Human Gene WIPI2 (uc003snv.3) Description and Page Index
  Description: Homo sapiens WD repeat domain, phosphoinositide interacting 2 (WIPI2), transcript variant 1, mRNA.
RefSeq Summary (NM_015610): WD40 repeat proteins are key components of many essential biologic functions. They regulate the assembly of multiprotein complexes by presenting a beta-propeller platform for simultaneous and reversible protein-protein interactions. Members of the WIPI subfamily of WD40 repeat proteins, such as WIPI2, have a 7-bladed propeller structure and contain a conserved motif for interaction with phospholipids (Proikas-Cezanne et al., 2004 [PubMed 15602573]).[supplied by OMIM, Mar 2008].
Transcript (Including UTRs)
   Position: hg19 chr7:5,229,835-5,273,486 Size: 43,652 Total Exon Count: 13 Strand: +
Coding Region
   Position: hg19 chr7:5,230,051-5,270,578 Size: 40,528 Coding Exon Count: 13 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr7:5,229,835-5,273,486)mRNA (may differ from genome)Protein (454 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
neXtProtOMIMPubMedReactomeStanford SOURCETreefam

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=WD repeat domain phosphoinositide-interacting protein 2; Short=WIPI-2; AltName: Full=WIPI49-like protein 2;
FUNCTION: Probable early component of the autophagy machinery being involved in formation of preautophagosomal structures and their maturation into mature phagosomes in response to PtdIns3P. May bind PtdIns3P.
SUBUNIT: Interacts with TECPR1.
SUBCELLULAR LOCATION: Preautophagosomal structure membrane; Peripheral membrane protein; Cytoplasmic side. Note=Enriched at preautophagosomal structure membranes in response to ptdIns3P.
TISSUE SPECIFICITY: Ubiquitously expressed (at protein level). Highly expressed in heart, skeletal muscle and pancreas. Expression is down-regulated in pancreatic and in kidney tumors.
SIMILARITY: Belongs to the WD repeat SVP1 family.
SIMILARITY: Contains 3 WD repeats.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): WIPI2
CDC HuGE Published Literature: WIPI2
Positive Disease Associations: Myocardial Infarction
Related Studies:
  1. Myocardial Infarction
    , , . [PubMed 0]

-  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: 30.89 RPKM in Testis
Total median expression: 745.47 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 -116.20216-0.538 Picture PostScript Text
3' UTR -1068.472908-0.367 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
IPR015943 - WD40/YVTN_repeat-like_dom
IPR001680 - WD40_repeat
IPR017986 - WD40_repeat_dom

SCOP Domains:
50960 - TolB, C-terminal domain
63829 - Calcium-dependent phosphotriesterase
69304 - Tricorn protease N-terminal domain
101898 - NHL repeat
75011 - 3-carboxy-cis,cis-mucoante lactonizing enzyme
101908 - Putative isomerase YbhE
50969 - YVTN repeat-like/Quinoprotein amine dehydrogenase
50974 - Nitrous oxide reductase, N-terminal domain
50978 - WD40 repeat-like
50993 - Prolyl oligopeptidase, N-terminal domain
69322 - Tricorn protease domain 2
50998 - Quinoprotein alcohol dehydrogenase-like
51004 - C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase
82171 - Dipeptidyl peptidase IV/CD26, N-terminal domain

ModBase Predicted Comparative 3D Structure on Q9Y4P8
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 orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 Protein Sequence    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0010314 phosphatidylinositol-5-phosphate binding
GO:0032266 phosphatidylinositol-3-phosphate binding
GO:0080025 phosphatidylinositol-3,5-bisphosphate binding

Biological Process:
GO:0000045 autophagosome assembly
GO:0000422 mitophagy
GO:0006497 protein lipidation
GO:0006914 autophagy
GO:0016236 macroautophagy
GO:0034497 protein localization to pre-autophagosomal structure
GO:0044804 nucleophagy
GO:0061739 protein lipidation involved in autophagosome assembly
GO:0098792 xenophagy
GO:0097352 autophagosome maturation

Cellular Component:
GO:0000407 pre-autophagosomal structure
GO:0005654 nucleoplasm
GO:0005829 cytosol
GO:0016020 membrane
GO:0019898 extrinsic component of membrane
GO:0032991 macromolecular complex
GO:0034045 pre-autophagosomal structure membrane
GO:0005776 autophagosome

-  Descriptions from all associated GenBank mRNAs
  AL080155 - Homo sapiens mRNA; cDNA DKFZp434J154 (from clone DKFZp434J154).
LF384067 - JP 2014500723-A/191570: Polycomb-Associated Non-Coding RNAs.
AK024279 - Homo sapiens cDNA FLJ14217 fis, clone NT2RP3003680, highly similar to WD repeat domain phosphoinositide-interacting protein 2.
BC007596 - Homo sapiens WD repeat domain, phosphoinositide interacting 2, mRNA (cDNA clone MGC:15650 IMAGE:3346710), complete cds.
AK023041 - Homo sapiens cDNA FLJ12979 fis, clone NT2RP2006334, highly similar to WD repeat domain phosphoinositide-interacting protein 2.
AK315468 - Homo sapiens cDNA, FLJ96528.
BC004116 - Homo sapiens WD repeat domain, phosphoinositide interacting 2, mRNA (cDNA clone MGC:11167 IMAGE:3842487), complete cds.
BC021200 - Homo sapiens WD repeat domain, phosphoinositide interacting 2, mRNA (cDNA clone MGC:11392 IMAGE:3957981), complete cds.
BC021012 - Homo sapiens WD repeat domain, phosphoinositide interacting 2, mRNA (cDNA clone IMAGE:2966543).
BC021068 - Homo sapiens WD repeat domain, phosphoinositide interacting 2, mRNA (cDNA clone IMAGE:2966543).
AB463348 - Synthetic construct DNA, clone: pF1KB8657, Homo sapiens WIPI2 gene for WD repeat domain, phosphoinositide interacting 2 protein, without stop codon, in Flexi system.
AM392901 - Synthetic construct Homo sapiens clone IMAGE:100002373 for hypothetical protein (WIPI2 gene).
AM393618 - Synthetic construct Homo sapiens clone IMAGE:100002463 for hypothetical protein (WIPI2 gene).
AM393628 - Synthetic construct Homo sapiens clone IMAGE:100001639 for hypothetical protein (WIPI2 gene).
CU675721 - Synthetic construct Homo sapiens gateway clone IMAGE:100019392 5' read WIPI2 mRNA.
KJ898596 - Synthetic construct Homo sapiens clone ccsbBroadEn_07990 WIPI2 gene, encodes complete protein.
AY691425 - Homo sapiens WIPI-2 beta mRNA, complete cds, alternatively spliced.
CR533530 - Homo sapiens full open reading frame cDNA clone RZPDo834F0219D for gene DKFZP434J154, DKFZP434J154 protein; complete cds, incl. stopcodon.
MA619644 - JP 2018138019-A/191570: Polycomb-Associated Non-Coding RNAs.
JD267481 - Sequence 248505 from Patent EP1572962.
JD127587 - Sequence 108611 from Patent EP1572962.
JD022051 - Sequence 3075 from Patent EP1572962.
JD030286 - Sequence 11310 from Patent EP1572962.
BC016912 - Homo sapiens WD repeat domain, phosphoinositide interacting 2, mRNA (cDNA clone IMAGE:4151640), with apparent retained intron.
AF151808 - Homo sapiens CGI-50 protein mRNA, complete cds.
AY691426 - Homo sapiens WIPI-2 delta mRNA, complete cds, alternatively spliced.
AK124974 - Homo sapiens cDNA FLJ42984 fis, clone BRTHA2008335.
BX537624 - Homo sapiens mRNA; cDNA DKFZp686P02188 (from clone DKFZp686P02188).
JD176899 - Sequence 157923 from Patent EP1572962.
JD103577 - Sequence 84601 from Patent EP1572962.
JD266761 - Sequence 247785 from Patent EP1572962.
JD299195 - Sequence 280219 from Patent EP1572962.
JD307621 - Sequence 288645 from Patent EP1572962.
JD511936 - Sequence 492960 from Patent EP1572962.
JD044870 - Sequence 25894 from Patent EP1572962.
JD385432 - Sequence 366456 from Patent EP1572962.
JD062845 - Sequence 43869 from Patent EP1572962.
JD448635 - Sequence 429659 from Patent EP1572962.
JD112206 - Sequence 93230 from Patent EP1572962.
LF360063 - JP 2014500723-A/167566: Polycomb-Associated Non-Coding RNAs.
JD509252 - Sequence 490276 from Patent EP1572962.
AK125007 - Homo sapiens cDNA FLJ43017 fis, clone BRTHA2016577.
LF360064 - JP 2014500723-A/167567: Polycomb-Associated Non-Coding RNAs.
MA595640 - JP 2018138019-A/167566: Polycomb-Associated Non-Coding RNAs.
MA595641 - JP 2018138019-A/167567: Polycomb-Associated Non-Coding RNAs.

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

Protein Q9Y4P8 (Reactome details) participates in the following event(s):

R-HSA-5679255 WIPI2 binds ATG12:ATG5:ATG16L
R-HSA-5676229 WIPIs bind PI3P
R-HSA-5678490 ATG16L1 complex transfers LC3 from ATG3 to PE
R-HSA-1632852 Macroautophagy
R-HSA-8953897 Cellular responses to external stimuli

-  Other Names for This Gene
  Alternate Gene Symbols: B3KNC2, CGI-50, NM_015610, NP_001265228, Q5MNZ8, Q6FI96, Q75L50, Q96IE4, Q9Y364, Q9Y4P8, WIPI2_HUMAN
UCSC ID: uc003snv.3
RefSeq Accession: NM_015610
Protein: Q9Y4P8 (aka WIPI2_HUMAN)
CCDS: CCDS5339.1, CCDS34593.1, CCDS47531.1

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: NM_015610.3
exon count: 13CDS single in 3' UTR: no RNA size: 4489
ORF size: 1365CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2701.00frame 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.