Human Gene BDNF (uc009yje.3) Description and Page Index
  Description: Homo sapiens brain-derived neurotrophic factor (BDNF), transcript variant 18, mRNA.
RefSeq Summary (NM_001143810): This gene encodes a member of the nerve growth factor family of proteins. Alternative splicing results in multiple transcript variants, at least one of which encodes a preproprotein that is proteolytically processed to generate the mature protein. Binding of this protein to its cognate receptor promotes neuronal survival in the adult brain. Expression of this gene is reduced in Alzheimer's, Parkinson's, and Huntington's disease patients. This gene may play a role in the regulation of the stress response and in the biology of mood disorders. [provided by RefSeq, Nov 2015].
Transcript (Including UTRs)
   Position: hg19 chr11:27,676,442-27,722,600 Size: 46,159 Total Exon Count: 3 Strand: -
Coding Region
   Position: hg19 chr11:27,679,368-27,695,831 Size: 16,464 Coding Exon Count: 2 

Page IndexSequence and LinksGenetic AssociationsMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA Descriptions
PathwaysOther NamesGeneReviewsModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr11:27,676,442-27,722,600)mRNA (may differ from genome)Protein (329 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
H-INVHGNCHPRDLynxMGIOMIM
PubMedReactomeStanford SOURCEUniProtKBWikipedia

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): BDNF
CDC HuGE Published Literature: BDNF
Positive Disease Associations: , ADHD | attention-deficit hyperactivity disorder , affective psychoses , alcoholism , Alzheimer's Disease , Alzheimer's disease; Parkinson's disease; multiple system atrophy , Amphetamine-Related Disorders , Angina, Unstable|Coronary Artery Disease , anorexia nervosa , anorexia nervosa; bulimia , BDNF serum concentrations , Bipolar disorder , body mass , Body mass index , Body Weight , brain activity , bulimia eating disorder , childhood-onset mood disorders , cognitive ability , cognitive function , cognitive function schizophrenia , depression , depression stroke , depressive disorder, major hippocampal volume , eating disorders , eating disorders mood disorders schizophrenia substance abuse , epilepsy , Epilepsy|Fragile X Syndrome , hippocampal volume , introversion and neuroticism , methamphetamine abuse; substance abuse , mood disorder , obsessive Compulsive Disorder , obsessive-compulsive disorder , Parkinson's Disease , Parkinson's disease; cognition , Parkinsons disease , personality disorders , personality traits , reasoning skills , rumination , Schizophrenia , schizophrenia weight gain , schizophrenia; psychoses , serotonin transporter availability , Smoking , smoking behavior , weight
Related Studies:

  1. Idan Shalev , et al. Psychoneuroendocrinology 2009 34(3):382-8, BDNF Val66Met polymorphism is associated with HPA axis reactivity to psychological stress characterized by genotype and gender interactions., Psychoneuroendocrinology 2009 34(3):382-8. [PubMed 18990498]
    These results indicate that a common, functionally significant polymorphism in the BDNF gene modulates HPA axis reactivity and regulation during the TSST differently in men and women.
  2. ADHD | attention-deficit hyperactivity disorder
    Robert D Oades , et al. Behavioral and brain functions 2008 4():48, The influence of serotonin- and other genes on impulsive behavioral aggression and cognitive impulsivity in children with attention-deficit/hyperactivity disorder (ADHD): Findings from a family-based association test (FBAT) analysis., Behavioral and brain functions 2008 4():48. [PubMed 18937842]
  3. affective psychoses
    Hong, C. J. et al. 2003, Association study of a brain-derived neurotrophic-factor genetic polymorphism and mood disorders, age of onset and suicidal behavior., Neuropsychobiology. 2003 ;48(4):186-9. [PubMed 14673216]
    Given the fact that the positive association between BDNF gene Val66Met polymorphism and bipolar disorder has only been demonstrated for a Caucasian population but not for a Japanese analog or our Chinese sample, it appears likely that this association is ethnicity dependent.
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: BDNF
Diseases sorted by gene-association score: bulimia nervosa, age of onset of weight loss in* (950), central hypoventilation syndrome, congenital* (767), anorexia nervosa* (606), obsessive-compulsive disorder* (335), bulimia nervosa (41), wagr syndrome* (32), bipolar disorder (28), mood disorder (26), huntington disease (24), bipolar i disorder (24), fetal alcohol spectrum disorder (23), cerebral artery occlusion (21), sydenham chorea (18), rett syndrome (16), transient global amnesia (15), psychotic disorder (14), status epilepticus (13), spinal cord injury (13), early-onset schizophrenia (13), wagro syndrome (13), eating disorder (12), postpartum depression (12), paranoid schizophrenia (12), cannabis abuse (11), relapsing-remitting multiple sclerosis (11), endogenous depression (10), temporal lobe epilepsy (10), segmental dystonia (10), anxiety disorder (10), substance abuse (10), mental depression (9), post-traumatic stress disorder (9), schizoaffective disorder (9), cervical dystonia (8), heroin dependence (8), traumatic brain injury (8), central nervous system disease (8), borderline personality disorder (8), disease of mental health (7), benign epilepsy with centrotemporal spikes (7), interstitial cystitis (7), generalized anxiety disorder (7), alcohol abuse (6), substance dependence (6), brain injury (6), dementia (6), childhood disintegrative disease (6), acute stress disorder (6), drug dependence (5), gilles de la tourette syndrome (5), toxic encephalopathy (5), neonatal hypoxic and ischemic brain injury (5), amnestic disorder (5), meningoencephalitis (5), nodular ganglioneuroblastoma (5), vertebral artery occlusion (4), tendinosis (4), pain disorder (4), attention deficit-hyperactivity disorder (4), motor neuron disease (4), sudden infant death syndrome (4), schizophrenia (3), brachial plexus lesion (3), valproate embryopathy, susceptibility to (3), alzheimer disease (3), fragile x syndrome (3), autism spectrum disorder (3), parkinson disease, late-onset (3), asthma (2), eye disease (2), multiple sclerosis, disease progression, modifier of (2), alcohol dependence (2), amyotrophic lateral sclerosis 1 (2), nervous system disease (2), autistic disorder (2), pervasive developmental disorder (1), neuroblastoma (1), autonomic nervous system neoplasm (1), peripheral nervous system neoplasm (1), specific developmental disorder (1), tetralogy of fallot (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 2.44 RPKM in Brain - Cerebellar Hemisphere
Total median expression: 23.76 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -32.30141-0.229 Picture PostScript Text
3' UTR -794.252926-0.271 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  Pfam Domains:
PF00243 - Nerve growth factor family

SCOP Domains:
57501 - Cystine-knot cytokines

ModBase Predicted Comparative 3D Structure on P23560-4
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
      
      
      
      
      

-  Descriptions from all associated GenBank mRNAs
  EF689009 - Homo sapiens brain derived neurotrophic factor variant (BDNF) mRNA, complete cds.
EF689010 - Homo sapiens brain derived neurotrophic factor variant (BDNF) mRNA, complete cds.
AY054399 - Homo sapiens brain-derived neurotrophic factor BDNF6A (BDNF) mRNA, complete cds, alternatively spliced.
AY054400 - Homo sapiens brain-derived neurotrophic factor BDNF6B (BDNF) mRNA, complete cds, alternatively spliced.
EF689017 - Homo sapiens brain derived neurotrophic factor variant (BDNF) mRNA, complete cds.
EF689018 - Homo sapiens brain derived neurotrophic factor variant (BDNF) mRNA, complete cds.
AY054398 - Homo sapiens brain-derived neurotrophic factor BDNF5 (BDNF) mRNA, complete cds, alternatively spliced.
EF689014 - Homo sapiens brain derived neurotrophic factor variant (BDNF) mRNA, complete cds.
EF689015 - Homo sapiens brain derived neurotrophic factor variant (BDNF) mRNA, complete cds.
EF689016 - Homo sapiens brain derived neurotrophic factor variant (BDNF) mRNA, complete cds.
EF689013 - Homo sapiens brain derived neurotrophic factor variant (BDNF) mRNA, complete cds.
EF689011 - Homo sapiens brain derived neurotrophic factor variant (BDNF) mRNA, complete cds.
EF689012 - Homo sapiens brain derived neurotrophic factor variant (BDNF) mRNA, complete cds.
EF689019 - Homo sapiens brain derived neurotrophic factor variant (BDNF) mRNA, complete cds.
EF689020 - Homo sapiens brain derived neurotrophic factor variant (BDNF) mRNA, complete cds.
AY054397 - Homo sapiens brain-derived neurotrophic factor BDNF4 (BDNF) mRNA, complete cds, alternatively spliced.
EF674521 - Homo sapiens brain derived neurotrophic factor transcript IV (BDNF) mRNA, complete cds, alternatively spliced.
AY054396 - Homo sapiens brain-derived neurotrophic factor BDNF3 (BDNF) mRNA, complete cds, alternatively spliced.
EF674520 - Homo sapiens brain derived neurotrophic factor transcript III (BDNF) mRNA, complete cds, alternatively spliced.
AY054393 - Homo sapiens brain-derived neurotrophic factor BDNF2A (BDNF) mRNA, complete cds, alternatively spliced.
AY054394 - Homo sapiens brain-derived neurotrophic factor BDNF2B (BDNF) mRNA, complete cds, alternatively spliced.
AY054395 - Homo sapiens brain-derived neurotrophic factor BDNF2C (BDNF) mRNA, complete cds, alternatively spliced.
EF674517 - Homo sapiens brain derived neurotrophic factor transcript IIa (BDNF) mRNA, complete cds, alternatively spliced.
EF674518 - Homo sapiens brain derived neurotrophic factor transcript IIb (BDNF) mRNA, complete cds, alternatively spliced.
EF674519 - Homo sapiens brain derived neurotrophic factor transcript IIc (BDNF) mRNA, complete cds, alternatively spliced.
AY054392 - Homo sapiens brain-derived neurotrophic factor BDNF1 (BDNF) mRNA, complete cds, alternatively spliced.
EF689021 - Homo sapiens brain derived neurotrophic factor variant (BDNF) mRNA, complete cds.
BC029795 - Homo sapiens brain-derived neurotrophic factor, mRNA (cDNA clone MGC:34632 IMAGE:5193877), complete cds.
E05934 - Base sequence of human BDNF cDNA.
X60201 - Human mRNA for brain-derived neurotrophic factor.
X91251 - H.sapiens mRNA for BDNF protein.
AY054406 - Homo sapiens brain-derived neurotrophic factor BDNF7 (BDNF) mRNA, complete cds, alternatively spliced.
M61176 - Homo sapiens brain-derived neurotrophic factor precursor (BDNF) mRNA, complete cds.
JD311341 - Sequence 292365 from Patent EP1572962.
JD214207 - Sequence 195231 from Patent EP1572962.
JD347353 - Sequence 328377 from Patent EP1572962.
AK289853 - Homo sapiens cDNA FLJ77015 complete cds, highly similar to Homo sapiens brain-derived neurotrophic factor (BDNF), transcript variant 3, mRNA.
AK289763 - Homo sapiens cDNA FLJ77010 complete cds, highly similar to Homo sapiens brain-derived neurotrophic factor (BDNF), transcript variant 4, mRNA.
AF400438 - Homo sapiens brain-derived neurotrophic factor (BDNF) mRNA, complete cds.
AY656701 - Homo sapiens brain-derived neurotrophic factor transcript variant 5 mRNA, complete cds.
DQ890811 - Synthetic construct clone IMAGE:100003441; FLH166124.01X; RZPDo839D0286D brain-derived neurotrophic factor (BDNF) gene, encodes complete protein.
KP229412 - Homo sapiens brain-derived neurotrophic factor (BDNF) mRNA, complete cds.
CU688744 - Synthetic construct Homo sapiens gateway clone IMAGE:100018605 5' read BDNF mRNA.
KJ896492 - Synthetic construct Homo sapiens clone ccsbBroadEn_05886 BDNF gene, encodes complete protein.
KR710721 - Synthetic construct Homo sapiens clone CCSBHm_00016104 BDNF (BDNF) mRNA, encodes complete protein.
DQ893966 - Synthetic construct Homo sapiens clone IMAGE:100008426; FLH166120.01L; RZPDo839D0285D brain-derived neurotrophic factor (BDNF) gene, encodes complete protein.
AB464470 - Synthetic construct DNA, clone: pF1KB9810, Homo sapiens BDNF gene for brain-derived neurotrophic factor, without stop codon, in Flexi system.
KU177943 - Homo sapiens brain-derived neurotrophic factor isoform 1 (BDNF) mRNA, partial cds.
KU177944 - Homo sapiens brain-derived neurotrophic factor isoform 2 (BDNF) mRNA, partial cds, alternatively spliced.
KU177945 - Homo sapiens brain-derived neurotrophic factor isoform 3 (BDNF) mRNA, partial cds, alternatively spliced.
KC855559 - Homo sapiens isolate EUN-5-9-12 brain-derived neurotrophic factor mRNA, partial cds.
AB038674 - Homo sapiens BDNF 4I-5 mRNA for brain-derived neurotrophic factor, partial cds.
AB038673 - Homo sapiens BDNF 4-5 mRNA for brain-derived neurotrophic factor, partial cds.
AB038672 - Homo sapiens BDNF 3-5 mRNA for brain-derived neurotrophic factor, partial cds.
AB038670 - Homo sapiens BDNF 1-5 mRNA for brain-derived neurotrophic factor, partial cds.
DQ250642 - Homo sapiens brain-derived neurotrophic factor preproprotein isoform 2 (BDNF) mRNA, partial cds.
AB038671 - Homo sapiens BDNF 2-5 mRNA for brain-derived neurotrophic factor, partial cds.
AY442188 - Homo sapiens brain-derived neurotrophic factor isoform 1 (BDNF) mRNA, partial cds, alternatively spliced.
JD221517 - Sequence 202541 from Patent EP1572962.
E05935 - Base sequence of human BDNF gene.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04010 - MAPK signaling pathway
hsa04722 - Neurotrophin signaling pathway
hsa05016 - Huntington's disease

Reactome (by CSHL, EBI, and GO)

Protein P23560 (Reactome details) participates in the following event(s):

R-HSA-9024906 BDNF binds NTRK2 (TRKB)
R-NUL-9025041 BDNF binds Ntrk2
R-HSA-9024967 BDNF-bound NTRK2 dimerizes
R-NUL-9025035 BDNF-bound Ntrk2 dimerizes
R-HSA-9026464 BDNF-bound NTRK2 dimers trans-autophosphorylate
R-HSA-9032502 Activated NTRK2 binds FYN
R-HSA-9032841 Activated NTRK2 binds CDK5
R-NUL-9030372 BDNF-bound Ntrk2 dimers trans-autophosphorylate
R-NUL-9032399 Activated Ntrk2 binds FRS3
R-NUL-9032516 Activated Ntrk2 binds Fyn
R-NUL-9032908 Activated Ntrk2 binds Cdk5
R-HSA-9033276 NTRK2 binds TIAM1
R-HSA-9032863 CDK5 phosphorylates NTRK2
R-NUL-9032961 Cdk5 phosphorylates Ntrk2
R-NUL-9033304 Ntrk2 binds Tiam1
R-HSA-9032854 NTRK2 phosphorylates CDK5
R-HSA-9026493 p-Y516 of p-5Y-NTRK2 recruits SHC1
R-HSA-9026531 p-Y817 of p-5Y-NTRK2 recruits PLCG1
R-HSA-9028730 Activated NTRK2 binds FRS2
R-HSA-9032402 Activated NTRK2 binds FRS3
R-NUL-9032361 Ntrk2-phosphorylated Frs2 binds Ptpn11
R-NUL-9032423 Ntrk2 phosphorylates FRS3
R-NUL-9030433 BDNF- or NTF4-activated Ntrk2 recruits Plcg1
R-NUL-9030473 BDNF- or NTF4-activated Ntrk2 binds Shc1
R-HSA-9026890 NTRK2 phosphorylates SHC1
R-HSA-9026579 NTRK2 phosphorylates PLCG1
R-HSA-9028328 SHC1 bound to activated NTRK2 recruits GRB2:SOS1
R-HSA-9028728 NTRK2 phosphorylates FRS2
R-HSA-9031981 NTRK2-phosphorylated FRS2 binds PTPN11
R-HSA-9032426 NTRK2 phosphorylates FRS3
R-HSA-9033292 NTRK2 and CDK5 promote activation of RAC1 by TIAM1
R-NUL-9033341 Ntrk2 and Cdk5 promote activation of Rac1 by Tiam1
R-NUL-9030450 BDNF- or NTF4-activated Ntrk2 phosphorylates Plcg1
R-NUL-9031971 Ntrk2 phosphorylates Frs2
R-HSA-9026891 NTRK2 activates RAS signaling through SHC1
R-HSA-9024909 BDNF activates NTRK2 (TRKB) signaling
R-HSA-9006115 Signaling by NTRK2 (TRKB)
R-HSA-9032500 Activated NTRK2 signals through FYN
R-HSA-9032845 Activated NTRK2 signals through CDK5
R-HSA-166520 Signaling by NTRKs
R-HSA-9032759 NTRK2 activates RAC1
R-HSA-9026519 Activated NTRK2 signals through RAS
R-HSA-9026527 Activated NTRK2 signals through PLCG1
R-HSA-9028335 Activated NTRK2 signals through PI3K
R-HSA-9028731 Activated NTRK2 signals through FRS2 and FRS3
R-HSA-9006934 Signaling by Receptor Tyrosine Kinases
R-HSA-162582 Signal Transduction

-  Other Names for This Gene
  Alternate Gene Symbols: NM_001143810, NP_733931, P23560-4
UCSC ID: uc009yje.3
RefSeq Accession: NM_001143810
Protein: P23560-4, splice isoform of P23560 CCDS: CCDS44558.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene BDNF:
hirschsprung-ov (Hirschsprung Disease Overview)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001143810.1
exon count: 3CDS single in 3' UTR: no RNA size: 4057
ORF size: 990CDS single in intron: no Alignment % ID: 99.95
txCdsPredict score: 1783.00frame shift in genome: no % Coverage: 99.95
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.