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VSTM2L Gene

protein-coding   GIFtS: 49
GCID: GC20P036531

V-Set And Transmembrane Domain Containing 2 Like

(Previous name: chromosome 20 open reading frame 102)
(Previous symbol: C20orf102)
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(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 2 Like1 2
C20orf1021 2 3
Chromosome 20 Open Reading Frame 1021
dJ1118M15.22
V-Set And Transmembrane Domain-Containing Protein 2-Like Protein2

External Ids:    HGNC: 160961   Entrez Gene: 1284342   Ensembl: ENSG000001328217   UniProtKB: Q96N033   

Export aliases for VSTM2L gene to outside databases

Previous GC identifers: GC20P035965 GC20P033266


(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 VSTM2L Gene:
VSTM2L (V-set and transmembrane domain containing 2 like) is a protein-coding gene. An important paralog of this gene is VSTM2B.


(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_000020.10  NC_018931.2  NT_011362.11  
Regulatory elements:
   Regulatory transcription factor binding sites in the VSTM2L gene promoter:
         AhR   Spz1   STAT1   p53   AML1a   STAT1beta   CUTL1   STAT1alpha   NRF-2   TGIF   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidVSTM2L promoter sequence
   Search Chromatin IP Primers for VSTM2L

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat VSTM2L


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

Entrez Gene cytogenetic band: 20q11.23   Ensembl cytogenetic band:  20q11.23   HGNC cytogenetic band: 20q11.23

VSTM2L Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
VSTM2L gene location

GeneLoc information about chromosome 20         GeneLoc Exon Structure

GeneLoc location for GC20P036531:  view genomic region     (about GC identifiers)

Start:
36,531,499 bp from pter      End:
36,573,752 bp from pter
Size:
42,254 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: VTM2L_HUMAN, Q96N03 (See protein sequence)
Recommended Name: V-set and transmembrane domain-containing protein 2-like protein precursor  
Size: 204 amino acids; 22349 Da
Secondary accessions: E1P5V7 Q5JWZ4 Q5JWZ5 Q8ND45 Q9BR37
Alternative splicing: 3 isoforms:  Q96N03-1   Q96N03-2   Q96N03-3   (Gene prediction based on EST data)

Explore the universe of human proteins at neXtProt for VSTM2L: NX_Q96N03

Explore proteomics data for VSTM2L at MOPED


See VSTM2L Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_542174.1  
ENSEMBL proteins: 
 ENSP00000362560   ENSP00000362558   ENSP00000406537   ENSP00000362557  

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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

5 InterPro protein domains:
 IPR027115 VSTM2L
 IPR013783 Ig-like_fold
 IPR013106 Ig_V-set
 IPR007110 Ig-like_dom
 IPR003599 Ig_sub

Graphical View of Domain Structure for InterPro Entry Q96N03

ProtoNet protein and cluster: Q96N03

1 Blocks protein domain: IPB003599 Immunoglobulin subtype

UniProtKB/Swiss-Prot: VTM2L_HUMAN, Q96N03
Similarity: Contains 1 Ig-like (immunoglobulin-like) domain


Find genes that share domains with VSTM2L           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 IPI16713569
     
Find genes that share ontologies with VSTM2L           About GenesLikeMe


Phenotypes:
     1 GenomeRNAi human phenotype for VSTM2L:
 Decreased Wnt reporter activit 

Animal Models:
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miRNA
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miRTarBase miRNAs that target VSTM2L:
hsa-mir-335-5p (MIRT017544)

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Selected qRT-PCR Assays for microRNAs that regulate VSTM2L (see all 22):
hsa-miR-148b* hsa-miR-520d-5p hsa-miR-320e hsa-miR-1323 hsa-miR-1293 hsa-miR-4257 hsa-miR-647 hsa-miR-548p
SwitchGear 3'UTR luciferase reporter plasmidVSTM2L 3' UTR sequence
Inhib. RNA
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Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat VSTM2L

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Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for VSTM2L


(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 COMPARTMENTS: 

CompartmentConfidence
extracellular2
cytoskeleton1
lysosome1
nucleus1
plasma membrane1

(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 VSTM2L
Interactions:

    Search GeneGlobe Interaction Network for VSTM2L

STRING Interaction Network Preview (showing 2 interactants - click image to see more details)

2 Interacting proteins for VSTM2L (Q96N031, 2, 3 ENSP000003625604) via UniProtKB, MINT, STRING, and/or I2D
InteractantInteraction Details
GeneCardExternal ID(s)
ATXN1P542531, 2, 3, ENSP000002447694EBI-948213,EBI-930964 MINT-2878653 MINT-2878634 MINT-2878672 I2D: score=3 STRING: ENSP00000244769
WIPF3ENSP000003868784STRING: ENSP00000386878
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 Small Molecules at EMD Millipore
   Browse drugs & compounds from Enzo Life Sciences
  Browse compounds at ApexBio 

Browse Tocris compounds for VSTM2L (VTM2L)



(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 VSTM2L gene: 
NM_080607.2  

Unigene Cluster for VSTM2L:

V-set and transmembrane domain containing 2 like
Hs.517029  [show with all ESTs]
Unigene Representative Sequence: NM_080607
4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000373461(uc002xhk.4) ENST00000373459 ENST00000448944 ENST00000373458

miRNA
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Selected qRT-PCR Assays for microRNAs that regulate VSTM2L (see all 22):
hsa-miR-148b* hsa-miR-520d-5p hsa-miR-320e hsa-miR-1323 hsa-miR-1293 hsa-miR-4257 hsa-miR-647 hsa-miR-548p
SwitchGear 3'UTR luciferase reporter plasmidVSTM2L 3' UTR sequence
Inhib. RNA
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Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat VSTM2L
Primer
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OriGene qPCR primer pairs and template standards for VSTM2L
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  QuantiFast Probe-based Assays in human, mouse, rat VSTM2L

Additional mRNA sequence: 

AK056177.1 AL834410.1 BC033818.1 

5 DOTS entries:

DT.212300  DT.100773009  DT.100780785  DT.100805462  DT.100752270 

Selected AceView cDNA sequences (see all 108):

BI822271 CA310563 CK821182 BI821282 BQ068223 CA946287 BI962569 AI653833 
AI783994 AI571493 AW054938 AI620799 AL834410 AW156979 CR619223 AI420351 
CK821181 AI198431 BX440669 BX459894 CB852861 BI918459 CA450044 BC033818 

GeneLoc Exon Structure

5 Alternative Splicing Database (ASD) splice patterns (SP) for VSTM2L    About this scheme

ExUns: 1a · 1b · 1c ^ 2a · 2b · 2c ^ 3 ^ 4 ^ 5a · 5b · 5c
SP1:                                            -                     
SP2:                    -                       -                     
SP3:                                                                  
SP4:                                      -     -                     
SP5:                    -     -     -     -     -                     


ECgene alternative splicing isoforms for VSTM2L

(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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VSTM2L expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: ATCCAGTCTG
VSTM2L Expression
About this image

VSTM2L Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

VSTM2L Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.517029
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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 VSTM2L gene from Selected species (see all 10)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Vstm2l1 , 5 V-set and transmembrane domain containing 2-like1, 5 88.45(n)1
92.08(a)1
  2 (78.48 cM)5
2774321  NM_198627.21  NP_941029.21 
 1579146535 
chicken
(Gallus gallus)
Aves VSTM2L1 V-set and transmembrane domain containing 2 like 84.75(n)
87.29(a)
  419297  XM_417469.3  XP_417469.3 
lizard
(Anolis carolinensis)
Reptilia VSTM2L6
V-set and transmembrane domain containing 2 like
72(a)
1 ↔ 1
GL343572.1(23245-66026)
tropical clawed frog
(Xenopus tropicalis)
Amphibia Str.191382 Transcribed sequence with weak similarity to protein more 79.01(n)    AL856246.2 
zebrafish
(Danio rerio)
Actinopterygii zgc661332 hypothetical protein MGC66133 79.93(n)   393468  BC055504.1 


ENSEMBL Gene Tree for VSTM2L (if available)
TreeFam Gene Tree for VSTM2L (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for VSTM2L gene
VSTM2B2  VSTM2A2  
2 SIMAP similar genes for VSTM2L using alignment to 2 protein entries:     VTM2L_HUMAN (see all proteins):
VSTM2B    VSTM2A

Find genes that share paralogs with VSTM2L           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 VSTM2L (see all 1022)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 20 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs739080111,2
C,F--36529551(+) TGGGGT/CTGAAG 1 -- us2k12Minor allele frequency- C:0.11WA 120
rs15699401,2
C,F,A,H--36529578(+) TCTGGT/CTAACA 1 -- us2k121Minor allele frequency- C:0.41NS EA NA WA CSA 2342
rs563000141,2
C--36529583(+) CTAACA/GTGGTG 1 -- us2k10--------
rs1893156471,2
--36529654(+) ATTTCA/GCTGGG 1 -- us2k10--------
rs60217551,2
--36529663(+) GGAGCA/GGGGTT 1 -- us2k10--------
rs1823086981,2
--36529684(+) AATGAA/GTGAGA 1 -- us2k10--------
rs1868203871,2
--36529719(+) GCCTGG/TCCAGC 1 -- us2k10--------
rs1466695511,2
--36529823(+) AGAAGG/TTTCGG 1 -- us2k10--------
rs11232911,2
C,F--36529854(-) GGTCCC/TAAGCG 1 -- us2k18Minor allele frequency- T:0.01NA EA 554
rs58412791,2
C,F--36530005(+) TGCTAC/-CCCCC 1 -- us2k1 tfbs3 trp32Minor allele frequency- -:0.50NA CSA 4

HapMap Linkage Disequilibrium report for VSTM2L (36531499 - 36573752 bp)

Structural Variations
     Database of Genomic Variants (DGV) 3 variations for VSTM2L:    About this table    
Variant IDTypeSubtypePubMed ID
esv2633566CNV Insertion19546169
nsv833970CNV Gain17160897
nsv833971CNV Gain17160897

Site Specific Mutation Identification with PCR Assays
SeqTarget long-range PCR primers for resequencing VSTM2L
DNA2.0 Custom Variant and Variant Library Synthesis for VSTM2L

(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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  --

(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 VSTM2L gene integrated from 10 sources:
(articles sorted by number of sources associating them with VSTM2L)
    Utopia: connect your pdf to the dynamic
world of online information

  1. 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. (Genome Res. 2004)
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
  3. The DNA sequence and comparative analysis of human chromosome 20. (PubMed id 11780052)1, 2 Deloukas P....Rogers J. (Nature 2001)
  4. VSTM2L is a novel secreted antagonist of the neuroprotective peptide Humanin. (PubMed id 21393573)1 Rossini L....Caricasole A. (FASEB J. 2011)
  5. The full-ORF clone resource of the German cDNA consortium. (PubMed id 17974005)2 Bechtel S.... Schupp I. (BMC Genomics 2007)
  6. A protein-protein interaction network for human inherited ataxias and disorders of Purkinje cell degeneration. (PubMed id 16713569)1 Lim J.... Zoghbi H.Y. (Cell 2006)
  7. 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. (Proc. Natl. Acad. Sci. U.S.A. 2002)
  8. CR16 forms a complex with N-WASP in brain and is a novel member of a conserved proline-rich actin-binding protein family. (PubMed id 11553796)1 Ho H.Y....Kirschner M.W. (Proc. Natl. Acad. Sci. U.S.A. 2001)

(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: 128434 HGNC: 16096 AceView: C20orf102 Ensembl:ENSG00000132821 euGenes: HUgn128434
ECgene: VSTM2L H-InvDB: VSTM2L

(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 VSTM2L 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 VSTM2L gene:
Search GeneIP for patents involving VSTM2L

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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