Human Gene LOC92270 (uc003khw.1)
  Description: V-type proton ATPase subunit S1-like protein
Transcript (Including UTRs)
   Position: hg18 chr5:81,636,509-81,649,903 Size: 13,395 Total Exon Count: 4 Strand: +
Coding Region
   Position: hg18 chr5:81,636,977-81,649,875 Size: 12,899 Coding Exon Count: 4 

Page IndexSequence and LinksUniProtKB CommentsPrimersMicroarray ExpressionRNA Structure
Protein StructureOther SpeciesGO AnnotationsmRNA DescriptionsOther NamesModel Information
Methods
Data last updated at UCSC: 2009-03-03

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:81,636,509-81,649,903)mRNA (may differ from genome)Protein (224 aa)
Gene SorterGenome BrowserOther Species FASTATable SchemaAlphaFoldBioGPS
EnsemblEntrez GeneExonPrimerGeneCardsGeneNetworkH-INV
HPRDMGIPubMedTreefamUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: VAS1L_HUMAN
DESCRIPTION: RecName: Full=V-type proton ATPase subunit S1-like protein; AltName: Full=Vacuolar proton pump subunit S1-like protein;
SUBCELLULAR LOCATION: Membrane; Single-pass membrane protein (Potential).
SIMILARITY: Belongs to the vacuolar ATPase subunit S1 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


-  Microarray Expression Data
 
Expression ratio colors:

GNF Expression Atlas 2 Data from U133A and GNF1H Chips

      
      
      
     
    
     
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Affymetrix All Exon Microarrays

           
Ratios

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -148.03468-0.316 Picture PostScript Text
3' UTR -4.8028-0.171 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
IPR008388 - ATPase_V1-cplx_s1su

Pfam Domains:
PF05827 - Vacuolar ATP synthase subunit S1 (ATP6S1)

ModBase Predicted Comparative 3D Structure on Q52LC2
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 orthologNo orthologNo orthologNo orthologNo ortholog
      
      
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0046933 proton-transporting ATP synthase activity, rotational mechanism
GO:0046961 proton-transporting ATPase activity, rotational mechanism

Biological Process:
GO:0015991 ATP hydrolysis coupled proton transport

Cellular Component:
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0033180 proton-transporting V-type ATPase, V1 domain


-  Descriptions from all associated GenBank mRNAs
  AK094973 - Homo sapiens cDNA FLJ37654 fis, clone BRHIP2010309, weakly similar to VACUOLAR ATP SYNTHASE SUBUNIT AC45 PRECURSOR (EC 3.6.1.34).
AK022625 - Homo sapiens cDNA FLJ12563 fis, clone NT2RM4000820, weakly similar to VACUOLAR ATP SYNTHASE SUBUNIT AC45 PRECURSOR (EC 3.6.1.34).
BC112191 - Homo sapiens V-type proton ATPase subunit S1-like protein, mRNA (cDNA clone MGC:138396 IMAGE:8327659), complete cds.
BC093982 - Homo sapiens V-type proton ATPase subunit S1-like protein, mRNA (cDNA clone MGC:121017 IMAGE:7939827), complete cds.
JD521954 - Sequence 502978 from Patent EP1572962.
JD481265 - Sequence 462289 from Patent EP1572962.
JD369951 - Sequence 350975 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: NM_001017971, NP_001017971, Q52LC2, VAS1L_HUMAN
UCSC ID: uc003khw.1
RefSeq Accession: NM_001017971
Protein: Q52LC2 (aka VAS1L_HUMAN)
CCDS: CCDS34196.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001017971.1
exon count: 4CDS single in 3' UTR: no RNA size: 758
ORF size: 675CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1270.50frame 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.