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Category Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21

GIFtS
-

VSTM2B Gene

protein-coding GIFtS: 36
GCID: GC19P030017

V-set and transmembrane domain containing 2B

Explore 1 disease affiliated with
VSTM2B via

MalaCards

our new
Human Malady Compendium

(According to ¹HGNC, ²Entrez Gene,
³UniProtKB/Swiss-Prot, ⁴UniProtKB/TrEMBL, ⁵OMIM, ⁶GeneLoc, ⁷Ensembl, ⁸DME, ⁹miRBase, and/or ¹⁰fRNAdb)
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

(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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section

RefSeq DNA sequence:

NC_000019.9 NC_018930.1 NT_011109.16

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 ¹UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to ²PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, 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 Uscn,
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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

VSTM2B Protein expression data from MOPED and PaxDb: About this image

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 ID	Qualified GO term	Evidence	PubMed IDs
GO:0016021	integral to membrane	IEA	--

VSTM2B for ontologies About GeneDecksing

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(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section

VSTM2B for domains About GeneDecksing

4 InterPro domains/families:

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

(According to ¹UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or ²DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
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, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
About This Section

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(Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, 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 Mar 2013 via Entrez Gene).
About This Section

Interactions:

Search SABiosciences Gene Network Central^TM Interacting Genes and Proteins Networks for VSTM2B

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
About This Section

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(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
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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)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: ACGTCCTACC

About this image

VSTM2B expression in embryonic tissues and stem cells

Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine About this table

4 LifeMap In Vivo Development Anatomical Compartments/Cells

Tissue

Anatomical Compartment

Cell

Category (developmental path)

Brain

Blood Brain Barrier

Postnatal Endothelial Cells

Blood Brain Barrier, Endothelium

Eye

Inner Nuclear Layer

Mature Rod Bipolar Cells

Bipolar, Retina

Brain

Neural Tube

Expression:

Positive

Negative

Selective marker

Experimental details:

Curated

Microarrays

In-situ hybridization

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

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In Situ
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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)
About This Section

This gene was present in the common ancestor of chordates.

Orthologs for VSTM2B gene from 4/9 species (see all 9) About this table

Organism	Taxonomic classification	Gene	Description	Human Similarity	Orthology Type	Details
mouse (Mus musculus)	Mammalia	Vstm2b^{1 , 5}	V-set and transmembrane domain containing 2B^{1, 5}	84.21(n)¹ 88.42(a)¹		7 (27.88 cM)⁵ 58188¹ NM_021387.3¹ NP_067362.1¹ 40899278⁵
chicken (Gallus gallus)	Aves	VSTM2B⁶	Uncharacterized protein	63(a)	1 ↔ 1	11(8900920-8918558)
lizard (Anolis carolinensis)	Reptilia	VSTM2B⁶	--	56(a)	1 ↔ 1	GL343441.1(672926-698557)
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

VSTM2L² VSTM2A²

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, UniProtKB, 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

SNP ID	Valid	Clinical significance	Chr 19 pos	Sequence	#	AA Chg	Type	More	#	Allele freq	Pop	Total sample	More
Genomic Data					Transcription Related Data				Allele Frequencies
				--	--	--		--	--
rs190069862^1,2		--	30018670(+)	`ACTTTC/GAGGAC`	1	--	int¹		0	--	--	--	--
rs73923869^1,2	C,F,	--	30018733(+)	`AAAGCC/TGGCAG`	1	--	int¹		5		WA NA CSA	126
rs73029454^1,2	C,F,	--	30018758(+)	`AGGGGC/AACAGA`	1	--	int¹		6		WA NA CSA	246
rs150367172^1,2		--	30018767(+)	`GAGGGA/GCCACT`	1	--	int¹		0	--	--	--	--
rs73029455^1,2	C,F,	--	30018768(+)	`AGGGGC/ACACTT`	1	--	int¹		4		NA CSA WA	123
rs145720900^1,2		--	30018938(+)	`CCTCCC/TGCTGG`	1	--	int¹		0	--	--	--	--
rs148923526^1,2		--	30019349(+)	`CAAATA/GAGGAT`	2	K E	mis¹		0	--	--	--	--
rs181281148^1,2		--	30019402(+)	`GGGAGA/TCCCCT`	1	--	int¹		0	--	--	--	--
rs185649978^1,2		--	30019464(+)	`GCGCAG/TGTGGG`	1	--	int¹		0	--	--	--	--
rs35111102^1,2	C,F,	--	30019505(+)	`TGCATC/TGGTGG`	1	--	int¹		7		NA WA EA	366

HapMap Linkage Disequilibrium report for VSTM2B (30017406 - 30055386 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV): 1 variation for VSTM2B
1 CNV: 67521

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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.)
About This Section

VSTM2B for disorders About GeneDecksing

1 disease for VSTM2B: About MalaCards

microcephaly

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

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

(in PubMed, OMIM, and NCBI Bookshelf)
About This Section

		AND	OR
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

Name	Description
PharmGKB entry for VSTM2B	Pharmacogenomics, SNPs, Pathways

Intellectual Property for VSTM2B gene
(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

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Category			VWF (GIFTS: 73) von Willebrand factor
GIFtS Group

The GeneCards human gene database gene index: 1 3 5 6 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

The GeneCards Human Gene Database

Developed at the Crown Human Genome Center, Department of Molecular Genetics, the Weizmann Institute of Science

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VSTM2B Gene

V-set and transmembrane domain containing 2B

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VSTM2B Gene

V-set and transmembrane domain containing 2B

Aliasesfor VSTM2B gene

Summariesfor VSTM2B gene

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External Searches for VSTM2B gene

Genome Databases showing VSTM2B gene

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Specialized Databases showing VSTM2B gene

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for VSTM2B gene

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for VSTM2B gene

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for VSTM2B gene

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