Human Gene VWA5A (ENST00000449321.5) from GENCODE V44
  Description: May play a role in tumorigenesis as a tumor suppressor. Altered expression of this protein and disruption of the molecular pathway it is involved in, may contribute directly to or modify tumorigenesis. (from UniProt O00534)
Gencode Transcript: ENST00000449321.5
Gencode Gene: ENSG00000110002.16
Transcript (Including UTRs)
   Position: hg38 chr11:124,115,404-124,124,841 Size: 9,438 Total Exon Count: 11 Strand: +
Coding Region
   Position: hg38 chr11:124,117,512-124,124,320 Size: 6,809 Coding Exon Count: 9 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr11:124,115,404-124,124,841)mRNA (may differ from genome)Protein (415 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblExonPrimerGencodeGeneCardsHGNC
HPRDLynxMGIneXtProtPubMedUniProtKB
Wikipedia

-  Comments and Description Text from UniProtKB
  ID: VMA5A_HUMAN
DESCRIPTION: RecName: Full=von Willebrand factor A domain-containing protein 5A; AltName: Full=Breast cancer suppressor candidate 1; Short=BCSC-1; AltName: Full=Loss of heterozygosity 11 chromosomal region 2 gene A protein;
FUNCTION: May play a role in tumorigenesis as a tumor suppressor. Altered expression of this protein and disruption of the molecular pathway it is involved in, may contribute directly to or modify tumorigenesis.
TISSUE SPECIFICITY: Expressed at low level in many tissues. Not expressed in 80% of tumor cell lines tested.
SIMILARITY: Contains 1 VIT domain.
SIMILARITY: Contains 1 VWFA 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


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 17.33 RPKM in Pituitary
Total median expression: 281.64 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 -66.00209-0.316 Picture PostScript Text
3' UTR -102.20521-0.196 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
IPR013694 - VIT
IPR002035 - VWF_A

Pfam Domains:
PF08487 - Vault protein inter-alpha-trypsin domain

ModBase Predicted Comparative 3D Structure on O00534
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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 orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
      
      
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm


-  Descriptions from all associated GenBank mRNAs
  AY366504 - Homo sapiens BCSC-1 isoform b/e (LOH11CR2A) mRNA, complete cds, alternatively spliced variant b.
AY366505 - Homo sapiens BCSC-1 isoform c/f (LOH11CR2A) mRNA, complete cds, alternatively spliced variant c.
AY366507 - Homo sapiens BCSC-1 isoform b/e (LOH11CR2A) mRNA, complete cds, alternatively spliced variant e.
AY366508 - Homo sapiens BCSC-1 isoform c/f (LOH11CR2A) mRNA, complete cds, alternatively spliced variant f.
AK291698 - Homo sapiens cDNA FLJ76886 complete cds, highly similar to Homo sapiens loss of heterozygosity, 11, chromosomal region 2, gene A (LOH11CR2A), transcript variant 1, mRNA.
AF002672 - Homo sapiens breast cancer suppressor candidate 1 (bcsc-1) mRNA, complete cds.
AK314934 - Homo sapiens cDNA, FLJ95844, highly similar to Homo sapiens loss of heterozygosity, 11, chromosomal region 2, gene A (LOH11CR2A), mRNA.
AY366503 - Homo sapiens BCSC-1 isoform a/d (LOH11CR2A) mRNA, complete cds, alternatively spliced variant a.
AY366506 - Homo sapiens BCSC-1 isoform a/d (LOH11CR2A) mRNA, complete cds, alternatively spliced variant d.
BC001234 - Homo sapiens von Willebrand factor A domain containing 5A, mRNA (cDNA clone MGC:4904 IMAGE:3461486), complete cds.
AK295247 - Homo sapiens cDNA FLJ55206 complete cds, highly similar to Loss of heterozygosity 11 chromosomal region 2 gene A protein.
KJ891553 - Synthetic construct Homo sapiens clone ccsbBroadEn_00947 VWA5A gene, encodes complete protein.
BT006655 - Homo sapiens loss of heterozygosity, 11, chromosomal region 2, gene A mRNA, complete cds.
JD263013 - Sequence 244037 from Patent EP1572962.
JD549773 - Sequence 530797 from Patent EP1572962.
JD330145 - Sequence 311169 from Patent EP1572962.
JD428608 - Sequence 409632 from Patent EP1572962.
JD485295 - Sequence 466319 from Patent EP1572962.
JD154086 - Sequence 135110 from Patent EP1572962.
JD133755 - Sequence 114779 from Patent EP1572962.
DL491375 - Novel nucleic acids.
DL490003 - Novel nucleic acids.
DL492078 - Novel nucleic acids.
DL490624 - Novel nucleic acids.
JD496654 - Sequence 477678 from Patent EP1572962.
JD128136 - Sequence 109160 from Patent EP1572962.
JD172638 - Sequence 153662 from Patent EP1572962.
JD563258 - Sequence 544282 from Patent EP1572962.
JD221852 - Sequence 202876 from Patent EP1572962.
JD046464 - Sequence 27488 from Patent EP1572962.
JD083588 - Sequence 64612 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: AY366506, BCSC1, ENST00000449321.1, ENST00000449321.2, ENST00000449321.3, ENST00000449321.4, LOH11CR2A, O00534, Q6UN19, Q6UN20, Q9BVF8, uc001pzs.1, uc001pzs.2, uc001pzs.3, uc001pzs.4, VMA5A_HUMAN
UCSC ID: ENST00000449321.5
RefSeq Accession: NM_198315
Protein: O00534 (aka VMA5A_HUMAN)
CCDS: CCDS8445.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.