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SNHG17 Gene

RNA gene   GIFtS: 17
GCID: GC20M037088

Small Nucleolar RNA Host Gene 17 (Non-Protein Coding)

  Search for SNHG17
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): processed_transcript

Quality score for this RNA gene is 3

Aliases
Small Nucleolar RNA Host Gene 17 (Non-Protein Coding)1 2

External Ids:    HGNC: 486001   Entrez Gene: 3887962   Ensembl: ENSG000001967567   

Export aliases for SNHG17 gene to outside databases

Previous GC identifer: GC20M037076


(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 SNHG17 Gene:
SNHG17 (small nucleolar RNA host gene 17 (non-protein coding)) is an RNA gene, and is affiliated with the processed_transcript 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:
   Search for regulatory transcription factor binding sites for SNHG17
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for SNHG17

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SNHG17


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

SNHG17 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SNHG17 gene location

GeneLoc information about chromosome 20         GeneLoc Exon Structure

GeneLoc location for GC20M037088:  view genomic region     (about GC identifiers)

Start:
37,049,235 bp from pter      End:
37,064,018 bp from pter
Size:
14,784 bases      Orientation:
minus strand
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for SNHG17

(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, 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)
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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, 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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(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 SNHG17
Interactions:

    Search GeneGlobe Interaction Network for SNHG17

(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 compounds at ApexBio 

Browse Tocris compounds for SNHG17



(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,
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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9 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000423536(processed_transcript) ENST00000436764(processed_transcript) ENST00000449469(processed_transcript) ENST00000414142(processed_transcript) ENST00000417578(processed_transcript)
ENST00000413755(processed_transcript) ENST00000456953(processed_transcript) ENST00000424235(processed_transcript) ENST00000362582(processed_transcript)
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Selected AceView cDNA sequences (see all 182):

AA654002 W95497 AA974245 AA513668 BC052370 AA062783 AI277243 N35265 
BM678826 BM562678 AW027666 AK022745 CR601352 Y11165 BM853469 AA694134 
BM988278 AA366536 AI874315 BX093504 BM720553 AA343039 CR614522 BU153111 

GeneLoc Exon Structure

Selected Alternative Splicing Database (ASD) splice patterns (SP) for SNHG17 (see all 18)    About this scheme

ExUns: 1a · 1b · 1c · 1d · 1e · 1f · 1g ^ 2 ^ 3a · 3b ^ 4a · 4b ^ 5 ^ 6 ^ 7a · 7b · 7c ^ 8a · 8b ^ 9a · 9b · 9c · 9d · 9e ^ 10 ^ 11a ·
SP1:                                      -                 -     -     -     -     -                                   -     -     -     -     -               
SP2:                                      -                 -     -     -     -           -                 -     -     -     -     -     -     -               
SP3:                                      -                 -     -     -           -                                                                           
SP4:                                      -                 -     -     -     -     -                       -     -     -     -     -     -     -               
SP5:                                      -                 -     -     -     -     -                                   -                                       

ExUns: 11b · 11c · 11d · 11e
SP1:                        
SP2:                        
SP3:                        
SP4:                        
SP5:                        


ECgene alternative splicing isoforms for SNHG17

(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 SNHG17:none

SNHG17 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: --
SNHG17 Expression
About this image

SNHG17 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

SNHG17 Protein Expression
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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 human and mouse.

Orthologs for SNHG17 gene from 1 species (see representative species )    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia 9430008C03Rik5 RIKEN cDNA 9430008C03 gene   --   2 (78.72 cM) 158355307 


ENSEMBL Gene Tree for SNHG17 (if available)
TreeFam Gene Tree for SNHG17 (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 SNHG17 (see all 170)    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 20 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1815198711,2
--37048759(+) TCACCC/TTACTC 1 -- ds50010--------
rs1861677731,2
--37048926(+) GACAGC/TTGATC 2 -- ds50010--------
rs1383143441,2
--37048928(+) CAGTTG/TATCTC 2 -- ds50010--------
rs17396521,2
C,F,A,H--37048959(+) GAGCCA/GCGTCA 2 -- ds500127Minor allele frequency- G:0.25NS EA NA WA CSA 2493
rs1492197561,2
--37048998(+) CATCAC/GACCTG 2 -- ds50010--------
rs1433214871,2
--37049318(+) GTTATC/TAAAGT 2 -- nc-transcript-variant0--------
rs1389606321,2
C--37049341(+) GGACAA/GAGGGA 2 -- nc-transcript-variant0--------
rs1421730031,2
--37049481(+) GTGACA/GCTTCA 2 -- nc-transcript-variant0--------
rs1885068421,2
--37049521(+) CCTCTC/TGTGCC 2 -- nc-transcript-variant0--------
rs37522751,2
C,F--37049538(+) CACCAC/TCAAGA 2 -- nc-transcript-variant1Minor allele frequency- T:0.01EA 1476

HapMap Linkage Disequilibrium report for SNHG17 (37049235 - 37064018 bp)

Structural Variations
      Database of Genomic Variants (DGV) variations for SNHG17: --
Site Specific Mutation Identification with PCR Assays
Search QIAGEN SeqTarget long-range PCR primers for resequencing SNHG17
DNA2.0 Custom Variant and Variant Library Synthesis for SNHG17

(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.)
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  --

(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 SNHG17 gene integrated from 10 sources:
(articles sorted by number of sources associating them with SNHG17)
    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. Transcriptome analysis of human gastric cancer. (PubMed id 16341674)1 Oh J.H.... Kim N.S. (Mamm. Genome 2005)
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1 Ota T.... Sugano S. (Nat. Genet. 2004)
  4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)
  5. Normalization and subtraction: two approaches to facilitate gene discovery. (PubMed id 8889548)1 Bonaldo M.F.... Soares M.B. (Genome Res. 1996)

(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: 388796 HGNC: 48600 AceView: LOC388796 Ensembl:ENSG00000196756 euGenes: HUgn388796
ECgene: SNHG17 H-InvDB: SNHG17

(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 SNHG17 gene:
Search GeneIP for patents involving SNHG17

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



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Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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