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RNY1 Gene

RNA gene   GIFtS: 19
GCID: GC07M148685

RNA, Ro-Associated Y1

(Previous names: RNA, Y1 small cytoplasmic (associated with Ro protein))
  See RNY1-related diseases
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): Y RNA

Quality score for this RNA gene is 5

Aliases
RNA, Ro-Associated Y11 2
Y12 5
RNA, Y1 Small Cytoplasmic (Associated With Ro Protein)1
HY12

External Ids:    HGNC: 102421   Entrez Gene: 60842   Ensembl: ENSG000002010987   OMIM: 6018215   
ORGUL members:    fRNAdb10:FR012907 FR126282 FR323454 FR274857 FR193825      
NCBI13:K01562 K01562    
NONCODE14:u3862    
Rfam:RF00019    

Export aliases for RNY1 gene to outside databases

Previous GC identifers: GC07U990082 GC07M148316 GC07M142763


(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 RNY1 Gene:
Y RNAs are small noncoding RNAs that were originally identified as the RNA component of soluble ribonucleoproteins
(RNPs) termed Ro RNPs. Ro RNPs are detected by autoimmune sera of patients suffering from rheumatic diseases,
such as from systemic lupus erythematosus (MIM 152700) and Sjogren syndrome (MIM 270200). Ro RNPs consist of a Y
RNA that is associated with the autoimmune antigen proteins Ro60 (TROVE2; MIM 600063) and La (SSB; MIM 109090),
as well as other proteins. Four human Y RNAs have been identified: Y1, Y3 (RNY3; MIM 601822), Y4 (RNY4; MIM
601823), and Y5 (RNY5; MIM 601824). (Y2 is a truncated form of Y1.) Y RNAs are transcribed by RNA polymerase III
and range in size from 83 to 112 nucleotides. They appear to have a functional role in chromosomal DNA
replication (Christov et al., 2006 (PubMed 16943439)).(supplied by OMIM, Apr 2009)

GeneCards Summary for RNY1 Gene:
RNY1 (RNA, Ro-associated Y1) is an RNA gene, and is affiliated with the Y RNA class. Diseases associated with RNY1 include sjogren's syndrome, and rheumatic disease.




(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:
   Regulatory transcription factor binding sites in the RNY1 gene promoter:
         E2F-4   E2F-3a   E2F-5   E2F-2   C/EBPalpha   CHOP-10   E2F   E2F-1   Pax-4a   En-1   
         Other transcription factors

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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat RNY1


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

Entrez Gene cytogenetic band: 7q36   Ensembl cytogenetic band:  7q36.1   HGNC cytogenetic band: 7q36

RNY1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
RNY1 gene location

GeneLoc information about chromosome 7         GeneLoc Exon Structure

GeneLoc location for GC07M148685:  view genomic region     (about GC identifiers)

Start:
148,684,228 bp from pter      End:
148,684,340 bp from pter
Size:
113 bases      Orientation:
minus strand

1 alternative location:
Chr7-,CRA_TCAG 148,022,614-148,022,726     
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for RNY1

(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:
RNY: Y RNAs (Ro-associated)

  --

(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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Molecular Function:
     Genatlas biochemistry entry for RNY1:
small cytoplasmic ribonucleoprotein RY1,component of Ro ribonucleoprotein

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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 RNY1
Interactions:

    GeneGlobe Interaction Network for RNY1

(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 RNY1

1 Novoseek inferred chemical compound relationship for RNY1 gene    About this table
Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
calcium 0 1 15850450 (1)



Find genes that share compounds with RNY1           About GenesLikeMe



(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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2 fRNAdb Secondary structures:


1 Ensembl transcript including schematic representation, and UCSC links where relevant:
ENST00000364228(misc_RNA)
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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™, 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 RNY1:none

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

RNY1 Protein expression data from MOPED1, PaxDb2 and MaxQB3 --
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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 RNY1 gene from Selected species (see all 3)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Rny15 RNA, Y1 small cytoplasmic, Ro-associated   --   6 (22.94 cM) 47788070 


ENSEMBL Gene Tree for RNY1 (if available)
TreeFam Gene Tree for RNY1 (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 RNY1 (see all 63)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 7 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1822683391,2
--148683735(+) GCGTGC/GTGGCG 1 -- ds50010--------
rs1868736021,2
C--148683744(+) CGCGCA/GCCTAT 1 -- ds50010--------
rs1917659841,2
--148683748(+) CGCCTA/GTAGTC 1 -- ds50010--------
rs26168571,2
C,F,A--148683797(-) GCCTCG/CTGGGT 1 -- ds50017Minor allele frequency- C:0.15NA WA CSA EA 249
rs566922091,2
C,F--148683842(+) CTCCAG/ACCTGG 1 -- ds50011Minor allele frequency- A:0.50WA 2
rs586508561,2
C--148683895(+) AAAAA-/AAAA/AAA
AA
/AAAAAAA
GAAAG
1 -- ds50011NA 2
rs560433501,2
C,F--148684073(+) GATGGG/TTTTTC 1 -- ds50015Minor allele frequency- T:0.18WA CSA NA 243
rs1826653041,2
--148684168(+) TTCAAC/TATTTT 1 -- ds50010--------
rs1495654581,2
--148684226(+) CTCTCA/GTAAAA 1 -- ds50010--------
rs1460783621,2
--148684231(+) GTAAAA/GGACTA 1 -- nc-transcript-variant0--------

HapMap Linkage Disequilibrium report for RNY1 (148684228 - 148684340 bp)

Structural Variations
      Database of Genomic Variants (DGV) variations for RNY1: --
Site Specific Mutation Identification with PCR Assays
Search QIAGEN SeqTarget long-range PCR primers for resequencing RNY1
DNA2.0 Custom Variant and Variant Library Synthesis for RNY1

(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: 601821    OMIM disorders: --

3 diseases for RNY1:    
About MalaCards
sjogren's syndrome    rheumatic disease    systemic lupus erythematosus


Find genes that share disorders with RNY1           About GenesLikeMe


Export disorders for RNY1 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 RNY1 gene, integrated from 10 sources (see all 19):
(articles sorted by number of sources associating them with RNY1)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Genes for two small cytoplasmic Ro RNAs are adjacent and appear to be single-copy in the human genome. (PubMed id 6187471)1, 3 Wolin S.L. and Steitz J.A. (Cell 1983)
  2. Functional requirement of noncoding Y RNAs for human chromosomal DNA replication. (PubMed id 16943439)1 Christov C.P....Krude T. (Mol. Cell. Biol. 2006)
  3. Gene encoding human Ro-associated autoantigen Y5 RNA. (PubMed id 8836182)1 Maraia R....Green E.D. (Nucleic Acids Res. 1996)
  4. Genes for murine Y1 and Y3 Ro RNAs have class 3 RNA polymerase III promoter structures and are unlinked on mouse chromosome 6. (PubMed id 8863726)9 Farris A.D....Harley J.B. (Gene 1996)
  5. A Y2 receptor mimetic aptamer directed against neuropeptide Y. (PubMed id 11756401)9 Proske D....Famulok M. (J. Biol. Chem. 2002)
  6. Substitutions and deletions in the cytoplasmic domain of the phagocytic receptor Fc gamma RIIA: effect on receptor tyrosine phosphorylation and phagocytosis. (PubMed id 7521687)9 Mitchell M.A....Schreiber A.D. (Blood 1994)
  7. DPP-IV inhibition enhances the antilipolytic action of NPY in human adipose tissue. (PubMed id 19175376)9 Kos K....McTernan P.G. (amp 2009)
  8. An arachidonic acid-preferring acyl-CoA synthetase is a hormone-dependent and obligatory protein in the signal transduction pathway of steroidogenic hormones. (PubMed id 15956337)9 Cornejo Maciel F....PodestA! E.J. (J. Mol. Endocrinol. 2005)
  9. Regional distribution of neuropeptide Y Y2 receptor messenger RNA in the human post mortem brain. (PubMed id 9692752)9 Caberlotto L....Hurd Y.L. (Neuroscience 1998)
  10. Neuropeptide Y expression, localization and cellular transducing effects in HUVEC. (PubMed id 15850450)9 Silva A.P....Grouzmann E. (Biol. Cell 2005)

(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: 6084 HGNC: 10242 Ensembl:ENSG00000201098 euGenes: HUgn6084 ECgene: RNY1
H-InvDB: RNY1

(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 RNY1 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 RNY1 gene:
Search GeneIP for patents involving RNY1

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



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