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Rattus norvegicus brain-derived neurotrophic factor (Bdnf), transcript variant 4, mRNA

NCBI Reference Sequence: NM_001270632.1

FASTA Graphics 

LOCUS       NM_001270632            4086 bp    mRNA    linear   ROD 08-DEC-2024
DEFINITION  Rattus norvegicus brain-derived neurotrophic factor (Bdnf),
            transcript variant 4, mRNA.
ACCESSION   NM_001270632
VERSION     NM_001270632.1
KEYWORDS    RefSeq.
SOURCE      Rattus norvegicus (Norway rat)
  ORGANISM  Rattus norvegicus
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
            Muroidea; Muridae; Murinae; Rattus.
REFERENCE   1  (bases 1 to 4086)
  AUTHORS   Balanya-Segura,M., Polishchuk,A., Just-Borras,L., Cilleros-Mane,V.,
            Silvera,C., Ardevol,A., Tomas,M., Lanuza,M.A., Hurtado,E. and
            Tomas,J.
  TITLE     Molecular Adaptations of BDNF/NT-4 Neurotrophic and Muscarinic
            Pathways in Ageing Neuromuscular Synapses
  JOURNAL   Int J Mol Sci 25 (15), 8018 (2024)
   PUBMED   39125587
  REMARK    GeneRIF: Molecular Adaptations of BDNF/NT-4 Neurotrophic and
            Muscarinic Pathways in Ageing Neuromuscular Synapses.
            Publication Status: Online-Only
REFERENCE   2  (bases 1 to 4086)
  AUTHORS   Harada,H., Mori,M., Murata,Y., Kohno,Y., Terada,K., Ohe,K. and
            Enjoji,M.
  TITLE     Divergent effects of chronic continuous and intermittent social
            defeat stress on emotional behaviors: Impact on phosphorylated CREB
            and BDNF protein levels in the rat hippocampus
  JOURNAL   Neurosci Lett 835, 137851 (2024)
   PUBMED   38838971
  REMARK    GeneRIF: Divergent effects of chronic continuous and intermittent
            social defeat stress on emotional behaviors: Impact on
            phosphorylated CREB and BDNF protein levels in the rat hippocampus.
REFERENCE   3  (bases 1 to 4086)
  AUTHORS   Hamze,M., Brier,C., Buhler,E., Zhang,J., Medina,I. and Porcher,C.
  TITLE     Regulation of Neuronal Chloride Homeostasis by Pro- and Mature
            Brain-Derived Neurotrophic Factor (BDNF) via KCC2 Cation-Chloride
            Cotransporters in Rat Cortical Neurons
  JOURNAL   Int J Mol Sci 25 (11), 6253 (2024)
   PUBMED   38892438
  REMARK    GeneRIF: Regulation of Neuronal Chloride Homeostasis by Pro- and
            Mature Brain-Derived Neurotrophic Factor (BDNF) via KCC2
            Cation-Chloride Cotransporters in Rat Cortical Neurons.
            Publication Status: Online-Only
REFERENCE   4  (bases 1 to 4086)
  AUTHORS   Avarlaid,A., Falkenberg,K., Lehe,K., Mudo,G., Belluardo,N., Di
            Liberto,V., Frinchi,M., Tuvikene,J. and Timmusk,T.
  TITLE     An upstream enhancer and MEF2 transcription factors fine-tune the
            regulation of the Bdnf gene in cortical and hippocampal neurons
  JOURNAL   J Biol Chem 300 (6), 107411 (2024)
   PUBMED   38796067
  REMARK    GeneRIF: An upstream enhancer and MEF2 transcription factors
            fine-tune the regulation of the Bdnf gene in cortical and
            hippocampal neurons.
REFERENCE   5  (bases 1 to 4086)
  AUTHORS   Campbell,T.S., Donoghue,K. and Roth,T.L.
  TITLE     Unlocking the epigenome: Stress and exercise induced Bdnf
            regulation in the prefrontal cortex
  JOURNAL   Neurotoxicol Teratol 103, 107353 (2024)
   PUBMED   38648864
  REMARK    GeneRIF: Unlocking the epigenome: Stress and exercise induced Bdnf
            regulation in the prefrontal cortex.
REFERENCE   6  (bases 1 to 4086)
  AUTHORS   Ernfors,P., Van De Water,T., Loring,J. and Jaenisch,R.
  TITLE     Complementary roles of BDNF and NT-3 in vestibular and auditory
            development
  JOURNAL   Neuron 14 (6), 1153-1164 (1995)
   PUBMED   7605630
  REMARK    Erratum:[Neuron 1995 Sep;15(3):739]
REFERENCE   7  (bases 1 to 4086)
  AUTHORS   Ohara,O., Gahara,Y., Teraoka,H. and Kitamura,T.
  TITLE     A rat brain-derived neurotrophic factor-encoding gene generates
            multiple transcripts through alternative use of 5' exons and
            polyadenylation sites
  JOURNAL   Gene 121 (2), 383-386 (1992)
   PUBMED   1446835
REFERENCE   8  (bases 1 to 4086)
  AUTHORS   Maisonpierre,P.C., Le Beau,M.M., Espinosa,R. 3rd, Ip,N.Y.,
            Belluscio,L., de la Monte,S.M., Squinto,S., Furth,M.E. and
            Yancopoulos,G.D.
  TITLE     Human and rat brain-derived neurotrophic factor and neurotrophin-3:
            gene structures, distributions, and chromosomal localizations
  JOURNAL   Genomics 10 (3), 558-568 (1991)
   PUBMED   1889806
REFERENCE   9  (bases 1 to 4086)
  AUTHORS   Hallbook,F., Ibanez,C.F. and Persson,H.
  TITLE     Evolutionary studies of the nerve growth factor family reveal a
            novel member abundantly expressed in Xenopus ovary
  JOURNAL   Neuron 6 (5), 845-858 (1991)
   PUBMED   2025430
REFERENCE   10 (bases 1 to 4086)
  AUTHORS   Yancopoulos,G.D., Maisonpierre,P.C., Ip,N.Y., Aldrich,T.H.,
            Belluscio,L., Boulton,T.G., Cobb,M.H., Squinto,S.P. and Furth,M.E.
  TITLE     Neurotrophic factors, their receptors, and the signal transduction
            pathways they activate
  JOURNAL   Cold Spring Harb Symp Quant Biol 55, 371-379 (1990)
   PUBMED   1966766
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            EF125677.1 and CN544668.1.
            
            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.
            
            Publication Note:  This RefSeq record includes a subset of the
            publications that are available for this gene. Please see the Gene
            record to access additional publications.
            
            ##Evidence-Data-START##
            Transcript exon combination :: EF125677.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN12840113, SAMN12840116
                                           [ECO:0000348]
            ##Evidence-Data-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-162               EF125677.1         1-162
            163-4029            EF125677.1         164-4030
            4030-4086           CN544668.1         1-57                c
FEATURES             Location/Qualifiers
     source          1..4086
                     /organism="Rattus norvegicus"
                     /mol_type="mRNA"
                     /strain="Sprague-Dawley"
                     /db_xref="taxon:10116"
                     /chromosome="3"
                     /map="3q34"
     gene            1..4086
                     /gene="Bdnf"
                     /note="brain-derived neurotrophic factor"
                     /db_xref="GeneID:24225"
                     /db_xref="RGD:2202"
     exon            1..416
                     /gene="Bdnf"
                     /inference="alignment:Splign:2.1.0"
     misc_feature    396..398
                     /gene="Bdnf"
                     /note="upstream in-frame stop codon"
     exon            417..4074
                     /gene="Bdnf"
                     /inference="alignment:Splign:2.1.0"
     CDS             438..1187
                     /gene="Bdnf"
                     /note="isoform 3 preproprotein is encoded by transcript
                     variant 4; brain derived neurothrophic factor; proBDNF;
                     neurotrophic factor BDNF precursor form"
                     /codon_start=1
                     /product="neurotrophic factor BDNF precursor form isoform
                     3 preproprotein"
                     /protein_id="NP_001257561.1"
                     /db_xref="GeneID:24225"
                     /db_xref="RGD:2202"
                     /translation="MTILFLTMVISYFGCMKAAPMKEANVHGQGNLAYPAVRTHGTLE
                     SVNGPRAGSRGLTTTSLADTFEHVIEELLDEDQKVRPNEENHKDADLYTSRVMLSSQV
                     PLEPPLLFLLEEYKNYLDAANMSMRVRRHSDPARRGELSVCDSISEWVTAADKKTAVD
                     MSGGTVTVLEKVPVSKGQLKQYFYETKCNPMGYTKEGCRGIDKRHWNSQCRTTQSYVR
                     ALTMDSKKRIGWRFIRIDTSCVCTLTIKRGR"
     sig_peptide     438..491
                     /gene="Bdnf"
                     /inference="COORDINATES: ab initio prediction:SignalP:6.0"
     mat_peptide     492..1184
                     /gene="Bdnf"
                     /product="Neurotrophic factor BDNF precursor form.
                     /id=PRO_0000447540"
                     /note="propagated from UniProtKB/Swiss-Prot (P23363.1)"
     misc_feature    612..617
                     /gene="Bdnf"
                     /note="Cleavage, by MBTPS1.
                     /evidence=ECO:0000250|UniProtKB:P23560; propagated from
                     UniProtKB/Swiss-Prot (P23363.1); cleavage site"
     misc_feature    804..806
                     /gene="Bdnf"
                     /note="N-linked (GlcNAc...) asparagine.
                     /evidence=ECO:0000255; propagated from
                     UniProtKB/Swiss-Prot (P23363.1); glycosylation site"
ORIGIN      
        1 gctttggcaa agccatccgc acgtgacaaa acgtaaggaa gtggaagaaa ccgtctagag
       61 caatatcaag taccacttaa ttagagaata tttttttaac cttttcctcc tgctgcgccg
      121 ggtgtgtgat ccgggcgagc agagtccatt cagcaccttg gacagagcca gcggatttgt
      181 ccgaggtggt agtacttcat ccaggtattc ttttcctcgc tgtcaagcca acccggtgtc
      241 gcccttaaaa agcgtctttt ccgaggttcg gctcacactg agatcggggc tggagagaga
      301 gtcagatttt ggagcggagc gtttggagag ccagccccag tttggtcccc tcattgagct
      361 cgctgaagtt ggcttcctag cggtgtaggc tggaatagac tcttggcaag ctccggttcc
      421 accaggtgag aagagtgatg accatccttt tccttactat ggttatttca tacttcggtt
      481 gcatgaaggc tgcgcccatg aaagaagcaa acgtccacgg acaaggcaac ttggcctacc
      541 cagctgtgcg gacccatggg actctggaga gcgtgaatgg gcccagggca ggttcgagag
      601 gtctgacgac gacgtccctg gctgacactt ttgagcacgt gatcgaagag ctgctggatg
      661 aggaccagaa ggttcggccc aacgaagaaa accataagga cgcggacttg tacacttccc
      721 gggtgatgct cagcagtcaa gtgcctttgg agcctcctct gctctttctg ctggaggaat
      781 acaaaaatta cctggatgcc gcaaacatgt ctatgagggt tcggcgccac tccgaccccg
      841 cccgccgtgg ggagctgagc gtgtgtgaca gtattagcga gtgggtcaca gcggcagata
      901 aaaagactgc agtggacatg tccggtggga cggtcacagt cctggagaaa gtcccggtat
      961 caaaaggcca actgaagcaa tatttctacg agaccaagtg taatcccatg ggttacacga
     1021 aggaaggctg caggggcata gacaaaaggc actggaactc gcaatgccga actacccaat
     1081 cgtatgttcg ggcccttact atggatagca aaaagagaat tggctggcgg ttcataagga
     1141 tagacacttc ctgtgtatgt acactgacca ttaaaagggg aagatagtgg atttatgttg
     1201 tatagattat attgagacaa aaattatcta tttgtatata tacataacag ggtaaattat
     1261 tcagttaaga aaaagataat tttatgaact gcatgtataa atgaagttta tacagtacag
     1321 tggttctaca atctatttat tggacatatc catgaccaga aagaaacagt catttgcgca
     1381 caactttaaa agtctgcatt acattcctcg ataatgttgt ggtttgttgc cgttgccaag
     1441 aattgaaaac aaaaagttaa aaaaaataat aaattgcatg ctgctttaat tgtgaattga
     1501 taataaactg tccctctttc agaaaacaga caaaaaaaca aaaaacaaaa aaaagcaaaa
     1561 acaaaaattt gaaccaaaac attccgttta cattttagac actaagtatc ttcgttcttg
     1621 ttagtactct gttctactgc tttcaacttc tcatagcgtt ggaattaaaa ctatgtcaag
     1681 gtgctgttgt cattgcttta ctggcttagg ggatggggaa cgggaggggt agatttctgt
     1741 ttgttttgtg ttttatttcg tttgtttgtt tgttttgttt ttttagttcc acccggagta
     1801 gggatggaga aaatttcttc actctccatt ctggttgata aagcgttaca tttgtatgtt
     1861 gtaaaaaatg tttgcaaaat ccaatcagat gactggaaaa cgaataaaaa ttaaggcaac
     1921 tgaataaaat gctcacacaa cactgcccat gatgtatctc cctggtcccc caggtcactc
     1981 ttctggcatg ggtcagggaa agctgctttt attggaaaga ccagcatttg tttaaagcac
     2041 attctttccc tccctcctcc cattttggtc cctttctttt ttgttttgtt ttaagaaaga
     2101 aaattaagtt gcgcgctttg aaatatttta tcactgctgt gaacagatga acaatgtgtg
     2161 tcatttcatg acactcgtgg aaaacagtga tttttttttt attttttgcc ctaaggagaa
     2221 acaagtaaga ataaccgaaa atgttctttt tttttaaagg cataaacagt ggataagtta
     2281 taatatggcc taacaatgtt tgcagataaa agatattgca tacagccaga tactagagca
     2341 gggatccaca ctgccactga aatgcgactg aatggccctg tggaggctaa gtggagctga
     2401 catactattt cctggcagag caggaggaat ttctgagtgg ccatcctgag gtctagatgg
     2461 aggtggggaa tggtacttga gacattccta aaggaaggct cggaagcacc cttcagagca
     2521 ggctctggaa tgatgtgtca agtttcttag gccttctgct ttaagtgcct acgttaccta
     2581 acagtgctca agaggttctc aattggagaa ccacactcaa atccatttat ggcctccatc
     2641 ccattttaaa taattatgga taaagttgga ttaacctgga gcagctttgg atccaaatat
     2701 ggcatagcag tgatgctatc agtgcagcat gatgggaaat gtttgctgtg aagagactta
     2761 actttctttg cgcttagact tcaggaagcc taggttttat ttatttattt ttttgagaca
     2821 ttttggtgaa aggaaaaaag aaagaagaaa acaaacaaac aaaaccagaa aaagcaccaa
     2881 aacttaggca gaatgagcaa tgtctgtctg taagggctag aatgacaagg cataggaagg
     2941 tgctttcact gtgaaagaga caagaacaca ggaggaaata ctgcttaagt gaagagcaca
     3001 gaaagctcct gatagttctg tccattcagc acaagggtcc cttctacact ttacctcttg
     3061 gggttaggag aagtcaagct ggaagcctga atgaatggcc ccaatgagaa ctagtgttaa
     3121 gcccatttcc ctagtgaggt tttccgccag cgcgaatgtg ttagtggtta cctgactggg
     3181 ctcctgggca tcagaaaaag aggcaaacaa ttgcttcatc ttaggagtgg aaagggtgaa
     3241 acaaagtggc tgtccactgt gactcaggga gtgaagatac catcagcaaa tagtttcttt
     3301 ttgttcaact gttcctttag aactagtctg tcttctggag tcccactgaa tcccctgttt
     3361 ttggaagact tcacgtagcc tagattgttt tgtgccgttt gacaacatta atctctgtca
     3421 tcatttttaa cctattaagg aatgctttga atatctgcta tatgctaact ttttgcagct
     3481 tcattctgag agacgttagt caaacaaata aaaggagccc catcacaatc tcacggtatt
     3541 cgaagggcca ggtcgattag gtggcttcat aggagaccct ccgcaactgt gtggtcagtg
     3601 gctggctctc atacccacta agatacatca tagctccatg tcggtggttt atgttgacct
     3661 gagattgatt tgttaaaatc tctcctctgt ttctgttcgt tctgtttccg tcctgttctg
     3721 ttctgttctg ttctgaaagt cttgctgtgg tctctttttg gcagaagtgt ttcatgcatg
     3781 gcagcaggcc tgatgctttt tatagtgatt cccattgaaa ctgtaagtaa atgtctgtgg
     3841 ccttgttctc tctatggtaa agatattatt caccatgtaa aacaagaaaa atatttattg
     3901 tattttagta tatttatata attatgttat tgaaaaaaat tggcattaaa acttaaccac
     3961 atcagaagcc tattgtaaat acaggttcta tttaagtgta ccaattaaca tataatatat
     4021 gttttaaata tagaattttt aatgttttta aatatatttt caaagtacat aaaaaaaaaa
     4081 aaaaaa
//
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