LOCUS       NM_007767               6613 bp    mRNA    linear   ROD 07-AUG-2023
DEFINITION  Mus musculus protocadherin alpha 6 (Pcdha6), mRNA.
ACCESSION   NM_007767 XM_908769
VERSION     NM_007767.4
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 6613)
  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 6613)
  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 6613)
  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 6613)
  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 6613)
  AUTHORS   Gendrel AV, Tang YA, Suzuki M, Godwin J, Nesterova TB, Greally JM,
            Heard E and Brockdorff N.
  TITLE     Epigenetic functions of smchd1 repress gene clusters on the
            inactive X chromosome and on autosomes
  JOURNAL   Mol Cell Biol 33 (16), 3150-3165 (2013)
   PUBMED   23754746
REFERENCE   6  (bases 1 to 6613)
  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 6613)
  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 6613)
  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 6613)
  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 6613)
  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 20, 2019 this sequence version replaced NM_007767.3.
            
            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 :: AY013764.1, D86917.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN01164131, SAMN01164132
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            CDS uses downstream in-frame AUG :: downstream AUG is associated
                                                with N-terminal localization
                                                signal
            RefSeq Select criteria           :: based on single protein-coding
                                                transcript
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-2513              AC020968.3         179150-181662
            2514-2572           AC020972.3         11539-11597         c
            2573-2661           AC020972.3         8399-8487           c
            2662-6613           AC020973.3         123819-127770
FEATURES             Location/Qualifiers
     source          1..6613
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="18"
                     /map="18 19.46 cM"
     gene            1..6613
                     /gene="Pcdha6"
                     /gene_synonym="CNR; Cnr2; Crnr2"
                     /note="protocadherin alpha 6"
                     /db_xref="GeneID:12937"
                     /db_xref="MGI:MGI:1298367"
     exon            1..2513
                     /gene="Pcdha6"
                     /gene_synonym="CNR; Cnr2; Crnr2"
                     /inference="alignment:Splign:2.1.0"
     CDS             132..2972
                     /gene="Pcdha6"
                     /gene_synonym="CNR; Cnr2; Crnr2"
                     /note="cadherin-related neuronal receptor 2"
                     /codon_start=1
                     /product="protocadherin alpha-6 precursor"
                     /protein_id="NP_031793.2"
                     /db_xref="CCDS:CCDS79618.1"
                     /db_xref="GeneID:12937"
                     /db_xref="MGI:MGI:1298367"
                     /translation="MDFTTEGRLGTRCMLLSLLLLAAWEAGSGQLHYSVPEEAKHGTF
                     VGRIAQDLGLELTELVPRLFRVASKDRGDLLEVNLQNGILFVNSRIDREELCGRSVEC
                     SIHLEVIVDRPLQVFHVEVEVRDINDNPPVFSVKEQRMLIYESRLPDSLFPLEGASDA
                     DVGLNSMLTYKLSPSEYFGLDVKSNSDGNKQIRLLLKKSLDREDAPEHKLLLTATDGG
                     KPELTGSVQLLVTVLDVNDNAPTFQHPEYEVRILENSDNGTTVIRLNASDKDEGTNSA
                     ISYSFNRLVPPKTLEQFSIDADTGEIITQGNLDFEQVDVYKIHVDATDKGHPPMVGHC
                     TVLVKVLDENDNVPQITLTSLSLPVREDAALSTVIALISVSDLDSGSNGQVTCSLSPH
                     VPFKLVSTFKNYYSLVLDSALDRETTADYQVVVTARDGGSPSLWTTASVSVEVADVND
                     NAPSFAQPDYTVFVKENNPPGAHIFTVSAMDADAQENALVSYSLVERRVGERLLSSYV
                     SVHAESGKVFALQPLDHEELELLQFQVSARDAGVPALGSNVTLQVFVLDENDNAPTLL
                     GPWTPGSGGVVSELVSPSVGAGQVVTKVRAVDADSGYNAWLSYELHPLAGGTRSLFRV
                     GLYTGEISTTRALEEADAPRHRLLVLVKDHGEPALIATATVLVSLVENSQTPKASSRA
                     QGATGQEVSLVNVNVYLIIAICAVSSLLVLTLMVYTALRCSVPPTEGVCGAGKPVLVC
                     SSAVGSWSYSQQRRQKVCSGEGPPKTDLMAFSPSLPPCPVVGEHQDLNDDHCSRPRQP
                     NPDWRYSASLRAGMHSSVHLEEAGILRAGPGGPDQQWPTVSSATPEPEAGEVSPPVGA
                     GVNSNSWTFKYGPGNPKQSGPGELPDKFIIPGSPAIISIRQEPANNQIDKSDFITFGK
                     KEETKKKKKKKKGNKTQEKKEKGNSTTDNSDQ"
     exon            2514..2572
                     /gene="Pcdha6"
                     /gene_synonym="CNR; Cnr2; Crnr2"
                     /inference="alignment:Splign:2.1.0"
     exon            2573..2661
                     /gene="Pcdha6"
                     /gene_synonym="CNR; Cnr2; Crnr2"
                     /inference="alignment:Splign:2.1.0"
     exon            2662..6613
                     /gene="Pcdha6"
                     /gene_synonym="CNR; Cnr2; Crnr2"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      
        1 ggtagctgga tcttccaaga ctgctgaagg atggcgaatg cagaagaact gaatcgatag
       61 actttgaatc atacagaatt ttatgcagag aaaaaaatct tctaatggaa acaaagcaag
      121 aagtatttga aatggatttt accactgaag gccgactggg aacacggtgt atgctgctct
      181 cgctcctgct cctcgcagcc tgggaggcag ggagcggcca gcttcattac tccgtcccag
      241 aggaggccaa acacggcacc ttcgtgggcc gcatcgcgca ggacctgggg ctggagctga
      301 cggagctggt gccccgcctg ttcagggtgg cgtccaagga ccgcggggac cttctggagg
      361 taaatctgca gaatggcatt ttgtttgtga attctcggat cgaccgggag gagctgtgcg
      421 ggcggagcgt ggagtgtagc atccacctgg aggtgatcgt ggacaggccg ctgcaggttt
      481 tccacgtgga ggtggaggtg agggacatta atgataaccc gcctgtgttc tcagtaaagg
      541 agcaaagaat gttaatttac gaatctaggc tgccagattc tttgtttcca ctagagggcg
      601 catcagatgc tgatgttgga ttaaattcta tgttaaccta taaactcagt cccagcgaat
      661 actttgggct agatgtgaaa tcaaacagcg atggcaacaa acaaattaga ctcttgttga
      721 aaaaatcctt ggacagagag gatgctcctg agcataagct actgctgaca gccacggatg
      781 gaggcaaacc tgagctcaca ggctctgttc agctgctggt cactgtgctg gatgtgaatg
      841 ataacgcccc tactttccag caccctgagt atgaagtgag aatcttggaa aactcagaca
      901 acggaacgac agttattaga ctgaatgctt ctgacaagga tgaagggacg aattcagcaa
      961 tttcgtactc ttttaataga ctggtgccgc ccaagactct tgagcagttt agcatagatg
     1021 cagatacagg agaaatcata actcaaggaa atttggactt tgagcaagta gatgtctaca
     1081 aaatccacgt tgatgcgacg gacaaaggac accctccgat ggtgggccat tgcactgttt
     1141 tagtgaaggt attggatgag aacgacaatg tgcctcagat cactttgact tccttatccc
     1201 tgcctgttcg agaggacgct gcactgagta ctgtcattgc tctaattagc gtttcggatc
     1261 tggactctgg atccaacggg caggtgacct gctccctgag tcctcatgtc cccttcaagt
     1321 tggtgtccac cttcaagaat tactattcgc ttgtgttgga cagcgccctg gaccgagaga
     1381 ccacagctga ctatcaggtg gtggtgacag cgcgggacgg gggttctcct tctttgtgga
     1441 ccacggctag cgtgtctgtg gaggtggccg atgtgaacga caatgcgcct tcatttgcgc
     1501 agcctgatta cacggtgttc gtgaaggaga acaaccctcc tggagcgcac atcttcacag
     1561 tatcggcgat ggacgcggat gcgcaggaga acgcgctggt gtcctactcg ctggtggagc
     1621 ggagggtggg cgagcgcttg ctgtcgagct atgtgtctgt gcacgcggaa agcggcaagg
     1681 tgttcgctct gcagcctctg gaccatgagg agctggaact gctgcagttc caggtgagcg
     1741 cgcgggatgc tggtgtgcct gccctgggca gcaatgtgac tctgcaggtg tttgtgctgg
     1801 atgagaacga caatgcgccc acgctgcttg gaccttggac accaggatct ggtggtgtag
     1861 tgagcgaact tgtgtcacct tcagtgggtg ctggccaggt ggtcacaaag gtgcgtgcag
     1921 tagatgcgga ttctggctat aatgcctggc tgtcttatga gctgcatcct ttagcaggtg
     1981 gaacgcggag tctgtttagg gtaggtctgt acacgggcga gatcagtacc acgcgtgccc
     2041 ttgaggaggc agatgcacca cgccatcgcc tattagtgct ggtgaaggac cacggggagc
     2101 cagcgctgat tgccacagcc actgtgttag tgtctctggt tgagaacagc cagactccaa
     2161 aagcctcttc gcgagcgcaa ggtgccactg gccaggaagt ttcgttagtg aatgtcaacg
     2221 tgtacctgat cattgccatc tgtgcggtgt ccagcctact agttctaacc ctcatggtat
     2281 acaccgcact gcggtgctca gttccaccta cagagggtgt gtgcggggca gggaagcctg
     2341 tgctggtgtg ctctagtgcg gtagggagct ggtcctactc acagcagagg agacagaagg
     2401 tttgttctgg agagggacca cccaaaaccg atctcatggc cttcagcccg agtcttcctc
     2461 cttgtccggt tgtgggtgag catcaggatt tgaacgacga tcattgctca agaccccggc
     2521 agcccaaccc tgactggcgc tactctgcct cgctaagagc aggcatgcac agctctgtgc
     2581 acctggagga ggctggcatt ctacgggctg gtccaggagg gcctgatcag cagtggccaa
     2641 cagtatccag tgcaacacca gaacctgagg caggagaggt gtcccctccg gtgggcgccg
     2701 gtgtcaacag caacagctgg acctttaaat acggaccagg caaccccaaa cagtccggtc
     2761 ccggtgagtt gccagacaaa ttcattatcc caggatctcc tgcaatcatc tccatccggc
     2821 aggagcctgc taacaaccaa attgacaaaa gcgattttat aaccttcggc aaaaaggagg
     2881 agaccaagaa aaagaagaaa aagaagaagg gtaacaagac ccaggagaaa aaagagaaag
     2941 ggaacagcac gacggacaac agtgaccagt gaggccacca aatggaaaca agccacttag
     3001 ccagtttttg taataatggc aaatctctcc catgtagcaa ctccccgctc ctttctccta
     3061 tgacatgagc cctcagaaat ctgcagaaag ttccctgtgt ctgtcttgat cgcatttaac
     3121 aggttttgtc ttaaaaagct ttcctaagtc tggtgttaac tctctctctc tccactctgg
     3181 cttgttttca gaacctaaaa agcagaccca ggtttccttt ctcccccgcc gcaaaggaga
     3241 agcttcccag ccccgccagt gagagttgga ctctctgccc tgtgcttcaa gcatcctgtc
     3301 ttgatgatat ttgcagggca ggctgaaagg tattcaggtt gagcagttgg gtgtttgtgg
     3361 tcactgggta tgtgtggcta ccaagagtgt tggagagcct ggtattggct gggatggtcc
     3421 agattagact agttaacaca aggagggctg gggctcaaag gcacatcaac accgggagtc
     3481 tttcatctgg agggggaaaa tgtgaaactt acaaggacca gactttctca atctctcaac
     3541 tagacatatg atggccatcc tctaacagac aaaaccatcc ccaccggcaa agctttagga
     3601 gcccctcaag tgtgctggct ataacatcac tgtattcaaa acctgcagta tgcacacgag
     3661 ccagcagttc aagcgtttaa caagagggtc ggccagggca acagaagcag atctgatgtg
     3721 tttcctgtac acgtccttgt gctcacgcta ttaaaaattc ttttgcacac aatgtttatg
     3781 aaaaggtctc atccttttcc aacaacacat atgcaaaagc aaaagaaaaa cccaagacct
     3841 cactttatgc tgtttgttgt ttgatagatt tattaaaaag aaaagagaaa gtcgatagct
     3901 ataaatcttt aaaggaatat gatgaataca atccccccaa ccttccctca aaagagaatc
     3961 cagtctacag ccatttgaaa tgatcgttgc tgctacagaa gtgctttaag agaattgcct
     4021 ggaacatctg tattatcccg gccacctgcc aatcacagct ttactctttc aggtcactct
     4081 ggggctgcct cttgcatgta ttaattacta aatagaagga tctttctctc ttttctaaga
     4141 aaaatgatgt gcactttgat tacacaacct tctctaaccc acgatatcaa gacccagaaa
     4201 ctgaagaaaa atcttgtttt ctcatgcata cagtgagcag acttttcatt cctctggttc
     4261 tgtggttgtc tcggtgtgct agcctacacc tccaccttgt ttagctttcc ttttctagaa
     4321 cactctgaat tgctaacctt actaacacct atgatgttac ctgaatcaat ctcccatatg
     4381 tatgctgtat gctattataa gactcctgag atatacttac tctgtgcttg tgtatgtgaa
     4441 tgttaatgca actattacct agagtgaact ttaagcttta ttgttgaatg taagcccatt
     4501 atatttcctt ttgtacacct gtggaaaagt ggaatagtgt tttttttaaa accattgtta
     4561 atcagctttt gtgtatgaaa gacacagtaa aatttctttc ttaaatcaag atgctggtga
     4621 ttcaaggaat tttatttatg gtcagccaag ggctgtctct tgccaagaat cctgctggca
     4681 agggaaaatg gataaagctg gttttttttt ttcctagtaa gaattctgga ataaatactg
     4741 aagaaagtcc ctgagggtat gcaagcacaa aattgtacca atctgacctc tttgaatttg
     4801 cagactgctt tgaaatgcta tccggaatat cagcttgtag aaagtaataa aatttactgt
     4861 taccataaat aagacatttt aagtttattg tgcacaactt agatgtttga ttaattatat
     4921 tatctactta aaagcatata aaagaggtag gagtctgttt taaaaggcat aaaaaatctc
     4981 aaaaaaaaaa aacctgtctt gtctactttt agcttcattc tcccatattt tgaagggtgt
     5041 gtaacttcag ctctgcagga ttgcatgggg taaaactcgt tgacagcgca tgtgaaccat
     5101 tgctacattg taggttgtga tcattttgcc ccactgaagc ccatgtaact gaccttacgt
     5161 gccttttgaa ctaggagaat cgggctataa tttattaatg atgataatga taatgtatat
     5221 gtacagcact ttttaacctt acaaagtgct ttccaattcg tgttagttat tagttattac
     5281 agctgtaagg ataaaacacg tcatgtggat tcatttttaa ttggtgctat tggtatttcc
     5341 tctgttcttg ctaataaatg gaaatggtgg tgtgaaagca atggtggtca tttctaagta
     5401 taagagtagg agaacacggg acactgatgg tcatgacccg ttactgctca agagtctggc
     5461 tgttacctgg atcttgtttg tcacggaggc aaacaagggt gggattaaga gtcacacgtt
     5521 acagccaggg gagtgatgat cacttcctgc tttgctattt caatctgaca agaactacag
     5581 taaatcggtt tttatgacta gagacccctt cctcggccat cctgtttaac tatttattta
     5641 gcccttgtac ctctctacaa ttagaaagcc aagtaatcac acaaacacag atacaccaca
     5701 gacactcact ccaacacaca tgcccatacc acacgaccac atacttcaca cacatacaca
     5761 cacactccac ccacacccac attatacacc cacacacata acacacacac acacacatat
     5821 cctacacaca tatactcaca cacgcctata acacaccaca acacagttca cacacatata
     5881 cacacccttc acacatatta cacacacaca cacacacaca cacacacaca cacacactac
     5941 actacacaca taccctccac atatatcctc ccatacatat actcacacac acctacaaca
     6001 caccccatac acaccacaca tatactttac acacacacta cacacataca caccccacac
     6061 acacccacac ccactacacc cccaccctcc ccacacacca cccctacaaa ttttcttttg
     6121 ttgatgacat agtacttaac ctccaccctc ctggataggt tcattccatg ctactacatt
     6181 ttctgttaac aagtagatag attatccttt tgaagcttaa attttgatga gcattggctt
     6241 tagattcgat agttctcagt gtggaacagt cctcctctct tccaaggtgg gaggagaggg
     6301 ggcatcagtt tatgtcagag atatttttgt cttccttaat tggaaatgag aatgctgtgg
     6361 ctttcattga gactaaagac actgctcaac accccacagt tcacaggaga ggccccccac
     6421 acacaagaaa cgaactttct agttcaaact gttaatagta acaagagtgg ggaagcttga
     6481 gagagggagt gacaaagtgg aagggaggtg ctgttaataa cccctctatg gtttccacaa
     6541 ggatggcagc agctgactgg ggtgtcagga ctacctacgc atgtaaataa catgatatct
     6601 ctctgtagct agc
//
