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Aliases for VTRNA2-1 Gene

Subcategory (RNA class) for VTRNA2-1 Gene

vault RNA

Quality Score for this RNA gene is

3

Aliases for VTRNA2-1 Gene

  • Vault RNA 2-1 2 3 5
  • MicroRNA 886 2 3
  • Cord Blood Lymphocyte-Derived Noncoding RNA 3 3
  • Noncoding RNA 886 3
  • Vault RNA 2 2
  • Hsa-Mir-886 3
  • SvtRNA2-1a 3
  • MIRN886 3
  • MIR886 3
  • VTRNA2 3
  • CBL-3 3
  • Hvg-5 3
  • Nc886 3
  • CBL3 3

External Ids for VTRNA2-1 Gene

ORGUL Members for VTRNA2-1 Gene

Previous HGNC Symbols for VTRNA2-1 Gene

  • MIR886
  • MIRN886
  • VTRNA2

Previous GeneCards Identifiers for VTRNA2-1 Gene

  • GC05M135417

Summaries for VTRNA2-1 Gene

Entrez Gene Summary for VTRNA2-1 Gene

  • This gene produces an RNA polymerase III transcript that resembles both a component of the ribonucleoprotein vault particle and a pre-microRNA. However, the RNA product does not function as a vault or microRNA; rather, it acts as a direct inhibitor of protein kinase R (also known as eukaryotic translation initiation factor 2-alpha kinase 2, EIF2AK2), and thereby plays an important role in the regulation of cell growth. This gene is located in the vicinity of a differentially methylated region (DMR) and is imprinted and may show allele-specific expression. This gene is also often hypermethylated and repressed in cancers. [provided by RefSeq, Nov 2015]

GeneCards Summary for VTRNA2-1 Gene

VTRNA2-1 (Vault RNA 2-1) is an RNA Gene, and is affiliated with the vault RNA class.

Additional gene information for VTRNA2-1 Gene

No data available for CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for VTRNA2-1 Gene

Genomics for VTRNA2-1 Gene

Regulatory Elements for VTRNA2-1 Gene

Enhancers for VTRNA2-1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH05H136079 1.4 FANTOM5 ENCODE 0.7 -0.3 -261 1 PKNOX1 ATF1 ARNT BRCA1 YY1 GTF3C2 GATA2 ZNF143 FOS ATF7 SMAD5 LECT2 SMAD5-AS1 ENSG00000278815 VTRNA2-1 ENSG00000277859
GH05H136082 0.8 ENCODE 0.7 -2.0 -2010 0 HDAC1 ELF3 RB1 NFRKB FEZF1 RAD21 YY1 ZNF143 SMARCA5 ZNF654 SMAD5 LECT2 SMAD5-AS1 ENSG00000278815 VTRNA2-1 ENSG00000277859
GH05H136087 1.1 Ensembl ENCODE 0.4 -8.1 -8076 3 HDAC1 LEF1 PKNOX1 ZNF175 ZMYM3 ZFHX2 ZNF316 CTBP1 EGR1 ATF7 SMAD5 SMAD5-AS1 LECT2 ENSG00000254239 IL9 ENSG00000278815 VTRNA2-1 ENSG00000277859
GH05H136093 0.9 ENCODE 0.4 -14.1 -14076 1 FOXA2 ATF1 ARID4B RAD21 THRB ZSCAN9 YY1 TCF12 CREM MIXL1 SMAD5 SMAD5-AS1 ENSG00000254239 IL9 VTRNA2-1 ENSG00000278815 ENSG00000277859
GH05H136122 1 ENCODE 0.3 -43.0 -43021 1 FOXA2 FEZF1 ZNF2 YY1 FOS YY2 TSHZ1 ZNF488 REST PPARG SMIM32 ENSG00000254239 IL9 LECT2 ENSG00000277859 ENSG00000278815 VTRNA2-1
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around VTRNA2-1 on UCSC Golden Path with GeneCards custom track

Promoters for VTRNA2-1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000187293 -3 1201 PKNOX1 ATF1 ARNT BRCA1 YY1 GTF3C2 GATA2 ZNF143 FOS ATF7

Genomic Location for VTRNA2-1 Gene

Chromosome:
5
Start:
136,080,471 bp from pter
End:
136,080,597 bp from pter
Size:
127 bases
Orientation:
Minus strand

Genomic View for VTRNA2-1 Gene

Genes around VTRNA2-1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
VTRNA2-1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for VTRNA2-1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for VTRNA2-1 Gene

Proteins for VTRNA2-1 Gene

Post-translational modifications for VTRNA2-1 Gene

No Post-translational modifications

No data available for DME Specific Peptides for VTRNA2-1 Gene

Domains & Families for VTRNA2-1 Gene

Gene Families for VTRNA2-1 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with VTRNA2-1: view

No data available for Protein Domains , Suggested Antigen Peptide Sequences and UniProtKB/Swiss-Prot for VTRNA2-1 Gene

Function for VTRNA2-1 Gene

Animal Model Products

CRISPR Products

miRNA Products

Clone Products

  • Applied Biological Materials Clones for VTRNA2-1
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

No data available for Molecular function , Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Gene Ontology (GO) - Molecular Function , Phenotypes , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for VTRNA2-1 Gene

Localization for VTRNA2-1 Gene

No data available for Subcellular locations from UniProtKB/Swiss-Prot , Subcellular locations from COMPARTMENTS , Subcellular locations from the Human Protein Atlas (HPA) and Gene Ontology (GO) - Cellular Components for VTRNA2-1 Gene

Pathways & Interactions for VTRNA2-1 Gene

SuperPathways for VTRNA2-1 Gene

No Data Available

Interacting Proteins for VTRNA2-1 Gene

Gene Ontology (GO) - Biological Process for VTRNA2-1 Gene

None

No data available for Pathways by source and SIGNOR curated interactions for VTRNA2-1 Gene

Drugs & Compounds for VTRNA2-1 Gene

No Compound Related Data Available

Transcripts for VTRNA2-1 Gene

mRNA/cDNA for VTRNA2-1 Gene

(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :

CRISPR Products

miRNA Products

Clone Products

  • Applied Biological Materials Clones for VTRNA2-1
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

Alternative Splicing Database (ASD) splice patterns (SP) for VTRNA2-1 Gene

No ASD Table

Relevant External Links for VTRNA2-1 Gene

GeneLoc Exon Structure for
VTRNA2-1
ECgene alternative splicing isoforms for
VTRNA2-1

Expression for VTRNA2-1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for VTRNA2-1 Gene

mRNA differential expression in normal tissues according to GTEx for VTRNA2-1 Gene

This gene is overexpressed in Adipose - Visceral (Omentum) (x5.9).
genes like me logo Genes that share expression patterns with VTRNA2-1: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for VTRNA2-1 Gene

Orthologs for VTRNA2-1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for VTRNA2-1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia Vault 34
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia Vault 34
  • 67 (a)
OneToOne
dog
(Canis familiaris)
Mammalia Vault 34
  • 64 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia Vault 34 34 34 34 34 34 34
  • 58 (a)
ManyToMany
oppossum
(Monodelphis domestica)
Mammalia Vault 34
  • 50 (a)
ManyToMany
chicken
(Gallus gallus)
Aves Vault 34
  • 64 (a)
OneToMany
lizard
(Anolis carolinensis)
Reptilia Vault 34
  • 57 (a)
ManyToMany
zebrafish
(Danio rerio)
Actinopterygii Vault 34 34 34
  • 50 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea Vault 34
  • 46 (a)
OneToMany
Species where no ortholog for VTRNA2-1 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)
  • mouse (Mus musculus)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • 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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for VTRNA2-1 Gene

ENSEMBL:
Gene Tree for VTRNA2-1 (if available)
TreeFam:
Gene Tree for VTRNA2-1 (if available)

Paralogs for VTRNA2-1 Gene

No data available for Paralogs for VTRNA2-1 Gene

Variants for VTRNA2-1 Gene

Sequence variations from dbSNP and Humsavar for VTRNA2-1 Gene

SNP ID Clin Chr 05 pos Sequence Context AA Info Type
rs1000150703 -- 136,080,207(+) CCGTC(C/T)TACTT downstream-variant-500B
rs1001822600 -- 136,081,644(+) GTCTC(C/T)CTATA upstream-variant-2KB
rs1001853642 -- 136,082,025(+) AGCTT(A/T)ATTTG upstream-variant-2KB
rs1003209359 -- 136,080,888(+) AGTAC(C/T)CCCGC upstream-variant-2KB
rs1003491182 -- 136,081,324(+) ATAAT(A/G)TCCCT upstream-variant-2KB

Structural Variations from Database of Genomic Variants (DGV) for VTRNA2-1 Gene

Variant ID Type Subtype PubMed ID
esv2759380 CNV loss 17122850
nsv5017 CNV insertion 18451855

Relevant External Links for VTRNA2-1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
VTRNA2-1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Variation tolerance for VTRNA2-1 Gene

Disorders for VTRNA2-1 Gene

Relevant External Links for VTRNA2-1

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
VTRNA2-1

No disorders were found for VTRNA2-1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for VTRNA2-1 Gene

Publications for VTRNA2-1 Gene

  1. Cell death/proliferation roles for nc886, a non-coding RNA, in the protein kinase R pathway in cholangiocarcinoma. (PMID: 22926522) Kunkeaw N … Lee YS (Oncogene 2013) 2 3 60
  2. Allelic methylation levels of the noncoding VTRNA2-1 located on chromosome 5q31.1 predict outcome in AML. (PMID: 22058117) Treppendahl MB … Grønbæk K (Blood 2012) 2 3 60
  3. Epstein-barr virus-induced expression of a novel human vault RNA. (PMID: 19298825) Nandy C … Polacek N (Journal of molecular biology 2009) 2 3 60
  4. Evolution of vault RNAs. (PMID: 19491402) Stadler PF … Ullmann K (Molecular biology and evolution 2009) 2 3 60
  5. Silencing nc886, a Non-Coding RNA, Induces Apoptosis of Human Endometrial Cancer Cells-1A In Vitro. (PMID: 28298621) Hu Z … Geng Y (Medical science monitor : international medical journal of experimental and clinical research 2017) 3 60

Products for VTRNA2-1 Gene

Sources for VTRNA2-1 Gene

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