Human Gene VPS35L (uc002dgn.3)
  Description: Homo sapiens chromosome 16 open reading frame 62 (VPS35L), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr16:19,566,737-19,712,485 Size: 145,749 Total Exon Count: 31 Strand: +
Coding Region
   Position: hg19 chr16:19,566,785-19,711,798 Size: 145,014 Coding Exon Count: 31 

Page IndexSequence and LinksUniProtKB CommentsPrimersGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA DescriptionsOther Names
Model InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr16:19,566,737-19,712,485)mRNA (may differ from genome)Protein (1052 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHPRDLynxMGIPubMedUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: E7EWW0_HUMAN
DESCRIPTION: SubName: Full=UPF0505 protein C16orf62;
CAUTION: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered as preliminary data.

-  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: 10.86 RPKM in Testis
Total median expression: 352.58 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 -11.3048-0.235 Picture PostScript Text
3' UTR -183.97687-0.268 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
  ModBase Predicted Comparative 3D Structure on E7EWW0
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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 BrowserGenome BrowserNo ortholog
Gene DetailsGene Details Gene DetailsGene Details 
Gene SorterGene Sorter Gene SorterGene Sorter 
 RGDEnsemblFlyBaseWormBase 
 Protein SequenceProtein SequenceProtein SequenceProtein Sequence 
 AlignmentAlignmentAlignmentAlignment 

-  Descriptions from all associated GenBank mRNAs
  BX537867 - Homo sapiens mRNA; cDNA DKFZp313H1733 (from clone DKFZp313H1733).
AK290286 - Homo sapiens cDNA FLJ75626 complete cds, highly similar to Homo sapiens esophageal cancer associated protein, mRNA.
AK095078 - Homo sapiens cDNA FLJ37759 fis, clone BRHIP2023888.
BC050464 - Homo sapiens chromosome 16 open reading frame 62, mRNA (cDNA clone MGC:54296 IMAGE:6061139), complete cds.
AL832159 - Homo sapiens mRNA; cDNA DKFZp686H1914 (from clone DKFZp686H1914).
BC058845 - Homo sapiens chromosome 16 open reading frame 62, mRNA (cDNA clone MGC:62059 IMAGE:6452778), complete cds.
EU832021 - Synthetic construct Homo sapiens clone HAIB:100067050; DKFZo004C0324 chromosome 16 open reading frame 62 protein (C16orf62) gene, encodes complete protein.
EU831926 - Synthetic construct Homo sapiens clone HAIB:100066955; DKFZo008C0323 chromosome 16 open reading frame 62 protein (C16orf62) gene, encodes complete protein.
BC014900 - Homo sapiens chromosome 16 open reading frame 62, mRNA (cDNA clone MGC:16824 IMAGE:3909068), complete cds.
AK024693 - Homo sapiens cDNA: FLJ21040 fis, clone CAE10642.
AF461052 - Homo sapiens esophageal cancer associated protein mRNA, complete cds.
AL136744 - Homo sapiens mRNA; cDNA DKFZp434B0212 (from clone DKFZp434B0212); complete cds.
AK294885 - Homo sapiens cDNA FLJ56313 complete cds.
LF207873 - JP 2014500723-A/15376: Polycomb-Associated Non-Coding RNAs.
AL833428 - Homo sapiens mRNA; cDNA DKFZp313M0539 (from clone DKFZp313M0539).
JD420309 - Sequence 401333 from Patent EP1572962.
MA443450 - JP 2018138019-A/15376: Polycomb-Associated Non-Coding RNAs.
JD516729 - Sequence 497753 from Patent EP1572962.
JD429254 - Sequence 410278 from Patent EP1572962.
JD235680 - Sequence 216704 from Patent EP1572962.
JD250738 - Sequence 231762 from Patent EP1572962.
JD285656 - Sequence 266680 from Patent EP1572962.
JD042482 - Sequence 23506 from Patent EP1572962.
JD433501 - Sequence 414525 from Patent EP1572962.
JD433502 - Sequence 414526 from Patent EP1572962.
JD534038 - Sequence 515062 from Patent EP1572962.
JD302506 - Sequence 283530 from Patent EP1572962.
JD113330 - Sequence 94354 from Patent EP1572962.
JD563680 - Sequence 544704 from Patent EP1572962.
JD078477 - Sequence 59501 from Patent EP1572962.
JD527966 - Sequence 508990 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: C16orf62, E7EWW0, E7EWW0_HUMAN, NM_020314, NP_064710, uc002dgn.2
UCSC ID: uc002dgn.3
RefSeq Accession: NM_020314
Protein: E7EWW0 CCDS: CCDS32397.2

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_020314.5
exon count: 31CDS single in 3' UTR: no RNA size: 3894
ORF size: 3159CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 6377.00frame 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.