LOCUS       NM_001081377            6231 bp    mRNA    linear   ROD 02-JUL-2024
DEFINITION  Mus musculus protocadherin 9 (Pcdh9), transcript variant 1, mRNA.
ACCESSION   NM_001081377 XM_006518774 XM_902471
VERSION     NM_001081377.3
KEYWORDS    RefSeq; RefSeq Select.
SOURCE      Mus musculus (house mouse)
  ORGANISM  Mus musculus
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
            Muroidea; Muridae; Murinae; Mus; Mus.
REFERENCE   1  (bases 1 to 6231)
  AUTHORS   Adams,D.J., Barlas,B., McIntyre,R.E., Salguero,I., van der
            Weyden,L., Barros,A., Vicente,J.R., Karimpour,N., Haider,A.,
            Ranzani,M., Turner,G., Thompson,N.A., Harle,V., Olvera-Leon,R.,
            Robles-Espinoza,C.D., Speak,A.O., Geisler,N., Weninger,W.J.,
            Geyer,S.H., Hewinson,J., Karp,N.A., Fu,B., Yang,F., Kozik,Z.,
            Choudhary,J., Yu,L., van Ruiten,M.S., Rowland,B.D., Lelliott,C.J.,
            Del Castillo Velasco-Herrera,M., Verstraten,R., Bruckner,L.,
            Henssen,A.G., Rooimans,M.A., de Lange,J., Mohun,T.J., Arends,M.J.,
            Kentistou,K.A., Coelho,P.A., Zhao,Y., Zecchini,H., Perry,J.R.B.,
            Jackson,S.P. and Balmus,G.
  CONSRTM   Sanger Mouse Genetics Project
  TITLE     Genetic determinants of micronucleus formation in vivo
  JOURNAL   Nature 627 (8002), 130-136 (2024)
   PUBMED   38355793
REFERENCE   2  (bases 1 to 6231)
  AUTHORS   Ye,Q., Bhojwani,A. and Hu,J.K.
  TITLE     Understanding the development of oral epithelial organs through
            single cell transcriptomic analysis
  JOURNAL   Development 149 (16) (2022)
   PUBMED   35831953
REFERENCE   3  (bases 1 to 6231)
  AUTHORS   Uemura,M., Furuse,T., Yamada,I., Kushida,T., Abe,T., Imai,K.,
            Nagao,S., Kudoh,M., Yoshizawa,K., Tamura,M., Kiyonari,H., Wakana,S.
            and Hirano,S.
  TITLE     Deficiency of protocadherin 9 leads to reduction in positive
            emotional behaviour
  JOURNAL   Sci Rep 12 (1), 11933 (2022)
   PUBMED   35831353
  REMARK    GeneRIF: Deficiency of protocadherin 9 leads to reduction in
            positive emotional behaviour.
            Publication Status: Online-Only
REFERENCE   4  (bases 1 to 6231)
  AUTHORS   Bedogni,F. and Hevner,R.F.
  TITLE     Cell-Type-Specific Gene Expression in Developing Mouse Neocortex:
            Intermediate Progenitors Implicated in Axon Development
  JOURNAL   Front Mol Neurosci 14, 686034 (2021)
   PUBMED   34321999
  REMARK    Publication Status: Online-Only
REFERENCE   5  (bases 1 to 6231)
  AUTHORS   Hertel,N. and Redies,C.
  TITLE     Absence of layer-specific cadherin expression profiles in the
            neocortex of the reeler mutant mouse
  JOURNAL   Cereb Cortex 21 (5), 1105-1117 (2011)
   PUBMED   20847152
REFERENCE   6  (bases 1 to 6231)
  AUTHORS   Kirchhof,P., Kahr,P.C., Kaese,S., Piccini,I., Vokshi,I.,
            Scheld,H.H., Rotering,H., Fortmueller,L., Laakmann,S., Verheule,S.,
            Schotten,U., Fabritz,L. and Brown,N.A.
  TITLE     PITX2c is expressed in the adult left atrium, and reducing Pitx2c
            expression promotes atrial fibrillation inducibility and complex
            changes in gene expression
  JOURNAL   Circ Cardiovasc Genet 4 (2), 123-133 (2011)
   PUBMED   21282332
REFERENCE   7  (bases 1 to 6231)
  AUTHORS   Krishna-K,K., Hertel,N. and Redies,C.
  TITLE     Cadherin expression in the somatosensory cortex: evidence for a
            combinatorial molecular code at the single-cell level
  JOURNAL   Neuroscience 175, 37-48 (2011)
   PUBMED   21129452
REFERENCE   8  (bases 1 to 6231)
  AUTHORS   Vanhalst,K., Kools,P., Staes,K., van Roy,F. and Redies,C.
  TITLE     delta-Protocadherins: a gene family expressed differentially in the
            mouse brain
  JOURNAL   Cell Mol Life Sci 62 (11), 1247-1259 (2005)
   PUBMED   15905963
REFERENCE   9  (bases 1 to 6231)
  AUTHORS   Mattar,P., Britz,O., Johannes,C., Nieto,M., Ma,L., Rebeyka,A.,
            Klenin,N., Polleux,F., Guillemot,F. and Schuurmans,C.
  TITLE     A screen for downstream effectors of Neurogenin2 in the embryonic
            neocortex
  JOURNAL   Dev Biol 273 (2), 373-389 (2004)
   PUBMED   15328020
REFERENCE   10 (bases 1 to 6231)
  AUTHORS   Strehl,S., Glatt,K., Liu,Q.M., Glatt,H. and Lalande,M.
  TITLE     Characterization of two novel protocadherins (PCDH8 and PCDH9)
            localized on human chromosome 13 and mouse chromosome 14
  JOURNAL   Genomics 53 (1), 81-89 (1998)
   PUBMED   9787079
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from CF745283.1, AC132470.3,
            AC122355.4, AC125095.3 and AC123919.4.
            
            On or before Feb 6, 2018 this sequence version replaced
            XM_006518774.3, NM_001081377.2.
            
            Summary: This gene encodes a member of the protocadherin family,
            and cadherin superfamily, of transmembrane proteins containing
            cadherin domains. These proteins mediate cell adhesion in neural
            tissues in the presence of calcium. The encoded protein may be
            involved in signaling at neuronal synaptic junctions. Sharing a
            characteristic with other protocadherin genes, this gene has a
            notably large exon that encodes multiple cadherin domains and a
            transmembrane region. Alternatively spliced transcript variants
            encoding multiple isoforms have been observed for this gene.
            [provided by RefSeq, Nov 2012].
            
            Transcript Variant: This variant (1) encodes the longest isoform
            (a, also known as 3).
            
            Sequence Note: This RefSeq record was created from transcript and
            genomic sequence data to make the sequence consistent with the
            reference genome assembly. The genomic coordinates used for the
            transcript record were based on transcript alignments.
            
            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 :: SRR1660815.87026.1,
                                           SRR10662774.1147985.1 [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMN00849374,
                                           SAMN00849385 [ECO:0006172]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-137               CF745283.1         1-137
            138-667             CF745283.1         139-668
            668-3741            AC132470.3         109582-112655       c
            3742-3843           AC122355.4         119958-120059
            3844-4045           AC125095.3         106510-106711       c
            4046-6231           AC123919.4         102814-104999       c
FEATURES             Location/Qualifiers
     source          1..6231
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="14"
                     /map="14 45.8 cM"
     gene            1..6231
                     /gene="Pcdh9"
                     /note="protocadherin 9"
                     /db_xref="GeneID:211712"
                     /db_xref="MGI:MGI:1306801"
     exon            1..549
                     /gene="Pcdh9"
                     /inference="alignment:Splign:2.1.0"
     exon            550..3741
                     /gene="Pcdh9"
                     /inference="alignment:Splign:2.1.0"
     CDS             706..4419
                     /gene="Pcdh9"
                     /note="isoform a precursor is encoded by transcript
                     variant 1"
                     /codon_start=1
                     /product="protocadherin-9 isoform a precursor"
                     /protein_id="NP_001074846.1"
                     /db_xref="CCDS:CCDS36992.1"
                     /db_xref="GeneID:211712"
                     /db_xref="MGI:MGI:1306801"
                     /translation="MDLRDFYLLAALIACLRLDSAIAQELIYTIREELPENVPIGNIP
                     KDLNISHINAATGTSASLVYRLVSKAGDAPLVKVSSSTGEIFTTSNRIDREKLCAGAS
                     YAEENECFFELEVVILPNDFFRLIKIKIIVKDTNDNAPMFPSPVINISIPENTLINSR
                     FPIPSATDPDTGFNGVQHYELLNGQSVFGLDIVETPEGEKWPQLIVQQNLDREQKDTY
                     VMKIKVEDGGTPQKSSTAILQVTVSDVNDNRPVFKEGQVEVHIPENAPVGTSVIQLHA
                     TDADIGSNAEIRYIFGAQVAPATKRLFALNNTTGLITVQRSLDREETAIHKVTVLASD
                     GSSTPARATVTINVTDVNDNPPNIDLRYIISPINGTVYLSEKDPVNTKIALITVSDKD
                     TDVNGKVICFIEREVPFHLKAVYDNQYLLETSSLLDYEGTKEFSFKIVASDSGKPSLN
                     QTALVRVKLEDENDNPPIFNQPVIELSVSENNRRGLYLTTISATDEDSGKNADIVYQL
                     GPNASFFDLDRKTGVLTASRVFNREEQERFIFTVTARDNGTPPLQSQAAVIVTVLDEN
                     DNSPKFTHNHFQFFVSENLPKYSTVGVITVTDEDAGENKAVTLSILNDNENFVLDPYS
                     GVIKSNVSFDREQQSSYTFDVKATDGGQPPRSSTAKVTINVMDVNDNSPVVISPPSNT
                     SFKLVPLSAIPGSVVAEVFAVDIDTGMNAELKYTIVSGNNKGLFRIDPVTGNITLEEK
                     PAPTDVGLHRLVVNISDLGYPKALHTLVLVFLYVNDTAGNTSYIYDLIRRTMETPLDR
                     NIGDSGQPYQNEDYLTIMIAIVAGAMVVIVVIFVTVLVRCRHASRFKAAQRSKQGAEW
                     MSPNQENKQNKKKKRKKRKSPKSSLLNFVTIEESKPDDAVHEPINGTISLPAELEEQG
                     IGRFDWGPAPPTTFKPNSPDLAKHYKSASPQPAFHLKPDTPVSVKKHHVIQELPLDNT
                     FVGGCDTLSKRSSTSSDHFSASECSSQGGFKTKGPLHTRQCNSYSKNDNIPVTHQKCP
                     GSTSFHIRENEESHSESQRRVTFHLPDGSQESCSDSGLGDHEPVGSGTLISHPLPLVQ
                     PQDEFYDQASPDKRTEADGNSDPNSDGPLGPRGLAEATEMCTQECLVLGHSDNCWMPP
                     GLGPYQHPKSPLSTFAPQKEWIKKDKLVNGHTLTRAWKEDTNRNQFNDRKQYGSNEGH
                     FNNGGHMADIPLANLKSYKQAGGTIESPKEHQL"
     exon            3742..3843
                     /gene="Pcdh9"
                     /inference="alignment:Splign:2.1.0"
     exon            3844..4045
                     /gene="Pcdh9"
                     /inference="alignment:Splign:2.1.0"
     exon            4046..6231
                     /gene="Pcdh9"
                     /inference="alignment:Splign:2.1.0"
     regulatory      6136..6141
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Pcdh9"
                     /note="hexamer: AATAAA"
     polyA_site      6155
                     /gene="Pcdh9"
                     /note="major polyA site"
     regulatory      6209..6214
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Pcdh9"
                     /note="hexamer: AATAAA"
     polyA_site      6227
                     /gene="Pcdh9"
                     /note="major polyA site"
ORIGIN      
        1 gagagaggag agggagaagg agaggggggc agaagagaag ggaaaaacga agagtacgcg
       61 aggtaggatg gagagcctca gtctcttaag cgcgaaagga ctcacggatt aagaatttgc
      121 cgggcaattg gcaccccggg aaaacatcca gaaaatcacc atcacccaac tctgacgttt
      181 cctactagaa gttagagact tcagcagtat tgccatcgga tgcaaatggt aggctggatg
      241 cggtgggata cactcccgag ctgaagaagt gcaattggat gtggtgtgcg ttaaatacca
      301 gaagagccca gacccagtgg gtaaaagcga ggaaatgtgg agagaatgac taacgacaaa
      361 tctgtgaatt tgttctcggg agttgctaat ttgccagccc gaagccacac attttacaag
      421 gagaaaacgt tttgctgctt ctgaattctc cccaaactgg tgctaccaga tgcatggctt
      481 tctatgtgtt ggagcaaatc cttcttaact gcagcctacc gggaaagggg caaggttgag
      541 gcaactaatt ggctgtctcc acataagaga tgagatgtaa tgcctcctcc tcctcctcct
      601 cctccttctc cagtccatgc acacttcctc ttgcagttcg tgcatcactc ctcagtggga
      661 acctttaaac tctaaaatcc aggaaaagaa cataaagaca ttatcatgga cctgagggat
      721 ttttacctgt tggctgctct gattgcctgt ttaaggctgg attccgcaat agctcaagaa
      781 cttatttaca ctattagaga ggaattgcct gaaaatgtgc ccataggaaa tataccaaag
      841 gatctgaata tttctcacat caatgctgcc acggggacca gtgccagcct tgtctacaga
      901 ctggtttcaa aagctgggga tgcccctctg gtgaaagtat cgagtagcac tggggagatt
      961 ttcacaacct ccaacagaat agacagagag aaactctgtg ctggggcttc atacgctgag
     1021 gagaacgagt gcttctttga acttgaagta gtgatcctcc ccaatgactt tttcaggctg
     1081 atcaaaatca agatcattgt caaggatacc aatgataatg cccccatgtt tccgtctcct
     1141 gtcatcaata tttccatccc agagaacact ttgatcaaca gccgctttcc aatcccatca
     1201 gccacagacc ctgacacggg cttcaatggg gtacagcatt atgaattact aaatggacag
     1261 agtgtttttg gactggatat cgtggaaact ccggagggag aaaagtggcc gcaattgatt
     1321 gttcagcaga acttggatag agaacaaaaa gatacctatg tgatgaaaat caaagtggag
     1381 gatgggggca cgccacagaa atcgagcaca gctattctcc aggtcacagt aagtgatgtc
     1441 aatgacaaca ggccagtgtt taaagagggt caagtagaag tgcatattcc agagaatgct
     1501 cctgtgggga cctctgtcat tcagctccat gccactgatg cagacatagg cagtaatgct
     1561 gaaatccggt atatttttgg tgcccaggtc gcccctgcaa ccaaaagact ctttgcttta
     1621 aataatacaa ctgggctgat aacagttcag aggtctttag atagggaaga gacagccatt
     1681 cacaaagtga cagtgctggc tagtgacggc agctccactc ctgccagagc caccgtgacc
     1741 atcaatgtca ccgatgtaaa tgataaccct ccaaacatag acctcaggta cattataagt
     1801 cccatcaatg gcacagtgta tctctctgag aaagaccctg tcaatacaaa gattgccctc
     1861 attacagttt cagataagga cacagatgtg aatggcaaag tgatctgttt tattgaaaga
     1921 gaggtcccat ttcatttgaa ggcagtgtat gacaaccagt atctgctaga gacctcttct
     1981 ctgctggact atgagggcac caaagaattc agctttaaaa tcgttgcctc tgattcgggg
     2041 aagcccagtt tgaatcagac tgccctggta agggttaagc tcgaggatga aaatgacaac
     2101 ccaccaattt tcaaccagcc tgtaattgag ctgtcagttt ctgaaaacaa ccgacgtggg
     2161 ttatacttaa caactattag tgctacagat gaagacagtg gaaaaaatgc agacattgtt
     2221 tatcagcttg gaccgaatgc ctccttcttt gatctggaca gaaagacagg agttttgaca
     2281 gcctccagag tctttaacag ggaggaacaa gagcggttca tttttacagt aactgccagg
     2341 gacaatggga cccctcccct ccagagccaa gcagcagtga tagttactgt tctggatgag
     2401 aatgacaata gccccaagtt tactcataat cactttcagt tttttgtgtc tgagaatctg
     2461 ccaaagtata gtactgtggg ggtaatcaca gtgacagacg aagacgctgg agagaataaa
     2521 gctgtgactc tttccattct aaatgacaat gaaaattttg tgttggatcc ctattcagga
     2581 gtcataaagt ccaatgtctc ctttgataga gagcagcaga gttcctacac gtttgacgtc
     2641 aaagccaccg acgggggaca gccaccacgg tcctctactg caaaagtaac tatcaatgtc
     2701 atggatgtca atgacaatag tccagttgtc atttctccac catccaacac ctcctttaag
     2761 ttggtgcccc tctcagccat tcctggttct gtggttgctg aagtgtttgc ggtggatatt
     2821 gacaccggaa tgaatgcaga actcaagtat accatagtga gcgggaacaa caagggatta
     2881 tttcggattg atccagtaac aggcaatatc accttagaag agaagccagc acctactgat
     2941 gtgggcctgc accgtcttgt ggtcaacata agtgacctgg ggtaccctaa ggctttgcac
     3001 actctcgtgc tggtatttct ttatgtgaac gacactgctg gaaacacctc atatatatat
     3061 gacttgatcc gtaggactat ggagacccca ctggaccgga acataggaga tagtggtcaa
     3121 ccttatcaga acgaggacta tctcaccatc atgattgcca tcgttgctgg ggccatggtg
     3181 gtcattgttg tgatctttgt cacggtgctg gtgcgctgtc gccatgcgtc caggttcaag
     3241 gccgctcaga ggagcaaaca aggggctgaa tggatgtccc caaaccagga gaataaacaa
     3301 aataagaaaa agaaacggaa gaaaagaaag tcgcccaaga gttctctttt gaactttgtt
     3361 actattgaag agtccaaacc cgatgatgcc gttcatgaac ccatcaatgg gaccataagc
     3421 ctgcctgccg agctggagga acagggtata ggaagatttg actggggccc agcccctcca
     3481 accaccttca agcctaacag ccctgacctg gccaagcact acaagtcggc ctctcctcag
     3541 cccgcttttc atctcaaacc tgacactcca gtttctgtga aaaagcacca cgtcattcaa
     3601 gagctcccgt tggacaacac ctttgttggg ggctgcgaca ccctttccaa acgctcctcc
     3661 actagttcag atcacttcag tgcctcagag tgcagctccc aaggaggctt caagacaaag
     3721 ggccccttac acaccagaca gtgtaactca tacagcaaaa atgacaatat tcctgtcaca
     3781 catcagaaat gtcccggctc taccagtttc cacattcgag agaatgaaga aagtcattct
     3841 gagtctcagc gccgtgttac ctttcacctt ccggatggct cccaggaaag ctgcagtgac
     3901 agtggtctgg gagaccacga gccggtgggt agtggaaccc tgatctcaca ccctcttcct
     3961 ctggttcagc cacaggacga attctacgac caggcctctc cggacaagag gaccgaagca
     4021 gatggcaact cggatcccaa ttctgatgga cctctgggtc cccgaggttt agctgaagct
     4081 acagagatgt gcactcaaga gtgtctggtt ttgggtcact ctgataattg ctggatgcct
     4141 cctggcttgg gtccatacca acaccctaaa tctcctctgt caacctttgc accccagaaa
     4201 gaatggatca agaaagacaa gcttgtgaat gggcacaccc tgacaagagc gtggaaagaa
     4261 gacaccaaca ggaaccaatt caatgaccgt aagcagtatg gctccaatga aggccatttc
     4321 aacaatggcg gccacatggc ggacattcct ctggcaaatc tgaagtccta taagcaagca
     4381 ggaggcacga ttgagagtcc taaggagcac caactttaag atgaagctgt atgggaccta
     4441 atacctttaa tctaaataga catgctaata ctgtgcgttg gagctttatg tattcgatag
     4501 atctctacaa ctatgcccct tatcgtaggg aatactcata actttgtgtt agcacgatgg
     4561 aggatacaat gctttgcagc ataagagaga aaatagttct actagccatg tgatgatgtt
     4621 ctttactaga attgattaaa ctctccagag atctctccat tgtgcaattt atttttatta
     4681 ctgcattttc ttttgaccct ggactgctgc tatgaacaat agaatatgca tttggagagt
     4741 aagaaagttc cacggattag agtgactgac aaaacatatc cagttagaaa tttgtgctct
     4801 ttttgtcttt gatttatgct gggacctcta tacttgacat tatacttcaa acaaaacttt
     4861 aaaagataag cattaaacct attgtgctgt taacaccgtt agtggacact tgtaagtcaa
     4921 tcagtgttaa agtatttgta aatagaagca agctattatt aacaattttg tgtacttata
     4981 gcactcacct acaaatgtta tagcataatt ctgtgttgat ggttgctcct ttccttttct
     5041 ctattgccct ctttcttctt atttttgttg tttctttcag tgaggtgttt ccgcgttagt
     5101 agtctgtctt ggcacacgtt gttcaaagaa tcttaaatat ttgtgtttta aaatggttct
     5161 gaaattttgc ttcttctatg ataacttaga atgttagaac tctgtaaaaa tataaagaca
     5221 aaagaaaata tgaaaacttc aaacaacaat agcagcagac aaatgcttct gcacactctt
     5281 ggaaattcag aacctctttt tgacatcctt attttcaaag taggcaaaat taaaaatgac
     5341 gtaattagta ccattaagtg agaaagtgat gggaagtgtt atccatcaag tgtgatataa
     5401 tattctgtac ttgttactct ttcaaaacta acgtattaaa atcagtatat attgaagaaa
     5461 aaatcattac tcaaaaaata gtttcaattg ggcaaatgtg tgtctccaac tttgttgaaa
     5521 tgacagagtt tgtgttgatc ctcatataca atactgttgt tgtaacacaa gtgttattag
     5581 accatagcca caaaatattt aatgtgttgt gccttcatga tgtaacagaa cattctccag
     5641 gtaggtagtt ggggaaaata aagggataaa tctctaatta ttgctgttta actgtttgtt
     5701 atcatagttg gtcaatgcct ggcaggtacc agcattttgt cacttgggtc aaaccaaggg
     5761 agtgacagat aatgttaata agatctcagt tgcacgtgca aacaaatcca aatttgaaca
     5821 ttcttaggag gttttttgtt aaggcatgac agatgattta aacaaataaa tagcatgcaa
     5881 caaaacgtct ttattgaaag gagtgaaagt tatattaacg ccacggttca ccatcaactt
     5941 taaagttaaa aaaaaagaaa aaagtttaaa aaaatcgcta atctgatagt taatttgttc
     6001 ttaccaaaaa taaagttact ttgtaaatag cagttcacat ttttccacag tataatggaa
     6061 aataatgggt aggggtgcat tgcttattga agtcattttt gtcggtttgt gaggggtgtt
     6121 tgatgacttt gacaaaataa atatctaaac aattatcctt gttactgctt tgccagttct
     6181 acgttattta caattattca gctcttgcaa taaatgttct gaattactga t
//
