Aliases for VSIR Gene

Aliases for VSIR Gene

  • V-Set Immunoregulatory Receptor 2 3 4 5
  • V-Type Immunoglobulin Domain-Containing Suppressor Of T-Cell Activation 3 4
  • V-Set Domain-Containing Immunoregulatory Receptor 3 4
  • V-Domain Ig Suppressor Of T Cell Activation 2 3
  • Stress-Induced Secreted Protein-1 3 4
  • PDCD1 Homolog 2 3
  • C10orf54 3 4
  • Sisp-1 3 4
  • SISP1 3 4
  • VISTA 3 4
  • Chromosome 10 Open Reading Frame 54 2
  • Stress Induced Secreted Protein 1 2
  • Platelet Receptor GI24 3
  • Platelet Receptor Gi24 4
  • Death Domain1alpha 3
  • DD1alpha 3
  • PP2135 3
  • B7-H5 3
  • Dies1 3
  • PD-1H 3
  • B7H5 3
  • GI24 3

External Ids for VSIR Gene

Previous HGNC Symbols for VSIR Gene

  • C10orf54

Summaries for VSIR Gene

GeneCards Summary for VSIR Gene

VSIR (V-Set Immunoregulatory Receptor) is a Protein Coding gene. Diseases associated with VSIR include Monckeberg Arteriosclerosis and Superficial Mycosis. Among its related pathways are Cell adhesion molecules (CAMs) and T Cell Co-Signaling Pathway: Ligand-Receptor Interactions. An important paralog of this gene is CLMP.

UniProtKB/Swiss-Prot Summary for VSIR Gene

  • Immunoregulatory receptor which inhibits the T-cell response (PubMed:24691993). May promote differentiation of embryonic stem cells, by inhibiting BMP4 signaling (By similarity). May stimulate MMP14-mediated MMP2 activation (PubMed:20666777).

Gene Wiki entry for VSIR Gene

Additional gene information for VSIR Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for VSIR Gene

Genomics for VSIR Gene

GeneHancer (GH) Regulatory Elements for VSIR Gene

Promoters and enhancers for VSIR 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
GH10J071762 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 553.5 +3.6 3590 14.1 HNRNPK ZBTB40 ZNF217 CTCF TCF12 SP1 GTF2E2 JUND PHF8 FOS VSIR CDH23 C10orf105 PSAP SPOCK2 lnc-C10orf105-4
GH10J071726 Promoter/Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 45.7 +45.9 45892 4.3 ZNF217 CTCF SP1 ZIC2 ZNF423 RFX1 REST CTBP1 EP300 EZH2 VSIR CDH23 C10orf105 PSAP lnc-C10orf105-3
GH10J071844 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 12.9 -75.4 -75365 8.1 HNRNPK ZSCAN5C SIN3A MYC NRF1 USF1 POLR2G JUND PHF8 FOS PSAP piR-51878-002 DNAJB12 VSIR C10orf105 ANAPC16 MICU1 DDIT4 RF00066-026 RNU7-38P
GH10J071745 Promoter/Enhancer 1.9 FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 15.5 +20.8 20808 15.3 CTCF SP1 GTF2E2 FOS EP300 REST ZBTB11 AFF1 TARDBP HES1 VSIR DNAJB12 CDH23 C10orf105 ANAPC16 lnc-C10orf105-4
GH10J071712 Promoter/Enhancer 1.4 Ensembl ENCODE CraniofacialAtlas dbSUPER 16.9 +59.4 59374 4.8 POLR2A ZBTB11 RBM25 CTCF NFRKB ZNF592 SPI1 ZFHX2 BCOR SKIL VSIR DNAJB12 lnc-C10orf105-3 C10orf105 CDH23
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around VSIR on UCSC Golden Path with GeneCards custom track

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

Genomic Locations for VSIR Gene

Genomic Locations for VSIR Gene
chr10:71,747,556-71,773,580
(GRCh38/hg38)
Size:
26,025 bases
Orientation:
Minus strand
chr10:73,507,313-73,533,337
(GRCh37/hg19)
Size:
26,025 bases
Orientation:
Minus strand

Genomic View for VSIR Gene

Genes around VSIR on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for VSIR Gene

Proteins for VSIR Gene

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

    Protein Symbol:
    Q9H7M9-VISTA_HUMAN
    Recommended name:
    V-type immunoglobulin domain-containing suppressor of T-cell activation
    Protein Accession:
    Q9H7M9
    Secondary Accessions:
    • A1L0X9
    • A4ZYV1
    • A8MVH5
    • Q6UXF3
    • Q8WUG3
    • Q8WYZ8

    Protein attributes for VSIR Gene

    Size:
    311 amino acids
    Molecular mass:
    33908 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=AAL55778.1; Type=Erroneous termination; Note=Truncated C-terminus.; Evidence={ECO:0000305}; Sequence=AAL55778.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Sequence of unknown origin in the N-terminal part.; Evidence={ECO:0000305}; Sequence=BAB15739.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for VSIR Gene

neXtProt entry for VSIR Gene

Post-translational modifications for VSIR Gene

Other Protein References for VSIR Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for VSIR Gene

Domains & Families for VSIR Gene

Gene Families for VSIR Gene

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

Protein Domains for VSIR Gene

Blocks:
  • Immunoglobulin V-set
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for VSIR Gene

GenScript: Design optimal peptide antigens:
  • C10orf54 protein (A1L0X9_HUMAN)
  • Stress induced secreted protein 1 (A4ZYV1_HUMAN)
  • Platelet receptor Gi24 (GI24_HUMAN)
  • C10orf54 protein (Q2TA85_HUMAN)
genes like me logo Genes that share domains with VSIR: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for VSIR Gene

Function for VSIR Gene

Molecular function for VSIR Gene

UniProtKB/Swiss-Prot Function:
Immunoregulatory receptor which inhibits the T-cell response (PubMed:24691993). May promote differentiation of embryonic stem cells, by inhibiting BMP4 signaling (By similarity). May stimulate MMP14-mediated MMP2 activation (PubMed:20666777).

Phenotypes From GWAS Catalog for VSIR Gene

Gene Ontology (GO) - Molecular Function for VSIR Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0019899 enzyme binding IPI 20666777
GO:0042802 identical protein binding IPI 26228159
GO:0061133 endopeptidase activator activity IDA 20666777
genes like me logo Genes that share ontologies with VSIR: view
genes like me logo Genes that share phenotypes with VSIR: view

Animal Models for VSIR Gene

MGI Knock Outs for VSIR:
  • Vsir Vsir<tm1Lex>
  • Vsir Vsir<tm1.1(KOMP)Vlcg>

Animal Model Products

  • Taconic Biosciences Mouse Models for VSIR

CRISPR Products

Inhibitory RNA Products

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

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for VSIR Gene

Localization for VSIR Gene

Subcellular locations from UniProtKB/Swiss-Prot for VSIR Gene

Cell 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 VSIR gene
Compartment Confidence
plasma membrane 5
extracellular 3
nucleus 3
cytoskeleton 2
mitochondrion 2
endoplasmic reticulum 2
cytosol 2
lysosome 2
peroxisome 1
endosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for VSIR Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IDA 20666777
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with VSIR: view

Pathways & Interactions for VSIR Gene

genes like me logo Genes that share pathways with VSIR: view

Pathways by source for VSIR Gene

1 KEGG pathway for VSIR Gene
1 R&D Systems pathway for VSIR Gene
1 Cell Signaling Technology pathway for VSIR Gene

Interacting Proteins for VSIR Gene

STRING Interaction Network Preview (showing top 2 STRING interactants - click image to see details)
STRING Interaction Network
Selected Interacting proteins: Q9H7M9-VISTA_HUMAN ENSP00000378409 for VSIR Gene via UniProtKB MINT STRING IID

;

Gene Ontology (GO) - Biological Process for VSIR Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0010628 positive regulation of gene expression IMP 20666777
GO:0010950 positive regulation of endopeptidase activity IDA 20666777
GO:0030335 positive regulation of cell migration IDA 20666777
GO:0031638 zymogen activation IDA 20666777
GO:0032689 negative regulation of interferon-gamma production IDA 24691993
genes like me logo Genes that share ontologies with VSIR: view

No data available for SIGNOR curated interactions for VSIR Gene

Transcripts for VSIR Gene

mRNA/cDNA for VSIR Gene

1 REFSEQ mRNAs :
10 NCBI additional mRNA sequence :
3 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 VSIR

Clone Products

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

No ASD Table

Relevant External Links for VSIR Gene

GeneLoc Exon Structure for
VSIR

Expression for VSIR Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for VSIR

mRNA Expression by UniProt/SwissProt for VSIR Gene:

Q9H7M9-VISTA_HUMAN
Tissue specificity: Expressed in spleen. Detected on a number of myeloid cells including CD11b monocytes, CD66b+ neutrophils, at low levels on CD4+ and CD8+ T-cells, and in a subset of NK cells. Not detected on B cells (at protein level). Expressed at high levels in placenta, spleen, plasma blood leukocytes, and lung. Expressed at moderate levels in lymph node, bone marrow, fat, uterus, and trachea. Has low expression levels in other tissues.

Evidence on tissue expression from TISSUES for VSIR Gene

  • Liver(4.7)
  • Nervous system(4.6)
  • Blood(4.5)
  • Spleen(4.4)
  • Lymph node(2)
genes like me logo Genes that share expression patterns with VSIR: view

No data available for mRNA expression in normal human tissues , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for VSIR Gene

Orthologs for VSIR Gene

This gene was present in the common ancestor of chordates.

Orthologs for VSIR Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia C10H10orf54 30
  • 99.36 (n)
C10orf54 31
  • 99 (a)
OneToOne
cow
(Bos Taurus)
Mammalia C28H10orf54 30
  • 86.99 (n)
MGC151567 31
  • 82 (a)
OneToOne
dog
(Canis familiaris)
Mammalia C10orf54 31
  • 80 (a)
OneToOne
mouse
(Mus musculus)
Mammalia 4632428N05Rik 31 30
  • 79.65 (n)
OneToOne
Vsir 17
rat
(Rattus norvegicus)
Mammalia MGC112715 30
  • 77.35 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia C10orf54 31
  • 62 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia C10orf54 31
  • 54 (a)
OneToOne
chicken
(Gallus gallus)
Aves C10ORF54 30
  • 64.81 (n)
C10orf54 31
  • 56 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia C10orf54 31
  • 57 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia c10orf54 30
  • 57.5 (n)
zebrafish
(Danio rerio)
Actinopterygii zgc:153073 30
  • 52.12 (n)
C13H10orf54 31
  • 38 (a)
OneToOne
Species where no ortholog for VSIR 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)
  • 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)
  • 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 VSIR Gene

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

Paralogs for VSIR Gene

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

Variants for VSIR Gene

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

SNP ID Clinical significance and condition Chr 10 pos Variation AA Info Type
rs3747869 - p.Asp187Glu

Additional dbSNP identifiers (rs#s) for VSIR Gene

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

Variant ID Type Subtype PubMed ID
esv1096295 CNV deletion 17803354
nsv1127122 CNV deletion 24896259
nsv1137935 CNV deletion 24896259
nsv1147297 CNV deletion 26484159
nsv470963 CNV loss 18288195
nsv831910 CNV loss 17160897

Variation tolerance for VSIR Gene

Residual Variation Intolerance Score: 77.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 8.55; 86.02% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for VSIR Gene

Human Gene Mutation Database (HGMD)
VSIR
SNPedia medical, phenotypic, and genealogical associations of SNPs for
VSIR

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

Disorders for VSIR Gene

MalaCards: The human disease database

(7) MalaCards diseases for VSIR Gene - From: DISEASES

Disorder Aliases PubMed IDs
monckeberg arteriosclerosis
  • monckeberg medial calcific sclerosis
superficial mycosis
  • piedra
gallbladder melanoma
  • malignant melanoma of gallbladder
combined thymoma
inflamed seborrheic keratosis
- elite association - COSMIC cancer census association via MalaCards
Search VSIR in MalaCards View complete list of genes associated with diseases

Additional Disease Information for VSIR

genes like me logo Genes that share disorders with VSIR: view

No data available for UniProtKB/Swiss-Prot and Genatlas for VSIR Gene

Publications for VSIR Gene

  1. VISTA is an immune checkpoint molecule for human T cells. (PMID: 24691993) Lines JL … Noelle R (Cancer research 2014) 2 3 4 54
  2. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PMID: 12975309) Clark HF … Gray A (Genome research 2003) 2 3 4 54
  3. Characterization of programmed death-1 homologue-1 (PD-1H) expression and function in normal and HIV infected individuals. (PMID: 25279955) Bharaj P … Shankar P (PloS one 2014) 2 3 54
  4. GI24 enhances tumor invasiveness by regulating cell surface membrane-type 1 matrix metalloproteinase. (PMID: 20666777) Sakr MA … Sato H (Cancer science 2010) 3 4 54
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 54

Products for VSIR Gene

Sources for VSIR Gene