orf111/SRRP130, CTBP1, CTBP2, KRT8, KRT18, KRT19, PS1D/PNO40, PPIG, RNPS1, SFRS4 and SRRM2. Identified in the spliceosome C complex.
INTERACTION: Q9UBC1:NFKBIL1; NbExp=1; IntAct=EBI-681904, EBI-1043728; Q15287:RNPS1; NbExp=1; IntAct=EBI-681904, EBI-395959;
SUBCELLULAR LOCATION: Nucleus speckle. Cell junction, desmosome. Note=Cell-cell contact area, predominantly desmosome of intercellular adherens junction. Not a nucleocytoplasmic shuttling protein.
TISSUE SPECIFICITY: Expressed in placenta, lung, liver, kidney, pancreas, spleen, thymus, prostate, testis, ovary, small intestine, colon, heart, epidermis, esophagus, brain and smooth and skeletal muscle. Expressed strongly in melanoma metastasis lesions and advanced primary tumors.
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR.
SIMILARITY: Belongs to the pinin 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


-  MalaCards Disease Associations
  MalaCards Gene Search: PNN
Diseases sorted by gene-association score: melanoma metastasis (7), premenstrual tension (2), epileptic encephalopathy, childhood-onset (1)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene
  • D013749 Tetrachlorodibenzodioxin
  • D001564 Benzo(a)pyrene
  • C049325 1,2-dithiol-3-thione
  • C532162 2-(1H-indazol-4-yl)-6-(4-methanesulfonylpiperazin-1-ylmethyl)-4-morpholin-4-ylthieno(3,2-d)pyrimidine
  • C030370 2-methoxy-5-(2',3',4'-trimethoxyphenyl)tropone
  • C518576 2-methylbutyric acid 4-((1,3)dioxan-5-ylmethoxyimino)-8-(2-(4-hydroxy-6-oxo-tetrahydropyran-2-yl)ethyl -7-methyl-6-oxo-1,2,3,4,6,7,8,8a-octahydronaphthyl)heptanoate
  • D015123 7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide
  • D000082 Acetaminophen
  • D016604 Aflatoxin B1
  • D002737 Chloroprene
          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: 86.51 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 2536.90 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 -6.1026-0.235 Picture PostScript Text
3' UTR -300.201357-0.221 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
IPR006786 - Pinin_SDK_MemA
IPR006787 - Pinin_SDK_N

Pfam Domains:
PF04696 - pinin/SDK/memA/ protein conserved region
PF04697 - pinin/SDK conserved region

ModBase Predicted Comparative 3D Structure on Q9H307
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 orthologGenome BrowserNo ortholog
Gene DetailsGene Details Gene DetailsGene Details 
Gene SorterGene Sorter Gene SorterGene Sorter 
 RGDEnsembl WormBase 
    Protein Sequence 
    Alignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003677 DNA binding
GO:0003723 RNA binding
GO:0005198 structural molecule activity
GO:0005515 protein binding

Biological Process:
GO:0000398 mRNA splicing, via spliceosome
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006397 mRNA processing
GO:0007155 cell adhesion
GO:0008380 RNA splicing

Cellular Component:
GO:0005634 nucleus
GO:0005681 spliceosomal complex
GO:0005882 intermediate filament
GO:0005886 plasma membrane
GO:0005911 cell-cell junction
GO:0016020 membrane
GO:0016607 nuclear speck
GO:0030054 cell junction
GO:0030057 desmosome
GO:0071013 catalytic step 2 spliceosome
GO:0035145 exon-exon junction complex


-  Descriptions from all associated GenBank mRNAs
  AK292579 - Homo sapiens cDNA FLJ75071 complete cds, highly similar to Homo sapiens pinin, desmosome associated protein (PNN), mRNA.
AF112222 - UNVERIFIED: Homo sapiens nuclear protein SDK3 mRNA, complete cds.
AK223612 - Homo sapiens mRNA for pinin, desmosome associated protein variant, clone: FCC133C12.
U77718 - Human desmosome associated protein pinin mRNA, complete cds.
BC062602 - Homo sapiens pinin, desmosome associated protein, mRNA (cDNA clone MGC:70809 IMAGE:5491466), complete cds.
KJ897351 - Synthetic construct Homo sapiens clone ccsbBroadEn_06745 PNN gene, encodes complete protein.
Y09703 - H.sapiens mRNA for MEMA protein.
Y10351 - H.sapiens mRNA for nuclear protein SDK3, partial.
AK303136 - Homo sapiens cDNA FLJ56911 complete cds, highly similar to Pinin.
AK300164 - Homo sapiens cDNA FLJ56361 complete cds, highly similar to Pinin.
AK304622 - Homo sapiens cDNA FLJ52602 complete cds, highly similar to Pinin.
U59479 - Human neutrophil protein mRNA, partial cds.
JD310051 - Sequence 291075 from Patent EP1572962.
JD044083 - Sequence 25107 from Patent EP1572962.
JD234641 - Sequence 215665 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: B4DZX8, DRS, ENST00000216832.1, ENST00000216832.2, ENST00000216832.3, ENST00000216832.4, ENST00000216832.5, ENST00000216832.6, ENST00000216832.7, ENST00000216832.8, MEMA, NM_002687, O60899, PININ_HUMAN, Q53EM7, Q6P5X4, Q7KYL1, Q99738, Q9H307, Q9UHZ9, Q9UQR9, uc317cse.1, uc317cse.2
UCSC ID: ENST00000216832.9_4
RefSeq Accession: NM_002687.4
Protein: Q9H307 (aka PININ_HUMAN)

-  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.