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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

VTRNA1-2 Gene

RNA gene   GIFtS: 18
GCID: GC05P140102

vault RNA 1-2

(Previous name: vault RNA component 2 )
(Previous symbol: VAULTRC2)
  Search for VTRNA1-2
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Biological research products
for VTRNA1-2    

Aliases
for VTRNA1-2 gene

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section
Subcategory (RNA class): vault RNA

Quality score for this RNA gene is 4

Aliases
Vault RNA 1-21 2     Hvg-21
HVG21 2 5     Vault RNA Component 21
VAULTRC21 2 5     VtRNA1-21
VR21 2     

External Ids:    HGNC: 126551   Entrez Gene: 566632   Ensembl: ENSG000002021117   OMIM: 6126965   
ORGUL members:    fRNAdb10:FR083011 FR154376      
Rfam:RF00006    

Export aliases for VTRNA1-2 gene to outside databases

Previous GC identifers: GC05P140082 GC05P135243 GC05P140100


Summaries
for VTRNA1-2 gene

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section
fRNAdb sequence ontology for VTRNA1-2:
Vault RNA - This family of RNAs are found as part of the enigmatic vault ribonucleoprotein complex. The complex consists of a major vault protein (MVP), two minor vault proteins (VPARP and TEP1), and several small untranslated RNA molecules. It has been suggested that the vault complex is involved in drug resistance. We have identified a putative novel vault RNA on chromosome 5 EMBL:AC005219.

Genomic Views
for VTRNA1-2 gene

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
 Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the VTRNA1-2 gene promoter:
         AML1a   Nkx2-5   HNF-4alpha1   AREB6   PPAR-gamma1   FOXO4   ARP-1   FOXO1a   PPAR-gamma2   FOXO1   
         Other transcription factors

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Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat VTRNA1-2


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 5q31.3   Ensembl cytogenetic band:  5q31.3   HGNC cytogenetic band: 5q31.3

VTRNA1-2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
VTRNA1-2 gene location

GeneLoc information about chromosome 5         GeneLoc Exon Structure

GeneLoc location for GC05P140102:  view genomic region     (about GC identifiers)

Start:
 140,098,510 bp from pter      End:
 140,098,598 bp from pter
Size:
 89 bases      Orientation:
 plus strand

Proteins
for VTRNA1-2 gene

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section
UniProtKB: --

Protein Domains /
Families
for VTRNA1-2 gene

(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section
   --

Function
for VTRNA1-2 gene

(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
About This Section
miRNA
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Inhib. RNA
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In Situ Assay
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Pathways & Interactions
for VTRNA1-2 gene

(Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
About This Section



Interactions:

    Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for VTRNA1-2

Drugs & Compounds
for VTRNA1-2 gene

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
About This Section
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Browse Tocris compounds for VTRNA1-2
Search CenterWatch for drugs/clinical trials and news about VTRNA1-2 

Transcripts
for VTRNA1-2 gene

(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from EMD Millipore,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
About This Section
1 Ensembl transcript including schematic representation, and UCSC links where relevant:
ENST00000365241(misc_RNA)

miRNA
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Inhib. RNA
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Clone
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Primer
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GeneLoc Exon Structure


Expression
for VTRNA1-2 gene

(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section

Expression evidence for VTRNA1-2:none

VTRNA1-2 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: --

Microarray
RNAseq (Illumina Body Map)
(100×FPKM)½
SAGE (Serial Analysis of Gene Expression)
About this image    SABiosciences Custom PCR Arrays for VTRNA1-2
Primer
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In Situ
Assay Products: 
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Orthologs
for VTRNA1-2 gene

(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
About This Section
   --

ENSEMBL Gene Tree for VTRNA1-2 (if available)
TreeFam Gene Tree for VTRNA1-2 (if available) 

Paralogs
for VTRNA1-2 gene

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
About This Section
Paralogs for VTRNA1-2 gene
ENSG000002519002  VTRNA1-32  ENSG000002522832  ENSG000002524852  VTRNA2-12  VTRNA1-12  VTRNA3-1P2  ENSG000002523282  

VTRNA1-2 for paralogs           About GeneDecksing



Genomic Variants
for VTRNA1-2 gene

(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
About This Section

10/63 NCBI SNPs in VTRNA1-2 are shown (see all 63)     About this table
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance		Chr 5 posSequence#AA
Chg		TypeMore#Allele
freq		PopTotal
sample		More
----------
rs1928810041,2
--140096546(+) AATTCC/TGAATT 1 -- us2k10--------
rs1850056801,2
--140096617(+) CATGGA/GGTGTT 1 -- us2k10--------
rs1879263711,2
--140096716(+) AGAGAA/GGCTTC 1 -- us2k10--------
rs1399713721,2
--140096721(+) GGCTTC/GTTTCA 1 -- us2k10--------
rs1418987521,2
--140096730(+) CAGGGC/GTTTCT 1 -- us2k10--------
rs1461716501,2
--140096772(+) GCATTC/TTGGTT 1 -- us2k10--------
rs1484029271,2
--140096802(+) AGTGCC/TTAGGT 1 -- us2k10--------
rs1928507191,2
--140096821(+) TGTAGA/GTACTG 1 -- us2k10--------
rs1844438121,2
--140096924(+) GATGAA/TCCTTA 1 -- us2k10--------
rs25632971,2
C,F,H,--140097072(-) GCTGCA/GGTAAT 1 -- us2k116Minor allele frequency- G:0.36EA NS NA WA 1832

HapMap Linkage Disequilibrium report for VTRNA1-2 (140098510 - 140098598 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV): 1 variation for VTRNA1-2
     1 CNV: 64316

SABiosciences Cancer Mutation PCR Assays
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Disorders / Diseases
for VTRNA1-2 gene

(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
About This Section
VTRNA1-2 for disorders           About MalaCards

VTRNA1-2 for disorders           About GeneDecksing

OMIM gene information: 612696    OMIM disorders: --


Export disorders for VTRNA1-2 gene to outside databases

Publications
for VTRNA1-2 gene

(in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
About This Section

PubMed articles for VTRNA1-2 gene integrated from 9 sources:
(articles sorted by number of sources associating them with VTRNA1-2)		    Utopia: connect your pdf to the dynamic
world of online information

  1. Evolution of vault RNAs. (PubMed id 19491402)1, 3 Stadler P.F....Ullmann K. (2009)
  2. Epstein-barr virus-induced expression of a novel huma n vault RNA. (PubMed id 19298825)1, 3 Nandy C....Polacek N. (2009)
  3. Vaults are up-regulated in multidrug-resistant cancer cell lines. (PubMed id 9535882)1, 3 Kickhoefer V.A....Rome L.H. (1998)
  4. The BTB and CNC homology 1 (BACH1) target genes are i nvolved in the oxidative stress response and in control of the cell cycle. (PubMed id 21555518)1 Warnatz H.J....Yaspo M.L. (2011)
  5. Vaults and telomerase share a common subunit, TEP1. (PubMed id 10551828)1 Kickhoefer V.A....Rome L.H. (1999)

External Searches for VTRNA1-2 gene

(in PubMed, OMIM, and NCBI Bookshelf)
About This Section
 ANDOR
Aliases
Free Text  
  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)

Genome Databases showing VTRNA1-2 gene

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
About This Section
Entrez Gene: 56663 HGNC: 12655 Ensembl:ENSG00000202111 euGenes: HUgn56663 ECgene: VTRNA1-2
H-InvDB: VTRNA1-2

Other Databases showing VTRNA1-2 gene

(According to HUGE)
About This Section
   --

Specialized Databases showing VTRNA1-2 gene

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section
NameDescription
PharmGKB entry for VTRNA1-2 Pharmacogenomics, SNPs, Pathways

Intellectual Property
for VTRNA1-2 gene

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
About This Section
Patent Information for VTRNA1-2 gene:
Search GeneIP for patents involving VTRNA1-2

GeneCards and IP:
Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



Products
for VTRNA1-2 gene

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