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RMST Gene

RNA gene   GIFtS: 27
GCID: GC12P097858

Rhabdomyosarcoma 2 Associated Transcript (Non-Protein Coding)

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(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): lncRNA

Quality score for this RNA gene is 5.4

Aliases
Rhabdomyosarcoma 2 Associated Transcript (Non-Protein Coding)1 2
NCRMS2 5
NCRNA000542 5
Long Intergenic Non-Protein Coding RNA 541
Non-Protein Coding RNA 541
LINC000542

External Ids:    HGNC: 298931   Entrez Gene: 1964752   Ensembl: ENSG000002557947   OMIM: 6070455   
ORGUL members:    fRNAdb10:FR146738 FR096436 FR071093 FR407690 FR359819      
H-InvDB12:HIT000012778    
NCBI13:AK056164 XR_000219 AF429306    
NONCODE14:u1773 n380503 n380796 n380793 n380977 see all 9    
RNAdb15:EVF34826 RNZ9447 RNZ9444 EVF34827 RNZ9448 see all 19    

Export aliases for RMST gene to outside databases

Previous GC identifers: GC12P096362 GC12U900573


(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 RMST Gene:
RMST (rhabdomyosarcoma 2 associated transcript (non-protein coding)) is an RNA gene, and is affiliated with the lncRNA class.

Gene Wiki entry for RMST Gene

fRNAdb sequence ontologies for RMST - the ORGUL cluster for this gene includes several descriptions:
nc_conserved_region - Non-coding region of sequence similarity by descent from a common ancestor.
ncRNA - An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product.

View fRNAdb secondary structures for RMST

(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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RefSeq DNA sequence at NCBI GenBank:
NC_000012.11  NC_018923.2  NT_029419.13  
Regulatory elements:
   Regulatory transcription factor binding sites in the RMST gene promoter:
         GR   TBP   STAT5B   POU3F1   POU6F1 (c2)   Tal-1beta   HEN1   FOXO4   GR-alpha   ITF-2   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat RMST


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

Entrez Gene cytogenetic band: 12q23.1|12q21   Ensembl cytogenetic band:  12q23.1   HGNC cytogenetic band: 12q23.1

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

GeneLoc information about chromosome 12         GeneLoc Exon Structure

GeneLoc location for GC12P097858:  view genomic region     (about GC identifiers)

Start:
97,825,431 bp from pter      End:
97,958,813 bp from pter
Size:
133,383 bases      Orientation:
plus strand
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for RMST

(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, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, 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:
LNCRNA: Long non-coding RNAs

  --

(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, 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, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, 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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    Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for RMST
Interactions:

    Search GeneGlobe Interaction Network for RMST

(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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Browse Tocris compounds for RMST



(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, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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5/17 fRNAdb Secondary structures (see all 17):


Unigene Cluster for RMST:

Rhabdomyosarcoma 2 associated transcript (non-protein coding)
Hs.652568  [show with all ESTs]
Unigene Representative Sequence: AK056164
6 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000538559(processed_transcript) ENST00000541282(processed_transcript) ENST00000548886(processed_transcript) ENST00000547996(processed_transcript) ENST00000552411(processed_transcript)
ENST00000547946(processed_transcript)
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Additional mRNA sequence: 

AF429305.1 AF429306.1 AK056164.1 NR_024037.1 

5 DOTS entries:

DT.408059  DT.95123408  DT.97835174  DT.95218774  DT.95365073 

Selected AceView cDNA sequences (see all 28):

BE468066 AA385037 AK056164 AW073558 AW873986 AA935956 AI693605 AI279904 
AF429306 AI860130 AW103716 BF448175 CD107083 AA460684 AA628719 BF195950 
BM719242 BG149972 AA905859 BE551303 AA460858 AF429305 BF447150 BE176737 

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 RMST:RNAdb

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


RMST expression in embryonic tissues and stem cells    About this table
Data from LifeMap, the Embryonic Development and Stem Cells Database
 selected tissues (see all 2) fully expand
 
 Inner Cell Mass (Early Embryonic Tissues)    fully expand to see all 2 entries
         C2a
 
 Thyroid (Endocrine System)
RMST Protein expression data from MOPED1, PaxDb2 and MaxQB3 --

SOURCE GeneReport for Unigene cluster: Hs.652568
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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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  --

ENSEMBL Gene Tree for RMST (if available)
TreeFam Gene Tree for RMST (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 RMST (see all 1254)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 12 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs710784861,2
C--97856825(-) GAGAG-/AGAG  
        
AGAGA
1 -- us2k11Minor allele frequency- AGAG:0.00NA 2
rs1462603791,2
--97856889(+) ACAAGC/GGCAAA 1 -- us2k10--------
rs1176356291,2
C,F--97856942(+) GCAGGC/TAGATG 1 -- us2k11Minor allele frequency- T:0.01NA 120
rs2021424801,2
C--97856987(+) CACAC-/AGTG  
  GAGCCG
ATTTC
1 -- us2k10--------
rs1892904121,2
--97857009(+) CGATGG/TCGAGA 1 -- us2k10--------
rs1808885551,2
--97857112(+) CTTTGG/TGTCTG 1 -- us2k10--------
rs1857180611,2
--97857114(+) TTGTGA/TCTGCA 1 -- us2k10--------
rs107778681,2
C,F,A,H--97857137(+) AAAGCA/GACTCT 1 -- us2k128Minor allele frequency- N:0.00NS EA NA WA CSA 2975
rs108602131,2
C,F,A,H--97857165(+) TGTGAG/AGGTAT 1 -- us2k19Minor allele frequency- A:0.13NS EA NA 802
rs1427397801,2
--97857273(+) GAGCTA/GCTTTT 1 -- us2k10--------

HapMap Linkage Disequilibrium report for RMST (97825431 - 97958813 bp)

Structural Variations
     Database of Genomic Variants (DGV) 5 variations for RMST:    About this table    
Variant IDTypeSubtypePubMed ID
esv2665672CNV Deletion23128226
nsv840CNV Insertion18451855
nsv438229CNV Loss16468122
nsv832495CNV Gain17160897
nsv7234OTHER Inversion18451855

Site Specific Mutation Identification with PCR Assays
Search QIAGEN SeqTarget long-range PCR primers for resequencing RMST
DNA2.0 Custom Variant and Variant Library Synthesis for RMST

(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: 607045    OMIM disorders: --


Find genes that share disorders with RMST           About GenesLikeMe

Genetic Association Database (GAD): RMST

Export disorders for RMST 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 RMST gene, integrated from 10 sources (see all 15):
(articles sorted by number of sources associating them with RMST)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Rmst is a novel marker for the mouse ventral mesencephalic floor plate and the anterior dorsal midline cells. (PubMed id 20062813)1, 3 Uhde C.W....Li M. (PLoS ONE 2010)
  2. Identification of a novel gene NCRMS on chromosome 12q21 with differential expression between rhabdomyosarcoma subtypes. (PubMed id 12082533)1, 3 Chan A.S....Zielenska M. (Oncogene 2002)
  3. Genome-wide SNP and CNV analysis identifies common and low-frequency variants associated with severe early-onset obesity. (PubMed id 23563609)1 Wheeler E....Farooqi I.S. (Nat. Genet. 2013)
  4. The long noncoding RNA RMST interacts with SOX2 to regulate neurogenesis. (PubMed id 23932716)1 Ng S.Y....Stanton L.W. (Mol. Cell 2013)
  5. Framingham Heart Study 100K Project: genome-wide associations for blood pressure and arterial stiffness. (PubMed id 17903302)4 Levy D....Mitchell G.F. (BMC Med. Genet. 2007)
  6. Genome-wide association with diabetes-related traits in the Framingham Heart Study. (PubMed id 17903298)4 Meigs J.B....Dupuis J. (BMC Med. Genet. 2007)
  7. Genome-wide association with select biomarker traits in the Framingham Heart Study. (PubMed id 17903293)4 Benjamin E.J....Vasan R.S. (BMC Med. Genet. 2007)
  8. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1 Ota T.... Sugano S. (Nat. Genet. 2004)
  9. (PubMed id 16628248)10 
  10. (PubMed id 15608161)10 

(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: 196475 HGNC: 29893 AceView: NCRMS Ensembl:ENSG00000255794 euGenes: HUgn196475
ECgene: RMST H-InvDB: RMST

(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 RMST 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 RMST gene:
Search GeneIP for patents involving RMST

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



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