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SNHG21 Gene

RNA gene   GIFtS: 15
GCID: GC15P083422

Small Nucleolar RNA Host Gene 21 (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 10.2

Aliases
Small Nucleolar RNA Host Gene 21 (Non-Protein Coding)1 2
FSD2 Antisense RNA 11
FSD2-AS12
SCARNA15HG2

External Ids:    HGNC: 502841   Entrez Gene: 1005056162   Ensembl: ENSG000002509887   
ORGUL members:    fRNAdb10:FR291048 FR070755 FR319535      
H-InvDB12:HIT000055032 HIT000383031    
NCBI13:BX538250 AL360137    
NONCODE14:n374660 n344791 n380677    
RNAdb15:RNZ13060 ASO3511 ASO3479    

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(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 SNHG21 Gene:
SNHG21 (small nucleolar RNA host gene 21 (non-protein coding)) is an RNA gene, and is affiliated with the lncRNA class.

fRNAdb sequence ontologies for SNHG21 - the ORGUL cluster for this gene includes several descriptions:
nc_conserved_region - Non-coding region of sequence similarity by descent from a common ancestor.
antisense_RNA - Antisense RNA is RNA that is transcribed from the coding, rather than the template, strand of DNA. It is therefore complementary to mRNA.

View fRNAdb secondary structures for SNHG21

(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_000015.9  NC_018926.2  NT_010194.18  
Regulatory elements:
   Search for regulatory transcription factor binding sites for SNHG21
         Other transcription factors

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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SNHG21


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

Ensembl cytogenetic band:  15q25.2   HGNC cytogenetic band: 15q25.2

SNHG21 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SNHG21 gene location

GeneLoc information about chromosome 15         GeneLoc Exon Structure

GeneLoc location for GC15P083422:  view genomic region     (about GC identifiers)

Start:
83,419,316 bp from pter      End:
83,425,958 bp from pter
Size:
6,643 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, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, 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:
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, 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, 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 SNHG21
Interactions:

    Search GeneGlobe Interaction Network for SNHG21

(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 SNHG21



(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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1 fRNAdb Secondary structure:


Unigene Cluster for SNHG21:

Uncharacterized LOC100505616
Hs.513091  [show with all ESTs]
Unigene Representative Sequence: BX538250
5 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000544685(antisense) ENST00000558687(antisense) ENST00000561107(antisense) ENST00000558174(antisense) ENST00000559366(antisense)

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Additional mRNA sequence: 

AL360137.1 BX538250.1 XR_110596.1 XR_110597.1 XR_159252.1 XR_159253.1 XR_172089.1 XR_172090.1 

5 DOTS entries:

DT.441771  DT.75131708  DT.75101703  DT.95217175  DT.95155336 

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 SNHG21:H-invDB

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

SNHG21 Protein expression data from MOPED1, PaxDb2 and MaxQB3 --

SOURCE GeneReport for Unigene cluster: Hs.513091
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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 SNHG21 (if available)
TreeFam Gene Tree for SNHG21 (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 SNHG21 (see all 160)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 15 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs28903131,2
C,F,H--63079863(+) aaaaaA/Caattg 2 -- us2k124Minor allele frequency- C:0.13NS EA NA WA CSA 2245
rs1885603241,2
--63079875(+) GAAGGA/CATAAA 2 -- us2k10--------
rs1461917761,2
--63079988(+) CTCTAC/TGCTCA 2 -- us2k10--------
rs116312091,2
C,F,A,H--63080113(+) ataatT/Agataa 2 -- us2k16Minor allele frequency- A:0.20NA EA 250
rs71781091,2
C,F--63080403(+) caccaA/Cgcccg 2 -- us2k11Minor allele frequency- C:0.00CSA 1
rs1498695941,2
--63080408(+) CGCCCA/GGCTAA 2 -- us2k10--------
rs1451020251,2
C--63080490(+) GATCCA/GCCCAC 2 -- us2k10--------
rs620116821,2
C,F--63080552(+) CCTACC/TCATCC 2 -- us2k13Minor allele frequency- T:0.11NA WA 240
rs1813658731,2
--63080626(+) TTGTAC/GTACAT 2 -- us2k10--------
rs1860306081,2
--63080684(+) TGTACA/TGGGTT 2 -- us2k10--------

HapMap Linkage Disequilibrium report for SNHG21 (83419316 - 83425958 bp)

Structural Variations
      Database of Genomic Variants (DGV) variations for SNHG21: --
Site Specific Mutation Identification with PCR Assays
Search QIAGEN SeqTarget long-range PCR primers for resequencing SNHG21
DNA2.0 Custom Variant and Variant Library Synthesis for SNHG21

(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 information: 612675    

Find genes that share disorders with SNHG21           About GenesLikeMe


Export disorders for SNHG21 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 SNHG21 gene integrated from 10 sources:
(articles sorted by number of sources associating them with SNHG21)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (Genome Res. 2006)
  2. Normalization and subtraction: two approaches to facilitate gene discovery. (PubMed id 8889548)1 Bonaldo M.F.... Soares M.B. (Genome Res. 1996)
  3. Generation and analysis of 280,000 human expressed sequence tags. (PubMed id 8889549)1 Hillier L.D....Marra M. (Genome Res. 1996)
  4. (PubMed id 16273071)10 
  5. (PubMed id 15608161)10 
  6. (PubMed id 15103394)10 
  7. (PubMed id 17451645)10 
  8. (PubMed id 18089548)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: 100505616 HGNC: 50284 Ensembl:ENSG00000250988 euGenes: HUgn100505616 ECgene: SNHG21
H-InvDB: SNHG21

(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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  --

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for SNHG21 gene:
Search GeneIP for patents involving SNHG21

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, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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