Human Gene PSENEN (ENST00000587708.7_4) from GENCODE V47lift37
  Description: presenilin enhancer, gamma-secretase subunit, transcript variant 1 (from RefSeq NM_172341.4)
Gencode Transcript: ENST00000587708.7_4
Gencode Gene: ENSG00000205155.8_8
Transcript (Including UTRs)
   Position: hg19 chr19:36,236,552-36,238,420 Size: 1,869 Total Exon Count: 4 Strand: +
Coding Region
   Position: hg19 chr19:36,236,832-36,237,748 Size: 917 Coding Exon Count: 3 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr19:36,236,552-36,238,420)mRNA (may differ from genome)Protein (101 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PEN2_HUMAN
DESCRIPTION: RecName: Full=Gamma-secretase subunit PEN-2; AltName: Full=Presenilin enhancer protein 2;
FUNCTION: Essential subunit of the gamma-secretase complex, an endoprotease complex that catalyzes the intramembrane cleavage of integral membrane proteins such as Notch receptors and APP (beta- amyloid precursor protein). Probably represents the last step of maturation of gamma-secretase, facilitating endoproteolysis of presenilin and conferring gamma-secretase activity.
SUBUNIT: Component of the gamma-secretase complex, a complex composed of a presenilin homodimer (PSEN1 or PSEN2), nicastrin (NCSTN), APH1 (APH1A or APH1B) and PSENEN/PEN2. Such minimal complex is sufficient for secretase activity, although other components may exist.
INTERACTION: P49755:TMED10; NbExp=3; IntAct=EBI-998468, EBI-998422;
SUBCELLULAR LOCATION: Endoplasmic reticulum membrane; Multi-pass membrane protein. Golgi apparatus, Golgi stack membrane; Multi- pass membrane protein. Note=Predominantly located in the endoplasmic reticulum and in the cis-Golgi.
TISSUE SPECIFICITY: Widely expressed. Expressed in leukocytes, lung, placenta, small intestine, liver, kidney, spleen thymus, skeletal muscle, heart and brain.
DISEASE: Defects in PSENEN are the cause of familial acne inversa type 2 (ACNINV2) [MIM:613736]. A chronic relapsing inflammatory disease of the hair follicles characterized by recurrent draining sinuses, painful skin abscesses, and disfiguring scars. Manifestations typically appear after puberty.
SIMILARITY: Belongs to the PEN-2 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: PSENEN
Diseases sorted by gene-association score: acne inversa, familial, 2* (919), dowling-degos disease* (164), acne (30), hidradenitis suppurativa (18), hidradenitis (17), alzheimer disease (11), anal canal squamous cell carcinoma (11), shipyard eye (8), pain agnosia (7), agnosia (7), sweat gland disease (5), sebaceous gland disease (4), specific developmental disorder (1)
* = Manually curated disease association

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

+  Common Gene Haplotype Alleles
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+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -56.20146-0.385 Picture PostScript Text
3' UTR -192.90672-0.287 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
IPR019379 - Gamma_Secretase_Asp_P_PEN2

Pfam Domains:
PF10251 - Presenilin enhancer-2 subunit of gamma secretase

ModBase Predicted Comparative 3D Structure on Q9NZ42
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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:0005515 protein binding

Biological Process:
GO:0006509 membrane protein ectodomain proteolysis
GO:0007219 Notch signaling pathway
GO:0007220 Notch receptor processing
GO:0016485 protein processing
GO:0034205 beta-amyloid formation
GO:0035333 Notch receptor processing, ligand-dependent
GO:0042982 amyloid precursor protein metabolic process
GO:0042987 amyloid precursor protein catabolic process
GO:0043085 positive regulation of catalytic activity

Cellular Component:
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0005794 Golgi apparatus
GO:0005886 plasma membrane
GO:0005887 integral component of plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0032580 Golgi cisterna membrane
GO:0070765 gamma-secretase complex


-  Descriptions from all associated GenBank mRNAs
  LF207608 - JP 2014500723-A/15111: Polycomb-Associated Non-Coding RNAs.
AF220053 - Homo sapiens uncharacterized hematopoietic stem/progenitor cells protein MDS033 mRNA, complete cds.
BC009575 - Homo sapiens presenilin enhancer 2 homolog (C. elegans), mRNA (cDNA clone MGC:14572 IMAGE:4096271), complete cds.
AK312233 - Homo sapiens cDNA, FLJ92524, Homo sapiens presenilin enhancer 2 (PEN2), mRNA.
JD054433 - Sequence 35457 from Patent EP1572962.
BC008939 - Homo sapiens lin-37 homolog (C. elegans), mRNA (cDNA clone IMAGE:2989481).
JD177788 - Sequence 158812 from Patent EP1572962.
LF206418 - JP 2014500723-A/13921: Polycomb-Associated Non-Coding RNAs.
JD196570 - Sequence 177594 from Patent EP1572962.
DQ893095 - Synthetic construct clone IMAGE:100005725; FLH193702.01X; RZPDo839B0279D presenilin enhancer 2 homolog (C. elegans) (PSENEN) gene, encodes complete protein.
DQ896368 - Synthetic construct Homo sapiens clone IMAGE:100010828; FLH193698.01L; RZPDo839B0269D presenilin enhancer 2 homolog (C. elegans) (PSENEN) gene, encodes complete protein.
KJ894274 - Synthetic construct Homo sapiens clone ccsbBroadEn_03668 PSENEN gene, encodes complete protein.
KR710357 - Synthetic construct Homo sapiens clone CCSBHm_00011813 PSENEN (PSENEN) mRNA, encodes complete protein.
LF367394 - JP 2014500723-A/174897: Polycomb-Associated Non-Coding RNAs.
LF354222 - JP 2014500723-A/161725: Polycomb-Associated Non-Coding RNAs.
LF354220 - JP 2014500723-A/161723: Polycomb-Associated Non-Coding RNAs.
JD365684 - Sequence 346708 from Patent EP1572962.
JD464840 - Sequence 445864 from Patent EP1572962.
LF354219 - JP 2014500723-A/161722: Polycomb-Associated Non-Coding RNAs.
JD493609 - Sequence 474633 from Patent EP1572962.
MA602971 - JP 2018138019-A/174897: Polycomb-Associated Non-Coding RNAs.
MA443185 - JP 2018138019-A/15111: Polycomb-Associated Non-Coding RNAs.
MA441995 - JP 2018138019-A/13921: Polycomb-Associated Non-Coding RNAs.
MA589799 - JP 2018138019-A/161725: Polycomb-Associated Non-Coding RNAs.
MA589797 - JP 2018138019-A/161723: Polycomb-Associated Non-Coding RNAs.
MA589796 - JP 2018138019-A/161722: Polycomb-Associated Non-Coding RNAs.

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

Protein Q9NZ42 (Reactome details) participates in the following event(s):

R-HSA-157353 NEXT1 is cleaved to produce NICD1
R-HSA-157640 NEXT2 is cleaved to produce NICD2
R-HSA-157648 NEXT4 is cleaved to produce NICD4
R-NUL-2197556 Gamma-secretase complex cleaves mNEXT2
R-HSA-2220988 NEXT1 PEST domain mutants are cleaved to produce NICD1 PEST domain mutants
R-HSA-9013361 NEXT3 is cleaved to produce NICD3
R-HSA-193682 gamma-secretase cleaves the p75NTR transmembrane domain
R-HSA-1251997 Cleavage of ERBB4m80 by gamma-scretase complex
R-HSA-205112 gamma-secretase cleaves p75NTR, releasing NRIF and TRAF6
R-HSA-157212 A third proteolytic cleavage releases NICD
R-HSA-2122948 Activated NOTCH1 Transmits Signal to the Nucleus
R-HSA-2979096 NOTCH2 Activation and Transmission of Signal to the Nucleus
R-HSA-1980150 Signaling by NOTCH4
R-HSA-2644606 Constitutive Signaling by NOTCH1 PEST Domain Mutants
R-HSA-2894862 Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants
R-HSA-9013507 NOTCH3 Activation and Transmission of Signal to the Nucleus
R-HSA-9017802 Noncanonical activation of NOTCH3
R-HSA-193692 Regulated proteolysis of p75NTR
R-HSA-1251985 Nuclear signaling by ERBB4
R-HSA-3928665 EPH-ephrin mediated repulsion of cells
R-HSA-205043 NRIF signals cell death from the nucleus
R-HSA-1980143 Signaling by NOTCH1
R-HSA-1980145 Signaling by NOTCH2
R-HSA-157118 Signaling by NOTCH
R-HSA-2644602 Signaling by NOTCH1 PEST Domain Mutants in Cancer
R-HSA-2894858 Signaling by NOTCH1 HD+PEST Domain Mutants in Cancer
R-HSA-9012852 Signaling by NOTCH3
R-HSA-193704 p75 NTR receptor-mediated signalling
R-HSA-1236394 Signaling by ERBB4
R-HSA-2682334 EPH-Ephrin signaling
R-HSA-204998 Cell death signalling via NRAGE, NRIF and NADE
R-HSA-162582 Signal Transduction
R-HSA-2644603 Signaling by NOTCH1 in Cancer
R-HSA-73887 Death Receptor Signalling
R-HSA-9006934 Signaling by Receptor Tyrosine Kinases
R-HSA-422475 Axon guidance
R-HSA-5663202 Diseases of signal transduction
R-HSA-1266738 Developmental Biology
R-HSA-1643685 Disease

-  Other Names for This Gene
  Alternate Gene Symbols: B2R5L9, ENST00000587708.1, ENST00000587708.2, ENST00000587708.3, ENST00000587708.4, ENST00000587708.5, ENST00000587708.6, MDS033, NM_172341, PEN2, PEN2_HUMAN, Q9NZ42, uc326rqd.1, uc326rqd.2
UCSC ID: ENST00000587708.7_4
RefSeq Accession: NM_172341.4
Protein: Q9NZ42 (aka PEN2_HUMAN)

-  Gene Model Information
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-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.