LOCUS       NM_009959               5376 bp    mRNA    linear   ROD 07-AUG-2023
DEFINITION  Mus musculus protocadherin alpha 5 (Pcdha5), mRNA.
ACCESSION   NM_009959
VERSION     NM_009959.2
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 5376)
  AUTHORS   Mancia Leon WR, Spatazza J, Rakela B, Chatterjee A, Pande V,
            Maniatis T, Hasenstaub AR, Stryker MP and Alvarez-Buylla A.
  TITLE     Clustered gamma-protocadherins regulate cortical interneuron
            programmed cell death
  JOURNAL   Elife 9, e55374 (2020)
   PUBMED   32633719
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 5376)
  AUTHORS   Elbert A, Vogt D, Watson A, Levy M, Jiang Y, Brule E, Rowland ME,
            Rubenstein J and Berube NG.
  TITLE     CTCF Governs the Identity and Migration of MGE-Derived Cortical
            Interneurons
  JOURNAL   J Neurosci 39 (1), 177-192 (2019)
   PUBMED   30377227
REFERENCE   3  (bases 1 to 5376)
  AUTHORS   Fan L, Lu Y, Shen X, Shao H, Suo L and Wu Q.
  TITLE     Alpha protocadherins and Pyk2 kinase regulate cortical neuron
            migration and cytoskeletal dynamics via Rac1 GTPase and WAVE
            complex in mice
  JOURNAL   Elife 7, e35242 (2018)
   PUBMED   29911975
  REMARK    Publication Status: Online-Only
REFERENCE   4  (bases 1 to 5376)
  AUTHORS   Toyoda S, Kawaguchi M, Kobayashi T, Tarusawa E, Toyama T, Okano M,
            Oda M, Nakauchi H, Yoshimura Y, Sanbo M, Hirabayashi M, Hirayama T,
            Hirabayashi T and Yagi T.
  TITLE     Developmental epigenetic modification regulates stochastic
            expression of clustered protocadherin genes, generating single
            neuron diversity
  JOURNAL   Neuron 82 (1), 94-108 (2014)
   PUBMED   24698270
REFERENCE   5  (bases 1 to 5376)
  AUTHORS   Esumi S, Kakazu N, Taguchi Y, Hirayama T, Sasaki A, Hirabayashi T,
            Koide T, Kitsukawa T, Hamada S and Yagi T.
  TITLE     Monoallelic yet combinatorial expression of variable exons of the
            protocadherin-alpha gene cluster in single neurons
  JOURNAL   Nat Genet 37 (2), 171-176 (2005)
   PUBMED   15640798
REFERENCE   6  (bases 1 to 5376)
  AUTHORS   Wu Q and Maniatis T.
  TITLE     Large exons encoding multiple ectodomains are a characteristic
            feature of protocadherin genes
  JOURNAL   Proc Natl Acad Sci U S A 97 (7), 3124-3129 (2000)
   PUBMED   10716726
REFERENCE   7  (bases 1 to 5376)
  AUTHORS   Sugino H, Hamada S, Yasuda R, Tuji A, Matsuda Y, Fujita M and Yagi
            T.
  TITLE     Genomic organization of the family of CNR cadherin genes in mice
            and humans
  JOURNAL   Genomics 63 (1), 75-87 (2000)
   PUBMED   10662547
REFERENCE   8  (bases 1 to 5376)
  AUTHORS   Senzaki K, Ogawa M and Yagi T.
  TITLE     Proteins of the CNR family are multiple receptors for Reelin
  JOURNAL   Cell 99 (6), 635-647 (1999)
   PUBMED   10612399
REFERENCE   9  (bases 1 to 5376)
  AUTHORS   Wu Q and Maniatis T.
  TITLE     A striking organization of a large family of human neural
            cadherin-like cell adhesion genes
  JOURNAL   Cell 97 (6), 779-790 (1999)
   PUBMED   10380929
REFERENCE   10 (bases 1 to 5376)
  AUTHORS   Kohmura N, Senzaki K, Hamada S, Kai N, Yasuda R, Watanabe M, Ishii
            H, Yasuda M, Mishina M and Yagi T.
  TITLE     Diversity revealed by a novel family of cadherins expressed in
            neurons at a synaptic complex
  JOURNAL   Neuron 20 (6), 1137-1151 (1998)
   PUBMED   9655502
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            AC020968.3, AC020972.3 and AC020973.3.
            
            On Feb 22, 2019 this sequence version replaced NM_009959.1.
            
            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.
            
            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 :: AY013763.1, SRR7345562.3702977.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN01164131, SAMN01164132
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on single protein-coding transcript
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-2510              AC020968.3         171801-174310
            2511-2569           AC020972.3         11539-11597         c
            2570-2658           AC020972.3         8399-8487           c
            2659-5376           AC020973.3         123819-126536
FEATURES             Location/Qualifiers
     source          1..5376
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="18"
                     /map="18 19.46 cM"
     gene            1..5376
                     /gene="Pcdha5"
                     /gene_synonym="Cnr6; Crnr6"
                     /note="protocadherin alpha 5"
                     /db_xref="GeneID:12941"
                     /db_xref="MGI:MGI:1298371"
     exon            1..2510
                     /gene="Pcdha5"
                     /gene_synonym="Cnr6; Crnr6"
                     /inference="alignment:Splign:2.1.0"
     CDS             165..2969
                     /gene="Pcdha5"
                     /gene_synonym="Cnr6; Crnr6"
                     /note="cadherin-related neuronal receptor 6"
                     /codon_start=1
                     /product="protocadherin alpha-5 precursor"
                     /protein_id="NP_034089.1"
                     /db_xref="CCDS:CCDS79617.1"
                     /db_xref="GeneID:12941"
                     /db_xref="MGI:MGI:1298371"
                     /translation="MVYFQRGSPGFRRLLISFVLLAAWEAGSGQLHYSIPEEAKHGTF
                     VGRIAQDLGLELTELVPRLFRVASKDRGDLLEVNLQNGILFVNSRIDREELCGRSAEC
                     SIHLEVIVDRPLQVFHVEVEVKDINDNPPKFSRPEQRLFILESRMPDSRFPVEGASDL
                     DIGANAALSYKINPNEYFDLDVKRNEEETSVLQLVLKKPLDREETQEHRLLLIAIDGG
                     KPELTGTVQLLIDVLDANDNAPEFDKSIYNVRLLENTPNGTLVIKLNASDADEGINKE
                     ILYFFSNLVLDDVKSKFTIDSSSGEIKVKGELDYEDCKVYEINIDAVDRSAFPLAGHC
                     KIIVKLVDVNDNVPEMAITSIFLPIKEDAPLATVIALISVSDRDSGANGQVTCSLTPH
                     IPFKLVSTFKNYYSLVLDRALDRETIANYDVVVTARDGGSPSLWATASVSVEVADVND
                     NVPAFAQPEYTVFVKENNPPGAHIFTVSAMDADAQENALVSYSLVERRVGERLLSSYV
                     SVHAESGKVFALQPLDHEELELLQFQVSARDAGVPALGSNVTLQVFVLDENDNAPTLL
                     GPQGSGGTIELLSRSVSSGHVVAKVRAVDADSGYNAWLSYELQPATGAVRSPFRVGLY
                     TGEISTTRVLDEADMPRQRLLVLVKDHGEPPLTATATFLVSLVENSQTPKVSSRVLVG
                     TSGSDSTLIDVNVYLIIAICAVSSLLVLTLLLYTAIRCSATPTDGACAPGKPVLVCSS
                     AVGTWSYSQQRRQRVCSGEGPPKTDLMAFSPSLPQGPSSTENPRQPNPDWRYSASLRA
                     GMHSSVHLEEAGILRAGPGGPDQQWPTVSSATPEPEAGEVSPPVGAGVNSNSWTFKYG
                     PGNPKQSGPGELPDKFIIPGSPAIISIRQEPANNQIDKSDFITFGKKEETKKKKKKKK
                     GNKTQEKKEKGNSTTDNSDQ"
     exon            2511..2569
                     /gene="Pcdha5"
                     /gene_synonym="Cnr6; Crnr6"
                     /inference="alignment:Splign:2.1.0"
     exon            2570..2658
                     /gene="Pcdha5"
                     /gene_synonym="Cnr6; Crnr6"
                     /inference="alignment:Splign:2.1.0"
     exon            2659..5376
                     /gene="Pcdha5"
                     /gene_synonym="Cnr6; Crnr6"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      
        1 ggagagtagt acattttact taggaaaagg atcttccatt tttggatctg ctacagaagc
       61 tcacaaaaag caaggaaatc aaatctattg taaattggaa ctaagttgtc aaaggacttt
      121 gtgtggtgct gcaatagaga ctggagaagt ggaacaagat tgcgatggta tatttccagc
      181 gaggaagtcc gggatttcgg cgcctgctga tctcctttgt gcttctcgca gcctgggagg
      241 cagggagcgg ccagctccac tactccatcc ccgaggaggc caaacacggc accttcgtgg
      301 gccgcatcgc gcaggacctg gggctggagc tgacggagct ggtgccccgc ctgttcagag
      361 tggcgtccaa ggaccgcggg gaccttctgg aggtaaatct gcagaatggc attttgtttg
      421 tgaattctcg gatcgaccgg gaggagctgt gtgggcggag cgcggagtgt agcatccacc
      481 tggaggtgat cgtggacagg ccgctgcagg ttttccacgt ggaggtggag gtgaaggaca
      541 ttaacgacaa cccgcctaaa ttctcacgac ctgaacaaag attatttatt ttagagtcaa
      601 gaatgccaga ctcgcggttt ccggtagagg gcgcatctga tttggatata ggagccaatg
      661 cagccttgag ttataagata aatcctaatg aatattttga cttggatgtt aaaagaaacg
      721 aagaagaaac aagcgtttta caactagttt tgaagaagcc cctagataga gaagaaaccc
      781 aagagcatcg tttgttgctc attgcaattg atggagggaa acctgaacta acaggtactg
      841 ttcagttact gattgatgtg ttggatgcaa atgataatgc tccggagttt gataaatcta
      901 tttataatgt tagattgtta gaaaatacac ccaacgggac attagtcatt aaactcaatg
      961 cttcagatgc ggatgaggga attaataaag aaatactgta tttctttagt aatcttgttc
     1021 ttgacgatgt aaaatctaaa tttacgatag attcttccag tggagaaata aaagttaagg
     1081 gcgaactgga ttacgaagac tgtaaagtat atgaaattaa tattgatgca gtggacagaa
     1141 gcgcattccc actagcagga cactgcaaaa ttatagtgaa actagtggat gtaaatgata
     1201 acgtgcctga gatggccata acctccattt ttttgcctat caaagaggat gctccattgg
     1261 cgactgtcat cgctctgatt agcgtgtcag atcgtgactc aggcgccaat gggcaggtga
     1321 cctgctcctt gacaccccac atccccttca agctggtgtc cactttcaag aattactatt
     1381 cgcttgtact ggacagagct ctggaccgag agactatcgc taactacgac gttgttgtga
     1441 ccgctcgcga tggaggctcg ccctccttgt gggccacggc cagcgtgtcc gtggaggtgg
     1501 ctgacgtgaa cgacaacgtg cctgcgtttg cgcagcccga atacactgtg ttcgtgaagg
     1561 agaacaaccc gcctggtgcg cacatcttca cggtgtcagc gatggacgct gatgcacagg
     1621 agaacgcgct ggtgtcctac tcgctggtgg agcggagggt gggcgagcgc ttgctgtcga
     1681 gctatgtgtc tgtgcacgcg gagagcggca aggtgtttgc gctgcagcct ctggaccatg
     1741 aggagctgga gctgctgcag ttccaggtga gcgcgcggga tgctggtgtg cctgccctgg
     1801 gcagcaatgt gactctgcag gtgtttgtgc tggatgagaa cgacaacgca cccacgctgc
     1861 tggggcctca gggtagcgga ggaactattg agttgttgtc caggtcagtg agttctggcc
     1921 atgtggttgc gaaggtgcgt gcagtggacg cggattctgg ctacaacgcg tggctgtctt
     1981 atgagttgca gcctgcgaca ggtgctgtgc gcagcccgtt ccgcgtgggg ctatacactg
     2041 gtgagatcag cacaactcgt gttctggatg aagcggacat gccgcgtcaa cgcttgttgg
     2101 tgctggtgaa ggatcacggc gagccacctc tgacagccac ggccactttc ctggtgtctc
     2161 ttgtggagaa cagccagacc ccgaaggtct catccagggt gttggttgga acctctggtt
     2221 cagactccac gctgatagat gtcaacgtgt acctaatcat cgccatttgt gcggtttcca
     2281 gtctgttggt gctcaccctg cttctgtaca cagcgattcg ctgctcagcg acgcccactg
     2341 atggagcctg tgctccagga aagccagtgc tggtgtgctc cagcgcggta gggacctggt
     2401 catactcgca gcagaggcga cagagggtgt gctctggaga aggtccaccc aagaccgacc
     2461 tcatggcctt cagtcccagc ctacctcagg gacccagctc tacagagaat ccccggcagc
     2521 ccaaccctga ctggcgctac tctgcctcgc taagagcagg catgcacagc tctgtgcacc
     2581 tggaggaggc tggcattcta cgggctggtc caggagggcc tgatcagcag tggccaacag
     2641 tatccagtgc aacaccagaa cctgaggcag gagaggtgtc ccctccggtg ggcgccggtg
     2701 tcaacagcaa cagctggacc tttaaatacg gaccaggcaa ccccaaacag tccggtcccg
     2761 gtgagttgcc agacaaattc attatcccag gatctcctgc aatcatctcc atccggcagg
     2821 agcctgctaa caaccaaatt gacaaaagcg attttataac cttcggcaaa aaggaggaga
     2881 ccaagaaaaa gaagaaaaag aagaagggta acaagaccca ggagaaaaaa gagaaaggga
     2941 acagcacgac ggacaacagt gaccagtgag gccaccaaat ggaaacaagc cacttagcca
     3001 gtttttgtaa taatggcaaa tctctcccat gtagcaactc cccgctcctt tctcctatga
     3061 catgagccct cagaaatctg cagaaagttc cctgtgtctg tcttgatcgc atttaacagg
     3121 ttttgtctta aaaagctttc ctaagtctgg tgttaactct ctctctctcc actctggctt
     3181 gttttcagaa cctaaaaagc agacccaggt ttcctttctc ccccgccgca aaggagaagc
     3241 ttcccagccc cgccagtgag agttggactc tctgccctgt gcttcaagca tcctgtcttg
     3301 atgatatttg cagggcaggc tgaaaggtat tcaggttgag cagttgggtg tttgtggtca
     3361 ctgggtatgt gtggctacca agagtgttgg agagcctggt attggctggg atggtccaga
     3421 ttagactagt taacacaagg agggctgggg ctcaaaggca catcaacacc gggagtcttt
     3481 catctggagg gggaaaatgt gaaacttaca aggaccagac tttctcaatc tctcaactag
     3541 acatatgatg gccatcctct aacagacaaa accatcccca ccggcaaagc tttaggagcc
     3601 cctcaagtgt gctggctata acatcactgt attcaaaacc tgcagtatgc acacgagcca
     3661 gcagttcaag cgtttaacaa gagggtcggc cagggcaaca gaagcagatc tgatgtgttt
     3721 cctgtacacg tccttgtgct cacgctatta aaaattcttt tgcacacaat gtttatgaaa
     3781 aggtctcatc cttttccaac aacacatatg caaaagcaaa agaaaaaccc aagacctcac
     3841 tttatgctgt ttgttgtttg atagatttat taaaaagaaa agagaaagtc gatagctata
     3901 aatctttaaa ggaatatgat gaatacaatc cccccaacct tccctcaaaa gagaatccag
     3961 tctacagcca tttgaaatga tcgttgctgc tacagaagtg ctttaagaga attgcctgga
     4021 acatctgtat tatcccggcc acctgccaat cacagcttta ctctttcagg tcactctggg
     4081 gctgcctctt gcatgtatta attactaaat agaaggatct ttctctcttt tctaagaaaa
     4141 atgatgtgca ctttgattac acaaccttct ctaacccacg atatcaagac ccagaaactg
     4201 aagaaaaatc ttgttttctc atgcatacag tgagcagact tttcattcct ctggttctgt
     4261 ggttgtctcg gtgtgctagc ctacacctcc accttgttta gctttccttt tctagaacac
     4321 tctgaattgc taaccttact aacacctatg atgttacctg aatcaatctc ccatatgtat
     4381 gctgtatgct attataagac tcctgagata tacttactct gtgcttgtgt atgtgaatgt
     4441 taatgcaact attacctaga gtgaacttta agctttattg ttgaatgtaa gcccattata
     4501 tttccttttg tacacctgtg gaaaagtgga atagtgtttt ttttaaaacc attgttaatc
     4561 agcttttgtg tatgaaagac acagtaaaat ttctttctta aatcaagatg ctggtgattc
     4621 aaggaatttt atttatggtc agccaagggc tgtctcttgc caagaatcct gctggcaagg
     4681 gaaaatggat aaagctggtt tttttttttc ctagtaagaa ttctggaata aatactgaag
     4741 aaagtccctg agggtatgca agcacaaaat tgtaccaatc tgacctcttt gaatttgcag
     4801 actgctttga aatgctatcc ggaatatcag cttgtagaaa gtaataaaat ttactgttac
     4861 cataaataag acattttaag tttattgtgc acaacttaga tgtttgatta attatattat
     4921 ctacttaaaa gcatataaaa gaggtaggag tctgttttaa aaggcataaa aaatctcaaa
     4981 aaaaaaaaac ctgtcttgtc tacttttagc ttcattctcc catattttga agggtgtgta
     5041 acttcagctc tgcaggattg catggggtaa aactcgttga cagcgcatgt gaaccattgc
     5101 tacattgtag gttgtgatca ttttgcccca ctgaagccca tgtaactgac cttacgtgcc
     5161 ttttgaacta ggagaatcgg gctataattt attaatgatg ataatgataa tgtatatgta
     5221 cagcactttt taaccttaca aagtgctttc caattcgtgt tagttattag ttattacagc
     5281 tgtaaggata aaacacgtca tgtggattca tttttaattg gtgctattgg tatttcctct
     5341 gttcttgcta ataaatggaa atggtggtgt gaaagc
//
