Human Gene WASHC3 (uc010svw.2)
  Description: Homo sapiens coiled-coil domain containing 53 (WASHC3), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr12:102,406,717-102,455,899 Size: 49,183 Total Exon Count: 7 Strand: -
Coding Region
   Position: hg19 chr12:102,406,886-102,455,740 Size: 48,855 Coding Exon Count: 7 

Page IndexSequence and LinksUniProtKB CommentsPrimersGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr12:102,406,717-102,455,899)mRNA (may differ from genome)Protein (194 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
HPRDLynxMGIneXtProtPubMedTreefam
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CCD53_HUMAN
DESCRIPTION: RecName: Full=WASH complex subunit CCDC53; AltName: Full=Coiled-coil domain-containing protein 53;
FUNCTION: Component of the WASH complex, a complex present at the surface of endosomes that recruits and activates the Arp2/3 complex to induce actin polymerization. The WASH complex plays 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, WASH5P or WASH6P), FAM21 (FAM21A, FAM21B or FAM21C), KIAA1033, KIAA0196 and CCDC53.
INTERACTION: Q96EZ8:MCRS1; NbExp=3; IntAct=EBI-712969, EBI-348259; Q96AQ6:PBXIP1; NbExp=3; IntAct=EBI-712969, EBI-740845;
SIMILARITY: Belongs to the CCDC53 family.

-  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


+  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: 69.33 RPKM in Testis
Total median expression: 751.19 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 -64.20159-0.404 Picture PostScript Text
3' UTR -23.91169-0.141 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
IPR019309 - WASH_CCDC53

Pfam Domains:
PF10152 - Subunit CCDC53 of WASH complex

ModBase Predicted Comparative 3D Structure on Q9Y3C0
FrontTopSide
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 orthologNo orthologGenome BrowserGenome BrowserGenome BrowserNo ortholog
Gene Details  Gene DetailsGene Details 
Gene Sorter  Gene SorterGene Sorter 
  EnsemblFlyBaseWormBase 
  Protein SequenceProtein SequenceProtein Sequence 
  AlignmentAlignmentAlignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding

Biological Process:
GO:0008150 biological_process
GO:0015031 protein transport

Cellular Component:
GO:0005768 endosome
GO:0005769 early endosome
GO:0071203 WASH complex


-  Descriptions from all associated GenBank mRNAs
  JD237731 - Sequence 218755 from Patent EP1572962.
AK223339 - Homo sapiens mRNA for CGI-116 protein variant, clone: TST05135.
AF151874 - Homo sapiens CGI-116 protein mRNA, complete cds.
AF155655 - Human protein x 0009 mRNA.
BC010889 - Homo sapiens coiled-coil domain containing 53, mRNA (cDNA clone MGC:13336 IMAGE:4272385), complete cds.
JD246020 - Sequence 227044 from Patent EP1572962.
JD172164 - Sequence 153188 from Patent EP1572962.
CR457171 - Homo sapiens full open reading frame cDNA clone RZPDo834E128D for gene CGI-116, CGI-116 protein; complete cds, incl. stopcodon.
AK314970 - Homo sapiens cDNA, FLJ95886, Homo sapiens CGI-116 protein (CGI-116), mRNA.
HQ448683 - Synthetic construct Homo sapiens clone IMAGE:100072125; CCSB006319_02 coiled-coil domain containing 53 (CCDC53) gene, encodes complete protein.
KJ898801 - Synthetic construct Homo sapiens clone ccsbBroadEn_08195 CCDC53 gene, encodes complete protein.
AB587430 - Synthetic construct DNA, clone: pF1KB6850, Homo sapiens CCDC53 gene for coiled-coil domain containing 53, without stop codon, in Flexi system.
CU679841 - Synthetic construct Homo sapiens gateway clone IMAGE:100017565 5' read CCDC53 mRNA.
JD128843 - Sequence 109867 from Patent EP1572962.
JD386282 - Sequence 367306 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: AD-016, B2RC74, CCD53_HUMAN, CCDC53, CGI-116, NM_016053, NP_057137, Q53FF0, Q6IAI4, Q96QK0, Q9Y3C0, x0009
UCSC ID: uc010svw.2
RefSeq Accession: NM_016053
Protein: Q9Y3C0 (aka CCD53_HUMAN)
CCDS: CCDS44959.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_016053.2
exon count: 7CDS single in 3' UTR: no RNA size: 923
ORF size: 585CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1259.00frame shift in genome: no % Coverage: 98.92
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.