LOCUS       NM_001191688            5595 bp    mRNA    linear   ROD 24-JUN-2024
DEFINITION  Rattus norvegicus protocadherin 9 (Pcdh9), mRNA.
ACCESSION   NM_001191688 XM_224429
VERSION     NM_001191688.1
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 5595)
  AUTHORS   Loh,K.H., Stawski,P.S., Draycott,A.S., Udeshi,N.D., Lehrman,E.K.,
            Wilton,D.K., Svinkina,T., Deerinck,T.J., Ellisman,M.H., Stevens,B.,
            Carr,S.A. and Ting,A.Y.
  TITLE     Proteomic Analysis of Unbounded Cellular Compartments: Synaptic
            Clefts
  JOURNAL   Cell 166 (5), 1295-1307 (2016)
   PUBMED   27565350
REFERENCE   2  (bases 1 to 5595)
  AUTHORS   Asahina,H., Masuba,A., Hirano,S. and Yuri,K.
  TITLE     Distribution of protocadherin 9 protein in the developing mouse
            nervous system
  JOURNAL   Neuroscience 225, 88-104 (2012)
   PUBMED   22982106
REFERENCE   3  (bases 1 to 5595)
  AUTHORS   Kim,S.Y., Chung,H.S., Sun,W. and Kim,H.
  TITLE     Spatiotemporal expression pattern of non-clustered protocadherin
            family members in the developing rat brain
  JOURNAL   Neuroscience 147 (4), 996-1021 (2007)
   PUBMED   17614211
COMMENT     PROVISIONAL REFSEQ: This record has not yet been subject to final
            NCBI review. The reference sequence was derived from
            JAXUCZ010000015.1.
            
            [WARNING] On Aug 21, 2024 this sequence was replaced by
            NM_001191688.2.
            
            On Jul 17, 2010 this sequence version replaced XM_224429.5.
            
            Sequence Note: The RefSeq transcript and protein were derived from
            genomic sequence to make the sequence consistent with the reference
            genome assembly. The genomic coordinates used for the transcript
            record were based on alignments.
            
            ##Evidence-Data-START##
            Transcript exon combination :: SRR26360176.893877.1,
                                           SRR26360194.1967505.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN12840110 [ECO:0000348]
            ##Evidence-Data-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-3112              JAXUCZ010000015.1  76640841-76643952   c
            3113-3214           JAXUCZ010000015.1  76313922-76314023   c
            3215-3416           JAXUCZ010000015.1  76065542-76065743   c
            3417-5595           JAXUCZ010000015.1  75748474-75750652   c
FEATURES             Location/Qualifiers
     source          1..5595
                     /organism="Rattus norvegicus"
                     /mol_type="mRNA"
                     /strain="BN"
                     /db_xref="taxon:10116"
                     /chromosome="15"
                     /map="15q21"
     gene            1..5595
                     /gene="Pcdh9"
                     /note="protocadherin 9"
                     /db_xref="GeneID:306091"
                     /db_xref="RGD:1306348"
     exon            1..3112
                     /gene="Pcdh9"
                     /inference="alignment:Splign:2.1.0"
     CDS             77..3790
                     /gene="Pcdh9"
                     /codon_start=1
                     /product="protocadherin-9 precursor"
                     /protein_id="NP_001178617.1"
                     /db_xref="GeneID:306091"
                     /db_xref="RGD:1306348"
                     /translation="MDLRDFYLLAALIACLRLDSAIAQELIYTIREELPENVPIGNIP
                     KDLNISHINAATGTSASLVYRLVSKAGDAPLVKVSSSTGEIFTTSNRIDREKLCAGAS
                     YAEENECFFELEVVILPNDFFRLIKIKIIVKDTNDNAPMFPSPVINISIPENTLINSR
                     FPIPSATDPDTGFNGVQHYELLNGQSVFGLDIVETPEGEKWPQLIVQQNLDREQKDTY
                     VMKIKVEDGGTPQKSSTAILQVTVSDVNDNRPVFKEGQVEVHIPENAPVGTSVIQLHA
                     TDADIGSNAEIRYIFGAQVAPATKRLFALNNTTGLITVQRSLDREETAIHKVTVLASD
                     GSSTPARATVTINVTDVNDNPPNIDLRYIISPINGTVYLSEKDPVNTKIALITVSDKD
                     TDVNGKVICFIEREVPFHLKAVYDNQYLLETSSLLDYEGTKEFSFKIVASDSGKPSLN
                     QTALVRVKLEDENDNPPIFNQPVIELSVSENNRRGLYLTTISATDEDSGKNADIVYQL
                     GPNASFFDLDRKTGVLTASRVFNREEQERFIFTVTARDNGTPPLQSQAAVIVTVLDEN
                     DNSPKFTHNHFQFFVSENLPKYSTVGVITVTDEDAGENKAVTLSILNDNENFVLDPYS
                     GVIKSNVSFDREQQSSYTFDVKATDGGQPPRSSTAKVTINVMDVNDNSPVVISPPSNT
                     SFKLVPLSAIPGSVVAEVFAVDIDTGMNAELKYTIVSGNNKGLFRIDPVTGNITLEEK
                     PAPTDVGLHRLVVNISDLGYPKALHTLVLVFLYVNDTAGNASYIYDLIRRTMETPLDR
                     NIGDSGQPYQNEDYLTIMIAIVAGAMVVIVVIFVTVLVRCRHASRFKAAQRSKQGAEW
                     MSPNQENKQNKKKKRKKRKSPKSSLLNFVTIEESKPDDAVHEPINGTISLPAELEEQS
                     IGRFDWGPAPPTTFKPNSPDLAKHYKSASPQPAFHLKPDTPVSVKKHHVIQELPLDNT
                     FVGGCDTLSKRSSTSSDHFSASECSSQGGFKTKGPLHTRQCNSHSKNDLIPVTHQKCP
                     SSTGFHIRENEESHSESQRRVTFHLPDGSQESCSDSGLGDHEPVGSGTLISHPLPLVQ
                     PQDEFYDQASPDKRTEADGNSDPNSDGPLGPRGLAEATEMCTQECLVLGHSDNCWMPP
                     GLGPYQHPKSPLSTFAPQKEWIKKDKLVNGHTLTRAWKEDTNRNQFNDRKQYGSNEGH
                     FSNGSHMADIPLANLKSYKQAGGTIESPKEHQL"
     exon            3113..3214
                     /gene="Pcdh9"
                     /inference="alignment:Splign:2.1.0"
     exon            3215..3416
                     /gene="Pcdh9"
                     /inference="alignment:Splign:2.1.0"
     exon            3417..5595
                     /gene="Pcdh9"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      
        1 cttgcaatcc gtgcatcatt cctcagtggg aacctttaaa ctctaaaatc caagggaaga
       61 aaataaagac attatcatgg acctgaggga tttttacctg ttggctgctc tgattgcctg
      121 tttaaggctg gattccgcaa tagctcaaga acttatttac actattagag aggaattgcc
      181 cgaaaatgtg cccataggaa atataccaaa ggatctgaat atttctcaca tcaacgctgc
      241 cacagggacg agtgccagcc ttgtctacag gctggtttct aaagctgggg atgcccctct
      301 ggtgaaagta tccagtagca ctggggagat tttcacaacc tccaacagaa tagacagaga
      361 gaaactctgt gccggagctt cttatgctga ggagaatgag tgtttctttg aacttgaggt
      421 ggtgatcctc cccaatgact ttttcagact gatcaaaatc aagatcattg tcaaggatac
      481 caatgataat gcccccatgt ttccgtctcc cgtcatcaat atttccatcc cagagaacac
      541 tttgatcaac agtcgctttc caatcccatc agccacagac cctgacacgg gcttcaatgg
      601 ggtacagcat tatgaattgc tgaatgggca gagtgttttt ggactggata tcgtggaaac
      661 tccggaggga gaaaagtggc cgcaattgat cgttcagcag aacttggata gagaacaaaa
      721 agatacctat gtgatgaaaa tcaaagtgga ggatgggggc actccacaga aatccagcac
      781 agccatactc caggtcacag taagtgatgt caatgacaac aggccagtgt ttaaagaggg
      841 tcaagtggaa gtgcatattc cagagaatgc tcctgtaggg acctctgtga ttcagctcca
      901 tgctactgat gcagacatag gcagcaatgc tgaaatccgg tacatctttg gtgcccaggt
      961 cgcccctgca accaaaagac tctttgcttt aaataacaca actgggctga ttacagttca
     1021 gaggtcctta gatagggaag agacagccat tcacaaagtg acagtgctgg ctagtgacgg
     1081 cagctccact cctgccagag ccaccgttac catcaatgtc acagatgtaa atgataatcc
     1141 tccaaacata gacctcaggt acattataag tcccatcaat ggcaccgtgt atctctctga
     1201 gaaagatcca gtcaatacaa agattgccct aattacagtt tcagataagg acacggatgt
     1261 gaatggcaaa gtgatctgtt ttattgaaag agaggtccca tttcatctga aggcagtgta
     1321 tgacaaccag tatctgctag agacctcgtc tctgctggac tatgagggca ccaaagaatt
     1381 cagctttaaa atcgttgcct ctgattctgg gaagcccagt ttgaatcaga ctgccctggt
     1441 aagggttaag cttgaggacg aaaatgacaa cccaccaatt ttcaaccagc ctgtaattga
     1501 gctgtcagtt tctgaaaaca accgacgtgg gttatactta acaactatta gtgctacgga
     1561 tgaagacagt gggaaaaatg cagacattgt ttatcagctt ggacccaatg cctccttctt
     1621 tgatctggac agaaagacag gagttctgac agcctccaga gtctttaaca gggaggaaca
     1681 agagcggttc atttttacag taactgccag ggacaacggg acccctcccc tgcagagcca
     1741 agcagccgtg atagttactg ttctggatga gaatgacaat agccccaagt tcactcataa
     1801 tcattttcag ttttttgtgt ctgagaatct gccaaagtat agtactgtgg gggtaatcac
     1861 agtgacagac gaggacgctg gagagaataa agctgtgact ctttccattc taaatgacaa
     1921 tgaaaatttc gtgttggatc cctattcagg agtcataaag tccaatgtct cctttgatag
     1981 agaacagcag agttcctaca cgtttgatgt caaagccact gacggaggac agccacctcg
     2041 gtcctctact gcaaaagtaa ctatcaatgt catggatgtc aatgacaata gtccagttgt
     2101 catttctcca ccatccaaca cctcctttaa gttggtgccc ctctcagcca ttcctggttc
     2161 cgtggttgct gaagtttttg ctgtggatat tgacaccggg atgaatgcag aacttaagta
     2221 taccatagtg agcgggaaca acaaaggatt atttcggatt gatccagtaa cgggcaatat
     2281 caccttagaa gaaaagccgg cacctactga cgtgggcctg caccgtctcg tggtcaacat
     2341 aagtgacctg gggtacccta aggctttgca cactcttgtg ctggtatttc tttacgtgaa
     2401 cgacactgct ggaaacgcct cgtatatata tgacttgatc cgtaggacta tggagacccc
     2461 gctggacagg aacataggag atagtggtca accttatcaa aacgaggact atctcaccat
     2521 catgattgcc atcgttgccg gggccatggt cgtcatcgtc gtgatctttg tcacggtgct
     2581 ggtgcgctgt cgccatgcgt cgaggttcaa ggctgctcag aggagcaaac aaggtgctga
     2641 atggatgtcc ccaaaccagg agaataaaca aaacaagaaa aagaaacgga agaaaagaaa
     2701 gtcgcccaag agttctcttt tgaactttgt tactatcgaa gagtccaaac ctgatgatgc
     2761 ggttcatgaa cctatcaatg ggaccataag cctgcctgct gagctggagg aacagagtat
     2821 aggaagattt gactggggcc cggcccctcc aacaaccttc aagcctaaca gccctgacct
     2881 ggccaagcac tacaaatctg cctctccaca gcctgcgttt catctcaaac cagacactcc
     2941 agtttccgtg aaaaagcacc acgtcattca agagctccct ttggacaaca cctttgttgg
     3001 gggctgcgac accctttcca aacgctcctc cactagttca gatcacttca gtgcctcaga
     3061 gtgcagctcc caaggaggct tcaagacaaa gggcccctta cacaccagac agtgtaactc
     3121 acacagcaaa aatgacctta ttcctgtcac acatcagaaa tgccccagct ctaccggttt
     3181 ccacattcga gagaatgaag aaagtcattc tgagtctcag cgtcgtgtta cctttcacct
     3241 tccggatggc tcccaggaaa gctgcagtga cagtggtctg ggagaccacg agccggtggg
     3301 tagtggaacc ctgatctcac accctcttcc tctggttcag ccacaggacg aattctacga
     3361 ccaggcctct ccggacaaga ggaccgaagc agacggcaac tcggacccca attctgatgg
     3421 acctctgggt ccccgagggt tagctgaagc tacagagatg tgcactcagg agtgtcttgt
     3481 tttgggtcac tctgataatt gctggatgcc ccctggcttg ggtccctacc aacaccctaa
     3541 atctcctctg tcaacctttg caccccagaa agaatggatc aagaaagaca agctcgtgaa
     3601 tggccacacc ctgacaagag cttggaaaga agataccaac aggaaccagt tcaatgaccg
     3661 taagcagtat ggctccaatg aaggccattt cagcaatggc agccacatgg cagacattcc
     3721 tctggcaaat ctgaagtcct ataagcaagc aggaggcacg attgagagtc ctaaggagca
     3781 ccaactttaa gacgaagctg tacgggacct aataacttta atctaaatag acatgctaat
     3841 actgtgtgtt ggagctttat gtattcgata gatctttaca gctatgcccc ttatagtagg
     3901 gaacactcat aactttgtgt tagcacgatg gagaatacaa tgctttgcaa cataagggag
     3961 gaaatagacc tcctagccat gcgatgacgt tctttactag aattgattaa actctccaga
     4021 gatgtctcca ttgtgcaatt tatttttatt actgcatttt cttttgaccc tggactgctg
     4081 ctatgaacaa tagaatatgc attcggagag taagaaagtc ccacagatta gagtgactga
     4141 caaaacatat ccagttagaa atttgtgctc tttttgtctt tgatttatgc tgggacctct
     4201 atacttgaca ttatacttca aactttaaaa gataagcatt aaacctattg tgctgttaac
     4261 accgttagtg gacacttgta agtcaatcag tgttaaagta tctgtaaata gaagcaagct
     4321 attattaaca acttttgtgt acttagagca ctcacctaaa aatgttgtag cataattctg
     4381 tgttgatggt tgcttctttc ctttttcgat ttccctcttt cttcttattt ctgttgtttc
     4441 tttcagtgag gtgtttctgc gttagtagtc tgtcttggca cacattgttc aaagaatctt
     4501 aaacatttgt gtttttaaac ggttctgaaa tcttgcttct tatatgataa cttagaatgt
     4561 tagaactctg taaacctata aagacaaaag aaaatatgaa aacttcaaac aacaagagta
     4621 gcagacgtat acttctgcaa actcttggaa attcagaacc tctttttttg atatccttat
     4681 tttcaaagta ggcaaaatta aaaacgactt aattagtacc attaagtgag aaagtgatgg
     4741 gaaagtgtta tccatcaagt gtgatgtaat attctgtact tgttactctt tcaaaactaa
     4801 tgtattaaaa tcagcatata ctgaagaaaa aatcattact caaaaatagt ttcaattggg
     4861 caaatgtgtg tcttcaactt tgttgaaatg acagagtttg tgttgatcct catatacaat
     4921 aatgttgttg taacacaagt gttattagac catagccaca aaatatttaa tgtgttgtgc
     4981 cttcatgatg taacagaaca ttctccaggt aggtagttgg ggaaaataaa gggataaatc
     5041 tctaattatt gctgtttaac tgtttcttat catagttggt caatgcctgg caggtaccag
     5101 cattttgtca cttgggtcaa accaagggag tgacagataa tgttaataag atctcagttg
     5161 cacgtgcaaa caaatccaaa tttgaacatt cttaggaggt tttttgttaa ggcatgacag
     5221 atgatttaaa caaataaata gcatgcaaca aaatgtcttt attgaaagga gtggaagtta
     5281 tattaatgcc acggttcacc atcaatttac acgttaaaaa aaaagaaaaa agtttaaaaa
     5341 aattgctaat ctgatagtta atttgttctt accaaaaatg aagttacttt gtaaatagca
     5401 gttcacattt ttccacagta taatggaaaa taatgggtag gggtgcattg cttattgaag
     5461 tcatttttgt cggtttgtga ggggtgtttg atgactttga caaaataaat atctaaacaa
     5521 ttatccttgt tacagctttg caagttctac gttatttaca cttatcagct cttgcaataa
     5581 atgttctgaa ttact
//
