Human Gene VOPP1 (ENST00000285279.10_9) from GENCODE V47lift37
  Description: VOPP1 WW domain binding protein, transcript variant 1 (from RefSeq NM_030796.5)
Gencode Transcript: ENST00000285279.10_9
Gencode Gene: ENSG00000154978.13_15
Transcript (Including UTRs)
   Position: hg19 chr7:55,538,306-55,640,195 Size: 101,890 Total Exon Count: 5 Strand: -
Coding Region
   Position: hg19 chr7:55,540,548-55,640,017 Size: 99,470 Coding Exon Count: 5 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr7:55,538,306-55,640,195)mRNA (may differ from genome)Protein (172 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: VOPP1_HUMAN
DESCRIPTION: RecName: Full=Vesicular, overexpressed in cancer, prosurvival protein 1; AltName: Full=EGFR-coamplified and overexpressed protein; Short=ECop; AltName: Full=Glioblastoma-amplified secreted protein; AltName: Full=Putative NF-kappa-B-activating protein 055N; Flags: Precursor;
FUNCTION: Increases the transcriptional activity of NFKB1 by facilitating its nuclear translocation, DNA-binding and associated apoptotic response, when overexpressed.
SUBCELLULAR LOCATION: Cytoplasmic vesicle membrane; Single-pass type I membrane protein. Note=When overexpressed, localizes in the nucleus and perinuclear regions.
TISSUE SPECIFICITY: Widely expressed with highest levels in thymus and ovary.
SIMILARITY: Belongs to the VOPP1/ECOP family.
SEQUENCE CAUTION: Sequence=AAK82888.1; Type=Erroneous translation; Note=Wrong choice of frame;

-  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           more ... click here to view the complete list

+  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: 58.00 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 687.84 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 -108.30178-0.608 Picture PostScript Text
3' UTR -782.502242-0.349 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
IPR026229 - VOPP1

ModBase Predicted Comparative 3D Structure on Q96AW1
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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 DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Biological Process:
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated

Cellular Component:
GO:0005768 endosome
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0030659 cytoplasmic vesicle membrane
GO:0031301 integral component of organelle membrane
GO:0031410 cytoplasmic vesicle


-  Descriptions from all associated GenBank mRNAs
  AL136610 - Homo sapiens mRNA; cDNA DKFZp564K0822 (from clone DKFZp564K0822).
BC016650 - Homo sapiens EGFR-coamplified and overexpressed protein, mRNA (cDNA clone MGC:17343 IMAGE:4342536), complete cds.
AF395824 - Homo sapiens glioblastoma amplified secreted protein (GASP) mRNA, complete cds.
AK092992 - Homo sapiens cDNA FLJ35673 fis, clone SPLEN2018285, highly similar to Homo sapiens EGFR-coamplified and overexpressed protein (ECOP), mRNA.
AX747841 - Sequence 1366 from Patent EP1308459.
AK090825 - Homo sapiens cDNA FLJ33506 fis, clone BRAMY2004756.
AX746636 - Sequence 161 from Patent EP1308459.
AB097004 - Homo sapiens mRNA for putative NFkB activating protein, complete cds, clone: 055N.
AK075391 - Homo sapiens cDNA PSEC0081 fis, clone NT2RP2004130.
AK315882 - Homo sapiens cDNA, FLJ79531 complete cds, highly similar to Homo sapiens EGFR-coamplified and overexpressed protein (ECOP).
AK309288 - Homo sapiens cDNA, FLJ99329.
CR533483 - Homo sapiens full open reading frame cDNA clone RZPDo834D0917D for gene DKFZP564K0822, hypothetical protein DKFZp564K0822; complete cds, incl. stopcodon.
AK225755 - Homo sapiens mRNA for EGFR-coamplified and overexpressed protein variant, clone: FCC135D05.
AK314338 - Homo sapiens cDNA, FLJ95099.
AM393121 - Synthetic construct Homo sapiens clone IMAGE:100001632 for hypothetical protein (ECOP gene).
AK000539 - Homo sapiens cDNA FLJ20532 fis, clone KAT10877.
AK126848 - Homo sapiens cDNA FLJ44900 fis, clone BRAMY3003723.
JD317692 - Sequence 298716 from Patent EP1572962.
JD114021 - Sequence 95045 from Patent EP1572962.
JD327320 - Sequence 308344 from Patent EP1572962.
JD067115 - Sequence 48139 from Patent EP1572962.
JD493135 - Sequence 474159 from Patent EP1572962.
JD219527 - Sequence 200551 from Patent EP1572962.
JD536272 - Sequence 517296 from Patent EP1572962.
JD322060 - Sequence 303084 from Patent EP1572962.
JD565886 - Sequence 546910 from Patent EP1572962.
JD529974 - Sequence 510998 from Patent EP1572962.
JD080274 - Sequence 61298 from Patent EP1572962.
JD227779 - Sequence 208803 from Patent EP1572962.
JD276661 - Sequence 257685 from Patent EP1572962.
JD073107 - Sequence 54131 from Patent EP1572962.
JD233415 - Sequence 214439 from Patent EP1572962.
JD363818 - Sequence 344842 from Patent EP1572962.
JD057895 - Sequence 38919 from Patent EP1572962.
JD528839 - Sequence 509863 from Patent EP1572962.
JD248168 - Sequence 229192 from Patent EP1572962.
JD227198 - Sequence 208222 from Patent EP1572962.
JD263962 - Sequence 244986 from Patent EP1572962.
JD382063 - Sequence 363087 from Patent EP1572962.
JD153880 - Sequence 134904 from Patent EP1572962.
JD417282 - Sequence 398306 from Patent EP1572962.
JD227118 - Sequence 208142 from Patent EP1572962.
JD261213 - Sequence 242237 from Patent EP1572962.
JD487280 - Sequence 468304 from Patent EP1572962.
JD068242 - Sequence 49266 from Patent EP1572962.
JD541081 - Sequence 522105 from Patent EP1572962.
JD436016 - Sequence 417040 from Patent EP1572962.
JD330182 - Sequence 311206 from Patent EP1572962.
JD352200 - Sequence 333224 from Patent EP1572962.
JD153704 - Sequence 134728 from Patent EP1572962.
JD327769 - Sequence 308793 from Patent EP1572962.
JD262691 - Sequence 243715 from Patent EP1572962.
JD131414 - Sequence 112438 from Patent EP1572962.
JD349952 - Sequence 330976 from Patent EP1572962.
JD163383 - Sequence 144407 from Patent EP1572962.
JD549653 - Sequence 530677 from Patent EP1572962.
JD143910 - Sequence 124934 from Patent EP1572962.
JD230318 - Sequence 211342 from Patent EP1572962.
JD203581 - Sequence 184605 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: B0AZU1, B2RAT4, B3KS72, C9JWR3, ECOP, ENST00000285279.1, ENST00000285279.2, ENST00000285279.3, ENST00000285279.4, ENST00000285279.5, ENST00000285279.6, ENST00000285279.7, ENST00000285279.8, ENST00000285279.9, GASP, NM_030796, Q6FIE3, Q8NBN8, Q96AW1, Q96RE5, Q9H0W4, uc317khi.1, uc317khi.2, VOPP1 , VOPP1_HUMAN
UCSC ID: ENST00000285279.10_9
RefSeq Accession: NM_030796.5
Protein: Q96AW1 (aka VOPP1_HUMAN)

-  Gene Model Information
  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.