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

VTRNA2-1 Gene

RNA gene   GIFtS: 18
GCID: GC05M135417

Vault RNA 2-1

(Previous names: microRNA 886, vault RNA 2)
(Previous symbols: MIR886, MIRN886, VTRNA2)
  See related diseases
at  

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

Subcategory (RNA class): vault RNA

Quality score for this RNA gene is 3

Aliases
Vault RNA 2-11 2     CBL-32
MIR8861 2     CBL32
MIRN8861 2     hsa-mir-8862
VTRNA21 2     hvg-52
MicroRNA 8861     nc8862
Vault RNA 21     

External Ids:    HGNC: 370541   Entrez Gene: 1001262992   Ensembl: ENSG000002701237   OMIM: 6149385   
ORGUL members:    fRNAdb10:FR085944      

Export aliases for VTRNA2-1 gene to outside databases


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

GeneCards Summary for VTRNA2-1 Gene: 
VTRNA2-1 (vault RNA 2-1) is an RNA gene, and is affiliated with the vault RNA class. Diseases associated with VTRNA2-1 include friedreich ataxia, and thyroid cancer.


(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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
Regulatory elements:
   Search SABiosciences Regulatory transcription factor binding sites for VTRNA2-1
         Other transcription factors

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Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat VTRNA2-1


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

Entrez Gene cytogenetic band: 5q31.1   Ensembl cytogenetic band:  5q31.1   HGNC cytogenetic band: 5q31.1

VTRNA2-1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
VTRNA2-1 gene location

GeneLoc information about chromosome 5         GeneLoc Exon Structure

GeneLoc location for GC05M135417:  view genomic region     (about GC identifiers)

Start:
135,416,160 bp from pter      End:
135,416,286 bp from pter
Size:
127 bases      Orientation:
minus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB: --


(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section
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,
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, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
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(Pathways according to EMD Millipore, 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 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 Oct 2013 via Entrez Gene).
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Interactions:

    Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for VTRNA2-1

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
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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,
Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from EMD Millipore,
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Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
About This Section

2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000602301(lincRNA) ENST00000365160(lincRNA)(uc021ydy.1)
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™, 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 VTRNA2-1:none

VTRNA2-1 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: --
VTRNA2-1 Expression
About this image

    SABiosciences Custom PCR Arrays for VTRNA2-1
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In Situ
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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)
About This Section
  --

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

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

(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) 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

10/58 SNPs in VTRNA2-1 are shown (see all 58)    About this table     
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 5 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1417266721,2
C--135415693(+) GGACAA/CGATGC 1 -- ds50010--------
rs1174796761,2
C,F--135415721(+) GTAGGT/CACAGG 1 -- ds50011Minor allele frequency- C:0.03EA 120
rs23460191,2
C,F,O,A,H--135415726(+) TACAGA/GCCGCC 1 -- ds500131Minor allele frequency- G:0.47NS EA NA WA CSA 2800
rs345777471,2
C--135415821(+) TGGCGG/TGTGGC 1 -- ds50012Minor allele frequency- T:0.04NA 122
rs2018228441,2
C--135416344(+) AGAGGG/CACGGG 1 -- us2k11Minor allele frequency- C:0.00EU 1213
rs1471000571,2
C--135416371(+) CCCCCA/GAGAGG 1 -- us2k10--------
rs93277401,2
C,F,H--135416547(+) TACCTA/GGGTCC 1 -- us2k17Minor allele frequency- G:0.12NS EA WA NA 660
rs1477222641,2
--135416767(+) GTTGAA/TTGAAT 1 -- us2k10--------
rs1488383911,2
--135416893(+) AATAAA/TTCATT 1 -- us2k10--------
rs752112141,2
C,F--135416913(+) CCCCAA/CCCCAT 1 -- us2k11Minor allele frequency- C:0.06WA 118

HapMap Linkage Disequilibrium report for VTRNA2-1 (135416160 - 135416286 bp)

Structural Variations
     Database of Genomic Variants (DGV) 2 variations for VTRNA2-1:    About this table     
Variant IDTypeSubtypePubMed ID
nsv5017CNV Insertion18451855
dgv1853e1CNV Complex17122850

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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
About This Section
OMIM gene information: 614938    OMIM disorders: --

5 diseases for VTRNA2-1:    About MalaCards
friedreich ataxia    thyroid cancer    thyroiditis    cholangiocarcinoma
ataxia


VTRNA2-1 for disorders           About GeneDecksing


Export disorders for VTRNA2-1 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)
About This Section

PubMed articles for VTRNA2-1 gene, integrated from 9 sources (see all 13):
(articles sorted by number of sources associating them with VTRNA2-1)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Cell death/proliferation roles for nc886, a non-coding RNA, in the protein kinase R pathway in cholangiocarcinoma. (PubMed id 22926522)1, 3 Kunkeaw N....Lee Y.S. (2012)
  2. Allelic methylation levels of the noncoding VTRNA2-1 l ocated on chromosome 5q31.1 predict outcome in AML. (PubMed id 22058117)1, 3 Treppendahl M.B....Gronbak K. (2012)
  3. Evolution of vault RNAs. (PubMed id 19491402)1, 3 Stadler P.F....Ullmann K. (2009)
  4. Epstein-barr virus-induced expression of a novel huma n vault RNA. (PubMed id 19298825)1, 3 Nandy C....Polacek N. (2009)
  5. miR-886-3p levels are elevated in Friedreich ataxia. (PubMed id 22764244)1 Mahishi L.H....Ratan R.R. (2012)
  6. Characterization of the direct physical interaction of nc886, a cellular non-coding RNA, and PKR. (PubMed id 22986343)1 Jeon S.H....Lee Y.S. (2012)
  7. MiR-886-3p regulates cell proliferation and migration , and is dysregulated in familial non-medullary thyroid cancer. (PubMed id 21998631)1 Xiong Y....Kebebew E. (2011)
  8. Precursor miR-886, a novel noncoding RNA repressed in cancer, associates with PKR and modulates its activity. (PubMed id 21518807)1 Lee K....Lee Y.S. (2011)
  9. Defining the RNA polymerase III transcriptome: Genome -wide localization of the RNA polymerase III transcription machinery in human c ells. (PubMed id 20413673)1 Canella D....Hernandez N. (2010)
  10. MiR-886-3p down regulates CXCL12 (SDF1) expression in human marrow stromal cells. (PubMed id 21179442)1 Pillai M.M....Torok-Storb B. (2010)

(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)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
About This Section
Entrez Gene: 100126299 HGNC: 37054 Ensembl:ENSG00000270123 euGenes: HUgn100126299 ECgene: VTRNA2-1
H-InvDB: VTRNA2-1

(According to HUGE)
About This Section
  --

(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 VTRNA2-1 Pharmacogenomics, SNPs, Pathways

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
About This Section
Patent Information for VTRNA2-1 gene:
Search GeneIP for patents involving VTRNA2-1

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, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, Cell lines from GenScript, and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
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