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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

VSTM2B Gene

protein-coding   GIFtS: 35
GCID: GC19P030017

V-Set And Transmembrane Domain Containing 2B

  See related disease
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

Aliases
V-Set And Transmembrane Domain Containing 2B1 2
V-Set And Transmembrane Domain-Containing Protein 2B2

External Ids:    HGNC: 335951   Entrez Gene: 3428652   Ensembl: ENSG000001871357   UniProtKB: A6NLU53   

Export aliases for VSTM2B gene to outside databases

Previous GC identifers: GC19P034708 GC19P026528


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

GeneCards Summary for VSTM2B Gene: 
VSTM2B (V-set and transmembrane domain containing 2B) is a protein-coding gene. Diseases associated with VSTM2B include microcephaly. An important paralog of this gene is VSTM2A.


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000019.9  NT_011109.16  NC_018930.2  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the VSTM2B gene promoter:
         HFH-3   POU3F1   MyoD   HNF-4alpha2   LCR-F1   RORalpha2   Gfi-1   HNF-4alpha1   FOXI1   SEF-1 (1)   
         Other transcription factors

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Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat VSTM2B


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 19q12   Ensembl cytogenetic band:  19q12   HGNC cytogenetic band: 19q12

VSTM2B Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
VSTM2B gene location

GeneLoc information about chromosome 19         GeneLoc Exon Structure

GeneLoc location for GC19P030017:  view genomic region     (about GC identifiers)

Start:
30,017,406 bp from pter      End:
30,055,386 bp from pter
Size:
37,981 bases      Orientation:
plus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: VTM2B_HUMAN, A6NLU5 (See protein sequence)
Recommended Name: V-set and transmembrane domain-containing protein 2B precursor  
Size: 285 amino acids; 30297 Da
Subcellular location: Membrane; Single-pass type I membrane protein (Potential)

Explore the universe of human proteins at neXtProt for VSTM2B: NX_A6NLU5

Explore proteomics data for VSTM2B at MOPED 

VSTM2B Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

VSTM2B Protein Expression

REFSEQ proteins: NP_001139811.1  
ENSEMBL proteins: 
 ENSP00000335038  

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Gene Ontology (GO): 1 cellular component term (GO ID links to tree view):    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0016021integral to membrane IEA--

VSTM2B for ontologies           About GeneDecksing



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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section
HGNC Gene Families: 
VSET: Immunoglobulin superfamily / V-set domain containing

4 InterPro protein domains:
 IPR007110 Ig-like_dom
 IPR003599 Ig_sub
 IPR013783 Ig-like_fold
 IPR013106 Ig_V-set

Graphical View of Domain Structure for InterPro Entry A6NLU5

ProtoNet protein and cluster: A6NLU5

UniProtKB/Swiss-Prot: VTM2B_HUMAN, A6NLU5
Similarity: Contains 1 Ig-like V-type (immunoglobulin-like) domain


VSTM2B for domains           About GeneDecksing


(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
About This Section

     Gene Ontology (GO): 1 molecular function term (GO ID links to tree view):    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005515protein binding ----
     
VSTM2B for ontologies           About GeneDecksing


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(Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene).
About This Section



Interactions:

    Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for VSTM2B

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
About This Section
Browse Small Molecules at EMD Millipore
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Browse Tocris compounds for VSTM2B (VTM2B)

Search CenterWatch for drugs/clinical trials and news about VSTM2B / VTM2B

(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from EMD Millipore,
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Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
About This Section

REFSEQ mRNAs for VSTM2B gene: 
NM_001146339.1  

Unigene Cluster for VSTM2B:

V-set and transmembrane domain containing 2B
Hs.451618  [show with all ESTs]
Unigene Representative Sequence: NM_001146339
1 Ensembl transcript including schematic representation, and UCSC links where relevant:
ENST00000335523(uc010xrl.1)
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1 DOTS entry:

DT.95133082 

3 AceView cDNA sequences:

BG716153 BG911226 AV727085 

GeneLoc Exon Structure


(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section

VSTM2B expression in normal human tissues (normalized intensities)      VSTM2B embryonic expression: see
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: ACGTCCTACC
VSTM2B Expression
About this image


VSTM2B expression in embryonic tissues and stem cells    About this table
Data from LifeMap, the Embryonic Development and Stem Cells Database 
 5/4 selected tissues (see all 4) fully expand
 
 Brain (Nervous System)    fully expand to see all 3 entries
         Medulla Oblongata
         brain/midbrain/lateral wall   
 
 Neural Tube (Nervous System)    fully expand to see all 2 entries
         Metencephalon
         brain/midbrain/lateral wall   
 
 Heart (Cardiovascular System)
         Atrioventricular Node Cells Atrioventricular Node
 
 Eye (Sensory Organs)
         Mature Rod Bipolar Cells Inner Nuclear Layer

See VSTM2B Protein Expression from SPIRE MOPED and PaxDB
SOURCE GeneReport for Unigene cluster: Hs.451618
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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for VSTM2B

(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
About This Section

This gene was present in the common ancestor of chordates.

Orthologs for VSTM2B gene from 3/8 species (see all 8)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Vstm2b1 , 5 V-set and transmembrane domain containing 2B1, 5 84.21(n)1
88.42(a)1
  7 (27.88 cM)5
581881  NM_021387.31  NP_067362.11 
 408992785 
lizard
(Anolis carolinensis)
Reptilia VSTM2B6
V-set and transmembrane domain containing 2B
58(a)
1 ↔ 1
GL343441.1(672152-751684)
zebrafish
(Danio rerio)
Actinopterygii zgc:1946781 zgc:194678 61.13(n)
57.14(a)
  793103  NM_001128778.1  NP_001122250.1 


ENSEMBL Gene Tree for VSTM2B (if available)
TreeFam Gene Tree for VSTM2B (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
About This Section
Paralogs for VSTM2B gene
VSTM2A2  VSTM2L2  
2 SIMAP similar genes for VSTM2B using alignment to 1 protein entry:     VTM2B_HUMAN:
VSTM2L    VSTM2A

VSTM2B for paralogs           About GeneDecksing



(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
About This Section

10/939 SNPs in VSTM2B are shown (see all 939)    About this table     
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 19 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1900698621,2
--30018670(+) ACTTTC/GAGGAC 1 -- int10--------
rs739238691,2
C,F--30018733(+) AAAGCC/TGGCAG 1 -- int15Minor allele frequency- T:0.06WA NA CSA 126
rs730294541,2
C,F--30018758(+) AGGGGC/AACAGA 1 -- int16Minor allele frequency- A:0.05WA NA CSA 246
rs1503671721,2
--30018767(+) GAGGGA/GCCACT 1 -- int10--------
rs730294551,2
C,F--30018768(+) AGGGGC/ACACTT 1 -- int14Minor allele frequency- A:0.05NA CSA WA 123
rs1457209001,2
--30018938(+) CCTCCC/TGCTGG 1 -- int10--------
rs1489235261,2
C--30019349(+) CAAATA/GAGGAT 2 K E mis10--------
rs1812811481,2
C--30019402(+) GGGAGA/TCCCCT 1 -- int10--------
rs1856499781,2
--30019464(+) GCGCAG/TGTGGG 1 -- int10--------
rs351111021,2
C,F--30019505(+) TGCATC/TGGTGG 1 -- int17Minor allele frequency- T:0.11NA WA EA 366

HapMap Linkage Disequilibrium report for VSTM2B (30017406 - 30055386 bp)

Structural Variations
     Database of Genomic Variants (DGV) 4 variations for VSTM2B:    About this table     
Variant IDTypeSubtypePubMed ID
nsv833798CNV Loss17160897
nsv833799CNV Gain17160897
esv21555CNV Gain19812545
esv275023CNV Gain+Loss21479260

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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
About This Section
2 diseases for VSTM2B:    About MalaCards
microcephaly    


VSTM2B for disorders           About GeneDecksing

Genetic Association Database (GAD): VSTM2B
Human Genome Epidemiology (HuGE) Navigator: VSTM2B (1 document)

Export disorders for VSTM2B gene to outside databases

(in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
About This Section

PubMed articles for VSTM2B gene integrated from 9 sources:
(articles sorted by number of sources associating them with VSTM2B)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Coeliac disease associated risk variants in TNFAIP3 and REL implicate altered NF-{kappa}B signalling. (PubMed id 19240061)1, 4 Trynka G....Wijmenga C. (2009)
  2. The DNA sequence and biology of human chromosome 19. (PubMed id 15057824)1, 2 Grimwood J.... Lucas S.M. (2004)
  3. Genetic variants associated with disordered eating. (PubMed id 23568457)1 Wade T.D....Martin N.G. (2013)
  4. Genome-wide meta-analysis for severe diabetic retinop athy. (PubMed id 21441570)1 Grassi M.A....Nicolae D.L. (2011)

(in PubMed, OMIM, and NCBI Bookshelf)
About This Section
 ANDOR
Aliases
Free Text  

  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
About This Section
Entrez Gene: 342865 HGNC: 33595 AceView: LOC342865 Ensembl:ENSG00000187135 euGenes: HUgn342865
ECgene: VSTM2B H-InvDB: VSTM2B

(According to HUGE)
About This Section
  --

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section
NameDescription
PharmGKB entry for VSTM2B Pharmacogenomics, SNPs, Pathways

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
About This Section
Patent Information for VSTM2B gene:
Search GeneIP for patents involving VSTM2B

GeneCards and IP:
Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, Cell lines from GenScript, and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
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About This Section

 
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GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 3 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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