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

Gene ID: 24225, updated on 15-Jul-2018
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; Myomorpha; 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]
Expression
Biased expression in Heart (RPKM 34.1), Lung (RPKM 27.0) and 3 other tissues See more
Orthologs
See Bdnf in Genome Data Viewer
Location:
3q34
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

  • 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

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 IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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
aging IEP
Inferred from Expression Pattern
more info
PubMed 
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
 
cell-cell signaling IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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
 
locomotion IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
mechanoreceptor differentiation ISO
Inferred from Sequence Orthology
more info
 
memory IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
mitochondrial electron transport, NADH to ubiquinone IMP
Inferred from Mutant Phenotype
more info
PubMed 
modulation of chemical synaptic transmission IBA
Inferred from Biological aspect of Ancestor
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 myotube differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
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
PubMed 
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 IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nerve development ISO
Inferred from Sequence Orthology
more info
 
nerve growth factor signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 projection morphogenesis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
neuron recognition ISO
Inferred from Sequence Orthology
more info
 
peripheral nervous system development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of DNA-binding transcription factor activity IDA
Inferred from Direct Assay
more info
PubMed 
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 receptor binding IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of receptor binding IEA
Inferred from Electronic Annotation
more info
 
positive regulation of receptor binding ISO
Inferred from Sequence Orthology
more info
 
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 neuron differentiation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 signaling receptor activity IEA
Inferred from Electronic Annotation
more info
 
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 
retrograde trans-synaptic signaling by neuropeptide, modulating synaptic transmission ISO
Inferred from Sequence Orthology
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
PubMed 
ureteric bud development ISO
Inferred from Sequence Orthology
more info
 
Component Evidence Code Pubs
axon IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 vesicle IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytoplasmic vesicle ISO
Inferred from Sequence Orthology
more info
 
dendrite IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
dendrite IDA
Inferred from Direct Assay
more info
PubMed 
dendrite ISO
Inferred from Sequence Orthology
more info
 
extracellular region IEA
Inferred from Electronic Annotation
more info
 
extracellular region TAS
Traceable Author Statement
more info
 
extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
extracellular space IDA
Inferred from Direct Assay
more info
PubMed 
mitochondrial crista IDA
Inferred from Direct Assay
more info
PubMed 
mitochondrion IEA
Inferred from Electronic Annotation
more info
 
mitochondrion ISO
Inferred from Sequence Orthology
more info
 
neuronal cell body IDA
Inferred from Direct Assay
more info
PubMed 
nuclear speck IEA
Inferred from Electronic Annotation
more info
 
nuclear speck ISO
Inferred from Sequence Orthology
more info
 
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 IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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

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
    ENSRNOP00000064356.2, ENSRNOT00000073636.2
    Conserved Domains (1) summary
    smart00140
    Location:248355
    NGF; Nerve growth factor (NGF or beta-NGF)
  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
    ENSRNOP00000072849.1, ENSRNOT00000077703.1
    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
    ENSRNOP00000073265.1, ENSRNOT00000080190.1
    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
    ENSRNOP00000073685.1, ENSRNOT00000090445.1
    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
    ENSRNOP00000075479.1, ENSRNOT00000089233.1
    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
    ENSRNOP00000074338.1, ENSRNOT00000083289.1
    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
    ENSRNOP00000072315.1, ENSRNOT00000078543.1
    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
    ENSRNOP00000073647.1, ENSRNOT00000083542.1
    Conserved Domains (1) summary
    smart00140
    Location:143250
    NGF; Nerve growth factor (NGF or beta-NGF)

RefSeqs of Annotated Genomes: Rattus norvegicus Annotation Release 106 details...Open this link in a new tab

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  brain-derived neurotrophic factor isoform X1

    Conserved Domains (1) summary
    smart00140
    Location:162269
    NGF; Nerve growth factor (NGF or beta-NGF)

Alternate Rn_Celera

Genomic

  1. AC_000071.1 Alternate Rn_Celera

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