Human Gene WASHC1 (uc010mgm.1)
  Description: Homo sapiens WAS protein family homolog 1 (WASHC1), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr9:14,511-29,739 Size: 15,229 Total Exon Count: 11 Strand: -
Coding Region
   Position: hg19 chr9:14,807-24,999 Size: 10,193 Coding Exon Count: 10 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr9:14,511-29,739)mRNA (may differ from genome)Protein (465 aa)
Gene SorterGenome BrowserOther Species FASTATable SchemaAlphaFoldBioGPS
EnsemblEntrez GeneExonPrimerGeneCardsGeneNetworkH-INV
HPRDLynxMalacardsMGIneXtProtOMIM
PubMedUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: WASH1_HUMAN
DESCRIPTION: RecName: Full=WAS protein family homolog 1; AltName: Full=CXYorf1-like protein on chromosome 9; AltName: Full=Protein FAM39E;
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.
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. Interacts with alpha-tubulin.
SUBCELLULAR LOCATION: Early endosome membrane. Recycling endosome membrane (By similarity). Note=Localization to the endodome membrane is mediated via its interaction with FAM21.
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.
SIMILARITY: Belongs to the WASH1 family.
SIMILARITY: Contains 1 WH2 domain.

-  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: WASHC1
Diseases sorted by gene-association score: wiskott-aldrich syndrome (4)

+  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: 6.41 RPKM in Testis
Total median expression: 191.95 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -31.30143-0.219 Picture PostScript Text
3' UTR -107.40296-0.363 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
IPR021854 - WASH_WASD

Pfam Domains:
PF11945 - WAHD domain of WASH complex

ModBase Predicted Comparative 3D Structure on A8K0Z3
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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 orthologGenome BrowserGenome BrowserGenome BrowserNo orthologNo ortholog
Gene DetailsGene Details Gene Details  
Gene SorterGene Sorter Gene Sorter  
 RGDEnsemblFlyBase  
 Protein SequenceProtein SequenceProtein Sequence  
 AlignmentAlignmentAlignment  

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003779 actin binding
GO:0005515 protein binding
GO:0031625 ubiquitin protein ligase binding
GO:0043014 alpha-tubulin binding

Biological Process:
GO:0006887 exocytosis
GO:0010507 negative regulation of autophagy
GO:0015031 protein transport
GO:0016197 endosomal transport
GO:0022617 extracellular matrix disassembly
GO:0030335 positive regulation of cell migration
GO:0031274 positive regulation of pseudopodium assembly
GO:0031396 regulation of protein ubiquitination
GO:0034314 Arp2/3 complex-mediated actin nucleation
GO:0042147 retrograde transport, endosome to Golgi
GO:0043553 negative regulation of phosphatidylinositol 3-kinase activity
GO:1990126 retrograde transport, endosome to plasma membrane

Cellular Component:
GO:0005737 cytoplasm
GO:0005768 endosome
GO:0005769 early endosome
GO:0005770 late endosome
GO:0005776 autophagosome
GO:0005814 centriole
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0016020 membrane
GO:0031410 cytoplasmic vesicle
GO:0031901 early endosome membrane
GO:0043231 intracellular membrane-bounded organelle
GO:0055037 recycling endosome
GO:0055038 recycling endosome membrane
GO:0071203 WASH complex
GO:0071437 invadopodium
GO:0000145 exocyst


-  Descriptions from all associated GenBank mRNAs
  BC094860 - Homo sapiens WAS protein family homolog 2 pseudogene, mRNA (cDNA clone IMAGE:4337266).
BC064371 - Homo sapiens cDNA clone IMAGE:5588748, partial cds.
BC073913 - Homo sapiens WAS protein family homolog 2 pseudogene, mRNA (cDNA clone IMAGE:5163655).
BC093083 - Homo sapiens WAS protein family homolog 2 pseudogene, mRNA (cDNA clone IMAGE:30388014).
BC063893 - Homo sapiens cDNA clone IMAGE:30368489, partial cds.
BC014406 - Homo sapiens CXYorf1-related protein, mRNA (cDNA clone IMAGE:4639282), with apparent retained intron.
BC027921 - Homo sapiens cDNA clone IMAGE:5225823, **** WARNING: chimeric clone ****.
JD043865 - Sequence 24889 from Patent EP1572962.
JD464022 - Sequence 445046 from Patent EP1572962.
JD464023 - Sequence 445047 from Patent EP1572962.
JD319762 - Sequence 300786 from Patent EP1572962.
JD439184 - Sequence 420208 from Patent EP1572962.
AK289708 - Homo sapiens cDNA FLJ75027 complete cds, highly similar to Homo sapiens CXYorf1-related protein (MGC52000), mRNA.
JD386972 - Sequence 367996 from Patent EP1572962.
JD469492 - Sequence 450516 from Patent EP1572962.
BC160141 - Synthetic construct Homo sapiens clone IMAGE:100064173, MGC:193256 WASH1 protein (WASH1) mRNA, encodes complete protein.
BC156859 - Synthetic construct Homo sapiens clone IMAGE:100062519, MGC:190539 WAS protein family homolog 1 (WASH1) mRNA, encodes complete protein.
JD371043 - Sequence 352067 from Patent EP1572962.
JD178321 - Sequence 159345 from Patent EP1572962.
JD371044 - Sequence 352068 from Patent EP1572962.
JD044295 - Sequence 25319 from Patent EP1572962.
JD433165 - Sequence 414189 from Patent EP1572962.
JD460507 - Sequence 441531 from Patent EP1572962.
AK296182 - Homo sapiens cDNA FLJ50976 complete cds.
JD406735 - Sequence 387759 from Patent EP1572962.
JD455749 - Sequence 436773 from Patent EP1572962.
JD115443 - Sequence 96467 from Patent EP1572962.
JD365642 - Sequence 346666 from Patent EP1572962.
JD123346 - Sequence 104370 from Patent EP1572962.
JD054019 - Sequence 35043 from Patent EP1572962.
JD309150 - Sequence 290174 from Patent EP1572962.
JD114876 - Sequence 95900 from Patent EP1572962.
JD270338 - Sequence 251362 from Patent EP1572962.
JD392218 - Sequence 373242 from Patent EP1572962.
AK309568 - Homo sapiens cDNA, FLJ99609.
JD520988 - Sequence 502012 from Patent EP1572962.
JD164536 - Sequence 145560 from Patent EP1572962.
JD145347 - Sequence 126371 from Patent EP1572962.
JD493632 - Sequence 474656 from Patent EP1572962.
JD295896 - Sequence 276920 from Patent EP1572962.
JD273037 - Sequence 254061 from Patent EP1572962.
JD267962 - Sequence 248986 from Patent EP1572962.
JD090362 - Sequence 71386 from Patent EP1572962.
JD090361 - Sequence 71385 from Patent EP1572962.
JD338175 - Sequence 319199 from Patent EP1572962.
JD544421 - Sequence 525445 from Patent EP1572962.
AK308540 - Homo sapiens cDNA, FLJ98581.
JD283908 - Sequence 264932 from Patent EP1572962.
JD405726 - Sequence 386750 from Patent EP1572962.
JD405727 - Sequence 386751 from Patent EP1572962.
JD127621 - Sequence 108645 from Patent EP1572962.
JD408497 - Sequence 389521 from Patent EP1572962.
JD100811 - Sequence 81835 from Patent EP1572962.
JD461476 - Sequence 442500 from Patent EP1572962.
JD170368 - Sequence 151392 from Patent EP1572962.
JD519949 - Sequence 500973 from Patent EP1572962.
JD042751 - Sequence 23775 from Patent EP1572962.
JD098685 - Sequence 79709 from Patent EP1572962.
JD151500 - Sequence 132524 from Patent EP1572962.
JD540282 - Sequence 521306 from Patent EP1572962.
JD442700 - Sequence 423724 from Patent EP1572962.
JD370682 - Sequence 351706 from Patent EP1572962.
AK308635 - Homo sapiens cDNA, FLJ98676.
AK024448 - Homo sapiens mRNA for FLJ00038 protein, partial cds.
JD488237 - Sequence 469261 from Patent EP1572962.
JD193028 - Sequence 174052 from Patent EP1572962.
JD172831 - Sequence 153855 from Patent EP1572962.
JD565176 - Sequence 546200 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: A8K0Z3, FAM39E, NM_182905, NP_878908, WASH1, WASH1_HUMAN
UCSC ID: uc010mgm.1
RefSeq Accession: NM_182905
Protein: A8K0Z3 (aka WASH1_HUMAN)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_182905.4
exon count: 11CDS single in 3' UTR: no RNA size: 1837
ORF size: 1398CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2993.00frame 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.