Atlas of Genetics and Cytogenetics in Oncology and Haematology

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BDNF (brain derived neurotrophic factor)

Identity

Other aliasANON2
BULN2
HGNC (Hugo) BDNF
LocusID (NCBI) 627
Atlas_Id 46287
Location 11p14.1  [Link to chromosome band 11p14]
Location_base_pair Starts at 27654895 and ends at 27659649 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2017)		Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
GPBP1 (5q11.2) / BDNF (11p14.1)SOCS7 (17q12) / BDNF (11p14.1)GPBP1 5q11.2 / BDNF 11p14.1

Note

Non-annotated gene. Preliminary data : if you are an author
who wish to write a full paper/card on this gene, go to  How to contribute

DNA/RNA

 

Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 2 ]
  t(5;11)(q11;p14) GPBP1/BDNF
t(11;17)(p14;q23) CLTC/BDNF

External links

Nomenclature
HGNC (Hugo)BDNF   1033
Cards
Entrez_Gene (NCBI)BDNF  627  brain derived neurotrophic factor
AliasesANON2; BULN2
GeneCards (Weizmann)BDNF
Ensembl hg19 (Hinxton)ENSG00000176697 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000176697 [Gene_View]  ENSG00000176697 [Sequence]  chr11:27654895-27659649 [Contig_View]  BDNF [Vega]
ICGC DataPortalENSG00000176697
TCGA cBioPortalBDNF
AceView (NCBI)BDNF
Genatlas (Paris)BDNF
WikiGenes627
SOURCE (Princeton)BDNF
Genetics Home Reference (NIH)BDNF
Genomic and cartography
GoldenPath hg38 (UCSC)BDNF  -     chr11:27654895-27659649 -  11p14.1   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)BDNF  -     11p14.1   [Description]    (hg19-Feb_2009)
GoldenPathBDNF - 11p14.1 [CytoView hg19]  BDNF - 11p14.1 [CytoView hg38]
ImmunoBaseENSG00000176697
Mapping of homologs : NCBIBDNF [Mapview hg19]  BDNF [Mapview hg38]
OMIM113505   
Gene and transcription
Genbank (Entrez)AB038670 AB038671 AB038672 AB038673 AB038674
RefSeq transcript (Entrez)NM_001143805 NM_001143806 NM_001143807 NM_001143808 NM_001143809 NM_001143810 NM_001143811 NM_001143812 NM_001143813 NM_001143814 NM_001143815 NM_001143816 NM_001709 NM_170731 NM_170732 NM_170733 NM_170734 NM_170735
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)BDNF
Alternative Splicing GalleryENSG00000176697
Gene ExpressionBDNF [ NCBI-GEO ]   BDNF [ EBI - ARRAY_EXPRESS ]   BDNF [ SEEK ]   BDNF [ MEM ]
Gene Expression Viewer (FireBrowse)BDNF [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)627
GTEX Portal (Tissue expression)BDNF
Human Protein AtlasENSG00000176697-BDNF [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtP23560   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP23560  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP23560
Splice isoforms : SwissVarP23560
PhosPhoSitePlusP23560
Domaine pattern : Prosite (Expaxy)NGF_1 (PS00248)    NGF_2 (PS50270)   
Domains : Interpro (EBI)Brain-der_neurotrophic_factor    Cystine-knot_cytokine    Nerve_growth_factor-like    Nerve_growth_factor-rel    Nerve_growth_factor_CS   
Domain families : Pfam (Sanger)NGF (PF00243)   
Domain families : Pfam (NCBI)pfam00243   
Domain families : Smart (EMBL)NGF (SM00140)  
Conserved Domain (NCBI)BDNF
DMDM Disease mutations627
Blocks (Seattle)BDNF
PDB (RSDB)1B8M    1BND   
PDB Europe1B8M    1BND   
PDB (PDBSum)1B8M    1BND   
PDB (IMB)1B8M    1BND   
Structural Biology KnowledgeBase1B8M    1BND   
SCOP (Structural Classification of Proteins)1B8M    1BND   
CATH (Classification of proteins structures)1B8M    1BND   
SuperfamilyP23560
Human Protein Atlas [tissue]ENSG00000176697-BDNF [tissue]
Peptide AtlasP23560
HPRD00214
IPIIPI00012058   IPI00336003   IPI00855724   IPI00917851   IPI00377232   IPI00979471   IPI00977029   
Protein Interaction databases
DIP (DOE-UCLA)P23560
IntAct (EBI)P23560
FunCoupENSG00000176697
BioGRIDBDNF
STRING (EMBL)BDNF
ZODIACBDNF
Ontologies - Pathways
QuickGOP23560
Ontology : AmiGOprotein binding  extracellular region  extracellular space  cytoplasm  mitochondrion  transmembrane receptor protein tyrosine kinase signaling pathway  activation of phospholipase C activity  nervous system development  axon guidance  synapse assembly  peripheral nervous system development  memory  synaptic vesicle  growth factor activity  negative regulation of myotube differentiation  positive regulation of neuron projection development  nuclear speck  nerve development  axon  dendrite  cytoplasmic vesicle  brain-derived neurotrophic factor receptor signaling pathway  positive regulation of brain-derived neurotrophic factor receptor signaling pathway  nerve growth factor signaling pathway  negative regulation of neuron apoptotic process  regulation of neuron differentiation  neurotrophin TRK receptor signaling pathway  perinuclear region of cytoplasm  collateral sprouting  positive regulation of collateral sprouting  neuron projection morphogenesis  modulation of chemical synaptic transmission  positive regulation of synapse assembly  positive regulation of receptor binding  positive regulation of non-membrane spanning protein tyrosine kinase activity  regulation of protein localization to cell surface  negative regulation of apoptotic signaling pathway  
Ontology : EGO-EBIprotein binding  extracellular region  extracellular space  cytoplasm  mitochondrion  transmembrane receptor protein tyrosine kinase signaling pathway  activation of phospholipase C activity  nervous system development  axon guidance  synapse assembly  peripheral nervous system development  memory  synaptic vesicle  growth factor activity  negative regulation of myotube differentiation  positive regulation of neuron projection development  nuclear speck  nerve development  axon  dendrite  cytoplasmic vesicle  brain-derived neurotrophic factor receptor signaling pathway  positive regulation of brain-derived neurotrophic factor receptor signaling pathway  nerve growth factor signaling pathway  negative regulation of neuron apoptotic process  regulation of neuron differentiation  neurotrophin TRK receptor signaling pathway  perinuclear region of cytoplasm  collateral sprouting  positive regulation of collateral sprouting  neuron projection morphogenesis  modulation of chemical synaptic transmission  positive regulation of synapse assembly  positive regulation of receptor binding  positive regulation of non-membrane spanning protein tyrosine kinase activity  regulation of protein localization to cell surface  negative regulation of apoptotic signaling pathway  
Pathways : KEGGMAPK signaling pathway    Neurotrophin signaling pathway    Huntington's disease    Cocaine addiction    Alcoholism   
NDEx NetworkBDNF
Atlas of Cancer Signalling NetworkBDNF
Wikipedia pathwaysBDNF
Orthology - Evolution
OrthoDB627
GeneTree (enSembl)ENSG00000176697
Phylogenetic Trees/Animal Genes : TreeFamBDNF
HOGENOMP23560
Homologs : HomoloGeneBDNF
Homology/Alignments : Family Browser (UCSC)BDNF
Gene fusions - Rearrangements
Fusion : MitelmanGPBP1/BDNF [5q11.2/11p14.1]  [t(5;11)(q11;p14)]  
Fusion PortalGPBP1 5q11.2 BDNF 11p14.1 LUAD
Fusion : QuiverBDNF
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerBDNF [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)BDNF
dbVarBDNF
ClinVarBDNF
1000_GenomesBDNF 
Exome Variant ServerBDNF
ExAC (Exome Aggregation Consortium)ENSG00000176697
GNOMAD BrowserENSG00000176697
Varsome BrowserBDNF
Genetic variants : HAPMAP627
Genomic Variants (DGV)BDNF [DGVbeta]
DECIPHERBDNF [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisBDNF 
Mutations
ICGC Data PortalBDNF 
TCGA Data PortalBDNF 
Broad Tumor PortalBDNF
OASIS PortalBDNF [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICBDNF  [overview]  [genome browser]  [tissue]  [distribution]  
Somatic Mutations in Cancer : COSMIC3DBDNF
Mutations and Diseases : HGMDBDNF
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch BDNF
DgiDB (Drug Gene Interaction Database)BDNF
DoCM (Curated mutations)BDNF (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)BDNF (select a term)
intoGenBDNF
Cancer3DBDNF(select the gene name)
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM113505   
Orphanet230   
DisGeNETBDNF
MedgenBDNF
Genetic Testing Registry BDNF
NextProtP23560 [Medical]
TSGene627
GENETestsBDNF
Target ValidationBDNF
Huge Navigator BDNF [HugePedia]
snp3D : Map Gene to Disease627
BioCentury BCIQBDNF
ClinGenBDNF
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD627
Chemical/Pharm GKB GenePA31891
Clinical trialBDNF
Miscellaneous
canSAR (ICR)BDNF (select the gene name)
HarmonizomeBDNF
DataMed IndexBDNF
Probes
Litterature
PubMed499 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineBDNF
EVEXBDNF
GoPubMedBDNF
iHOPBDNF
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

Search in all EBI   NCBI

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indexed on : Sun May 10 12:08:08 CEST 2020
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