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Category Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21

GIFtS
-

VSTM1 Gene

protein-coding GIFtS: 41
GCID: GC19M054544

V-set and transmembrane domain containing 1

Search for VSTM1
in

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 1¹ ²		OSCAR-Like Transcript-1²
UNQ3033¹ ²		Signal Inhibitory Receptor On Leukocytes-1²
SIRL1²		V-Set And Transmembrane Domain-Containing Protein 1²
LAIR Homolog²

External Ids:	HGNC: 29455¹	Entrez Gene: 284415²	Ensembl: ENSG00000189068⁷	UniProtKB: Q6UX27³

Export aliases for VSTM1 gene to outside databases

Previous GC identifers: GC19M059236 GC19M050859

(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 VSTM1 gene promoter:
MEF-2 HSF1 (long) C/EBPalpha AREB6 MEF-2A c-Rel IRF-2 SEF-1 (1) HSF1short aMEF-2
Other transcription factors

SwitchGear Promoter luciferase reporter plasmid: VSTM1 promoter sequence

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Epigenetics:

QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat VSTM1

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

Entrez Gene cytogenetic band: 19q13.42 Ensembl cytogenetic band: 19q13.42 HGNC cytogenetic band: 19q13.42

VSTM1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
VSTM1 gene location

GeneLoc information about chromosome 19 GeneLoc Exon Structure

GeneLoc location for GC19M054544: view genomic region (about GC identifiers)

Start:	54,544,079 bp from pter	End:	54,567,207 bp from pter
Size:	23,129 bases	Orientation:	minus 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,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: VSTM1_HUMAN, Q6UX27 (See protein sequence)

Recommended Name: V-set and transmembrane domain-containing protein 1 precursor

Size: 236 amino acids; 26109 Da

Subcellular location: Membrane; Single-pass membrane protein (Potential)

Secondary accessions: D2DJS3 Q496B6 Q496B7

Alternative splicing: 3 isoforms: Q6UX27-1 Q6UX27-2 Q6UX27-3 (May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay. No experimental confirmation available)

Explore the universe of human proteins at neXtProt for VSTM1: NX_Q6UX27

VSTM1 Protein expression data from MOPED and PaxDb: About this image

REFSEQ proteins: NP_940883.2

ENSEMBL proteins:

ENSP00000409412 ENSP00000343366 ENSP00000401926 ENSP00000365813 ENSP00000444153

ENSP00000413006

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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	--

VSTM1 for ontologies About GeneDecksing

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	Uscn ELISAs and CLIAs for VSTM1

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

VSTM1 for domains About GeneDecksing

3 InterPro domains/families:

IPR007110 Ig-like_dom

IPR003599 Ig_sub

IPR013783 Ig-like_fold

Graphical View of Domain Structure for InterPro Entry Q6UX27

ProtoNet protein and cluster: Q6UX27

2 Blocks protein families:

IPB003599 Immunoglobulin subtype

IPB013106 Immunoglobulin V-set

UniProtKB/Swiss-Prot: VSTM1_HUMAN, Q6UX27

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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3 GenomeRNAi human phenotypes for VSTM1:

Decreased BPV1 E2 protein expr

Increased G2M DNA content

Increased HPV18 LCR reporter a

(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 VSTM1

(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,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
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Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
About This Section

REFSEQ mRNAs for VSTM1 gene:

NM_198481.3

Unigene Cluster for VSTM1:

V-set and transmembrane domain containing 1

Hs.444431 [show with all ESTs]

Unigene Representative Sequence: NM_198481

6 Ensembl transcripts including schematic representations, and UCSC links where relevant:

ENST00000419106 ENST00000338372(uc002qcw.4 uc021vbe.1 uc021vbf.1 uc002qcx.4 uc021vbg.1)

ENST00000447872(uc010erb.3) ENST00000376626 ENST00000366170 ENST00000425006

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Additional cDNA sequence:

AY358542.1 BC100943.2 DQ479397.1 FJ584316.1 FJ584317.1 FJ584318.1 FJ584319.1 FJ584320.1

FJ882051.1 FN398145.1

3 DOTS entries:

DT.101977072 DT.100017246 DT.40218164

15 AceView cDNA sequences:

BX098691 BQ446547 BQ446114 AY358542 AI498747 NM_198481 CB055158 AI056326

AW026120 AI359561 AI075298 BG189223 AI457604 BF891852 BQ337552

GeneLoc Exon Structure

2 Alternative Splicing Database (ASD) splice patterns (SP) for VSTM1 About this scheme

ExUns:	1	^	2	^	3	^	4	^	5
SP1:
SP2:							-

ECgene alternative splicing isoforms for VSTM1

(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

VSTM1 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: AATATGCGGC

About this image
See VSTM1 Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for VSTM1

SOURCE GeneReport for Unigene cluster: Hs.444431

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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

--

ENSEMBL Gene Tree for VSTM1 (if available)
TreeFam Gene Tree for VSTM1 (if available)

(Paralogs according to ¹HomoloGene,
²Ensembl, and ³SIMAP, Pseudogenes according to ⁴Pseudogene.org Build 68)
About This Section

(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
				--	--	--		--	--
rs68002308^1,2	C	--	50878091(+)	`CTTTC-/TTTTTT`	1	--	int¹		0	--	--	--	--
rs68122616^1,2	C,F	--	54543612(+)	`TTTTTG/TTTTTT`	1	--	ds500¹		3		NA CSA	6
rs2433725^1,2	C,F,A,H,	--	54543618(-)	`AAAAAC/AAAAAA`	1	--	ds500¹		4		NA WA	8
rs138299926^1,2		--	54543655(+)	`CCATTA/GCCCAG`	1	--	ds500¹		0	--	--	--	--
rs142390977^1,2		--	54543747(+)	`AGTAGC/TGGGGA`	1	--	ds500¹		0	--	--	--	--
rs146585577^1,2		--	54543761(+)	`CAGGCA/GCCTGC`	1	--	ds500¹		0	--	--	--	--
rs71365425^1,2	C,F,	--	54543764(+)	`GCGCCC/TGCCAC`	1	--	ds500¹		3		NA CSA	6
rs71365426^1,2	C,F,	--	54543787(+)	`ATTTTT/GTATTT`	1	--	ds500¹		4		NA CSA	126
rs202029576^1,2		--	54543840(+)	`AACTC-/TTGACC`	1	--	ds500¹		0	--	--	--	--
rs186598125^1,2		--	54543979(+)	`GGTCAA/GTCATT`	1	--	ds500¹		0	--	--	--	--

HapMap Linkage Disequilibrium report for VSTM1 (54544079 - 54567207 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV): 10 variations for VSTM1
9 CNVs: 89310 78266 35674 58891 102876 67605 30919 0519 23143
1 Indel: 58890

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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

(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 VSTM1 gene integrated from 9 sources:
(articles sorted by number of sources associating them with VSTM1)

Utopia: connect your pdf to the dynamic
world of online information

The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PubMed id 12975309)^{1, 2, 3} Clark H.F.... Gray A.M. (2003)
Signal peptide prediction based on analysis of experimentally verified cleavage sites. (PubMed id 15340161)^{1, 2} Zhang Z. and Henzel W.J. (2004)
The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)^{1, 2} Gerhard D.S....Malek J. (2004)
Signal inhibitory receptor on leukocytes-1 is a novel functional inhibitory immune receptor expressed on human phagocytes. (PubMed id 20375307)¹ Steevels T.A....Meyaard L. (2010)
The DNA sequence and biology of human chromosome 19. (PubMed id 15057824)² Grimwood J.... Lucas S.M. (2004)
Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)¹ Strausberg R.L....Marra M.A. (2002)
Creation of genome-wide protein expression libraries using random activation of gene expression. (PubMed id 11329013)¹ Harrington J.J.... Ducar M. (2001)
Hepatitis C virus core protein interacts with 14-3-3 protein and activates the kinase Raf-1. (PubMed id )² Aoki H.... Hino O. (2000)

(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: 284415	HGNC: 29455	AceView: UNQ3033	Ensembl:ENSG00000189068	euGenes: HUgn284415
ECgene: VSTM1	H-InvDB: VSTM1

(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 VSTM1	Pharmacogenomics, SNPs, Pathways

Intellectual Property for VSTM1 gene
(Patent information from GeneIP, Licensable technologies from WIS Yeda, Salk, Tufts, IP news from LifeMap Sciences, Inc.)

About This Section

Patent Information for VSTM1 gene:
Search GeneIP for patents involving VSTM1

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, Uscn, Thermo Fisher Scientific, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, 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),
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VSTM1 Gene

V-set and transmembrane domain containing 1

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VSTM1 Gene

V-set and transmembrane domain containing 1

Aliasesfor VSTM1 gene

Summariesfor VSTM1 gene

Genomic Viewsfor VSTM1 gene

Proteinsfor VSTM1 gene

Protein Domains /Familiesfor VSTM1 gene

Functionfor VSTM1 gene

Pathways & Interactionsfor VSTM1 gene

Drugs & Compoundsfor VSTM1 gene

Transcriptsfor VSTM1 gene

Expression for VSTM1 gene

Orthologsfor VSTM1 gene

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Genomic Variantsfor VSTM1 gene

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Publicationsfor VSTM1 gene

External Searches for VSTM1 gene

Genome Databases showing VSTM1 gene

Other Databases showing VSTM1 gene

Specialized Databases showing VSTM1 gene

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for VSTM1 gene

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for VSTM1 gene

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for VSTM1 gene

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for VSTM1 gene

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for VSTM1 gene

Function
for VSTM1 gene

Pathways & Interactions
for VSTM1 gene

Drugs & Compounds
for VSTM1 gene

Transcripts
for VSTM1 gene

Expression
for VSTM1 gene

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for VSTM1 gene

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for VSTM1 gene

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for VSTM1 gene

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for VSTM1 gene

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for VSTM1 gene

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for VSTM1 gene