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    Bdnf brain-derived neurotrophic factor [ Rattus norvegicus (Norway rat) ]

    Gene ID: 24225, updated on 14-Jan-2025

    Summary

    Official Symbol
    Bdnfprovided by RGD
    Official Full Name
    brain-derived neurotrophic factorprovided by RGD
    Primary source
    RGD:2202
    See related
    EnsemblRapid:ENSRNOG00000047466 AllianceGenome:RGD:2202
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Enables neurotrophin TRKB receptor binding activity. Involved in several processes, including behavioral response to cocaine; cellular response to norepinephrine stimulus; and regulation of neuronal synaptic plasticity. Acts upstream of or within positive regulation of DNA-binding transcription factor activity; positive regulation of glucocorticoid receptor signaling pathway; and positive regulation of peptidyl-serine phosphorylation. Located in several cellular components, including mitochondrial crista; perikaryon; and secretory vesicle. Used to study several diseases, including alcohol dependence; cystitis; eye disease (multiple); neuropathy (multiple); and status epilepticus. Biomarker of several diseases, including alcohol dependence; alcohol use disorder; amphetamine abuse; anxiety disorder (multiple); and attention deficit hyperactivity disorder. Human ortholog(s) of this gene implicated in several diseases, including cocaine dependence; cognitive disorder (multiple); congenital central hypoventilation syndrome; neurodegenerative disease (multiple); and obstructive sleep apnea. Orthologous to human BDNF (brain derived neurotrophic factor). [provided by Alliance of Genome Resources, Jan 2025]
    Expression
    Biased expression in Heart (RPKM 34.1), Lung (RPKM 27.0) and 3 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See Bdnf in Genome Data Viewer
    Location:
    3q34
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 3 NC_086021.1 (116619633..116670212)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 3 NC_051338.1 (96165042..96215621)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 3 NC_005102.4 (100768637..100819216)

    Chromosome 3 - NC_086021.1Genomic Context describing neighboring genes Neighboring gene transfer RNA alanine (anticodon GGC) 3 Neighboring gene adenosylhomocysteinase, pseudogene 7 Neighboring gene lin-7 homolog C, crumbs cell polarity complex component Neighboring gene leucine-rich repeat-containing G protein-coupled receptor 4

    Genomic regions, transcripts, and products

    Expression

    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Clone Names

    • MGC105254

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables growth factor activity  
    enables growth factor activity  
    enables growth factor activity PubMed 
    enables nerve growth factor receptor binding  
    enables neurotrophin TRKB receptor binding PubMed 
    Items 1 - 25 of 98
    Process Evidence Code Pubs
    acts_upstream_of_or_within axon extension  
    acts_upstream_of_or_within axon guidance  
    acts_upstream_of_or_within axon target recognition  
    acts_upstream_of_or_within behavioral fear response  
    involved_in behavioral response to cocaine PubMed 
    involved_in cell surface receptor protein tyrosine kinase signaling pathway  
    involved_in cellular response to nerve growth factor stimulus PubMed 
    involved_in cellular response to norepinephrine stimulus PubMed 
    involved_in cellular response to potassium ion PubMed 
    involved_in cellular response to tumor necrosis factor PubMed 
    involved_in chronic inflammatory response PubMed 
    involved_in circadian rhythm  
    involved_in cognition PubMed 
    involved_in collateral sprouting  
    involved_in collateral sprouting  
    involved_in conditioned place preference PubMed 
    acts_upstream_of_or_within dendrite development  
    acts_upstream_of_or_within dendrite extension  
    involved_in excitatory postsynaptic potential PubMed 
    acts_upstream_of_or_within fear response  
    acts_upstream_of_or_within feeding behavior  
    acts_upstream_of_or_within gamma-aminobutyric acid signaling pathway  
    acts_upstream_of_or_within glutamate secretion  
    acts_upstream_of_or_within inhibitory postsynaptic potential  
    acts_upstream_of_or_within inner ear development  
    involved_in learning PubMed 
    acts_upstream_of_or_within learning or memory  
    acts_upstream_of_or_within mechanoreceptor differentiation  
    involved_in mitochondrial electron transport, NADH to ubiquinone PubMed 
    involved_in modulation of chemical synaptic transmission  
    acts_upstream_of_or_within negative regulation of apoptotic process  
    involved_in negative regulation of apoptotic signaling pathway  
    involved_in negative regulation of myotube differentiation PubMed 
    acts_upstream_of_or_within negative regulation of neuroblast proliferation  
    involved_in negative regulation of neuron apoptotic process  
    acts_upstream_of_or_within negative regulation of neuron apoptotic process  
    acts_upstream_of_or_within negative regulation of programmed cell death  
    involved_in negative regulation of striated muscle tissue development PubMed 
    acts_upstream_of_or_within negative regulation of synaptic transmission, GABAergic  
    involved_in nerve development  
    acts_upstream_of_or_within nerve development  
    involved_in nerve growth factor signaling pathway  
    involved_in nervous system development PubMed 
    acts_upstream_of neuron apoptotic process  
    involved_in neuron differentiation PubMed 
    involved_in neuron projection extension PubMed 
    involved_in neuron projection morphogenesis  
    acts_upstream_of_or_within neuron recognition  
    acts_upstream_of peptidyl-serine phosphorylation  
    acts_upstream_of_or_within positive regulation of DNA-binding transcription factor activity PubMed 
    NOT acts_upstream_of_or_within positive regulation of axon extension  
    involved_in positive regulation of axon regeneration PubMed 
    involved_in positive regulation of collateral sprouting  
    acts_upstream_of_or_within positive regulation of collateral sprouting  
    involved_in positive regulation of collateral sprouting  
    acts_upstream_of_or_within positive regulation of glucocorticoid receptor signaling pathway PubMed 
    involved_in positive regulation of long-term neuronal synaptic plasticity PubMed 
    involved_in positive regulation of neuron apoptotic process PubMed 
    acts_upstream_of_or_within positive regulation of neuron differentiation  
    involved_in positive regulation of neuron projection development  
    acts_upstream_of_or_within positive regulation of peptidyl-serine phosphorylation PubMed 
    acts_upstream_of_or_within positive regulation of peptidyl-serine phosphorylation  
    involved_in positive regulation of synapse assembly  
    involved_in positive regulation of synapse assembly  
    involved_in regeneration PubMed 
    involved_in regulation of axon extension PubMed 
    acts_upstream_of_or_within regulation of collateral sprouting  
    involved_in regulation of long-term neuronal synaptic plasticity PubMed 
    acts_upstream_of_or_within regulation of neuron apoptotic process  
    acts_upstream_of_or_within regulation of retinal cell programmed cell death  
    involved_in regulation of short-term neuronal synaptic plasticity PubMed 
    acts_upstream_of_or_within regulation of synaptic plasticity  
    involved_in response to L-glutamate PubMed 
    involved_in response to activity PubMed 
    involved_in response to anesthetic PubMed 
    involved_in response to auditory stimulus PubMed 
    involved_in response to electrical stimulus PubMed 
    involved_in response to ethanol PubMed 
    involved_in response to food PubMed 
    involved_in response to hormone PubMed 
    involved_in response to hyperoxia PubMed 
    involved_in response to hypoxia PubMed 
    involved_in response to light intensity PubMed 
    involved_in response to light stimulus PubMed 
    involved_in response to morphine PubMed 
    involved_in response to nerve growth factor PubMed 
    involved_in response to nutrient levels PubMed 
    involved_in response to potassium ion PubMed 
    involved_in response to tumor necrosis factor PubMed 
    involved_in response to vitamin A PubMed 
    involved_in response to xenobiotic stimulus PubMed 
    acts_upstream_of_or_within response to xenobiotic stimulus  
    involved_in signal transduction  
    involved_in synapse assembly  
    involved_in synapse assembly  
    acts_upstream_of_or_within taste bud development  
    involved_in trans-synaptic signaling by BDNF, modulating synaptic transmission  
    acts_upstream_of_or_within ureteric bud development  
    Items 1 - 25 of 98
    Items 1 - 20 of 27
    Component Evidence Code Pubs
    is_active_in axon  
    located_in axon PubMed 
    located_in axon  
    located_in cytoplasm  
    located_in cytoplasm  
    located_in cytoplasmic vesicle  
    is_active_in dendrite  
    located_in dendrite PubMed 
    located_in dendrite  
    located_in extracellular region  
    located_in extracellular region  
    is_active_in extracellular space  
    located_in extracellular space PubMed 
    is_active_in glutamatergic synapse  
    is_active_in hippocampal mossy fiber to CA3 synapse  
    located_in mitochondrial crista PubMed 
    located_in neuronal cell body PubMed 
    is_active_in neuronal dense core vesicle  
    located_in perikaryon PubMed 
    located_in perinuclear region of cytoplasm  
    located_in perinuclear region of cytoplasm  
    located_in postsynapse  
    located_in secretory granule PubMed 
    located_in secretory granule  
    is_active_in synaptic vesicle  
    located_in synaptic vesicle PubMed 
    located_in terminal bouton PubMed 
    Items 1 - 20 of 27

    General protein information

    Preferred Names
    neurotrophic factor BDNF precursor form; brain-derived neurotrophic factor
    Names
    brain derived neurothrophic factor
    proBDNF

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001270630.1NP_001257559.1  neurotrophic factor BDNF precursor form isoform 1

      See identical proteins and their annotated locations for NP_001257559.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1, also known as VI) encodes the longest isoform (1).
      Source sequence(s)
      CN544668, EF125680
      UniProtKB/TrEMBL
      A0A0H2UI28, A6HP02
      Related
      ENSRNOP00000064356.2, ENSRNOT00000073636.4
      Conserved Domains (1) summary
      smart00140
      Location:248355
      NGF; Nerve growth factor (NGF or beta-NGF)
    2. NM_001270631.1NP_001257560.1  neurotrophic factor BDNF precursor form isoform 3 preproprotein

      See identical proteins and their annotated locations for NP_001257560.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3, also known as IIC) has an alternate 5' exon and uses a downstream start codon, compared to variant 1. The resulting isoform (3) has a shorter N-terminus, compared to isoform 1. Variants 3-10 encode the same isoform 3.
      Source sequence(s)
      CN544668, EF125678
      UniProtKB/Swiss-Prot
      P23363, Q53YL8
      UniProtKB/TrEMBL
      A6HP04
      Related
      ENSRNOP00000072849.1, ENSRNOT00000077703.3
      Conserved Domains (1) summary
      smart00140
      Location:135242
      NGF; Nerve growth factor (NGF or beta-NGF)
    3. NM_001270632.1NP_001257561.1  neurotrophic factor BDNF precursor form isoform 3 preproprotein

      See identical proteins and their annotated locations for NP_001257561.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4, also known as IIB) has an alternate 5' exon and uses a downstream start codon, compared to variant 1. The resulting isoform (3) has a shorter N-terminus, compared to isoform 1. Variants 3-10 encode the same isoform 3.
      Source sequence(s)
      CN544668, EF125677
      UniProtKB/Swiss-Prot
      P23363, Q53YL8
      UniProtKB/TrEMBL
      A6HP04
      Conserved Domains (1) summary
      smart00140
      Location:135242
      NGF; Nerve growth factor (NGF or beta-NGF)
    4. NM_001270633.1NP_001257562.1  neurotrophic factor BDNF precursor form isoform 3 preproprotein

      See identical proteins and their annotated locations for NP_001257562.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5, also known as IV) has an alternate 5' exon and uses a downstream start codon, compared to variant 1. The resulting isoform (3) has a shorter N-terminus, compared to isoform 1. Variants 3-10 encode the same isoform 3.
      Source sequence(s)
      CN544668, EF125679
      UniProtKB/Swiss-Prot
      P23363, Q53YL8
      UniProtKB/TrEMBL
      A6HP04
      Related
      ENSRNOP00000073265.1, ENSRNOT00000080190.3
      Conserved Domains (1) summary
      smart00140
      Location:135242
      NGF; Nerve growth factor (NGF or beta-NGF)
    5. NM_001270634.1NP_001257563.1  neurotrophic factor BDNF precursor form isoform 3 preproprotein

      See identical proteins and their annotated locations for NP_001257563.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (6, also known as 6B) has an alternate 5' exon and an additional exon in the 5' region, and uses a downstream start codon, compared to variant 1. The resulting isoform (3) has a shorter N-terminus, compared to isoform 1. Variants 3-10 encode the same isoform 3.
      Source sequence(s)
      AY559250, CN544668, EF125689
      UniProtKB/Swiss-Prot
      P23363, Q53YL8
      UniProtKB/TrEMBL
      A6HP04
      Conserved Domains (1) summary
      smart00140
      Location:135242
      NGF; Nerve growth factor (NGF or beta-NGF)
    6. NM_001270635.1NP_001257564.1  neurotrophic factor BDNF precursor form isoform 3 preproprotein

      See identical proteins and their annotated locations for NP_001257564.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (7, also known as III) has an alternate 5' exon and uses a downstream start codon, compared to variant 1. The resulting isoform (3) has a shorter N-terminus, compared to isoform 1. Variants 3-10 encode the same isoform 3.
      Source sequence(s)
      CN544668, EF125686
      UniProtKB/Swiss-Prot
      P23363, Q53YL8
      UniProtKB/TrEMBL
      A6HP04
      Related
      ENSRNOP00000075479.1, ENSRNOT00000089233.3
      Conserved Domains (1) summary
      smart00140
      Location:135242
      NGF; Nerve growth factor (NGF or beta-NGF)
    7. NM_001270636.1NP_001257565.1  neurotrophic factor BDNF precursor form isoform 3 preproprotein

      See identical proteins and their annotated locations for NP_001257565.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (8, also known as VII or 6A) has an alternate 5' exon and uses a downstream start codon, compared to variant 1. The resulting isoform (3) has a shorter N-terminus, compared to isoform 1. Variants 3-10 encode the same isoform 3.
      Source sequence(s)
      CN544668, EF125688
      UniProtKB/Swiss-Prot
      P23363, Q53YL8
      UniProtKB/TrEMBL
      A6HP04
      Conserved Domains (1) summary
      smart00140
      Location:135242
      NGF; Nerve growth factor (NGF or beta-NGF)
    8. NM_001270637.1NP_001257566.1  neurotrophic factor BDNF precursor form isoform 3 preproprotein

      See identical proteins and their annotated locations for NP_001257566.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (9, also known as IIA) has an alternate 5' exon and uses a downstream start codon, compared to variant 1. The resulting isoform (3) has a shorter N-terminus, compared to isoform 1. Variants 3-10 encode the same isoform 3.
      Source sequence(s)
      CN544668, EF125676
      UniProtKB/Swiss-Prot
      P23363, Q53YL8
      UniProtKB/TrEMBL
      A6HP04
      Conserved Domains (1) summary
      smart00140
      Location:135242
      NGF; Nerve growth factor (NGF or beta-NGF)
    9. NM_001270638.1NP_001257567.1  neurotrophic factor BDNF precursor form isoform 3 preproprotein

      See identical proteins and their annotated locations for NP_001257567.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (10, also known as V) has an alternate 5' exon and uses a downstream start codon, compared to variant 1. The resulting isoform (3) has a shorter N-terminus, compared to isoform 1. Variants 3-10 encode the same isoform 3.
      Source sequence(s)
      CN544668, EF125687
      UniProtKB/Swiss-Prot
      P23363, Q53YL8
      UniProtKB/TrEMBL
      A6HP04
      Related
      ENSRNOP00000072315.1, ENSRNOT00000078543.3
      Conserved Domains (1) summary
      smart00140
      Location:135242
      NGF; Nerve growth factor (NGF or beta-NGF)
    10. NM_012513.4NP_036645.2  neurotrophic factor BDNF precursor form isoform 2 preproprotein

      See identical proteins and their annotated locations for NP_036645.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2, also known as I) has an alternate 5' exon, compared to variant 1. The resulting isoform (2) is shorter and has a distinct N-terminus, compared to isoform 1.
      Source sequence(s)
      CN544668, EF125675
      UniProtKB/TrEMBL
      A0A0G2K624, A6HP01
      Related
      ENSRNOP00000073647.1, ENSRNOT00000083542.3
      Conserved Domains (1) summary
      smart00140
      Location:143250
      NGF; Nerve growth factor (NGF or beta-NGF)

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCr8

    Genomic

    1. NC_086021.1 Reference GRCr8

      Range
      116619633..116670212
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006234684.5XP_006234746.1  brain-derived neurotrophic factor isoform X1

      Related
      ENSRNOP00000104100.1, ENSRNOT00000122945.1
      Conserved Domains (1) summary
      smart00140
      Location:162269
      NGF; Nerve growth factor (NGF or beta-NGF)
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