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Category Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21

GIFtS
-

SNORD50A Gene

RNA gene GIFtS: 21
GCID: GC06M086393

small nucleolar RNA, C/D box 50A

(Previous names: RNA, U50 small nuclear )
(Previous symbol: RNU50)

Explore 4 diseases affiliated with
SNORD50A via

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our new
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(According to ¹HGNC, ²Entrez Gene,
³UniProtKB/Swiss-Prot, ⁴UniProtKB/TrEMBL, ⁵OMIM, ⁶GeneLoc, ⁷Ensembl, ⁸DME, ⁹miRBase, and/or ¹⁰fRNAdb)
About This Section

Subcategory (RNA class): snoRNA

Quality score for this RNA gene is 5

Aliases
Small Nucleolar RNA, C/D Box 50A¹ ²
RNU50¹ ² ⁵
U50¹ ²
RNA, U50 Small Nuclear¹

External Ids:	HGNC: 10200¹	Entrez Gene: 26799²	Ensembl: ENSG00000207066⁷	OMIM: 613117⁵

ORGUL members:	fRNAdb¹⁰:FR153161 FR081615
	H-InvDB:HIT000383109
	NCBI:X96662
	NONCODE:u5081
	Rfam:RF00278

Export aliases for SNORD50A gene to outside databases

Previous GC identifers: GC06M086448 GC06M086452 GC06M086455 GC06M086458 GC06M086459 GC06M086463 GC06M086389 GC06M086391 GC06M083612

(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 SNORD50A:

SNORD50A belongs to the C/D box class of small nucleolar RNAs (snoRNAs), which are thought to function as guide RNAs in

the site-specific ribose methylation of preribosomal RNA (Kiss-Laszlo et al., 1996 (PubMed 8674114)).(supplied by

OMIM, Nov 2009)

fRNAdb sequence ontologies for SNORD50A - the ORGUL cluster for this gene includes several descriptions:
Small nucleolar RNA SNORD50 - U50 belongs to the C/D class of snoRNA which contain the C (UGAUGA) and D (CUGA) box motifs. Most of the members of the box C/D family function in directing site-specific 2'-O-methylation of substrate RNAs [1]. U50 is an intronic snoRNA gene located on chromosome 6q15, at the breakpoint of chromosomal translocation t(3;6)(q27;q15). The U50HG gene is composed of six exons, whose spliced transcripts have little potential for coding a protein, and its introns produce both U50 and U50-like (U50') snoRNAs that are localised in nucleoli [3].
C_D_box_snoRNA - Most box C/D snoRNAs also contain long (>10 nt) sequences complementary to rRNA. Boxes C and D, as well as boxes C' and D', are usually located in close proximity, and form a structure known as the box C/D motif. This motif is important for snoRNA stability, processing, nucleolar targeting and function. A small number of box C/D snoRNAs are involved in rRNA processing; most, however, are known or predicted to serve as guide RNAs in ribose methylation of rRNA. Targeting involves direct base pairing of the snoRNA at the rRNA site to be modified and selection of a rRNA nucleotide a fixed distance from box D or D'.

View fRNAdb secondary structures for SNORD50A

(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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section

Regulatory elements:

SABiosciences Regulatory transcription factor binding sites in the SNORD50A 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:

QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat SNORD50A

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

SNORD50A Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SNORD50A gene location

GeneLoc information about chromosome 6 GeneLoc Exon Structure

GeneLoc location for GC06M086393: view genomic region (about GC identifiers)

Start:	86,387,012 bp from pter	End:	86,387,086 bp from pter
Size:	75 bases	Orientation:	minus strand

(According to ¹UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to ²PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, 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 Uscn,
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About This Section

UniProtKB: --

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

(According to ¹UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or ²DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
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, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
About This Section

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(Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, 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 Mar 2013 via Entrez Gene).
About This Section

Interactions:

Search SABiosciences Gene Network Central^TM Interacting Genes and Proteins Networks for SNORD50A

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, 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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(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 235 Homo sapiens; Mar 10 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,
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About This Section

1 fRNAdb Secondary structure:

1 Ensembl transcript including schematic representation, and UCSC links where relevant:

ENST00000384338(snoRNA)

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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™, 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 SNORD50A:H-invDB

SNORD50A expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: --

About this image
Genevestigator expression for SNORD50A

SABiosciences Custom PCR Arrays for SNORD50A

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In Situ
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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

--

ENSEMBL Gene Tree for SNORD50A (if available)
TreeFam Gene Tree for SNORD50A (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, UniProtKB, 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

SNP ID	Valid	Clinical significance	Chr 6 pos	Sequence	#	AA Chg	Type	More	#	Allele freq	Pop	Total sample	More
Genomic Data					Transcription Related Data				Allele Frequencies
				--	--	--		--	--
rs183223970^1,2		--	86386555(+)	`AAGCAA/TCCAGG`	2	--	ds500¹ int¹		0	--	--	--	--
rs188085142^1,2		--	86386572(+)	`AAATTA/CTAGTT`	2	--	int¹ ds500¹		0	--	--	--	--
rs144346987^1,2	C,	--	86386617(+)	`AACAA-/TTAC TTCTA`	2	--	ds500¹ int¹		0	--	--	--	--
rs191400554^1,2		--	86386624(+)	`ACTTCC/TAATTC`	2	--	ds500¹ int¹		0	--	--	--	--
rs183928665^1,2		--	86386647(+)	`TCTTAC/GACTGA`	2	--	int¹ ds500¹		0	--	--	--	--
rs80236938^1,2	F,	--	86386688(+)	`AACCCG/AAAACA`	2	--	int¹ ds500¹		1		WA	118
rs112084658^1,2		--	86386711(+)	`AATTTG/CATTAC`	2	--	int¹ ds500¹		1		CSA	2
rs79011497^1,2	F,	--	86386843(+)	`AAGAGC/TTTTTT`	3	--	nc-transcript-variantds500¹		1		WA	118
rs149080830^1,2		--	86386962(+)	`ACATAC/TGTAAA`	3	--	ds500¹ int¹		0	--	--	--	--
rs188165652^1,2		--	86386974(+)	`GCATTA/GAAAGT`	3	--	ds500¹ int¹		0	--	--	--	--

HapMap Linkage Disequilibrium report for SNORD50A (86387012 - 86387086 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV) variations for SNORD50A: --
Human Gene Mutation Database (HGMD): SNORD50A

SABiosciences Cancer Mutation PCR Assays

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(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.)
About This Section

SNORD50A for disorders           About GeneDecksing

OMIM gene information: 613117 122550 143400 604519 608545
4 diseases for SNORD50A:    About MalaCards

b-cell lymphomas prostate cancer breast cancer prostatitis

Human Genome Epidemiology (HuGE) Navigator: SNORD50A (1 document)

Export disorders for SNORD50A 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 SNORD50A gene, integrated from 9 sources (see all 11):
(articles sorted by number of sources associating them with SNORD50A)

Utopia: connect your pdf to the dynamic
world of online information

Site-specific ribose methylation of preribosomal RNA: a novel function for small nucleolar RNAs. (PubMed id 8674114)^{1, 3} Kiss-Laszlo Z....Kiss T. (1996)
Eukaryotic snoRNAs: a paradigm for gene expression fl exibility. (PubMed id 19446021)¹ Dieci G....Montanini B. (2009)
Implication of snoRNA U50 in human breast cancer. (PubMed id 19683667)¹ Dong X.Y....Dong J.T. (2009)
SnoRNA U50 is a candidate tumor-suppressor gene at 6q14.3 with a mutation associated with clinically significant prostate cancer. (PubMed id 18202102)¹ Dong X.Y....Dong J.T. (2008)
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 Tanaka R....Mori S. (2000)
(PubMed id 12215523)¹⁰
(PubMed id 8797828)¹⁰
(PubMed id 10736225)¹⁰
(PubMed id 15103394)¹⁰
(PubMed id 18089548)¹⁰

(in PubMed, OMIM, and NCBI Bookshelf)
About This Section

		AND	OR
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: 26799	HGNC: 10200	Ensembl:ENSG00000207066	euGenes: HUgn26799	ECgene: SNORD50A
H-InvDB: SNORD50A

(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

Name	Description
PharmGKB entry for SNORD50A	Pharmacogenomics, SNPs, Pathways

Intellectual Property for SNORD50A gene
(Patent information from GeneIP, Licensable technologies from WIS Yeda, Salk, Tufts, IP news from LifeMap Sciences, Inc.)

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Patent Information for SNORD50A gene:
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GeneCards and IP:
Japan Patent Office Licenses GeneCards European Patent Office Licenses GeneCards Improving the IP Search

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small nucleolar RNA, C/D box 50A

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SNORD50A Gene

small nucleolar RNA, C/D box 50A

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Disorders / Diseases
for SNORD50A gene

Publications
for SNORD50A gene

Intellectual Property
for SNORD50A gene

Products
for SNORD50A gene