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VTRNA1-2 Gene

RNA gene   GIFtS: 18
GCID: GC05P140113

Vault RNA 1-2

(Previous name: vault RNA component 2)
(Previous symbol: VAULTRC2)
  Search for VTRNA1-2
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Subcategory (RNA class): vault RNA

Quality score for this RNA gene is 3

Aliases
Vault RNA 1-21 2
VAULTRC21 2 5
HVG22 5
Vault RNA Component 21
VR22
hvg-22

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

Export aliases for VTRNA1-2 gene to outside databases

Previous GC identifers: GC05P140082 GC05P135243 GC05P140100 GC05P140102


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for VTRNA1-2 Gene:
VTRNA1-2 (vault RNA 1-2) is an RNA gene, and is affiliated with the vault RNA class.


(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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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Regulatory elements:
   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:
DNA Methylation CpG Assay Predesigned for Pyrosequencing 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 GC05P140113:  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

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, 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 Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB: --


(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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HGNC Gene Families:
VAULT: Vault RNAs (vtRNAs)

  --

(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Animal Models:
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(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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  --

(SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, 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 Apr 2014 via Entrez Gene).
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(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 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,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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1 Ensembl transcript including schematic representation, and UCSC links where relevant:
ENST00000365241(misc_RNA)
miRNA
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GeneLoc Exon Structure


(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™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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Expression evidence for VTRNA1-2:none

See probesets specificity/sensitivity at GeneAnnot
CGAP TAG: --

VTRNA1-2 Protein expression data from MOPED1, PaxDb2 and MaxQB3 --
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(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)
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This gene was present in the common ancestor of chordates.

Orthologs for VTRNA1-2 gene from Selected species (see all 8)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
chicken
(Gallus gallus)
Aves Vault6
Vault RNA
57(a)
1 → many
13(380747-380840) ENSGALG00000025591
lizard
(Anolis carolinensis)
Reptilia Vault6
Vault RNA
63(a)
many ↔ many
1(228113067-228113154)
zebrafish
(Danio rerio)
Actinopterygii Vault6
Vault6
(see all 3)
Vault RNA
(see all 3)
53(a)
52(a)
(see all 3)
many ↔ many
many ↔ many
(see all 3)
14(2309500-2309603)
14(2309883-2309986)
        Species with no ortholog for VTRNA1-2

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

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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  --

(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, 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), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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Selected SNPs for VTRNA1-2 (see all 77)    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
C--140096716(+) AGAGAA/GGCTTC 1 -- us2k10--------
rs1399713721,2
C--140096721(+) GGCTTC/GTTTCA 1 -- us2k10--------
rs1418987521,2
C--140096730(+) CAGGGC/GTTTCT 1 -- us2k10--------
rs1461716501,2
C--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--------
rs3741910751,2
C--140096977(+) TTGTA-/TTTCT 
CCCATAAC
TTTCT
1 -- us2k10--------

HapMap Linkage Disequilibrium report for VTRNA1-2 (140098510 - 140098598 bp)

Structural Variations
     Database of Genomic Variants (DGV) 6 variations for VTRNA1-2:    About this table    
Variant IDTypeSubtypePubMed ID
esv2661261CNV Deletion23128226
esv2730832CNV Deletion23290073
esv2730833CNV Deletion23290073
esv23837CNV Loss19812545
nsv882950CNV Loss21882294
nsv830508CNV Loss17160897

Site Specific Mutation Identification with PCR Assays
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(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.)
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OMIM gene information: 612696    OMIM disorders: --


VTRNA1-2 for disorders           About GeneDecksing


Export disorders for VTRNA1-2 gene to outside databases

(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)
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PubMed articles for VTRNA1-2 gene integrated from 10 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. (Mol. Biol. Evol. 2009)
  2. Epstein-barr virus-induced expression of a novel human vault RNA. (PubMed id 19298825)1, 3 Nandy C....Polacek N. (J. Mol. Biol. 2009)
  3. Vaults are up-regulated in multidrug-resistant cancer cell lines. (PubMed id 9535882)1, 3 Kickhoefer V.A....Rome L.H. (J. Biol. Chem. 1998)
  4. The BTB and CNC homology 1 (BACH1) target genes are involved in the oxidative stress response and in control of the cell cycle. (PubMed id 21555518)1 Warnatz H.J....Yaspo M.L. (J. Biol. Chem. 2011)
  5. Vaults and telomerase share a common subunit, TEP1. (PubMed id 10551828)1 Kickhoefer V.A....Rome L.H. (J. Biol. Chem. 1999)

(in PubMed, OMIM, and NCBI Bookshelf)
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 ANDOR
Aliases
Free Text  

  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)

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

(According to HUGE)
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  --

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

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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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



(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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