Aliases for VSTM2B Gene

Aliases for VSTM2B Gene

  • V-Set And Transmembrane Domain Containing 2B 2 3 5
  • V-Set And Transmembrane Domain-Containing Protein 2B 3 4
  • VSTM2B 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 JAM3.

Additional gene information for VSTM2B Gene

No data available for Entrez Gene Summary , CIViC Summary , UniProtKB/Swiss-Prot Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for VSTM2B Gene

Genomics for VSTM2B Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for VSTM2B Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around VSTM2B on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for VSTM2B

Top Transcription factor binding sites by QIAGEN in the VSTM2B gene promoter:
  • FOXI1
  • Gfi-1
  • HFH-3
  • HNF-4alpha1
  • HNF-4alpha2
  • LCR-F1
  • MyoD
  • POU3F1
  • RORalpha2
  • SEF-1 (1)

Genomic Locations for VSTM2B Gene

Genomic Locations for VSTM2B Gene
chr19:29,525,431-29,564,555
(GRCh38/hg38)
Size:
39,125 bases
Orientation:
Plus strand
chr19:30,017,406-30,055,386
(GRCh37/hg19)
Size:
37,981 bases
Orientation:
Plus strand

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 intracellular proteins

Protein Domains for VSTM2B Gene

Suggested Antigen Peptide Sequences for VSTM2B Gene

GenScript: Design optimal peptide antigens:
  • V-set and transmembrane domain-containing protein 2B (VTM2B_HUMAN)
genes like me logo Genes that share domains with VSTM2B: view

No data available for Graphical View of Domain Structure and 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

CRISPR Products

miRNA for VSTM2B Gene

miRTarBase miRNAs that target VSTM2B

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for VSTM2B

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 2
extracellular 1
endoplasmic reticulum 1
peroxisome 0
lysosome 0

Gene Ontology (GO) - Cellular Components for VSTM2B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IBA 21873635
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

PathCards logo

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

1 REFSEQ mRNAs :
1 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for VSTM2B

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

No ASD Table

Relevant External Links for VSTM2B Gene

GeneLoc Exon Structure for
VSTM2B

Expression for VSTM2B Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and 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

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for 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 30 31
  • 98.67 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia VSTM2B 30 31
  • 87.89 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Vstm2b 30 17 31
  • 84.21 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Vstm2b 30
  • 83.86 (n)
Cow
(Bos Taurus)
Mammalia VSTM2B 31
  • 79 (a)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia VSTM2B 31
  • 75 (a)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia VSTM2B 31
  • 55 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia vstm2b 30
  • 65.87 (n)
Zebrafish
(Danio rerio)
Actinopterygii zgc:194678 30
  • 60.25 (n)
VSTM2B 31
  • 55 (a)
OneToOne
Species where no ortholog for VSTM2B was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (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)
Aminode:
Evolutionary constrained regions (ECRs) for VSTM2B: view image

Paralogs for VSTM2B Gene

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

  • VTM2B_HUMAN
genes like me logo Genes that share paralogs with VSTM2B: view

Variants for VSTM2B Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for VSTM2B Gene

SNP ID Clinical significance and condition Chr 19 pos Variation AA Info Type
777466 Benign: not provided 29,530,187(+) G/C SYNONYMOUS_VARIANT

Additional dbSNP identifiers (rs#s) for VSTM2B Gene

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
Open Targets Platform

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 41
  2. The DNA sequence and biology of human chromosome 19. (PMID: 15057824) Grimwood J … Lucas SM (Nature 2004) 3 4
  3. Genetic variants associated with disordered eating. (PMID: 23568457) Wade TD … Martin NG (The International journal of eating disorders 2013) 3
  4. Genome-wide meta-analysis for severe diabetic retinopathy. (PMID: 21441570) Grassi MA … Nicolae DL (Human molecular genetics 2011) 3
  5. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. (PMID: 21873635) Gaudet P … Thomas PD (Briefings in bioinformatics 2011) 3

Products for VSTM2B Gene

Sources for VSTM2B Gene