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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

GeneHancer (GH) Regulatory Elements for VTRNA2-1 Gene

Promoters and enhancers for VTRNA2-1 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
GH05I136079 Promoter/Enhancer 1.8 FANTOM5 Ensembl ENCODE 550.8 -0.3 -260 1.7 PKNOX1 ATF1 ARNT IRF4 BRCA1 YY1 NCOA2 GTF3C2 POLR2B GATA2 ENSG00000278815 GC05M136082 VTRNA2-1 SMAD5 LECT2 SMAD5-AS1 ENSG00000277859
GH05I136082 Enhancer 0.8 ENCODE 0.8 -2.0 -2010 0.2 HDAC1 ELF3 RB1 NFRKB MZF1 FEZF1 RAD21 ZBTB40 YY1 ZNF143 SMAD5 LECT2 SMAD5-AS1 ENSG00000278815 VTRNA2-1 ENSG00000277859
GH05I136087 Enhancer 1 Ensembl ENCODE 0.4 -8.1 -8076 3.1 HDAC1 MEIS2 LEF1 PKNOX1 ZBTB6 ZMYM3 ZBTB40 ZFHX2 CTBP1 ZNF316 SMAD5 SMAD5-AS1 LECT2 ENSG00000254239 IL9 ENSG00000278815 VTRNA2-1 ENSG00000277859
GH05I136093 Enhancer 0.8 ENCODE 0.4 -14.1 -14076 1.6 FOXA2 ARID4B RAD21 THRB ZSCAN9 ZBTB40 ETS1 YY1 TCF12 CREM SMAD5 SMAD5-AS1 ENSG00000254239 IL9 ENSG00000278815 VTRNA2-1 ENSG00000277859
GH05I136122 Enhancer 0.9 ENCODE 0.3 -43.0 -43021 1.5 FOXA2 FEZF1 ZNF2 YY1 ZNF213 FOS YY2 TSHZ1 ZNF488 REST SMIM32 ENSG00000254239 IL9 LECT2 ENSG00000277859 ENSG00000278815 VTRNA2-1 GC05M136114
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

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

Genomic Locations for VTRNA2-1 Gene

Genomic Locations for VTRNA2-1 Gene
chr5:136,080,471-136,080,597
(GRCh38/hg38)
Size:
127 bases
Orientation:
Minus strand
chr5:135,416,160-135,416,286
(GRCh37/hg19)

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

miRNA Products

Clone Products

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 :

miRNA Products

Clone Products

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 Variation AA Info Type
rs1000150703 -- 136,080,207(-) C/T downstream_transcript_variant
rs1001822600 -- 136,081,644(-) C/G/T upstream_transcript_variant
rs1001853642 -- 136,082,025(-) T/A upstream_transcript_variant
rs1003209359 -- 136,080,888(-) C/T upstream_transcript_variant
rs1003491182 -- 136,081,324(-) G/A upstream_transcript_variant

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

Additional Variant Information 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

Additional Disease Information for 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 58
  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 58
  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 58
  4. Evolution of vault RNAs. (PMID: 19491402) Stadler PF … Ullmann K (Molecular biology and evolution 2009) 2 3 58
  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 58

Products for VTRNA2-1 Gene

Sources for VTRNA2-1 Gene

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