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BDNF-AS Gene

RNA gene   GIFtS: 22
GCID: GC11P027531

BDNF Antisense RNA

(Previous names: BDNF opposite strand (non-protein coding), BDNF antisense...)
(Previous symbol: BDNFOS)
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(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 5.4

Aliases
BDNF Antisense RNA1 2     Non-Protein Coding RNA 491
BDNFOS1 2     ANTI-BDNF2
BDNF Antisense RNA (Non-Protein Coding)1     BDNF2
BDNF Antisense RNA 1 (Non-Protein Coding)1     BDNF-AS12
BDNF Opposite Strand (Non-Protein Coding)1     NCRNA000492

External Ids:    HGNC: 206081   Entrez Gene: 4972582   Ensembl: ENSG000002455737   OMIM: 6114685   
ORGUL members:    fRNAdb10:FR194521 FR256372 FR066047 FR031513 FR189117      
NCBI13:AY054404 AY054391 AY054401 AY054403    
NONCODE14:n380314 n379488 n340997 n380349 n380309 see all 11    
RNAdb15:ASO3572 EVF31936 ASO3768 ASO3541 RNZ6557 see all 14    

Export aliases for BDNF-AS gene to outside databases


(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 BDNF-AS Gene:
BDNF-AS (BDNF antisense RNA) is an RNA gene, and is affiliated with the lncRNA class. Diseases associated with BDNF-AS include substance abuse, and neuronitis.

summary for BDNF-AS Gene:
Trk (neurotrophin) receptors are single transmembrane catalytic receptors with intracellular tyrosine kinase
activity. Trk receptors are coupled to the Ras, Cdc42/Rac/RhoG, MAPK, PI 3-K and PLCgamma signaling
pathways. There are four members of the Trk family; TrkA, TrkB and TrkC and a related p75NTR receptor.
p75NTR lacks tyrosine kinase activity and signals via NF-kappaB activation. Each family member binds
different neurotrophins with varying affinities. TrkA potently binds nerve growth factor (NGF) and is
involved in differentiation and survival of neurons and in control of gene expression of enzymes involved in
neurotransmitter synthesis. TrkB has highest affinity for brain-derived neurotrophic factor (BDNF) and is
involved in neuronal plasticity, longterm potentiation and apoptosis of CNS neurons. TrkC is activated by
neurotrophin-3 (NT-3) and is found on proprioceptive sensory neurons. p75NTR binds neurotrophin precursors
with high affinity and retains low affinity to the mature cleaved forms. TrkA was originally identified as
an oncogene as it is commonly mutated in cancers, particularly colon and thyroid carcinomas.



fRNAdb sequence ontologies for BDNF-AS - the ORGUL cluster for this gene includes several descriptions:
antisense_RNA - Antisense RNA is RNA that is transcribed from the coding, rather than the template, strand of DNA. It is therefore complementary to mRNA.
nc_conserved_region - Non-coding region of sequence similarity by descent from a common ancestor.

View fRNAdb secondary structures for BDNF-AS

(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:
   Search for regulatory transcription factor binding sites for BDNF-AS
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 4): BDNF-AS promoter sequence
   Search Chromatin IP Primers for BDNF-AS

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat BDNF-AS


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

Entrez Gene cytogenetic band: 11p14.1   Ensembl cytogenetic band:  11p14.1   HGNC cytogenetic band: 11p14.1

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

GeneLoc information about chromosome 11         GeneLoc Exon Structure

GeneLoc location for GC11P027531:  view genomic region     (about GC identifiers)

Start:
27,528,385 bp from pter      End:
27,719,721 bp from pter
Size:
191,337 bases      Orientation:
plus strand
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for BDNF-AS

(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, and/or Cloud-Clone Corp.)
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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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Animal Models:
   inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for BDNF-AS
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Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for BDNF-AS


(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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Selected Downloadable PowerPoint Slides of GeneGlobe Pathway Central Maps for BDNF-AS (see all 60)
    Nuclear Receptor Activation by Vitamin-A
Paxillin Interactions
Telomerase Components in Cell Signaling
Mitochondrial Apoptosis
Molecular Mechanisms of Cancer


    Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for BDNF-AS
Interactions:

    Search GeneGlobe Interaction Network for BDNF-AS

(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 Small Molecules at EMD Millipore
   Browse drugs & compounds from Enzo Life Sciences
  Browse compounds at ApexBio 

Compounds for BDNF-AS available from Tocris Bioscience    About this table
CompoundAction CAS #
BDNF (human)Activates TrkB and p75 receptors[218441-99-7]
ANA 12TrkB receptor antagonist[219766-25-3]
GNF 5837 Potent Trk inhibitor; inhibits TrkA, TrkB and TrkC [1033769-28-6]
TLQP 21VGF-derived peptide[869988-94-3]
7,8-Dihydroxyflavone TrkB agonist[38183-03-8]



(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,
Conferences by KenesGroup, 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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5/9 fRNAdb Secondary structures (see all 9):


9 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000530686(antisense) ENST00000532965(antisense) ENST00000501176(antisense) ENST00000499008(antisense) ENST00000502161(antisense)
ENST00000500662(antisense) ENST00000499568(antisense) ENST00000530313(antisense) ENST00000501663(antisense)

miRNA
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SwitchGear 3'UTR luciferase reporter plasmidBDNF-AS 3' UTR sequence
Inhib. RNA
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GenScript Custom all cDNA clones Services for BDNF-AS
DNA2.0 Custom Codon Optimized Gene Synthesis Service for BDNF-AS
Search Vector BioLabs for ready-to-use adenovirus/AAV for human, mouse, rat BDNF-AS
Primer
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Search Pre-validated RT2 qPCR Primer Assays in human, mouse, rat BDNF-AS
  Search QuantiTect SYBR Green Assays in human, mouse, rat BDNF-AS
  QuantiFast Probe-based Assays in human, mouse, rat BDNF-AS

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 BDNF-AS:none

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

BDNF-AS Protein expression data from MOPED1, PaxDb2 and MaxQB3 --
    Custom PCR Arrays for BDNF-AS
Primer
Products:
OriGene qSTAR qPCR primer pairs in human, mouse for BDNF-AS
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Search QuantiTect SYBR Green Assays in human, mouse, rat BDNF-AS
QuantiFast Probe-based Assays in human, mouse, rat BDNF-AS
In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for BDNF-AS

(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 BDNF-AS (if available)
TreeFam Gene Tree for BDNF-AS (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 BDNF-AS (see all 2052)    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 11 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs358338111,2
C--27460863(+) GTCTC-/AAAAAA 5 -- int10--------
rs679242151,2
C--27462128(+) AGTCT-/ATGGATT 5 -- int12Minor allele frequency- AT:0.25NA 4
rs728895941,2
C,F--27530412(+) ACTTTT/CCTGCA 5 -- int11Minor allele frequency- C:0.10EA 120
rs1118526401,2
C,F--27530626(+) AAACAG/ATTTTG 5 -- int11Minor allele frequency- A:0.00CSA 1
rs676269181,2
C--27530811(-) AAAAA-/AGTCCA 5 -- int12Minor allele frequency- A:0.00NA CSA 4
rs742337401,2
C--27530811(+) TGGACC/TTTTTT 5 -- int10--------
rs1824949271,2
--27530932(+) GGCTGC/GAATGC 5 -- int10--------
rs1429575871,2
--27530997(+) CATGCA/GTCAGC 5 -- int10--------
rs2013298171,2
C--27531037(+) GCCACC/TGCACC 5 -- int10--------
rs1170636011,2
F--27531098(+) AGCTGG/ACCTCA 5 -- int11Minor allele frequency- A:0.01EA 120

HapMap Linkage Disequilibrium report for BDNF-AS (27528385 - 27719721 bp)

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

(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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OMIM gene information: 611468OMIM information: 113505    
5 diseases for BDNF-AS:    About MalaCards
substance abuse    neuronitis    thyroiditis    parkinson's disease
obesity


BDNF-AS for disorders           About GeneDecksing


Congresses - knowledge worth sharing:
Alzheimer's & Parkinson's Diseases Congress (ADPD) 18 - 22 March 2015

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

  1. Inhibition of natural antisense transcripts in vivo results in gene-specific transcriptional upregulation. (PubMed id 22446693)1, 3 Modarresi F....Wahlestedt C. (Nat. Biotechnol. 2012)
  2. Human brain derived neurotrophic factor (BDNF) genes, splicing patterns, and assessments of associations with substance abuse and Parkinson's Disease. (PubMed id 15666411)1, 3 Liu Q.-R.... Uhl G.R. (Am. J. Med. Genet. B Neuropsychiatr. Genet. 2005)
  3. Genome wide association study identifies KCNMA1 contributing to human obesity. (PubMed id 21708048)1 Jiao H....Dahlman I. (BMC Med Genomics 2011)
  4. Genome-wide meta-analyses identify multiple loci associated with smoking behavior. (PubMed id 20418890)1 (Nat. Genet. 2010)
  5. Genome-wide association yields new sequence variants at seven loci that associate with measures of obesity. (PubMed id 19079260)1 Thorleifsson G....Stefansson K. (Nat. Genet. 2009)
  6. Dissecting the human BDNF locus: bidirectional transcription, complex splicing, and multiple promoters. (PubMed id 17629449)1 Pruunsild P.... Timmusk T. (Genomics 2007)
  7. Rodent BDNF genes, novel promoters, novel splice variants, and regulation by cocaine. (PubMed id 16376315)9 Liu Q.R....Uhl G.R. (Brain Res. 2006)
  8. (PubMed id 15608161)10 
  9. (PubMed id 16628248)10 
  10. (PubMed id 16273071)10 

(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: 497258 HGNC: 20608 Ensembl:ENSG00000245573 euGenes: HUgn497258 ECgene: BDNF-AS
H-InvDB: BDNF-AS

(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 BDNF-AS 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 BDNF-AS gene:
Search GeneIP for patents involving BDNF-AS

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
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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