Human Gene VSTM2A (uc010kzf.3)
  Description: Homo sapiens V-set and transmembrane domain containing 2A (VSTM2A), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr7:54,610,019-54,636,948 Size: 26,930 Total Exon Count: 5 Strand: +
Coding Region
   Position: hg19 chr7:54,610,424-54,636,778 Size: 26,355 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: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr7:54,610,019-54,636,948)mRNA (may differ from genome)Protein (236 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCHPRDLynxMGIneXtProt
PubMedUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: VTM2A_HUMAN
DESCRIPTION: RecName: Full=V-set and transmembrane domain-containing protein 2A; Flags: Precursor;
SUBCELLULAR LOCATION: Secreted (Potential).
SIMILARITY: Contains 1 Ig-like V-type (immunoglobulin-like) domain.
SEQUENCE CAUTION: Sequence=AAH28404.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=EAL23809.1; Type=Erroneous initiation; Note=Translation N-terminally extended;

-  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
  • C548651 2-(1'H-indolo-3'-carbonyl)thiazole-4-carboxylic acid methyl ester
  • D013749 Tetrachlorodibenzodioxin

+  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: 13.66 RPKM in Brain - Frontal Cortex (BA9)
Total median expression: 67.21 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 -161.74405-0.399 Picture PostScript Text
3' UTR -30.17170-0.177 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
IPR013106 - Ig_V-set

Pfam Domains:
PF00047 - Immunoglobulin domain
PF07679 - Immunoglobulin I-set domain
PF07686 - Immunoglobulin V-set domain
PF13927 - Immunoglobulin domain

SCOP Domains:
48726 - Immunoglobulin

ModBase Predicted Comparative 3D Structure on Q8TAG5
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 orthologGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
  Ensembl   
  Protein Sequence   
  Alignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0042802 identical protein binding

Biological Process:
GO:0010628 positive regulation of gene expression
GO:0010884 positive regulation of lipid storage
GO:0030154 cell differentiation
GO:0070352 positive regulation of white fat cell proliferation
GO:0071773 cellular response to BMP stimulus
GO:0090336 positive regulation of brown fat cell differentiation

Cellular Component:
GO:0005576 extracellular region
GO:0005886 plasma membrane
GO:0016021 integral component of membrane
GO:0005634 nucleus


-  Descriptions from all associated GenBank mRNAs
  BC028404 - Homo sapiens V-set and transmembrane domain containing 2A, mRNA (cDNA clone MGC:33530 IMAGE:4820705), complete cds.
JD063802 - Sequence 44826 from Patent EP1572962.
JD437911 - Sequence 418935 from Patent EP1572962.
JD368499 - Sequence 349523 from Patent EP1572962.
JD517757 - Sequence 498781 from Patent EP1572962.
JD258048 - Sequence 239072 from Patent EP1572962.
JD516770 - Sequence 497794 from Patent EP1572962.
JD405634 - Sequence 386658 from Patent EP1572962.
CU688494 - Synthetic construct Homo sapiens gateway clone IMAGE:100023459 5' read VSTM2A mRNA.
HQ448214 - Synthetic construct Homo sapiens clone IMAGE:100071613; CCSB001780_01 V-set and transmembrane domain containing 2 (VSTM2A) gene, encodes complete protein.
KJ904037 - Synthetic construct Homo sapiens clone ccsbBroadEn_13431 VSTM2A gene, encodes complete protein.

-  Other Names for This Gene
  Alternate Gene Symbols: A4D2E9, B5MC94, NM_182546, NP_872352, Q8TAG5, VSTM2, VTM2A_HUMAN
UCSC ID: uc010kzf.3
RefSeq Accession: NM_182546
Protein: Q8TAG5 (aka VTM2A_HUMAN)
CCDS: CCDS5512.2

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_182546.2
exon count: 5CDS single in 3' UTR: no RNA size: 1286
ORF size: 711CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1589.00frame 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.