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WASH3P Gene

pseudogene   GIFtS: 32
GCID: GC15P102501

WAS Protein Family Homolog 3 Pseudogene

(Previous names: family with sequence similarity 39, member D pseudogene)
(Previous symbol: FAM39DP)
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(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
WAS Protein Family Homolog 3 Pseudogene1 2
FAM39DP1 2 3
Family With Sequence Similarity 39, Member D Pseudogene1
Protein FAM39DP3

External Ids:    HGNC: 243621   Entrez Gene: 3746662   Ensembl: ENSG000001855967   UniProtKB: C4AMC73   

Export aliases for WASH3P gene to outside databases

Previous GC identifers: GC15P100321 GC15U900980


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for WASH3P Gene:
WASH3P (WAS protein family homolog 3 pseudogene) is a pseudogene. GO annotations related to this gene include actin binding and alpha-tubulin binding.

UniProtKB/Swiss-Prot: WASH3_HUMAN, C4AMC7
Function: Acts as a nucleation-promoting factor at the surface of endosomes, where it recruits and activates the
Arp2/3 complex to induce actin polymerization, playing a key role in the fission of tubules that serve as
transport intermediates during endosome sorting (By similarity)




(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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000015.9  NC_018926.2  NT_010194.18  
Regulatory elements:
   Regulatory transcription factor binding sites in the WASH3P gene promoter:
         FOXF2   MEF-2   POU3F1   E4BP4   MEF-2A   POU2F1a   POU2F1b   aMEF-2   POU2F1c   RSRFC4   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for WASH3P

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat WASH3P


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

Entrez Gene cytogenetic band: 15q26.3   Ensembl cytogenetic band:  15q26.3   HGNC cytogenetic band: 15q26.3

WASH3P Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
WASH3P gene location

GeneLoc information about chromosome 15         GeneLoc Exon Structure

GeneLoc location for GC15P102501:  view genomic region     (about GC identifiers)

Start:
102,501,016 bp from pter      End:
102,516,808 bp from pter
Size:
15,793 bases      Orientation:
plus strand
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for WASH3P

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, 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, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: WASH3_HUMAN, C4AMC7 (See protein sequence)
Recommended Name: Putative WAS protein family homolog 3  
Size: 463 amino acids; 49995 Da
Subunit: Component of the WASH complex, composed of F-actin-capping protein subunit alpha (CAPZA1, CAPZA2 or
CAPZA3), F-actin-capping protein subunit beta (CAPZB), WASH (WASH1, WASH2P, WASH3P, WASH4P or WASH6P), FAM21
(FAM21A, FAM21B or FAM21C), KIAA1033, KIAA0196 and CCDC53. Interacts (via WHD1 region) with FAM21C; the
interaction is direct (By similarity)
Miscellaneous: WASH genes duplicated to multiple chromosomal ends during primate evolution, with highest copy
number reached in humans, whose WASH repertoires probably vary extensively among individuals (PubMed:18159949).
It is therefore difficult to determine which gene is functional or not. The telomeric region of chromosome 9p is
paralogous to the pericentromeric regions of chromosome 9 as well as to 2q. Paralogous regions contain 7
transcriptional units. Duplicated WASH genes are also present in the Xq/Yq pseudoautosomal region, as well as on
chromosome 1 and 15. The chromosome 16 copy seems to be a pseudogene

Explore the universe of human proteins at neXtProt for WASH3P: NX_C4AMC7


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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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HGNC Gene Families:
WASH: WAS protein homologs

3 InterPro protein domains:
 IPR028290 WASH1
 IPR003124 WH2_dom
 IPR021854 WASH1_WAHD

Graphical View of Domain Structure for InterPro Entry C4AMC7

ProtoNet protein and cluster: C4AMC7

UniProtKB/Swiss-Prot: WASH3_HUMAN, C4AMC7
Similarity: Belongs to the WASH1 family
Similarity: Contains 1 WH2 domain


Find genes that share domains with WASH3P           About GenesLikeMe


(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, genOway,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Molecular Function:

     UniProtKB/Swiss-Prot Summary: WASH3_HUMAN, C4AMC7
Function: Acts as a nucleation-promoting factor at the surface of endosomes, where it recruits and activates the
Arp2/3 complex to induce actin polymerization, playing a key role in the fission of tubules that serve as
transport intermediates during endosome sorting (By similarity)

     Gene Ontology (GO): 2 molecular function terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0003779actin binding IEA--
GO:0043014alpha-tubulin binding ISS--
     
Find genes that share ontologies with WASH3P           About GenesLikeMe


Phenotypes:
     1 GenomeRNAi human phenotype for WASH3P:
 Synthetic lethal with Ras 

Animal Models:
   genOway: Develop your customized and physiologically relevant rodent model for WASH3P

miRNA
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miRTarBase miRNAs that target WASH3P:
hsa-mir-149-5p (MIRT045560), hsa-mir-183-5p (MIRT047160), hsa-mir-331-3p (MIRT043400), hsa-mir-93-3p (MIRT038874)

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(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Subcellular locations from UniProtKB/Swiss-Prot
WASH3_HUMAN, C4AMC7: Early endosome membrane (By similarity). Recycling endosome membrane (By similarity).
Note=Localization to the endodome membrane is mediated via its interaction with FAM21 (By similarity)

Gene Ontology (GO): Selected cellular component terms (see all 7):    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005769early endosome ISS--
GO:0030027lamellipodium IDA18159949
GO:0030175filopodium IDA18159949
GO:0031901early endosome membrane IEA--
GO:0055037recycling endosome ISS--

Find genes that share ontologies with WASH3P           About GenesLikeMe


(SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, 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 Apr 2014 via Entrez Gene).
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    Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for WASH3P
Interactions:

    Search GeneGlobe Interaction Network for WASH3P

2 Interacting proteins for WASH3P (C4AMC73) via UniProtKB, MINT, STRING, and/or I2D
InteractantInteraction Details
GeneCardExternal ID(s)
EXOC7Q9UPT53I2D: score=2 
MAPK10P537793I2D: score=2 
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Gene Ontology (GO): 3 biological process terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0016197endosomal transport ISS--
GO:0034314Arp2/3 complex-mediated actin nucleation IDA18159949
GO:0042147retrograde transport, endosome to Golgi ISS--

Find genes that share ontologies with WASH3P           About GenesLikeMe



(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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Browse Small Molecules at EMD Millipore
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  Browse compounds at ApexBio 

Browse Tocris compounds for WASH3P (WASH3)



(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 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,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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REFSEQ mRNAs for WASH3P gene: 
NM_199163.2  

Unigene Cluster for WASH3P:

WAS protein family homolog 3 pseudogene
Hs.459573  [show with all ESTs]
Unigene Representative Sequence: AK092583
10 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000559884(uc002cdj.3) ENST00000558686 ENST00000559163 ENST00000354296
ENST00000557932 ENST00000558784 ENST00000560956 ENST00000338304(uc021szk.1 uc010utt.1 uc010bpl.1 uc010bpk.1 uc010utu.2)
ENST00000398121(uc002cdi.3 uc010bpo.3 uc002cdq.3 uc002cdr.3)
ENST00000378819
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Primer
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Additional mRNA sequence: 

AK056232.1 AK092583.1 AK095183.1 AK097269.1 AK290087.1 AK291582.1 AK295256.1 AK300161.1 
AK308540.1 AK308566.1 AK308574.1 AK309926.1 AK310139.1 BC048328.1 BC053987.1 BC063470.1 
BC063555.1 BC094698.1 BC110991.1 BC110996.1 NR_003659.2 NR_024540.1 

Selected DOTS entries (see all 84):

DT.454253  DT.95172025  DT.100851542  DT.95364255  DT.86999703  DT.100848231  DT.121055053  DT.92045715 
DT.95172022  DT.65284869  DT.95243425  DT.97860170  DT.100840652  DT.121055064  DT.100653448  DT.100803430 
DT.121417481  DT.121475240  DT.100654144  DT.85101946  DT.121184997  DT.121185067  DT.121417477  DT.121456739 

9 AceView cDNA sequences:

BI830790 BI830792 BV188241 BU570288 BI550667 BE145464 BM691866 BG197266 
AI310707 

GeneLoc Exon Structure


(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™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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WASH3P expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: GGGGGACGGC
WASH3P Expression
About this image

WASH3P Protein expression data from MOPED1, PaxDb2 and MaxQB3 --

SOURCE GeneReport for Unigene cluster: Hs.459573
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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)
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ENSEMBL Gene Tree for WASH3P (if available)
TreeFam Gene Tree for WASH3P (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for WASH3P gene
8 SIMAP similar genes for WASH3P using alignment to 1 protein entry:     WASH3_HUMAN:
WASH1    WASH2P    WASH6P    WASH4P    WASH    DKFZp686C24272
DKFZp434K1323    FLJ00075

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(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, 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), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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Selected SNPs for WASH3P (see all 183)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 15 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1417154501,2
C--102499152(+) AGGTCC/TAGGAT 1 -- us2k10--------
rs1154571851,2
C--102499423(+) ATTACA/CAAGTA 1 -- us2k10--------
rs2009781661,2
C--102499489(+) GGTACA/GATCAT 1 -- us2k10--------
rs3705574211,2
C--102499673(+) CTCTCA/GGTCAG 1 -- us2k10--------
rs2015201551,2
C--102499694(+) GTGCTA/GGGATT 1 -- us2k10--------
rs3725053191,2
C--102499717(+) CACCAC/GCCCAG 1 -- us2k10--------
rs1997662061,2
C--102502988(+) GACCAC/TACACT 1 -- int10--------
rs1997944041,2
C--102503074(+) ACAAAA/GTATGA 1 -- int10--------
rs2007525341,2
C--102503078(+) AATATC/GAAGAT 1 -- int10--------
rs3740913771,2
C--102503116(+) ACAAA-/TGTT  
        
GTTTG
1 -- int10--------

HapMap Linkage Disequilibrium report for WASH3P (102501016 - 102516808 bp)

Structural Variations
     Database of Genomic Variants (DGV) 7 variations for WASH3P:    About this table    
Variant IDTypeSubtypePubMed ID
nsv820527CNV Duplication20802225
nsv471523CNV Duplication19718026
nsv1695CNV Insertion18451855
esv27561CNV Gain19812545
nsv904622CNV Gain21882294
nsv9315CNV Gain+Loss18304495
nsv514760CNV Complex21397061

Site Specific Mutation Identification with 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.)
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(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 WASH3P gene, integrated from 10 sources (see all 11):
(articles sorted by number of sources associating them with WASH3P)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Human subtelomeric WASH genes encode a new subclass of the WASP family. (PubMed id 18159949)1, 2, 3 Linardopoulou E.V.... Trask B.J. (PLoS Genet. 2007)
  2. Analysis of the DNA sequence and duplication history of human chromosome 15. (PubMed id 16572171)1, 2 Zody M.C....Nusbaum C. (Nature 2006)
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
  4. Characterization of the murine orthologue of a novel human subtelomeric multigene family. (PubMed id 11701968)1, 3 Gianfrancesco F....D'Urso M. (Cytogenet. Cell Genet. 2001)
  5. Differentially regulated and evolved genes in the fully sequenced Xq/Yq pseudoautosomal region. (PubMed id 10655549)1, 2 Ciccodicola A.... D'Urso M. (Hum. Mol. Genet. 2000)
  6. Systematic and quantitative assessment of the ubiquitin-modified proteome. (PubMed id 21906983)1 Kim W....Gygi S.P. (Mol. Cell 2011)
  7. Interactions of pathological hallmark proteins: tubulin polymerization promoting protein/p25, beta-amyloid, and alpha-synuclein. (PubMed id 21832049)1 OlA!h J....OvA!di J. (J. Biol. Chem. 2011)
  8. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (Genome Res. 2006)
  9. Transcriptome analysis of human gastric cancer. (PubMed id 16341674)1 Oh J.H.... Kim N.S. (Mamm. Genome 2005)
  10. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1 Ota T.... Sugano S. (Nat. Genet. 2004)

(in PubMed, OMIM, and NCBI Bookshelf)
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 ANDOR
Aliases
Free Text  

  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 374666 HGNC: 24362 AceView: FLJ25222.1 Ensembl:ENSG00000185596 euGenes: HUgn374666
ECgene: WASH3P H-InvDB: WASH3P

(According to HUGE)
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(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for WASH3P gene:
Search GeneIP for patents involving WASH3P

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



(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, eBioscience, antibodies-online, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from genOway)
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 Search www.enzolifesciences.com for proteins, assays, substrates, inhibitors & antibodies

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  Search antibodies-online for antibodies for WASH3P
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GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014 , 21 Aug 2014 , 8 Sep 2014 , 7 Oct 2014

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