Human Gene VSTM1 (uc002qcw.4)
  Description: Homo sapiens V-set and transmembrane domain containing 1 (VSTM1), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr19:54,544,080-54,567,207 Size: 23,128 Total Exon Count: 9 Strand: -
Coding Region
   Position: hg19 chr19:54,544,215-54,567,031 Size: 22,817 Coding Exon Count: 9 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr19:54,544,080-54,567,207)mRNA (may differ from genome)Protein (236 aa)
Gene SorterGenome BrowserOther Species FASTATable SchemaAlphaFoldBioGPS
EnsemblEntrez GeneExonPrimerGeneCardsGeneNetworkHGNC
HPRDLynxMGIneXtProtOMIMPubMed
TreefamUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: VSTM1_HUMAN
DESCRIPTION: RecName: Full=V-set and transmembrane domain-containing protein 1; Flags: Precursor;
SUBCELLULAR LOCATION: Membrane; Single-pass membrane protein (Potential).
SIMILARITY: Contains 1 Ig-like V-type (immunoglobulin-like) 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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): VSTM1
CDC HuGE Published Literature: VSTM1
Positive Disease Associations: Heart Failure
Related Studies:
  1. Heart Failure
    , , . [PubMed 0]

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

+  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: 11.31 RPKM in Whole Blood
Total median expression: 20.36 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 -69.76176-0.396 Picture PostScript Text
3' UTR -32.80135-0.243 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
IPR007110 - Ig-like
IPR013783 - Ig-like_fold
IPR003599 - Ig_sub

Pfam Domains:
PF00047 - Immunoglobulin domain
PF13895 - Immunoglobulin domain
PF13927 - Immunoglobulin domain

SCOP Domains:
48726 - Immunoglobulin

ModBase Predicted Comparative 3D Structure on Q6UX27
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:0005125 cytokine activity

Biological Process:
GO:0002376 immune system process
GO:0010469 regulation of receptor activity

Cellular Component:
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0016020 membrane
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  LP896142 - Sequence 1006 from Patent EP3253886.
AX721201 - Sequence 161 from Patent WO0220754.
AY358542 - Homo sapiens clone DNA119510 LAIR hlog (UNQ3033) mRNA, complete cds.
BC100942 - Homo sapiens V-set and transmembrane domain containing 1, mRNA (cDNA clone MGC:119160 IMAGE:40004094), complete cds.
BC100943 - Homo sapiens V-set and transmembrane domain containing 1, mRNA (cDNA clone MGC:119161 IMAGE:40004095), complete cds.
FN398145 - Homo sapiens mRNA for V-set and transmembrane domain containing 1 (VSTM1 gene).
DQ479397 - Homo sapiens OSCAR-like transcript-1 mRNA, complete cds.
FJ584316 - Homo sapiens V-set and transmembrane domain containing 1 isoform a (VSTM1) mRNA, complete cds.
FJ584317 - Homo sapiens V-set and transmembrane domain containing 1 isoform a (VSTM1) mRNA, complete cds.
FJ584318 - Homo sapiens V-set and transmembrane domain containing 1 isoform b (VSTM1) mRNA, complete cds.
FJ584319 - Homo sapiens V-set and transmembrane domain containing 1 isoform c (VSTM1) mRNA, complete cds.
FJ584320 - Homo sapiens V-set and transmembrane domain containing 1 isoform d (VSTM1) mRNA, complete cds.
FJ882051 - Homo sapiens V-set and transmembrane domain containing 1 isoform e (VSTM1) mRNA, complete cds, alternatively spliced.
KJ904134 - Synthetic construct Homo sapiens clone ccsbBroadEn_13528 VSTM1 gene, encodes complete protein.

-  Other Names for This Gene
  Alternate Gene Symbols: D2DJS3, NM_198481, NP_940883, Q496B6, Q496B7, Q6UX27, UNQ3033/PRO9835, VSTM1_HUMAN
UCSC ID: uc002qcw.4
RefSeq Accession: NM_198481
Protein: Q6UX27 (aka VSTM1_HUMAN)
CCDS: CCDS12872.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_198481.3
exon count: 9CDS single in 3' UTR: no RNA size: 1034
ORF size: 711CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1266.00frame shift in genome: no % Coverage: 98.84
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.