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brain cytoplasmic RNA 1(Previous names: brain cytoplasmic RNA 1, Bc1 analog (mouse), brain cytoplasmic...)
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Aliases
for BCYRN1 gene
(According to
1HGNC,
2Entrez Gene,
3UniProtKB/Swiss-Prot,
4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc,
7Ensembl,
8DME,
9miRBase,
and/or 10fRNAdb)
About This Section
|
Subcategory (RNA class): lncRNA
Quality score for this RNA gene is 3
| Aliases |
|---|
| Brain Cytoplasmic RNA 11 2 | | NCRNA000041 2 | | BC2001 2 | | Brain Cytoplasmic RNA 1 (Non-Protein Coding)1 | | BC200a1 2 | | Brain Cytoplasmic RNA 1, Bc1 Analog (Mouse)1 | | LINC000041 2 | | |
Export aliases for BCYRN1 gene to outside databasesPrevious GC identifers: GC02U990008 GC02P047415 GC02P047299 |
Summaries
for BCYRN1 gene(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 BCYRN1:
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 isdivided into three domains: a 5' portion homologous to the Alu Lm, a central adenosine-rich region, and the terminal43-nt nonrepetitive domain. It is believed that this gene was retropositionally generated and recruited into afunction regulating dendritic protein biosynthesis. At least two pseudogenes of this gene have been identified.(provided by RefSeq, Jul 2008)
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Genomic Views
for BCYRN1 gene
(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 BCYRN1 gene promoter:
STAT5B USF1 USF-1:USF-2 AP-4 STAT5A HNF-3beta N-Myc USF-1 Pax-4a ATF6
Other transcription factors
Search SABiosciences Chromatin IP Primers for BCYRN1
Epigenetics:
| | QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays 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: 2p16BCYRN1 Gene in genomic location: bands according to Ensembl, locations according to
 (and/or Entrez Gene and/or Ensembl if different)
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:
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47,571,656 bp from pter |
Size:
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13,458 bases |
Orientation:
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plus strand |
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Proteins
for BCYRN1 gene
(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,
Biochemical Assays by
EMD Millipore,
R&D Systems,
OriGene,
GenScript,
Cell Signaling Technology,
Enzo Life Sciences, and/or
Uscn,
Ontologies according to Gene
Ontology Consortium 01 Mar 2013 and
Entrez Gene,
Antibodies by
EMD Millipore,
R&D Systems,
GenScript,
Cell Signaling Technology,
OriGene,
Novus Biologicals,
Thermo Fisher Scientific,
Abcam, and/or
Uscn)
About This Section
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UniProtKB: --
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Protein
Domains /
Families
for BCYRN1 gene(According to InterPro, ProtoNet,
UniProtKB, and/or BLOCKS,
Sets of similar genes according to GeneDecks)
About This Section
| -- |
Function
for BCYRN1 gene
(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
|
Function Summary:
Genatlas biochemistry entry for BCYRN1:brain specific,200 nucleotide non-translatable RNA,component of a ribonucleoprotein complex,localized to dendrite-richneuropil areas of the retina,hippocampus,neocortex
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Pathways & Interactions
for BCYRN1 gene
(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
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Interactions:
Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for BCYRN1
|
Drugs & Compounds
for BCYRN1 gene(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
|
BCYRN1 for compounds About GeneDecksing
 Browse Tocris compounds for BCYRN1
1 Novoseek 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) |
Search CenterWatch for drugs/clinical trials and news about BCYRN1 
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Transcripts
for BCYRN1 gene(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,
RNAi Products from
EMD Millipore,
siRNAs from
OriGene,
QIAGEN,
shRNA from
OriGene,
microRNA from QIAGEN,
Tagged/untagged cDNA clones from
OriGene,
SwitchGear Genomics,
GenScript,
DNA2.0,
Vector BioLabs,
Primers from
OriGene,
SABiosciences, and/or
QIAGEN
)
About This Section
|
1 Ensembl transcript including schematic representation, and UCSC links where relevant: ENST00000418539(lincRNA)
GeneLoc Exon Structure
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Expression
for BCYRN1 gene
(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 BCYRN1:none
BCYRN1 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: --
About this image SABiosciences Custom PCR Arrays for BCYRN1
Primer
Products: |  | Browse OriGene genome-wide validated SYBR primer pairs
Browse OriGene validated miRNA SYBR primer pairs
| | | Search SABiosciences RT2 qPCR
Primer Assays in human, mouse, rat BCYRN1 | | | Search QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat BCYRN1 | | | QIAGEN QuantiFast Probe-based Assays in human, mouse, rat BCYRN1 |
Orthologs
for BCYRN1 gene
(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
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--
ENSEMBL Gene Tree for BCYRN1 (if available)
TreeFam Gene Tree for BCYRN1 (if available) |
Paralogs
for BCYRN1 gene(Paralogs according to
1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
About This Section
| -- |
Genomic Variants
for BCYRN1 gene(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
|
| Genomic Data | Transcription Related Data | Allele Frequencies | | SNP ID | Valid | Clinical
significance | Chr 2 pos | Sequence | # | AA
Chg | Type | More | # | Allele
freq | Pop | Total
sample | More |
|---|
HapMap Linkage Disequilibrium report for BCYRN1 (47558199 - 47571656 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV): 23 variations for BCYRN1
11 CNVs: 7797 33169 33168 4155 6739 96746 83584 83583 53034 96745 96752
11 Indels: 96748 83588 96749 83585 96747 74004 83586 83582 96750 96751 83587
1 Inversion: 37386 | SABiosciences Cancer Mutation PCR Assays |
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Disorders
/ Diseases
for BCYRN1 gene
(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.)
About This Section
|
BCYRN1 for disorders About GeneDecksing
OMIM gene information: 606089
OMIM disorders: --
3  diseases for BCYRN1: About MalaCardsalzheimer's disease breast cancer neuronitis
1 Novoseek 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
|
Publications
for BCYRN1 gene (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 BCYRN1 gene, integrated from 9 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 |
- BC200 RNA in invasive and preinvasive breast cancer. (PubMed id 15240511)1, 3, 9 Iacoangeli A....Tiedge H. (2004)
- Dendritic BC200 RNA in aging and in Alzheimer's disease. (PubMed id 17553964)1, 3, 9 Mus E....Tiedge H. (2007)
- 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. (1993)
- 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. (1998)
- 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. (2001)
- Primary structure, neural-specific expression, and dendritic location of human BC200 RNA. (PubMed id 7684772)1, 9 Tiedge H....Brosius J. (1993)
- Application of the BC1 RNA gene promoter for short hairpin RNA expression in cultured neuronal cells. (PubMed id 16054886)1 Kobayashi S....Anzai K. (2005)
- Expression of neural BC200 RNA in human tumours. (PubMed id 9422992)9 Chen W....Tiedge H. (1997)
- SYNCRIP, a component of dendritically localized mRNPs, binds to the translation regulator BC200 RNA. (PubMed id 18045242)9 Duning K....Kremerskothen J. (2008)
- 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. (2007)
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External Searches for BCYRN1 gene
(in PubMed,
OMIM, and NCBI Bookshelf)
About This Section
|
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Genome Databases showing BCYRN1 gene
(According to
Entrez Gene,
HGNC,
AceView,
euGenes,
Ensembl,
miRBase,
ECgene,
Kegg,
and/or
H-InvDB)
About This Section
|
|
Other Databases showing BCYRN1 gene
(According to HUGE)
About This Section
| -- |
Specialized Databases showing BCYRN1 gene(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 BCYRN1 | Pharmacogenomics, SNPs, Pathways |
|
| | |
About This Section
| 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
|
Products
for BCYRN1 gene(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Uscn, Thermo Fisher Scientific, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or
Enzo Life Sciences),
In Situ Hybridization Assays from
Advanced Cell Diagnostics
About This Section
|
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|  | QIAGEN Custom miScript Target Protector blocks miRNA-binding site of in human, mouse, rat BCYRN1 | | | Search QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing BCYRN1 | | | QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat BCYRN1 | | | QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat BCYRN1 | | | QIAGEN QuantiFast Probe-based Assays in human, mouse, rat BCYRN1 | | | Search QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat BCYRN1 |
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| | | | Search Tocris compounds for BCYRN1 |
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 | | | | |  |  |  | | | | Search ThermoFisher Antibodies for BCYRN1 |
| | | Search Vector BioLabs for ready-to-use adenovirus/AAV for human, mouse, rat BCYRN1 |
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