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

    Gene ID: 24225, updated on 22-Aug-2016
    Official Symbol
    Bdnfprovided by RGD
    Official Full Name
    brain-derived neurotrophic factorprovided by RGD
    Primary source
    RGD:2202
    See related
    Ensembl:ENSRNOG00000047466
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Sciurognathi; Muroidea; Muridae; Murinae; Rattus
    Summary
    plays a role in the development of hippocampal long term potentiation; involved in regulation of synaptic plasticity [RGD, Feb 2006]
    Orthologs
    Location:
    3q33
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    106 current Rnor_6.0 (GCF_000001895.5) 3 NC_005102.4 (100768637..100819216)
    104 previous assembly Rnor_5.0 (GCF_000001895.4) 3 NC_005102.3 (107371329..107421908)

    Chromosome 3 - NC_005102.4Genomic Context describing neighboring genes Neighboring gene similar to Adenosylhomocysteinase (S-adenosyl-L-homocysteine hydrolase) (AdoHcyase) (Liver copper-binding protein) (CUBP) Neighboring gene glyceraldehyde-3-phosphate dehydrogenase-like Neighboring gene lin-7 homolog C, crumbs cell polarity complex component Neighboring gene leucine-rich repeat-containing G protein-coupled receptor 4

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Markers

    Homology

    Clone Names

    • MGC105254

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    growth factor activity IEA
    Inferred from Electronic Annotation
    more info
     
    growth factor activity TAS
    Traceable Author Statement
    more info
    PubMed 
    neurotrophin TRKB receptor binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Process Evidence Code Pubs
    Ras protein signal transduction TAS
    Traceable Author Statement
    more info
     
    activation of MAPKK activity TAS
    Traceable Author Statement
    more info
     
    activation of phospholipase C activity TAS
    Traceable Author Statement
    more info
     
    axon extension ISO
    Inferred from Sequence Orthology
    more info
     
    axon guidance ISO
    Inferred from Sequence Orthology
    more info
     
    axon target recognition ISO
    Inferred from Sequence Orthology
    more info
     
    behavioral fear response ISO
    Inferred from Sequence Orthology
    more info
     
    cellular response to nerve growth factor stimulus IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    cellular response to norepinephrine stimulus IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    cellular response to tumor necrosis factor IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    chronic inflammatory response IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    circadian rhythm ISO
    Inferred from Sequence Orthology
    more info
     
    cognition IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    collateral sprouting IEA
    Inferred from Electronic Annotation
    more info
     
    collateral sprouting ISO
    Inferred from Sequence Orthology
    more info
     
    dendrite development ISO
    Inferred from Sequence Orthology
    more info
     
    dendrite extension ISO
    Inferred from Sequence Orthology
    more info
     
    excitatory postsynaptic potential IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    fear response ISO
    Inferred from Sequence Orthology
    more info
     
    feeding behavior ISO
    Inferred from Sequence Orthology
    more info
     
    gamma-aminobutyric acid signaling pathway ISO
    Inferred from Sequence Orthology
    more info
     
    glutamate secretion ISO
    Inferred from Sequence Orthology
    more info
     
    inhibitory postsynaptic potential ISO
    Inferred from Sequence Orthology
    more info
     
    inner ear development ISO
    Inferred from Sequence Orthology
    more info
     
    learning IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    learning or memory ISO
    Inferred from Sequence Orthology
    more info
     
    mechanoreceptor differentiation ISO
    Inferred from Sequence Orthology
    more info
     
    mitochondrial electron transport, NADH to ubiquinone IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    negative regulation of apoptotic process ISO
    Inferred from Sequence Orthology
    more info
     
    negative regulation of cell death ISO
    Inferred from Sequence Orthology
    more info
     
    negative regulation of neuroblast proliferation ISO
    Inferred from Sequence Orthology
    more info
     
    negative regulation of neuron apoptotic process IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    negative regulation of neuron apoptotic process ISO
    Inferred from Sequence Orthology
    more info
     
    negative regulation of neuron death IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    negative regulation of striated muscle tissue development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    negative regulation of synaptic transmission, GABAergic ISO
    Inferred from Sequence Orthology
    more info
     
    nerve development ISO
    Inferred from Sequence Orthology
    more info
     
    nervous system development IDA
    Inferred from Direct Assay
    more info
    PubMed 
    neuron differentiation TAS
    Traceable Author Statement
    more info
    PubMed 
    neuron projection extension IDA
    Inferred from Direct Assay
    more info
    PubMed 
    neuron recognition ISO
    Inferred from Sequence Orthology
    more info
     
    neurotrophin TRK receptor signaling pathway TAS
    Traceable Author Statement
    more info
     
    positive regulation of apoptotic process TAS
    Traceable Author Statement
    more info
     
    NOT positive regulation of axon extension ISO
    Inferred from Sequence Orthology
    more info
     
    positive regulation of collateral sprouting IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of collateral sprouting ISO
    Inferred from Sequence Orthology
    more info
     
    positive regulation of glucocorticoid receptor signaling pathway IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of long-term neuronal synaptic plasticity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of neuron differentiation ISO
    Inferred from Sequence Orthology
    more info
     
    positive regulation of peptidyl-serine phosphorylation IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    positive regulation of peptidyl-serine phosphorylation ISO
    Inferred from Sequence Orthology
    more info
     
    positive regulation of sequence-specific DNA binding transcription factor activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of synapse assembly IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of synapse assembly ISO
    Inferred from Sequence Orthology
    more info
     
    regeneration IDA
    Inferred from Direct Assay
    more info
    PubMed 
    regulation of axon extension IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    regulation of collateral sprouting ISO
    Inferred from Sequence Orthology
    more info
     
    regulation of long-term neuronal synaptic plasticity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    regulation of metabolic process ISO
    Inferred from Sequence Orthology
    more info
     
    regulation of neuron apoptotic process ISO
    Inferred from Sequence Orthology
    more info
     
    regulation of retinal cell programmed cell death ISO
    Inferred from Sequence Orthology
    more info
     
    regulation of short-term neuronal synaptic plasticity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    regulation of synaptic plasticity ISO
    Inferred from Sequence Orthology
    more info
     
    response to L-glutamate IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    response to activity IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    response to anesthetic IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    response to auditory stimulus IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    response to drug IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    response to drug ISO
    Inferred from Sequence Orthology
    more info
     
    response to electrical stimulus IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    response to food IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    response to hormone IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    response to hyperoxia IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    response to hypoxia IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    response to light intensity IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    response to light stimulus IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    response to nerve growth factor IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    response to nutrient levels IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    response to potassium ion IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    response to tumor necrosis factor IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    response to vitamin A IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    small GTPase mediated signal transduction TAS
    Traceable Author Statement
    more info
     
    synapse assembly IEA
    Inferred from Electronic Annotation
    more info
     
    synapse assembly ISO
    Inferred from Sequence Orthology
    more info
     
    taste bud development ISO
    Inferred from Sequence Orthology
    more info
     
    transmembrane receptor protein tyrosine kinase signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    ureteric bud development ISO
    Inferred from Sequence Orthology
    more info
     
    Component Evidence Code Pubs
    axon IDA
    Inferred from Direct Assay
    more info
    PubMed 
    axon ISO
    Inferred from Sequence Orthology
    more info
     
    cytoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    cytoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    cytoplasmic, membrane-bounded vesicle ISO
    Inferred from Sequence Orthology
    more info
     
    dendrite IDA
    Inferred from Direct Assay
    more info
    PubMed 
    dendrite ISO
    Inferred from Sequence Orthology
    more info
     
    extracellular region TAS
    Traceable Author Statement
    more info
     
    extracellular space IDA
    Inferred from Direct Assay
    more info
    PubMed 
    mitochondrial crista IDA
    Inferred from Direct Assay
    more info
    PubMed 
    neuronal cell body IDA
    Inferred from Direct Assay
    more info
    PubMed 
    perikaryon IDA
    Inferred from Direct Assay
    more info
    PubMed 
    perinuclear region of cytoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    perinuclear region of cytoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    postsynapse IEA
    Inferred from Electronic Annotation
    more info
     
    secretory granule ISO
    Inferred from Sequence Orthology
    more info
     
    synaptic vesicle IDA
    Inferred from Direct Assay
    more info
    PubMed 
    terminal bouton IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Preferred Names
    brain-derived neurotrophic factor
    Names
    brain derived neurothrophic factor
    brain derived neurotrophic factor

    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  brain-derived neurotrophic factor 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/Swiss-Prot
      P23363
      UniProtKB/TrEMBL
      A0A0H2UI28
      Related
      ENSRNOP00000064356, ENSRNOT00000073636
      Conserved Domains (1) summary
      pfam00243
      Location:245362
      NGF; Nerve growth factor family
    2. NM_001270631.1NP_001257560.1  brain-derived neurotrophic factor 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
      Related
      ENSRNOP00000072849, ENSRNOT00000077703
      Conserved Domains (1) summary
      smart00140
      Location:135242
      NGF; Nerve growth factor (NGF or beta-NGF)
    3. NM_001270632.1NP_001257561.1  brain-derived neurotrophic factor 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
      Conserved Domains (1) summary
      smart00140
      Location:135242
      NGF; Nerve growth factor (NGF or beta-NGF)
    4. NM_001270633.1NP_001257562.1  brain-derived neurotrophic factor 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
      Related
      ENSRNOP00000073265, ENSRNOT00000080190
      Conserved Domains (1) summary
      smart00140
      Location:135242
      NGF; Nerve growth factor (NGF or beta-NGF)
    5. NM_001270634.1NP_001257563.1  brain-derived neurotrophic factor 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
      Related
      ENSRNOP00000073685, ENSRNOT00000090445
      Conserved Domains (1) summary
      smart00140
      Location:135242
      NGF; Nerve growth factor (NGF or beta-NGF)
    6. NM_001270635.1NP_001257564.1  brain-derived neurotrophic factor 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
      Related
      ENSRNOP00000075479, ENSRNOT00000089233
      Conserved Domains (1) summary
      smart00140
      Location:135242
      NGF; Nerve growth factor (NGF or beta-NGF)
    7. NM_001270636.1NP_001257565.1  brain-derived neurotrophic factor 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
      Related
      ENSRNOP00000074338, ENSRNOT00000083289
      Conserved Domains (1) summary
      smart00140
      Location:135242
      NGF; Nerve growth factor (NGF or beta-NGF)
    8. NM_001270637.1NP_001257566.1  brain-derived neurotrophic factor 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
      Conserved Domains (1) summary
      smart00140
      Location:135242
      NGF; Nerve growth factor (NGF or beta-NGF)
    9. NM_001270638.1NP_001257567.1  brain-derived neurotrophic factor 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
      Related
      ENSRNOP00000072315, ENSRNOT00000078543
      Conserved Domains (1) summary
      smart00140
      Location:135242
      NGF; Nerve growth factor (NGF or beta-NGF)
    10. NM_012513.4NP_036645.2  brain-derived neurotrophic factor 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/Swiss-Prot
      P23363
      UniProtKB/TrEMBL
      A0A0G2K624
      Related
      ENSRNOP00000073647, ENSRNOT00000083542
      Conserved Domains (1) summary
      pfam00243
      Location:140257
      NGF; Nerve growth factor family

    RefSeqs of Annotated Genomes: Rattus norvegicus Annotation Release 106 details...

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

    Reference Rnor_6.0 Primary Assembly

    Genomic

    1. NC_005102.4 Reference Rnor_6.0 Primary Assembly

      Range
      100768637..100819216
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006234684.3XP_006234746.1  

      Conserved Domains (1) summary
      pfam00243
      Location:159276
      NGF; Nerve growth factor family

    Alternate Rn_Celera

    Genomic

    1. AC_000071.1 Alternate Rn_Celera

      Range
      95191318..95241949
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)