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BCYRN1 Gene

RNA gene   GIFtS: 19
GCID: GC02P047558

Brain Cytoplasmic RNA 1

(Previous names: brain cytoplasmic RNA 1, Bc1 analog (mouse), brain cytoplasmic...)
  See 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): lncRNA

Quality score for this RNA gene is 3

Aliases
Brain Cytoplasmic RNA 11 2     Non-Protein Coding RNA 41
Brain Cytoplasmic RNA 1 (Non-Protein Coding)1     BC2002
Brain Cytoplasmic RNA 1, Bc1 Analog (Mouse)1     BC200a2
Brain Cytoplasmic RNA 200-Alpha1     LINC000042
Long Intergenic Non-Protein Coding RNA 41     NCRNA000042

External Ids:    HGNC: 10221   Entrez Gene: 6182   Ensembl: ENSG000002368247   OMIM: 6060895   
ORGUL members:         

Export aliases for BCYRN1 gene to outside databases

Previous GC identifers: GC02U990008 GC02P047415 GC02P047299


(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 BCYRN1 Gene:
This gene, which encodes a neural small non-messenger RNA, is a member of the family of interspersed repetitive
DNA, and its product represents an example of a primate tissue-specific RNA polymerase III transcript. The RNA
sequence is divided into three domains: a 5' portion homologous to the Alu Lm, a central adenosine-rich region,
and the terminal 43-nt nonrepetitive domain. It is believed that this gene was retropositionally generated and
recruited into a function regulating dendritic protein biosynthesis. At least two pseudogenes of this gene have
been identified. (provided by RefSeq, Jul 2008)

GeneCards Summary for BCYRN1 Gene:
BCYRN1 (brain cytoplasmic RNA 1) is an RNA gene, and is affiliated with the lncRNA class. Diseases associated with BCYRN1 include alzheimer's disease, and neuronitis.




(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 BCYRN1 gene promoter:
         STAT5B   USF1   USF-1:USF-2   AP-4   STAT5A   HNF-3beta   N-Myc   USF-1   Pax-4a   ATF6   
         Other transcription factors

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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat BCYRN1


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

Entrez Gene cytogenetic band: 2p21   Ensembl cytogenetic band:  2p21   HGNC cytogenetic band: 2p16

BCYRN1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
BCYRN1 gene location

GeneLoc information about chromosome 2         GeneLoc Exon Structure

GeneLoc location for GC02P047558:  view genomic region     (about GC identifiers)

Start:
47,558,199 bp from pter      End:
47,571,656 bp from pter
Size:
13,458 bases      Orientation:
plus strand

1 alternative location:
Chr7-,CRA_TCAG 130,095,824-130,095,868     

(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, 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, 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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Molecular Function:
     Genatlas biochemistry entry for BCYRN1:
brain specific,200 nucleotide non-translatable RNA,component of a ribonucleoprotein complex,localized to
dendrite-rich neuropil areas of the retina,hippocampus,neocortex

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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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Interactions:

    Search GeneGlobe Interaction Network for BCYRN1

(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 drugs & compounds from Enzo Life Sciences
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Browse Tocris compounds for BCYRN1

1 Novoseek inferred chemical compound relationship for BCYRN1 gene    About this table
Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
adenylate 26.6 2 17175535 (1), 17387282 (1)



BCYRN1 for compounds           About GeneDecksing



(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, Primers from OriGene, and/or QIAGEN )
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1 Ensembl transcript including schematic representation, and UCSC links where relevant:
ENST00000418539(lincRNA)
miRNA
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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 BCYRN1:none

BCYRN1 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: --
BCYRN1 Expression
About this image

BCYRN1 Protein expression data from MOPED1, PaxDb2 and MaxQB3 --
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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)
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  --

ENSEMBL Gene Tree for BCYRN1 (if available)
TreeFam Gene Tree for BCYRN1 (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 BCYRN1 (see all 58)    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 2 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs44043271,2
C,F,H--47560497(+) TGCCAC/TCGCAT 1 -- us2k113Minor allele frequency- T:0.16NS EA NA CSA WA 1200
rs170364781,2
C,F,H--47560548(+) GGTTCC/TGGCTT 1 -- us2k18Minor allele frequency- T:0.02NA NS EA WA 678
rs1159920761,2
C,F--47560645(+) TGTTTC/TGTGTT 1 -- us2k11Minor allele frequency- T:0.04WA 118
rs1820487051,2
--47560694(+) ACACCC/TTTTTT 1 -- us2k10--------
rs1866989311,2
--47560743(+) CTGTTG/TACTGG 1 -- us2k10--------
rs728827121,2
C,F--47560818(+) CATTAT/CGGAAG 1 -- us2k12Minor allele frequency- C:0.04WA 120
rs2000729091,2
C--47560838(+) GCCTC-/AAAT  
        
AAAAT
1 -- us2k10--------
rs1128990741,2
F--47560925(+) CTGAGG/TTGGGC 1 -- us2k11Minor allele frequency- T:0.50CSA 2
rs557936241,2
C--47560971(+) TAACAC/TGGTGA 1 -- us2k10--------
rs1117578141,2
C,F--47560990(+) TCTCTG/ACTAAA 1 -- us2k11Minor allele frequency- A:0.50WA 2

HapMap Linkage Disequilibrium report for BCYRN1 (47558199 - 47571656 bp)

Structural Variations
     Database of Genomic Variants (DGV) Selected variations for BCYRN1 (see all 17):    About this table    
Variant IDTypeSubtypePubMed ID
esv2740215CNV Deletion23290073
esv2740214CNV Deletion23290073
esv2740213CNV Deletion23290073
nsv508781CNV Insertion20534489
nsv6954CNV Insertion18451855
nsv425542CNV Loss16902084
nsv9952CNV Loss18304495
nsv9951CNV Loss18304495
nsv512678CNV Loss21212237
esv33082CNV Loss17666407

Site Specific Mutation Identification with PCR Assays
Search QIAGEN SeqTarget long-range PCR primers for resequencing BCYRN1
DNA2.0 Custom Variant and Variant Library Synthesis for BCYRN1

(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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OMIM gene information: 606089    OMIM disorders: --

3 diseases for BCYRN1:    
About MalaCards
alzheimer's disease    neuronitis    breast cancer


BCYRN1 for disorders           About GeneDecksing

1 Novoseek inferred disease relationship for BCYRN1 gene    About this table

Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
carcinoma 0 2 9422992 (1), 15240511 (1)


Export disorders for BCYRN1 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 BCYRN1 gene, integrated from 10 sources (see all 19):
(articles sorted by number of sources associating them with BCYRN1)
    Utopia: connect your pdf to the dynamic
world of online information

  1. BC200 RNA in invasive and preinvasive breast cancer. (PubMed id 15240511)1, 3, 9 Iacoangeli A....Tiedge H. (Carcinogenesis 2004)
  2. Dendritic BC200 RNA in aging and in Alzheimer's disease. (PubMed id 17553964)1, 3, 9 Mus E....Tiedge H. (Proc. Natl. Acad. Sci. U.S.A. 2007)
  3. BC200 RNA: a neural RNA polymerase III product encoded by a monomeric Alu element. (PubMed id 8265590)1, 3, 9 Martignetti J.A. and Brosius J. (Proc. Natl. Acad. Sci. U.S.A. 1993)
  4. Assignment of the human BC200 RNA gene (BCYRN1) to chromosome 2p16 by radiation hybrid mapping. (PubMed id 9858834)1, 3, 9 Basile V....Kennedy J.L. (Cytogenet. Cell Genet. 1998)
  5. Birth of a gene: locus of neuronal BC200 snmRNA in three prosimians and human BC200 pseudogenes as archives of change in the Anthropoidea lineage. (PubMed id 11399078)1, 3 Kuryshev V.Y....Brosius J. (J. Mol. Biol. 2001)
  6. Primary structure, neural-specific expression, and dendritic location of human BC200 RNA. (PubMed id 7684772)1, 9 Tiedge H....Brosius J. (J. Neurosci. 1993)
  7. Application of the BC1 RNA gene promoter for short hairpin RNA expression in cultured neuronal cells. (PubMed id 16054886)1 Kobayashi S....Anzai K. (Biochem. Biophys. Res. Commun. 2005)
  8. Expression of neural BC200 RNA in human tumours. (PubMed id 9422992)9 Chen W....Tiedge H. (J. Pathol. 1997)
  9. SYNCRIP, a component of dendritically localized mRNPs, binds to the translation regulator BC200 RNA. (PubMed id 18045242)9 Duning K....Kremerskothen J. (J. Neurochem. 2008)
  10. Two primate-specific small non-protein-coding RNAs in transgenic mice: neuronal expression, subcellular localization and binding partners. (PubMed id 17175535)9 Khanam T....Skryabin B.V. (Nucleic Acids Res. 2007)

(in PubMed, OMIM, and NCBI Bookshelf)
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 ANDOR
Aliases
Disorders
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: 618 HGNC: 1022 Ensembl:ENSG00000236824 euGenes: HUgn618 ECgene: BCYRN1
H-InvDB: BCYRN1

(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 BCYRN1 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 BCYRN1 gene:
Search GeneIP for patents involving BCYRN1

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, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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