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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

ZFYVE28 Gene

protein-coding   GIFtS: 51
GCID: GC04M002271

zinc finger, FYVE domain containing 28

  Search for ZFYVE28
in our new
 Human Malady Compendium 
Biological research products
for ZFYVE28
    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section

Aliases
Zinc Finger, FYVE Domain Containing 281 2     HLst21
KIAA16431 3     LYST22
Zinc Finger FYVE Domain-Containing Protein 282 3     Lateral Signaling Target Protein 2 Homolog2
LST22 3     

External Ids:    HGNC: 293341   Entrez Gene: 577322   Ensembl: ENSG000001597337   OMIM: 6141765   UniProtKB: Q9HCC93   

Export aliases for ZFYVE28 gene to outside databases

Previous GC identifers: GC04M002233 GC04M002238


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

UniProtKB/Swiss-Prot: LST2_HUMAN, Q9HCC9
Function: Negative regulator of epidermal growth factor receptor (EGFR) signaling. Acts by promoting EGFR degradation
in endosomes when not monoubiquitinated




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000004.11  NC_018915.1  NT_006051.18  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the ZFYVE28 gene promoter:
         E2F-3a   E2F-4   E2F-5   E2F-2   CUTL1   E2F-1   E2F   ARP-1   Pax-4a   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidZFYVE28 promoter sequence
   Search SABiosciences Chromatin IP Primers for ZFYVE28

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat ZFYVE28


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 4p16.3   Ensembl cytogenetic band:  4p16.3   HGNC cytogenetic band: 4p16.3

ZFYVE28 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
ZFYVE28 gene location

GeneLoc information about chromosome 4         GeneLoc Exon Structure

GeneLoc location for GC04M002271:  view genomic region     (about GC identifiers)

Start:
2,271,309 bp from pter      End:
2,420,390 bp from pter
Size:
149,082 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: LST2_HUMAN, Q9HCC9 (See protein sequence)
Recommended Name: Lateral signaling target protein 2 homolog  
Size: 887 amino acids; 96490 Da
Subunit: Interacts with TRIM3
Subcellular location: Cytoplasm, cytosol. Early endosome membrane. Note=Localizes to early endosome membrane in absence
of Lys-87 monoubiquitination. Localizes to cytosol when monoubiquitinated
Sequence caution: Sequence=AAH53664.1; Type=Erroneous initiation; Note=Translation N-terminally extended;
Sequence=BAB13469.1; Type=Erroneous initiation;
Secondary accessions: B2RP83 B3KX50 B7Z1Q7 B7Z2G9 B7Z2M2 B7ZB19 E9PB54 E9PG77 Q7Z6J3
Alternative splicing: 7 isoforms:  Q9HCC9-1   Q9HCC9-2   Q9HCC9-3   Q9HCC9-4   Q9HCC9-5   Q9HCC9-6   Q9HCC9-7   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for ZFYVE28: NX_Q9HCC9

Post-translational modifications:

  • Monoubiquitination at Lys-87 prevents binding to phosphatidylinositol 3-phosphate (PI3P) and localization to early
  • endosome membranes1
  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q9HCC9

  • ZFYVE28 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins (6 alternative transcripts): 
    NP_001166127.1  NP_001166128.1  NP_001166129.1  NP_001166130.1  NP_001166131.1  NP_066023.2  

    ENSEMBL proteins: 
     ENSP00000427654   ENSP00000290974   ENSP00000425706   ENSP00000426299   ENSP00000425766  
     ENSP00000422638   ENSP00000423694   ENSP00000427471  

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    Uscn Proteins for ZFYVE28

    Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005829cytosol IDA19460345
    GO:0031901early endosome membrane IDA19460345


    ZFYVE28 for ontologies           About GeneDecksing



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    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    ZFYVE28 for domains           About GeneDecksing

    4 InterPro domains/families:
     IPR000306 Znf_FYVE
     IPR017455 Znf_FYVE-rel
     IPR013083 Znf_RING/FYVE/PHD
     IPR011011 Znf_FYVE_PHD

    Graphical View of Domain Structure for InterPro Entry Q9HCC9

    ProtoNet protein and cluster: Q9HCC9

    1 Blocks protein family: IPB000306 Zn-finger

    UniProtKB/Swiss-Prot: LST2_HUMAN, Q9HCC9
    Domain: The FYVE-type zinc finger mediates the interaction with phosphatidylinositol 3-phosphate (PI3P) and
    localization to early endosome membranes when not monoubiquitinated at Lys-87
    Similarity: Belongs to the lst-2 family
    Similarity: Contains 1 FYVE-type zinc finger


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section

    Function Summary:

         UniProtKB/Swiss-Prot: LST2_HUMAN, Q9HCC9
    Function: Negative regulator of epidermal growth factor receptor (EGFR) signaling. Acts by promoting EGFR degradation
    in endosomes when not monoubiquitinated

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    hsa-miR-4317 hsa-miR-136 hsa-miR-216b hsa-miR-885-5p hsa-miR-500a hsa-miR-548a-3p hsa-miR-3150b-3p hsa-miR-3121-3p
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    Gene Ontology (GO): 3 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding IPI19460345
    GO:0032266phosphatidylinositol-3-phosphate binding IDA19460345
    GO:0046872metal ion binding IEA--


    ZFYVE28 for ontologies           About GeneDecksing


    1 GenomeRNAi human phenotype for ZFYVE28:
     Increased gamma-H2AX phosphory 


    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
    About This Section

    Unified GeneCards pathways  About this table 
    See pathways by source

    Super-pathwaycontained gene-specific pathways
    1Internalization of ErbB1
    Internalization of ErbB11.00


    1 BioSystems Pathway for ZFYVE28 
        Internalization of ErbB1


    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for ZFYVE28

    STRING Interaction Network Preview (showing 5 interactants - click image to see 9)

    5/10 Interacting proteins for ZFYVE28 (Q9HCC93 ENSP000002909744) via UniProtKB, MINT, STRING, and/or I2D (see all 10)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    UBCP0CG483, ENSP000003448184I2D: score=1 STRING: ENSP00000344818
    EGFP011333, ENSP000002651714I2D: score=1 STRING: ENSP00000265171
    EGFRP005333, ENSP000002754934I2D: score=1 STRING: ENSP00000275493
    RAB4AP203383, ENSP000003556514I2D: score=1 STRING: ENSP00000355651
    RAB5AP203393, ENSP000002730474I2D: score=1 STRING: ENSP00000273047
    About this table

    Gene Ontology (GO): 2 biological process terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0007175negative regulation of epidermal growth factor-activated receptor activity IMP19460345
    GO:0042059negative regulation of epidermal growth factor receptor signaling pathway IMP19460345


    ZFYVE28 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
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    Browse Tocris compounds for ZFYVE28
    Search CenterWatch for drugs/clinical trials and news about ZFYVE28 / LST2 

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for ZFYVE28 gene (6 alternative transcripts): 
    NM_001172656.1  NM_001172657.1  NM_001172658.1  NM_001172659.1  NM_001172660.1  NM_020972.2  

    Unigene Cluster for ZFYVE28:

    Zinc finger, FYVE domain containing 28
    Hs.292056  [show with all ESTs]
    Unigene Representative Sequence: AK126692
    11 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000508471 ENST00000290974(uc003gew.2 uc011bvk.2 uc003gex.2 uc011bvl.2)
    ENST00000511071 ENST00000515312 ENST00000514248 ENST00000515169(uc003gey.4)
    ENST00000509171(uc003gez.3) ENST00000503000(uc021xkq.1) ENST00000508184
    ENST00000504743 ENST00000505421

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    Additional cDNA sequence: 

    AB046863.1 AK126692.1 AK293775.1 AK294710.1 AK294874.1 AK316484.1 BC032605.1 BC035793.1 
    BC041866.1 BC053664.1 BC137309.1 BC137310.1 

    6 DOTS entries:

    DT.439461  DT.95345136  DT.101971065  DT.101964122  DT.100681700  DT.91748011 

    24/41 AceView cDNA sequences (see all 41):

    CB069515 BX089483 BM677125 BM721483 BC053664 AB046863 BQ005210 BM672438 
    BC041866 AW271792 CA307118 BM129246 BM686438 BC035793 AK126692 AL698726 
    AA977137 BV195638 AW054793 AA961044 CA433241 AW130023 AA324976 BE327635 

    GeneLoc Exon Structure

    5/9 Alternative Splicing Database (ASD) splice patterns (SP) for ZFYVE28 (see all 9)    About this scheme

    ExUns: 1a · 1b · 1c ^ 2a · 2b · 2c ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7 ^ 8 ^ 9a · 9b · 9c ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19a ·
    SP1:                    -     -     -           -     -           -     -     -                                   -                 -     -                     
    SP2:                                                                                                                                                            
    SP3:                    -     -     -           -     -           -     -     -                                                                                 
    SP4:                                            -     -           -     -     -                                                                                 
    SP5:                    -     -     -     -     -     -           -     -     -                                                                                 

    ExUns: 19b ^ 20a · 20b ^ 21
    SP1:              -         
    SP2:              -         
    SP3:                        
    SP4:                        
    SP5:                        


    ECgene alternative splicing isoforms for ZFYVE28

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    ZFYVE28 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: GGGGTCCGAC

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)

    About this image
    See ZFYVE28 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for ZFYVE28

    SOURCE GeneReport for Unigene cluster: Hs.292056
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    In Situ
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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

    This gene was present in the common ancestor of animals.

    Orthologs for ZFYVE28 gene from 6/19 species (see all 19)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Zfyve281 , 5 zinc finger, FYVE domain containing 281, 5 82.77(n)1
    84.24(a)1
      5 (17.85 cM)5
    2311251  NM_001015039.11  NP_001015039.11 
     341948745 
    chicken
    (Gallus gallus)
    Aves ZFYVE281 zinc finger, FYVE domain containing 28 66.63(n)
    71.31(a)
      422889  XM_420832.3  XP_420832.3 
    lizard
    (Anolis carolinensis)
    Reptilia ZFYVE286
    --
    54(a)
    1 ↔ 1
    2(145473145-145476170)
    zebrafish
    (Danio rerio)
    Actinopterygii idibd13742 idibd1374 82.9(n)   338253  57093083 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG60516
    --
    28(a)
    1 ↔ 1
    3R(22950481-22976791)
    worm
    (Caenorhabditis elegans)
    Secernentea lst-26
    Lateral signaling target protein 2
    39(a)
    1 ↔ 1
    X(4378005-4383341)


    ENSEMBL Gene Tree for ZFYVE28 (if available)
    TreeFam Gene Tree for ZFYVE28 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for ZFYVE28 gene
    PIKFYVE2  ZFYVE212  
    1 SIMAP similar gene for ZFYVE28 using alignment to 4 protein entries:     LST2_HUMAN (see all proteins):
    MTMR3

    ZFYVE28 for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 13 variations for ZFYVE28
         2 CNVs: 98610 7440
         11 Indels: 27613 46620 68623 98609 12387 98608 68622 62155 43136 11233 27614
    SABiosciences Cancer Mutation PCR Assays
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section

    ZFYVE28 for disorders           About MalaCards

    ZFYVE28 for disorders           About GeneDecksing

    OMIM gene information: 614176    OMIM disorders: --

    Human Genome Epidemiology (HuGE) Navigator: ZFYVE28 (1 document)

    Export disorders for ZFYVE28 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for ZFYVE28 gene, integrated from 9 sources (see all 12):
    (articles sorted by number of sources associating them with ZFYVE28)
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    1. Prediction of the coding sequences of unidentified human genes. XVIII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PubMed id 10997877)1, 2, 3 Nagase T.... Ohara O. (2000)
    2. Monoubiquitinylation regulates endosomal localization of Lst2, a negative regulator of EGF receptor signaling. (PubMed id 19460345)1, 2 Mosesson Y.... Yarden Y. (2009)
    3. Methods for quantification of in vivo changes in prote in ubiquitination following proteasome and deubiquitinase inhibition. (PubMed id 22505724)1 Udeshi N.D....Carr S.A. (2012)
    4. Systematic and quantitative assessment of the ubiquiti n-modified proteome. (PubMed id 21906983)1 Kim W....Gygi S.P. (2011)
    5. Ubiquitin ligase substrate identification through qua ntitative proteomics at both the protein and peptide levels. (PubMed id 21987572)1 Lee K.A....Doedens J.R. (2011)
    6. A proteome-wide, quantitative survey of in vivo ubiqui tylation sites reveals widespread regulatory roles. (PubMed id 21890473)1 Wagner S.A....Choudhary C. (2011)
    7. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)1 Rose J.E....Uhl G.R. (2010)
    8. Protein microarray analysis identifies human cellular prion protein interactors. (PubMed id 18482256)1 Satoh J....Tabunoki H. (2009)
    9. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. (PubMed id 15815621)2 Hillier L.W....Wilson R.K. (2005)
    10. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S....Malek J. (2004)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 57732 HGNC: 29334 AceView: ZFYVE28 Ensembl:ENSG00000159733 euGenes: HUgn57732
    ECgene: ZFYVE28 H-InvDB: ZFYVE28

    (According to HUGE)
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    HUGE: KIAA1643

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for ZFYVE28 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for ZFYVE28 gene:
    Search GeneIP for patents involving ZFYVE28

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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