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DSCR9 Gene

RNA gene   GIFtS: 32
GCID: GC21P038580

Down Syndrome Critical Region Gene 9 (Non-Protein Coding)

  Search for DSCR9
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): lncRNA

Quality score for this RNA gene is 3

Aliases
Down Syndrome Critical Region Gene 9 (Non-Protein Coding)1 2
Non-Protein Coding RNA 381
NCRNA000382

External Ids:    HGNC: 163011   Entrez Gene: 2572032   Ensembl: ENSG000002303667   UniProtKB: P590203   

Export aliases for DSCR9 gene to outside databases

Previous GC identifers: GC21P035170 GC21P037513 GC21P037502 GC21P024056


(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 DSCR9 Gene:
DSCR9 (Down syndrome critical region gene 9 (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_000021.8  NC_018932.2  NT_011512.12  
Regulatory elements:
   Regulatory transcription factor binding sites in the DSCR9 gene promoter:
         AP-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidDSCR9 promoter sequence
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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat DSCR9


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

Entrez Gene cytogenetic band: 21q22.13   Ensembl cytogenetic band:  21q22.13   HGNC cytogenetic band: 21q22

DSCR9 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
DSCR9 gene location

GeneLoc information about chromosome 21         GeneLoc Exon Structure

GeneLoc location for GC21P038580:  view genomic region     (about GC identifiers)

Start:
38,580,804 bp from pter      End:
38,594,037 bp from pter
Size:
13,234 bases      Orientation:
plus strand
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for DSCR9

(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/Swiss-Prot: DSCR9_HUMAN, P59020 (See protein sequence)
Recommended Name: Down syndrome critical region protein 9  
Size: 149 amino acids; 16743 Da
Secondary accessions: B2R8P8

Explore the universe of human proteins at neXtProt for DSCR9: NX_P59020

Explore proteomics data for DSCR9 at MOPED


See DSCR9 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB


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(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

ProtoNet protein and cluster: P59020


(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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     Gene Ontology (GO): 1 molecular function term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0003674molecular_function ND--
     
Find genes that share ontologies with DSCR9           About GenesLikeMe


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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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Gene Ontology (GO): 1 cellular component term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005575cellular_component ND--

Find genes that share ontologies with DSCR9           About GenesLikeMe


(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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Interactions:

    Search GeneGlobe Interaction Network for DSCR9

Gene Ontology (GO): 1 biological process term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0008150biological_process ND--

Find genes that share ontologies with DSCR9           About GenesLikeMe



(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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REFSEQ mRNAs for DSCR9 gene: 
NM_148675.3  

Unigene Cluster for DSCR9:

Down syndrome critical region gene 9 (non-protein coding)
Hs.505159  [show with all ESTs]
Unigene Representative Sequence: BC066653
6 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000581640(lincRNA) ENST00000578829(lincRNA)(uc010gni.3) ENST00000585273(lincRNA)(uc010gng.3)
ENST00000584840(lincRNA)(uc010gnh.3) ENST00000454482(lincRNA)(uc010gnj.3 uc011aef.2)
ENST00000543267(lincRNA)(uc010gnk.2)
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Additional mRNA sequence: 

AB066100.1 AB212286.1 AB212287.1 AB212288.1 AB212289.1 AB212290.1 AB212291.1 AK313458.1 
BC029827.1 BC066653.1 NR_026719.2 

1 DOTS entry:

DT.210120 

Selected AceView cDNA sequences (see all 30):

AA973296 AB066100 BF508967 BC066653 AI075910 AI125524 AI125493 AA255898 
BQ223675 AI419824 AA432171 CD673555 AW295935 AI291000 BI826306 AI206596 
AI918692 NM_148675 AA256098 BC029827 BF062278 AW510868 AI631552 AW236642 

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 DSCR9:none

DSCR9 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: AAGCCCTGGG
DSCR9 Expression
About this image

DSCR9 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

DSCR9 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.505159

UniProtKB/Swiss-Prot: DSCR9_HUMAN, P59020
Tissue specificity: Testis specific

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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 DSCR9 (if available)
TreeFam Gene Tree for DSCR9 (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 DSCR9 (see all 335)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 21 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs750403721,2
C,F--38578809(+) GGAAAT/CATAAA 1 -- us2k12Minor allele frequency- C:0.13WA EA 238
rs1414500171,2
--38578834(+) GCAGGA/GTGATA 1 -- us2k10--------
rs1470011281,2
--38578838(+) GGTGAC/TAGGGT 1 -- us2k10--------
rs1928777361,2
--38578852(+) GATTCA/GTGTCC 1 -- us2k10--------
rs1150683911,2
C,F--38578890(+) GAAGGG/TCCTGG 1 -- us2k11Minor allele frequency- T:0.07WA 118
rs7149601,2
C,F,A--38578906(-) ATCCAA/GTCACC 1 -- us2k15Minor allele frequency- G:0.17NA 128
rs732185951,2
C,F--38579087(+) CAGCCA/GTGCTT 1 -- us2k11Minor allele frequency- G:0.02NA 120
rs785726921,2
C,F--38579183(+) GAGAAC/GGGACC 1 -- us2k11Minor allele frequency- G:0.03WA 118
rs1379307041,2
C--38579184(+) AGAACA/GGACCA 1 -- us2k10--------
rs1837386901,2
C--38579272(+) TTGCTC/GTTCTC 1 -- us2k10--------

HapMap Linkage Disequilibrium report for DSCR9 (38580804 - 38594037 bp)

Structural Variations
     Database of Genomic Variants (DGV) 2 variations for DSCR9:    About this table    
Variant IDTypeSubtypePubMed ID
nsv3512CNV Loss18451855
dgv70n68CNV Gain17160897

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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.)
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Find genes that share disorders with DSCR9           About GenesLikeMe

Human Genome Epidemiology (HuGE) Navigator: DSCR9 (1 document)

Export disorders for DSCR9 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 DSCR9 gene integrated from 10 sources:
(articles sorted by number of sources associating them with DSCR9)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Identification of two novel primate-specific genes in DSCR. (PubMed id 12168953)1, 2, 3 Takamatsu K....Takeda T. (DNA Res. 2002)
  2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
  3. Interactions of pathological hallmark proteins: tubulin polymerization promoting protein/p25, beta-amyloid, and alpha-synuclein. (PubMed id 21832049)1 OlA!h J....OvA!di J. (J. Biol. Chem. 2011)
  4. Digital quantification of human eye color highlights genetic association of three new loci. (PubMed id 20463881)1 Liu F....Kayser M. (PLoS Genet. 2010)
  5. hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes. (PubMed id 17207965)1 Lamesch P.... Vidal M. (Genomics 2007)
  6. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)2 Ota T.... Sugano S. (Nat. Genet. 2004)
  7. 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)
  8. The DNA sequence of human chromosome 21. (PubMed id 10830953)2 Hattori M.... Yaspo M.-L. (Nature 2000)

(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: 257203 HGNC: 16301 AceView: DSCR9 Ensembl:ENSG00000230366 euGenes: HUgn257203
ECgene: DSCR9 H-InvDB: DSCR9

(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 DSCR9 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 DSCR9 gene:
Search GeneIP for patents involving DSCR9

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



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Developed at the Crown Human Genome Center, Department of Molecular Genetics, the Weizmann Institute of Science

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