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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

BDNF-AS Gene

RNA gene   GIFtS: 29
GCID: GC11P027531

BDNF antisense RNA

(Previous names: BDNF opposite strand (non-protein coding), BDNF antisense...)
(Previous symbol: BDNFOS)
 Explore 3 diseases affiliated with
BDNF-AS via
MalaCards
our new
 Human Malady Compendium 
Biological research products
for BDNF-AS    

Aliases
for BDNF-AS 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 5

Aliases
BDNF Antisense RNA1 2     BT2C1
BDNF-AS11 2     BT2D1
BDNFOS1 2     BDNF Antisense RNA (Non-Protein Coding)1
NCRNA000491 2     BDNF Opposite Strand (Non-Protein Coding)1
BT2A1     ANTI-BDNF2
BT2B1     BDNF2

External Ids:    HGNC: 206081   Entrez Gene: 4972582   Ensembl: ENSG000002455737   OMIM: 6114685   
ORGUL members:    fRNAdb10:FR194521 FR176978 FR066047 FR031513      
NCBI:AY054404 AY054403 AY054391 AY054401    
NONCODE:n379542 n379589 n380349 n380314 n379316 see all 8    
RNAdb:ASO3572 ASO3898 ASO3768 ASO3541    

Export aliases for BDNF-AS gene to outside databases


Summaries
for BDNF-AS gene

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section
summary for BDNF-AS:
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 ontology for BDNF-AS:
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.

Genomic Views
for BDNF-AS 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
RefSeq DNA sequence:
NC_000011.9  NC_018922.1  NT_009237.18  
Regulatory elements:
   Search SABiosciences Regulatory transcription factor binding sites for BDNF-AS
         Other transcription factors

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

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays 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)

  • n380314
  • n380349
  • FR0031513
  • n379640
  • n340997
  • FR0066047
  • n379488
  • n379316
  • FR0194521
  • FR0176978
  • n379542
  • n379589
27528384 27624090 27719795 chr11

Proteins
for BDNF-AS 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
UniProtKB: --

Protein Domains /
Families
for BDNF-AS gene

(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section
   --

Function
for BDNF-AS 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
miRNA
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Pathways & Interactions
for BDNF-AS 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



Interactions:

    Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for BDNF-AS

Drugs & Compounds
for BDNF-AS 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
Browse Small Molecules at EMD Millipore
Browse drugs & compounds from Enzo Life Sciences

Compounds for BDNF-AS available from Tocris Bioscience    About this table
CompoundAction CAS #
BDNF (human)Activates TrkB and p75 receptors[218441-99-7]
Search CenterWatch for drugs/clinical trials and news about BDNF-AS 

Transcripts
for BDNF-AS 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,
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Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
About This Section

Unigene Cluster for BDNF-AS:

BDNF antisense RNA
Hs.675323  [show with all ESTs]
Unigene Representative Sequence: AY054403
9 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000530686(lincRNA) ENST00000532965(lincRNA) ENST00000501176(lincRNA)(uc009yiq.3 uc001mrp.3 uc009yij.3 uc009yik.3 uc009yil.3 uc009yin.3 uc009yio.3 uc009yim.3 uc009yip.3 uc001mrn.3 uc001mro.3)
ENST00000499008(lincRNA)(uc001mrm.3) ENST00000502161(lincRNA)(uc009yir.3 uc009yis.3 uc009yiu.3 uc009yix.3 uc009yiy.3 uc009yiw.3 uc009yiz.3 uc009yit.3 uc009yja.3 uc009yjb.3)
ENST00000500662(lincRNA)(uc001mrr.4 uc009yiv.3) ENST00000499568(lincRNA)(uc001mrq.4)
ENST00000530313(lincRNA) ENST00000501663(lincRNA)

miRNA
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Inhib. RNA
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Additional cDNA sequence: 

AJ011597.1 AY054391.4 AY054401.3 AY054402.3 AY054403.4 AY054404.4 AY054405.4 AY513486.3 
EF689022.1 EF689023.1 EF689024.1 EF689025.1 EF689026.1 EF689027.1 EF689028.1 EF689029.1 
EF689030.1 EF689031.1 EF689032.1 EF689033.1 EF689034.1 EF689035.1 EF689036.1 EF689037.1 
EF689038.1 EF689039.1 EF689040.1 EF689041.1 EF689042.1 NR_002832.2 NR_033312.1 NR_033313.1 
NR_033314.1 NR_033315.1 

7 DOTS entries:

DT.91658493  DT.95313710  DT.100794509  DT.100794503  DT.91720198  DT.40291086  DT.91939479 

GeneLoc Exon Structure


Expression
for BDNF-AS 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 BDNF-AS:none

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

Genevestigator expression for BDNF-AS

SOURCE GeneReport for Unigene cluster: Hs.675323
    SABiosciences Custom PCR Arrays for BDNF-AS

Primer
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In Situ
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Orthologs
for BDNF-AS 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
   --

ENSEMBL Gene Tree for BDNF-AS (if available)
TreeFam Gene Tree for BDNF-AS (if available) 

Paralogs
for BDNF-AS gene

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
About This Section
  --

Genomic Variants
for BDNF-AS 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

10/1994 NCBI SNPs in BDNF-AS are shown (see all 1994)     About this table
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance		Chr 11 posSequence#AA
Chg		TypeMore#Allele
freq		PopTotal
sample		More
----------
rs728895941,2
C,F,--27530412(+) ACTTTT/CCTGCA 5 -- int11Minor allele frequency- C:0.10EA 120
rs1118526401,2
--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--------
rs1170636011,2
--27531098(+) AGCTGG/ACCTCA 5 -- int11Minor allele frequency- A:0.01EA 120
rs1477510671,2
--27531162(+) CAGGCA/GTGAGC 5 -- int10--------
rs743333041,2
C,F,--27531177(+) ACACCC/TGGGTG 5 -- int11Minor allele frequency- T:0.02EA 120
rs749489401,2
F--27531209(+) TCATAG/AAATTT 5 -- int11Minor allele frequency- A:0.50NA 4

HapMap Linkage Disequilibrium report for BDNF-AS (27528385 - 27719721 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
      Database of Genomic Variants (DGV) variations for BDNF-AS: --

SABiosciences Cancer Mutation PCR Assays
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Disorders / Diseases
for BDNF-AS gene

(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.)
About This Section
BDNF-AS for disorders           About GeneDecksing

OMIM gene information: 611468 113505    
3 diseases for BDNF-AS:    About MalaCards
substance abuse    obesity    parkinson's disease


Export disorders for BDNF-AS gene to outside databases

Publications
for BDNF-AS 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 BDNF-AS gene integrated from 9 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 re sults in gene-specific transcriptional upregulation. (PubMed id 22446693)1, 3 Modarresi F....Wahlestedt C. (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. (2005)
  3. Genome wide association study identifies KCNMA1 contr ibuting to human obesity. (PubMed id 21708048)1 Jiao H....Dahlman I. (2011)
  4. Genome-wide association yields new sequence variants at seven loci that associate with measures of obesity. (PubMed id 19079260)1 Thorleifsson G....Stefansson K. (2009)
  5. Dissecting the human BDNF locus: Bidirectional transcription, complex splicing, and multiple promoters. (PubMed id 17629449)1 Pruunsild P.... Timmusk T. (2007)
  6. Rodent BDNF genes, novel promoters, novel splice variants, and regulation by cocaine. (PubMed id 16376315)9 Liu Q.R....Uhl G.R. (2006)
  7. (PubMed id 15608161)10 

External Searches for BDNF-AS gene

(in PubMed, OMIM, and NCBI Bookshelf)
About This Section
 ANDOR
Aliases
Free Text  
  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)

Genome Databases showing BDNF-AS gene

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
About This Section
Entrez Gene: 497258 HGNC: 20608 Ensembl:ENSG00000245573 euGenes: HUgn497258 ECgene: BDNF-AS
H-InvDB: BDNF-AS

Other Databases showing BDNF-AS gene

(According to HUGE)
About This Section
   --

Specialized Databases showing BDNF-AS 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
NameDescription
PharmGKB entry for BDNF-AS Pharmacogenomics, SNPs, Pathways

Intellectual Property
for BDNF-AS gene

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
About This Section
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



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