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Aliases for VSTM2B Gene

Aliases for VSTM2B Gene

  • V-Set And Transmembrane Domain Containing 2B 2 3 5

External Ids for VSTM2B Gene

Previous GeneCards Identifiers for VSTM2B Gene

  • GC19P034708
  • GC19P030017
  • GC19P026528

Summaries for VSTM2B Gene

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.

Additional gene information for VSTM2B Gene

No data available for Entrez Gene Summary , CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for VSTM2B Gene

Genomics for VSTM2B Gene

GeneHancer (GH) Regulatory Elements for VSTM2B Gene

Promoters and enhancers for VSTM2B Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH19I029526 Promoter/Enhancer 1.1 EPDnew dbSUPER 550.8 +1.1 1103 0.1 CTCF ZNF189 ZIC2 ZNF2 ZBTB7A ZNF335 GLIS2 ZBTB48 GLIS1 ZNF341 ENSG00000266248 LOC284395 VSTM2B
GH19I029525 Enhancer 1 ENCODE dbSUPER 550.8 -0.3 -282 0.2 KLF17 SIN3A ZNF2 ZNF335 GLIS2 ZNF416 ZNF391 ZNF202 SP3 ZNF280D ENSG00000266248 LOC284395 VSTM2B RPL9P32 ENSG00000279387
GH19I029524 Enhancer 0.6 ENCODE dbSUPER 550.8 -1.0 -1042 0.2 CTCF ZNF335 EZH2 LOC284395 VSTM2B ENSG00000266248 ENSG00000279387
GH19I029488 Enhancer 0.5 dbSUPER 12.1 -34.1 -34060 5 ZNF121 ZNF777 ZNF621 ZNF547 ZNF341 ZSCAN5C NFE2 RPL9P32 VSTM2B URI1 ENSG00000279387 LOC284395 ENSG00000266248 ENSG00000267574
GH19I029528 Enhancer 1.1 ENCODE dbSUPER 0.8 +3.7 3728 1.5 SIN3A ZNF2 ZNF121 GLIS2 ZNF213 ZNF143 KLF7 KLF13 SP3 REST RPL9P32 URI1 ENSG00000266248 VSTM2B POP4
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around VSTM2B on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the VSTM2B gene promoter:

Genomic Locations for VSTM2B Gene

Genomic Locations for VSTM2B Gene
chr19:29,525,431-29,564,551
(GRCh38/hg38)
Size:
39,121 bases
Orientation:
Plus strand
chr19:30,017,406-30,055,386
(GRCh37/hg19)

Genomic View for VSTM2B Gene

Genes around VSTM2B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
VSTM2B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for VSTM2B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for VSTM2B Gene

Proteins for VSTM2B Gene

  • Protein details for VSTM2B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    A6NLU5-VTM2B_HUMAN
    Recommended name:
    V-set and transmembrane domain-containing protein 2B
    Protein Accession:
    A6NLU5

    Protein attributes for VSTM2B Gene

    Size:
    285 amino acids
    Molecular mass:
    30297 Da
    Quaternary structure:
    No Data Available

neXtProt entry for VSTM2B Gene

Post-translational modifications for VSTM2B Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for VSTM2B Gene

No data available for DME Specific Peptides for VSTM2B Gene

Domains & Families for VSTM2B Gene

Gene Families for VSTM2B Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted secreted proteins

Protein Domains for VSTM2B Gene

Suggested Antigen Peptide Sequences for VSTM2B Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with VSTM2B: view

No data available for UniProtKB/Swiss-Prot for VSTM2B Gene

Function for VSTM2B Gene

Phenotypes From GWAS Catalog for VSTM2B Gene

genes like me logo Genes that share phenotypes with VSTM2B: view

Animal Model Products

  • Taconic Biosciences Mouse Models for VSTM2B

miRNA for VSTM2B Gene

miRTarBase miRNAs that target VSTM2B

Clone Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for VSTM2B Gene

Localization for VSTM2B Gene

Subcellular locations from UniProtKB/Swiss-Prot for VSTM2B Gene

Membrane; Single-pass type I membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for VSTM2B gene
Compartment Confidence
plasma membrane 4
extracellular 2
peroxisome 1
endoplasmic reticulum 1
lysosome 1

Gene Ontology (GO) - Cellular Components for VSTM2B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IBA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IBA --
genes like me logo Genes that share ontologies with VSTM2B: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for VSTM2B Gene

Pathways & Interactions for VSTM2B Gene

SuperPathways for VSTM2B Gene

No Data Available

Interacting Proteins for VSTM2B Gene

Gene Ontology (GO) - Biological Process for VSTM2B Gene

None

No data available for Pathways by source and SIGNOR curated interactions for VSTM2B Gene

Drugs & Compounds for VSTM2B Gene

No Compound Related Data Available

Transcripts for VSTM2B Gene

mRNA/cDNA for VSTM2B Gene

(6) REFSEQ mRNAs :
(0) Additional mRNA sequences :
-
(3) Selected AceView cDNA sequences:
(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for VSTM2B Gene

V-set and transmembrane domain containing 2B:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for VSTM2B Gene

No ASD Table

Relevant External Links for VSTM2B Gene

GeneLoc Exon Structure for
VSTM2B
ECgene alternative splicing isoforms for
VSTM2B

Expression for VSTM2B Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for VSTM2B Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for VSTM2B Gene

This gene is overexpressed in Brain - Anterior cingulate cortex (BA24) (x5.3), Brain - Amygdala (x4.6), Brain - Frontal Cortex (BA9) (x4.6), Brain - Putamen (basal ganglia) (x4.4), Brain - Nucleus accumbens (basal ganglia) (x4.3), Brain - Cortex (x4.2), and Brain - Substantia nigra (x4.2).

Protein differential expression in normal tissues from HIPED for VSTM2B Gene

This gene is overexpressed in Vitreous humor (49.1) and Pancreatic juice (19.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for VSTM2B Gene



Protein tissue co-expression partners for VSTM2B Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of VSTM2B Gene:

VSTM2B

SOURCE GeneReport for Unigene cluster for VSTM2B Gene:

Hs.451618
genes like me logo Genes that share expression patterns with VSTM2B: view

No data available for mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for VSTM2B Gene

Orthologs for VSTM2B Gene

This gene was present in the common ancestor of chordates.

Orthologs for VSTM2B Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia VSTM2B 33 34
  • 98.67 (n)
dog
(Canis familiaris)
Mammalia VSTM2B 33 34
  • 87.89 (n)
mouse
(Mus musculus)
Mammalia Vstm2b 33 16 34
  • 84.21 (n)
rat
(Rattus norvegicus)
Mammalia Vstm2b 33
  • 83.86 (n)
cow
(Bos Taurus)
Mammalia VSTM2B 34
  • 79 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia VSTM2B 34
  • 75 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia VSTM2B 34
  • 55 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia vstm2b 33
  • 65.87 (n)
zebrafish
(Danio rerio)
Actinopterygii zgc:194678 33
  • 60.25 (n)
VSTM2B 34
  • 55 (a)
OneToOne
Species where no ortholog for VSTM2B was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for VSTM2B Gene

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

Paralogs for VSTM2B Gene

Paralogs for VSTM2B Gene

(2) SIMAP similar genes for VSTM2B Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with VSTM2B: view

Variants for VSTM2B Gene

Sequence variations from dbSNP and Humsavar for VSTM2B Gene

SNP ID Clin Chr 19 pos Variation AA Info Type
rs1000075523 -- 29,530,736(+) G/C intron_variant
rs1000148578 -- 29,530,110(+) C/A coding_sequence_variant, missense_variant
rs1000158084 -- 29,534,175(+) C/A intron_variant
rs1000227855 -- 29,526,493(+) C/T 5_prime_UTR_variant, genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant
rs1000248101 -- 29,560,638(+) C/T intron_variant

Structural Variations from Database of Genomic Variants (DGV) for VSTM2B Gene

Variant ID Type Subtype PubMed ID
esv21555 CNV gain 19812545
esv275023 CNV gain+loss 21479260
esv3583340 CNV loss 25503493
nsv1061604 CNV loss 25217958
nsv833798 CNV loss 17160897
nsv833799 CNV gain 17160897

Variation tolerance for VSTM2B Gene

Gene Damage Index Score: 4.96; 68.07% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for VSTM2B Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
VSTM2B

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for VSTM2B Gene

Disorders for VSTM2B Gene

Additional Disease Information for VSTM2B

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for VSTM2B Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for VSTM2B Gene

Publications for VSTM2B Gene

  1. Coeliac disease-associated risk variants in TNFAIP3 and REL implicate altered NF-kappaB signalling. (PMID: 19240061) Trynka G … Wijmenga C (Gut 2009) 3 44 58
  2. The DNA sequence and biology of human chromosome 19. (PMID: 15057824) Grimwood J … Lucas SM (Nature 2004) 3 4 58
  3. Genetic variants associated with disordered eating. (PMID: 23568457) Wade TD … Martin NG (The International journal of eating disorders 2013) 3 58
  4. Genome-wide meta-analysis for severe diabetic retinopathy. (PMID: 21441570) Grassi MA … Nicolae DL (Human molecular genetics 2011) 3 58

Products for VSTM2B Gene

Sources for VSTM2B Gene

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