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WIPI2 WD repeat domain, phosphoinositide interacting 2 [ Homo sapiens (human) ]

Gene ID: 26100, updated on 24-Sep-2024

Summary

Official Symbol
WIPI2provided by HGNC
Official Full Name
WD repeat domain, phosphoinositide interacting 2provided by HGNC
Primary source
HGNC:HGNC:32225
See related
Ensembl:ENSG00000157954 MIM:609225; AllianceGenome:HGNC:32225
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
Atg21; ATG18B; CGI-50; IDDSSA; WIPI-2
Summary
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]
Expression
Ubiquitous expression in testis (RPKM 20.8), brain (RPKM 12.7) and 25 other tissues See more
Orthologs
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Genomic context

See WIPI2 in Genome Data Viewer
Location:
7p22.1
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (5190233..5233855)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (5307988..5351615)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (5229864..5273486)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene zinc finger protein 890, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25570 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25571 Neighboring gene MPRA-validated peak6354 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17908 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17909 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17910 Neighboring gene RNA, U6 small nuclear 215, pseudogene Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr7:5257932-5259131 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:5262434-5263183 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25574 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17911 Neighboring gene Sharpr-MPRA regulatory region 13937 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25575 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17912 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:5323448-5324013 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:5324014-5324580 Neighboring gene Sharpr-MPRA regulatory region 9837 Neighboring gene Sharpr-MPRA regulatory region 3727 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17913 Neighboring gene solute carrier family 29 member 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:5350589-5351090 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:5351091-5351590 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:5362189-5362722 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:5362723-5363256 Neighboring gene trinucleotide repeat containing 18 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:5387551-5388392 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:5390077-5390917 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:5395754-5396256 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:5421456-5422020 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:5422021-5422584 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25576 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:5441055-5441556 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:5443987-5444488 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:5447331-5447920 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:5447921-5448510 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:5458249-5458998 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17914 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:5467243-5467992 Neighboring gene long intergenic non-protein coding RNA 2983 Neighboring gene long intergenic non-protein coding RNA 3073

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • FLJ12979, FLJ14217, FLJ42984, DKFZp434J154, DKFZp686P02188

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables phosphatidylinositol-3,5-bisphosphate binding IBA
Inferred from Biological aspect of Ancestor
more info
 
enables phosphatidylinositol-3,5-bisphosphate binding IDA
Inferred from Direct Assay
more info
PubMed 
enables phosphatidylinositol-3-phosphate binding IBA
Inferred from Biological aspect of Ancestor
more info
 
enables phosphatidylinositol-3-phosphate binding IDA
Inferred from Direct Assay
more info
PubMed 
enables phosphatidylinositol-5-phosphate binding IDA
Inferred from Direct Assay
more info
PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
involved_in autophagosome assembly IDA
Inferred from Direct Assay
more info
PubMed 
involved_in autophagosome assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
NOT involved_in autophagosome maturation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in autophagy of mitochondrion IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in autophagy of peroxisome IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in cellular response to starvation IDA
Inferred from Direct Assay
more info
PubMed 
involved_in glycophagy IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in nucleophagy IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in protein lipidation involved in autophagosome assembly IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in protein localization to phagophore assembly site IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in protein localization to phagophore assembly site IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in xenophagy IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
NOT colocalizes_with autophagosome IDA
Inferred from Direct Assay
more info
PubMed 
is_active_in cytosol IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in cytosol IDA
Inferred from Direct Assay
more info
PubMed 
located_in cytosol TAS
Traceable Author Statement
more info
 
colocalizes_with membrane IDA
Inferred from Direct Assay
more info
PubMed 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
 
located_in phagophore assembly site IDA
Inferred from Direct Assay
more info
PubMed 
is_active_in phagophore assembly site membrane IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in phagophore assembly site membrane IDA
Inferred from Direct Assay
more info
PubMed 
part_of protein-containing complex IDA
Inferred from Direct Assay
more info
 

General protein information

Preferred Names
WD repeat domain phosphoinositide-interacting protein 2
Names
WD40 repeat protein interacting with phosphoinositides 2
WIPI49-like protein 2

NCBI Reference Sequences (RefSeq)

NEW Try the new Transcript table

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001033518.2NP_001028690.1  WD repeat domain phosphoinositide-interacting protein 2 isoform c

    See identical proteins and their annotated locations for NP_001028690.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) uses an alternate in-frame splice junction in a 3' exon compared to variant 1. The resulting isoform (c) has the same N- and C-termini but is shorter compared to isoform a.
    Source sequence(s)
    AC093376, AL080155
    Consensus CDS
    CCDS47531.1
    UniProtKB/TrEMBL
    B3KMZ0
    Related
    ENSP00000385297.3, ENST00000404704.7
    Conserved Domains (3) summary
    COG2319
    Location:37290
    WD40; WD40 repeat [General function prediction only]
    sd00039
    Location:161200
    7WD40; WD40 repeat [structural motif]
    cl02567
    Location:184363
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
  2. NM_001033519.2NP_001028691.1  WD repeat domain phosphoinositide-interacting protein 2 isoform d

    See identical proteins and their annotated locations for NP_001028691.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) lacks an alternate in-frame 5' exon and uses an alternate in-frame splice junction in a 3' exon compared to variant 1. The resulting isoform (d) has the same N- and C-termini but is shorter compared to isoform a.
    Source sequence(s)
    AC093376, AL080155
    Consensus CDS
    CCDS47532.1
    UniProtKB/TrEMBL
    B3KMZ0
    Related
    ENSP00000371821.2, ENST00000382384.6
    Conserved Domains (2) summary
    COG2319
    Location:21272
    WD40; WD40 repeat [General function prediction only]
    sd00039
    Location:143182
    7WD40; WD40 repeat [structural motif]
  3. NM_001033520.1NP_001028692.1  WD repeat domain phosphoinositide-interacting protein 2 isoform e

    See identical proteins and their annotated locations for NP_001028692.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR and coding sequence and uses an alternate in-frame splice junction in a 3' exon compared to variant 1. The resulting isoform (e) has a shorter and distinct N-terminus and lacks an alternate internal segment compared to isoform a.
    Source sequence(s)
    AC093376, AY691426, BC016912
    Consensus CDS
    CCDS47533.1
    UniProtKB/TrEMBL
    B3KMZ0
    Related
    ENSP00000429654.1, ENST00000484262.1
    Conserved Domains (3) summary
    COG2319
    Location:9231
    WD40; WD40 repeat [General function prediction only]
    sd00039
    Location:102141
    7WD40; WD40 repeat [structural motif]
    cl02567
    Location:125304
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
  4. NM_001278299.2NP_001265228.1  WD repeat domain phosphoinositide-interacting protein 2 isoform f

    See identical proteins and their annotated locations for NP_001265228.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) uses an alternate splice junction in a 5' exon compared to variant 1. This difference causes translation initiation at a downstream AUG and results in an isoform (f) with a shorter N-terminus, compared to isoform a.
    Source sequence(s)
    AC093376, AI074985, AK315468, AL080155
    UniProtKB/Swiss-Prot
    Q9Y4P8
    Conserved Domains (3) summary
    COG2319
    Location:2216
    WD40; WD40 repeat [General function prediction only]
    sd00039
    Location:1756
    7WD40; WD40 repeat [structural motif]
    cl02567
    Location:40219
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
  5. NM_015610.4NP_056425.1  WD repeat domain phosphoinositide-interacting protein 2 isoform a

    See identical proteins and their annotated locations for NP_056425.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (a).
    Source sequence(s)
    AC093376, AL080155
    Consensus CDS
    CCDS5339.1
    UniProtKB/Swiss-Prot
    B3KNC2, Q5MNZ8, Q6FI96, Q75L50, Q96IE4, Q9Y364, Q9Y4P8
    UniProtKB/TrEMBL
    B3KMZ0
    Related
    ENSP00000288828.4, ENST00000288828.9
    Conserved Domains (3) summary
    COG2319
    Location:37290
    WD40; WD40 repeat [General function prediction only]
    sd00039
    Location:161200
    7WD40; WD40 repeat [structural motif]
    cl02567
    Location:184363
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
  6. NM_016003.4NP_057087.2  WD repeat domain phosphoinositide-interacting protein 2 isoform b

    See identical proteins and their annotated locations for NP_057087.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame 5' exon compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a.
    Source sequence(s)
    AC093376, AK024279
    Consensus CDS
    CCDS34593.1
    UniProtKB/TrEMBL
    B3KMZ0
    Related
    ENSP00000384945.3, ENST00000401525.7
    Conserved Domains (2) summary
    COG2319
    Location:21272
    WD40; WD40 repeat [General function prediction only]
    sd00039
    Location:143182
    7WD40; WD40 repeat [structural motif]

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    5190233..5233855
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006715685.2XP_006715748.1  WD repeat domain phosphoinositide-interacting protein 2 isoform X1

    See identical proteins and their annotated locations for XP_006715748.1

    Conserved Domains (3) summary
    COG2319
    Location:2216
    WD40; WD40 repeat [General function prediction only]
    sd00039
    Location:1756
    7WD40; WD40 repeat [structural motif]
    cl02567
    Location:40219
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    5307988..5351615
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054357839.1XP_054213814.1  WD repeat domain phosphoinositide-interacting protein 2 isoform X1