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VSTM2B Gene

protein-coding   GIFtS: 36
GCID: GC19P030017

V-Set And Transmembrane Domain Containing 2B

  Search for VSTM2B
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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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, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for VSTM2B Gene:
VSTM2B (V-set and transmembrane domain containing 2B) is a protein-coding gene. 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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000019.9  NT_011109.17  NC_018930.2  
Regulatory elements:
   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:
DNA Methylation CpG Assay Predesigned for Pyrosequencing 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 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, 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, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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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

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

Explore proteomics data for VSTM2B at MOPED


See VSTM2B Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_001139811.1  
ENSEMBL proteins: 
 ENSP00000335038  

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

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

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


Find genes that share domains with VSTM2B           About GenesLikeMe


(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,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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     Gene Ontology (GO): 1 molecular function term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005515protein binding ----
     
Find genes that share ontologies with VSTM2B           About GenesLikeMe


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(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Subcellular locations from UniProtKB/Swiss-Prot
VTM2B_HUMAN, A6NLU5: Membrane; Single-pass type I membrane protein (Potential)
Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
extracellular2
plasma membrane2
endoplasmic reticulum1
lysosome1
peroxisome1

Gene Ontology (GO): 1 cellular component term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0016021integral component of membrane IEA--

Find genes that share ontologies with VSTM2B           About GenesLikeMe


(SuperPaths according to PathCards, Pathways according to 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 QIAGEN, 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 Apr 2014 via Entrez Gene).
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    Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for VSTM2B
Interactions:

    Search GeneGlobe Interaction Network for VSTM2B

STRING Interaction Network Preview (showing 1 interactants - click image to see more details)

1 Interacting protein for VSTM2B (ENSP000003350384) via UniProtKB, MINT, STRING, and/or I2D
InteractantInteraction Details
GeneCardExternal ID(s)
IGKV4-1ENSP000003747784STRING: ENSP00000374778
About this table

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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Browse Tocris compounds for 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,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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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™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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VSTM2B expression in normal human tissues (normalized intensities)
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
 selected tissues (see all 5) fully expand
 
 Heart (Cardiovascular System)
         Atrioventricular Node Cells Atrioventricular Node
 
 Neurons
         Mature Rod Bipolar Cells Inner Nuclear Layer
 
 Neural Tube (Nervous System)
         Metencephalon
 
 Eye (Sensory Organs)
         Mature Rod Bipolar Cells Inner Nuclear Layer
 
 Brain (Nervous System)
         Medulla Oblongata
VSTM2B Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

VSTM2B Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.451618
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In Situ
Assay Products:
 

 
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(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)
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This gene was present in the common ancestor of chordates.

Orthologs for VSTM2B gene from Selected species (see all 9)    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
55(a)
1 ↔ 1
GL343441.1(672152-751684)
tropical clawed frog
(Xenopus tropicalis)
Amphibia vstm2b1 V-set and transmembrane domain containing 2B 65.87(n)
66.4(a)
  780250  NM_001079321.1  NP_001072789.1 
zebrafish
(Danio rerio)
Actinopterygii zgc:1946781 zgc:194678 60.25(n)
56.07(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)
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Paralogs for VSTM2B gene
VSTM2A2  VSTM2L2  
2 SIMAP similar genes for VSTM2B using alignment to 1 protein entry:     VTM2B_HUMAN:
VSTM2L    VSTM2A

Find genes that share paralogs with VSTM2B           About GenesLikeMe



(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), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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Selected SNPs for VSTM2B (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, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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Find genes that share disorders with VSTM2B           About GenesLikeMe

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)
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PubMed articles for VSTM2B gene integrated from 10 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-kappaB signalling. (PubMed id 19240061)1, 4 Trynka G....Wijmenga C. (Gut 2009)
  2. The DNA sequence and biology of human chromosome 19. (PubMed id 15057824)1, 2 Grimwood J.... Lucas S.M. (Nature 2004)
  3. Genetic variants associated with disordered eating. (PubMed id 23568457)1 Wade T.D....Martin N.G. (Int J Eat Disord 2013)
  4. Genome-wide meta-analysis for severe diabetic retinopathy. (PubMed id 21441570)1 Grassi M.A....Nicolae D.L. (Hum. Mol. Genet. 2011)

(in PubMed, OMIM, and NCBI Bookshelf)
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 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)
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Entrez Gene: 342865 HGNC: 33595 AceView: LOC342865 Ensembl:ENSG00000187135 euGenes: HUgn342865
ECgene: VSTM2B H-InvDB: VSTM2B

(According to HUGE)
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  --

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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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.)
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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, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014 , 21 Aug 2014 , 8 Sep 2014

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