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

SNHG11 Gene

RNA gene   GIFtS: 30
GCID: GC20P037075

Small Nucleolar RNA Host Gene 11 (Non-Protein Coding)

(Previous name: chromosome 20 open reading frame 198)
(Previous symbol: C20orf198)
  See related disease
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): lncRNA

Quality score for this RNA gene is 13.2

Aliases
Small Nucleolar RNA Host Gene 11 (Non-Protein Coding)1 2
C20orf1981 2
Chromosome 20 Open Reading Frame 1981
Long Intergenic Non-Protein Coding RNA 1011
LINC001012
NCRNA001012

External Ids:    HGNC: 250461   Entrez Gene: 1284392   Ensembl: ENSG000001743657   
ORGUL members:    fRNAdb10:FR177408      
H-InvDB12: HIT000383021 HIT000383015    
NONCODE14:n378028 n378842 n383906 n378381 n378521 see all 14      
RNAdb15:RNZ21397    

Export aliases for SNHG11 gene to outside databases

Previous GC identifers: GC20P036520 GC20P036523 GC20P036526 GC20P036529 GC20P033810


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

Entrez Gene summary for SNHG11 Gene:
This gene is a member of the non-protein-coding multiple snoRNA host gene family. Two snoRNAs are derived from the
introns of this host gene. Although many alternative splice variants have been observed, the gene is thought to
have no protein-coding potential. (provided by RefSeq, Jul 2008)

GeneCards Summary for SNHG11 Gene: 
SNHG11 (small nucleolar RNA host gene 11 (non-protein coding)) is an RNA gene, and is affiliated with the lncRNA class. Diseases associated with SNHG11 include obesity.



fRNAdb sequence ontology for SNHG11:
nc_conserved_region - Non-coding region of sequence similarity by descent from a common ancestor.

View fRNAdb secondary structures for SNHG11

(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
RefSeq DNA sequence:
NC_000020.10  NC_018931.2  NT_011362.10  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the SNHG11 gene promoter:
         GR   Elk-1   GR-beta   HSF1 (long)   HSF1short   GR-alpha   POU3F2   RORalpha2   
         Other transcription factors

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Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat SNHG11


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

Entrez Gene cytogenetic band: 20q11.23   Ensembl cytogenetic band:  20q11.23   HGNC cytogenetic band: 20q11.23

SNHG11 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SNHG11 gene location

GeneLoc information about chromosome 20         GeneLoc Exon Structure

GeneLoc location for GC20P037075:  view genomic region     (about GC identifiers)

Start:
37,075,221 bp from pter      End:
37,079,564 bp from pter
Size:
4,344 bases      Orientation:
plus strand
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for SNHG11

(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.)
About This Section

UniProtKB: --


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

Animal Models:
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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).
About This Section



Interactions:

    Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for SNHG11

(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)
About This Section
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Search CenterWatch for drugs/clinical trials and news about SNHG11

(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
1 fRNAdb Secondary structure:


REFSEQ mRNAs for SNHG11 gene: 
NM_139016.2  

Unigene Cluster for SNHG11:

Small nucleolar RNA host gene 11 (non-protein coding)
Hs.16936  [show with all ESTs]
Unigene Representative Sequence: AK091209
16 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000453698(uc002xiq.1) ENST00000400436(uc002xir.1 uc002xis.1 uc002xit.1)
ENST00000483342(uc002xiu.1) ENST00000421599 ENST00000449351 ENST00000420006
ENST00000359074 ENST00000440918 ENST00000432153 ENST00000437028 ENST00000434729
ENST00000418383 ENST00000457218 ENST00000442419 ENST00000444816 ENST00000365032

miRNA
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Additional mRNA sequence: 

AF454939.1 AF497716.1 AK055434.1 AK091209.1 AK290212.1 BC040237.1 NR_003239.1 

12 DOTS entries:

DT.100818998  DT.100819002  DT.40270856  DT.91746588  DT.100818997  DT.101965303  DT.120817917  DT.120817930 
DT.446553  DT.100028340  DT.100818996  DT.97842894 

24/143 AceView cDNA sequences (see all 143):

BM717353 CB147515 CA454357 BQ685452 BQ888199 AW411323 BQ709000 BG753439 
T25024 BU620235 BI438282 BQ777178 BF525766 CB142876 AF497716 BM727499 
BU073306 AF454939 BI325028 BI851004 AX746850 BE646607 BM717910 CF455261 

GeneLoc Exon Structure

5/13 Alternative Splicing Database (ASD) splice patterns (SP) for SNHG11 (see all 13)    About this scheme

ExUns: 1a · 1b · 1c ^ 2a · 2b · 2c · 2d ^ 3a · 3b ^ 4 ^ 5 ^ 6a · 6b · 6c · 6d ^ 7a · 7b · 7c · 7d · 7e
SP1:                                -     -                             -           -     -                                 
SP2:                                      -                 -           -           -     -                                 
SP3:                                                        -           -           -     -                                 
SP4:                                      -                 -           -                                                   
SP5:                                      -                                                                                 


ECgene alternative splicing isoforms for SNHG11

(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 SNHG11:H-invDB

SNHG11 expression in normal human tissues (normalized intensities)      SNHG11 embryonic expression: see
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: GCCCAGGAAG
SNHG11 Expression
About this image


SNHG11 expression in embryonic tissues and stem cells    About this table
Data from LifeMap, the Embryonic Development and Stem Cells Database 
 5/6 selected tissues (see all 6) fully expand
 
 Brain (Nervous System)    fully expand to see all 23 entries
         Thalamus
         Olfactory Bulb   
 
 Neural Tube (Nervous System)    fully expand to see all 5 entries
         Telencephalon
         brain/midbrain/lateral wall   
 
 Peripheral Nervous System (Nervous System)    fully expand to see all 4 entries
         autonomic/sympathetic/ganglion   
 
 Spinal Cord (Nervous System)    fully expand to see all 3 entries
         Dorsal Horn   
 
 Gut Tube (Gastrointestinal Tract)    fully expand to see all 2 entries
         Midgut

Genevestigator expression for SNHG11

SOURCE GeneReport for Unigene cluster: Hs.16936
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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

This gene was present in the common ancestor of human and mouse.

Orthologs for SNHG11 gene from 1 species (see representative species )    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Snhg115 small nucleolar RNA host gene 11   --   2 (78.72 cM) 158375638 


ENSEMBL Gene Tree for SNHG11 (if available)
TreeFam Gene Tree for SNHG11 (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

10/45 SNPs in SNHG11 are shown (see all 45)    About this table     
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 20 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1906464401,2
--37073541(+) GCACGG/TGGGAG 1 -- us2k10--------
rs1465263521,2
--37073652(+) TGTGCA/GCCTGT 1 -- us2k10--------
rs1829041001,2
--37073674(+) CTCAGA/GAGGCT 1 -- us2k10--------
rs1881614221,2
--37073838(+) CGCTAC/GTGCTT 1 -- us2k10--------
rs60702011,2
C--37074178(+) ttgtgC/Tagtac 1 -- us2k10--------
rs75092531,2
C--37074180(+) GTGCAC/GTACAC 1 -- us2k10--------
rs8055301,2
C,F,A,H--37074199(+) CAACCG/ATATGT 1 -- us2k1 tfbs339Minor allele frequency- A:0.22NA EA NS WA CSA 3583
rs1501453501,2
--37074294(+) AATCAA/GAGCAA 1 -- us2k10--------
rs1454867761,2
--37074325(+) CCAGAA/GAGAGA 1 -- us2k10--------
rs1912519731,2
--37074350(+) ACAGGA/GATGGA 1 -- us2k10--------

HapMap Linkage Disequilibrium report for SNHG11 (37075221 - 37079564 bp)

Structural Variations
     Database of Genomic Variants (DGV) 4 variations for SNHG11:    About this table     
Variant IDTypeSubtypePubMed ID
nsv509769CNV Insertion20534489
nsv817893CNV Gain17921354
esv35121CNV Gain17911159
dgv1327e1CNV 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
2 diseases for SNHG11:    About MalaCards
obesity    


SNHG11 for disorders           About GeneDecksing

Genetic Association Database (GAD): SNHG11
Human Genome Epidemiology (HuGE) Navigator: SNHG11 (1 document)

Export disorders for SNHG11 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 SNHG11 gene integrated from 9 sources:
(articles sorted by number of sources associating them with SNHG11)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Use of genome-wide expression data to mine the ' Gray Zone' of GWA studies leads to novel candidate obesity genes. (PubMed id 20532202)1, 4 Naukkarinen J....Peltonen L. (2010)
  2. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1, 3 Strausberg R.L....Marra M.A. (2002)
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1 Ota T.... Sugano S. (2004)
  4. The sequence of the human genome. (PubMed id 11181995)1 Venter J.C.... Zhu X. (2001)
  5. (PubMed id 16273071)10 
  6. (PubMed id 15608161)10 

(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: 128439 HGNC: 25046 AceView: LOC128439 Ensembl:ENSG00000174365 euGenes: HUgn128439
ECgene: SNHG11 H-InvDB: SNHG11

(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 SNHG11 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 SNHG11 gene:
Search GeneIP for patents involving SNHG11

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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About This Section

 
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 lentivirus expression plasmids for stable overexpression
 adenovirus for overexpression
 Search LSBio for Antibodies for SNHG11
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GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 4 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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transforming growth factor, beta 1
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