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SNHG5 Gene

RNA gene   GIFtS: 25
GCID: GC06M086386

Small Nucleolar RNA Host Gene 5 (Non-Protein Coding)

(Previous name: chromosome 6 open reading frame 160)
(Previous symbol: C6orf160)
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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 3

Aliases
Small Nucleolar RNA Host Gene 5 (Non-Protein Coding)1 2     Non-Protein Coding RNA 441
C6orf1601 2     LINC000442
U50HG2 5     NCRNA000442
Chromosome 6 Open Reading Frame 1601     bA33E24.22
Long Intergenic Non-Protein Coding RNA 441     

External Ids:    HGNC: 210261   Entrez Gene: 3870662   Ensembl: ENSG000002038757   OMIM: 6132635   
ORGUL members:         

Export aliases for SNHG5 gene to outside databases

Previous GC identifers: GC06M086447 GC06M086451 GC06M086454 GC06M086457 GC06M086461 GC06M086465 GC06M083611


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for SNHG5 Gene:
This gene is a member of both the non-protein-coding multiple snoRNA host gene family and the 5'-terminal
oligopyrimidine (5' TOP) class of genes. Two snoRNAs are derived from the introns of this host gene but, although
many alternative splice variants have been observed, the gene is thought to have no protein-coding potential. The
gene is located at the chromosomal translocation breakpoint involved in B-cell lymphoma. (provided by RefSeq, Jul
2008)

GeneCards Summary for SNHG5 Gene:
SNHG5 (small nucleolar RNA host gene 5 (non-protein coding)) is an RNA gene, and is affiliated with the lncRNA 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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RefSeq DNA sequence at NCBI GenBank:
NC_000006.11  NC_018917.2  NT_025741.16  
Regulatory elements:
   Regulatory transcription factor binding sites in the SNHG5 gene promoter:
         Pbx1a   AP-2gamma   Egr-4   Egr-2   POU2F1   TFIID   POU2F1a   AP-2beta   AP-2alpha   AP-2alphaA   
         Other transcription factors

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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SNHG5


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

Entrez Gene cytogenetic band: 6q14.3   Ensembl cytogenetic band:  6q14.3   HGNC cytogenetic band: 6q14.3

SNHG5 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SNHG5 gene location

GeneLoc information about chromosome 6         GeneLoc Exon Structure

GeneLoc location for GC06M086386:  view genomic region     (about GC identifiers)

Start:
86,370,710 bp from pter      End:
86,388,451 bp from pter
Size:
17,742 bases      Orientation:
minus 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 SNHG5
Interactions:

    Search GeneGlobe Interaction Network for SNHG5

(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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(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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Unigene Cluster for SNHG5:

Small nucleolar RNA host gene 5 (non-protein coding)
Hs.292457  [show with all ESTs]
Unigene Representative Sequence: CD048516
14 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000589187(processed_transcript) ENST00000587692(processed_transcript) ENST00000369605(processed_transcript) ENST00000427501(processed_transcript) ENST00000435947(processed_transcript)
ENST00000428833(processed_transcript) ENST00000453754(processed_transcript) ENST00000420199(processed_transcript) ENST00000414002(processed_transcript) ENST00000431043(processed_transcript)
ENST00000433843(processed_transcript) ENST00000425170(processed_transcript) ENST00000384338(processed_transcript) ENST00000364995(processed_transcript)
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Additional mRNA sequence: 

AK311192.1 BC009220.2 BC108291.1 NR_003038.2 

20 DOTS entries:

DT.100713080  DT.100847883  DT.75155507  DT.100060459  DT.97844648  DT.97844650  DT.100713072  DT.100698627 
DT.100059048  DT.100870552  DT.97765018  DT.97773458  DT.121390926  DT.100857790  DT.102829863  DT.121390889 
DT.121390896  DT.121390928  DT.100810714  DT.315448 

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 SNHG5:none

SNHG5 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: TAATTTTGGA
SNHG5 Expression
About this image

SNHG5 Protein expression data from MOPED1, PaxDb2 and MaxQB3 --

SOURCE GeneReport for Unigene cluster: Hs.292457
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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 SNHG5 (if available)
TreeFam Gene Tree for SNHG5 (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 SNHG5 (see all 33)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 6 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1413874111,2
--86386371(+) AGTATC/GAGATA 1 -- int10--------
rs1469889721,2
--86386445(+) ACCAGA/GTTGTT 1 -- int10--------
rs1919195961,2
--86386488(+) ATAAAC/GTGCTA 1 -- int10--------
rs132132921,2
H--86386508(+) TATTGT/GGCTCC 1 -- int14Minor allele frequency- G:0.00NS EA 418
rs1832239701,2
--86386555(+) AAGCAA/TCCAGG 2 -- ds5001 int10--------
rs1880851421,2
--86386572(+) AAATTA/CTAGTT 2 -- ds5001 int10--------
rs1443469871,2
C--86386617(+) AACAA-/TTAC  
        
TTCTA
2 -- ds5001 int10--------
rs1914005541,2
--86386624(+) ACTTCC/TAATTC 2 -- ds5001 int10--------
rs1839286651,2
--86386647(+) TCTTAC/GACTGA 2 -- ds5001 int10--------
rs802369381,2
F--86386688(+) AACCCG/AAAACA 2 -- ds5001 int11Minor allele frequency- A:0.04WA 118

HapMap Linkage Disequilibrium report for SNHG5 (86370710 - 86388451 bp)

Structural Variations
     Database of Genomic Variants (DGV) 1 variation for SNHG5:    About this table    
Variant IDTypeSubtypePubMed ID
nsv886334CNV Loss21882294

Site Specific Mutation Identification with PCR Assays
Search QIAGEN SeqTarget long-range PCR primers for resequencing SNHG5
DNA2.0 Custom Variant and Variant Library Synthesis for SNHG5

(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: 613263    OMIM disorders: --


Find genes that share disorders with SNHG5           About GenesLikeMe


Export disorders for SNHG5 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 SNHG5 gene integrated from 10 sources:
(articles sorted by number of sources associating them with SNHG5)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Intronic U50 small-nucleolar-RNA (snoRNA) host gene of no protein-coding potential is mapped at the chromosome breakpoint t(3;6)(q27;q15) of human B-cell lymphoma. (PubMed id 10792466)1, 3 Tanaka R....Mori S. (amp 2000)
  2. 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)

(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: 387066 HGNC: 21026 Ensembl:ENSG00000203875 euGenes: HUgn387066 ECgene: SNHG5
H-InvDB: SNHG5

(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 SNHG5 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 SNHG5 gene:
Search GeneIP for patents involving SNHG5

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