LOCUS       NM_009957               5334 bp    mRNA    linear   ROD 03-AUG-2024
DEFINITION  Mus musculus protocadherin alpha 7 (Pcdha7), mRNA.
ACCESSION   NM_009957 XM_908860
VERSION     NM_009957.2
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 5334)
  AUTHORS   Mancia Leon,W.R., Spatazza,J., Rakela,B., Chatterjee,A., Pande,V.,
            Maniatis,T., Hasenstaub,A.R., Stryker,M.P. 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 5334)
  AUTHORS   Elbert,A., Vogt,D., Watson,A., Levy,M., Jiang,Y., Brule,E.,
            Rowland,M.E., Rubenstein,J. and Berube,N.G.
  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 5334)
  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 5334)
  AUTHORS   Goodman,K.M., Rubinstein,R., Thu,C.A., Bahna,F., Mannepalli,S.,
            Ahlsen,G., Rittenhouse,C., Maniatis,T., Honig,B. and Shapiro,L.
  TITLE     Structural Basis of Diverse Homophilic Recognition by Clustered
            alpha- and beta-Protocadherins
  JOURNAL   Neuron 90 (4), 709-723 (2016)
   PUBMED   27161523
REFERENCE   5  (bases 1 to 5334)
  AUTHORS   Thompson,C.L., Ng,L., Menon,V., Martinez,S., Lee,C.K.,
            Glattfelder,K., Sunkin,S.M., Henry,A., Lau,C., Dang,C.,
            Garcia-Lopez,R., Martinez-Ferre,A., Pombero,A., Rubenstein,J.L.R.,
            Wakeman,W.B., Hohmann,J., Dee,N., Sodt,A.J., Young,R., Smith,K.,
            Nguyen,T.N., Kidney,J., Kuan,L., Jeromin,A., Kaykas,A., Miller,J.,
            Page,D., Orta,G., Bernard,A., Riley,Z., Smith,S., Wohnoutka,P.,
            Hawrylycz,M.J., Puelles,L. and Jones,A.R.
  TITLE     A high-resolution spatiotemporal atlas of gene expression of the
            developing mouse brain
  JOURNAL   Neuron 83 (2), 309-323 (2014)
   PUBMED   24952961
REFERENCE   6  (bases 1 to 5334)
  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 5334)
  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 5334)
  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 5334)
  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 5334)
  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_009957.1.
            
            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 :: AY013765.1, SRR7652917.1264783.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN00849384, SAMN00849389
                                           [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
            1-2468              AC020968.3         185336-187803
            2469-2527           AC020972.3         11539-11597         c
            2528-2616           AC020972.3         8399-8487           c
            2617-5334           AC020973.3         123819-126536
FEATURES             Location/Qualifiers
     source          1..5334
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="18"
                     /map="18 19.46 cM"
     gene            1..5334
                     /gene="Pcdha7"
                     /gene_synonym="Cnr4; Crnr4"
                     /note="protocadherin alpha 7"
                     /db_xref="GeneID:12939"
                     /db_xref="MGI:MGI:1298369"
     exon            1..2468
                     /gene="Pcdha7"
                     /gene_synonym="Cnr4; Crnr4"
                     /inference="alignment:Splign:2.1.0"
     CDS             87..2927
                     /gene="Pcdha7"
                     /gene_synonym="Cnr4; Crnr4"
                     /note="cadherin-related neuronal receptor 4; PCDH-alpha-7"
                     /codon_start=1
                     /product="protocadherin alpha-7 precursor"
                     /protein_id="NP_034087.2"
                     /db_xref="CCDS:CCDS79619.1"
                     /db_xref="GeneID:12939"
                     /db_xref="MGI:MGI:1298369"
                     /translation="MRIKRQQFEMVNLRGYNWKSQQLLLFLIIVAAWEAGSGQLHYSV
                     PEEAKHGTFVGRIAQDLGLELTELVPRLFRVASKDRGDLLEVNLQNGILFVNSRIDRE
                     ELCGRSAECSIHLEVIVDRPLQVFHVEVEVKDINDNPPMFPATQKALFILESRLLDSR
                     FPLEGASDADVGSNALLTYRLSTNEHFSLDVPPNHEQVKPLGLVLRKPLDREEAAEIR
                     LLLTATDGGKPELTGTVQLLITVLDVNDNAPVFDRSLYTVKLPENVPNGTLVIKVNAS
                     DLDEGVNGDVMYSFSSDVSSDIKSKFHMDTVSGEITVIGIIDFEESKAYKIPLEARDK
                     GFPQLPGHCTILVEVVDANDNAPQLTVSSLSLPVSEDSQPGRVVTLISVFDRDSGANG
                     QVTCSLTPHIPFKLVSTFKNYYSLVLDSALDRETIANYDVIVTARDGGSPSLWATASV
                     SVEVADVNDNAPLFAQPEYTVFVKENNPPGAHIFTVSAMDADAQENALVSYSLVERRV
                     GERLLSSYVSVHAESGKVFALQPLDHEELELLQFQVSARDAGVPALGSNVTLQVFVLD
                     ENDNAPTLLGPLANGVGGTMNEVVSRALVPGQVVAKVRAVDEDSGYNAWLSFELQPVA
                     GGVRSPFRVGLYTGEISTTRALEETDALRQCLLVLVKDHGEPSLTATATVLLSLVDSG
                     QTQKVSSKVSAGASRVDQRLVDVNVYLIIAICAVSSLLVLTLLLYTALRCSATPTDGA
                     CAPGKPMLVCSSAVGSWSYSQQRRQRVCSGEGPPKTDLMAFSPSLPQGPSSTDNPRQP
                     NPDWRYSASLRAGMHSSVHLEEAGILRAGPGGPDQQWPTVSSATPEPEAGEVSPPVGA
                     GVNSNSWTFKYGPGNPKQSGPGELPDKFIIPGSPAIISIRQEPANNQIDKSDFITFGK
                     KEETKKKKKKKKGNKTQEKKEKGNSTTDNSDQ"
     exon            2469..2527
                     /gene="Pcdha7"
                     /gene_synonym="Cnr4; Crnr4"
                     /inference="alignment:Splign:2.1.0"
     exon            2528..2616
                     /gene="Pcdha7"
                     /gene_synonym="Cnr4; Crnr4"
                     /inference="alignment:Splign:2.1.0"
     exon            2617..5334
                     /gene="Pcdha7"
                     /gene_synonym="Cnr4; Crnr4"
                     /inference="alignment:Splign:2.1.0"
     regulatory      5308..5313
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Pcdha7"
                     /gene_synonym="Cnr4; Crnr4"
                     /note="hexamer: AATAAA"
     polyA_site      5332
                     /gene="Pcdha7"
                     /gene_synonym="Cnr4; Crnr4"
                     /note="major polyA site"
ORIGIN      
        1 actcttcggt tgctccacaa tggccagcat ctcgggactg gaatgaagaa ataaaaaacc
       61 tccagaattt gggataactg tcgcgaatga gaataaaacg tcagcaattt gaaatggtaa
      121 acctgagagg atacaactgg aagagccaac aattactcct gttcctgata attgtggcag
      181 cctgggaggc agggagcggc cagctccact actccgtccc agaggaagcc aaacacggca
      241 ccttcgtggg ccgcatcgcg caggacctgg ggctggagct gacggagctg gtgccccgcc
      301 tgttcagggt ggcgtccaag gaccgcgggg accttctgga ggtaaatctt cagaatggca
      361 ttttgtttgt gaattctcgc atcgaccggg aggaactgtg cgggcggagc gcggagtgta
      421 gcatccacct ggaggtgatc gtggacaggc cgctgcaggt tttccacgtg gaggtggagg
      481 tgaaggacat taatgacaac cctcccatgt ttccagcgac acaaaaggct ctgtttatcc
      541 tggagtccag actgcttgac tcgcggtttc cactagaggg cgcgtcagat gcagatgtcg
      601 gttccaatgc tctgctgact tacagactga gcaccaatga acatttctct ctggatgtac
      661 cgcccaacca cgagcaggtg aaacctcttg ggctggtttt gcggaaacct ttagacagag
      721 aagaagctgc agagattcgc ttattgctca cggccaccga cggaggcaaa ccggagctga
      781 caggcaccgt tcaattactc atcaccgtgc tggatgtcaa tgacaatgct ccagtttttg
      841 acagatctct gtatactgtg aaattgccag aaaacgttcc aaatggaaca ttggtaatca
      901 aagtcaatgc ctcagatttg gacgaaggcg tgaatgggga cgttatgtac tcattttcta
      961 gtgatgtttc ttcagatata aaatccaagt tccacatgga cactgtgagt ggagagatta
     1021 cagttatagg aattattgat ttcgaagaga gtaaagctta caagattcca ttggaggcac
     1081 gtgataaagg gttcccacaa ctgcctggac actgtaccat tcttgtggaa gttgtagatg
     1141 ctaatgacaa cgctccacag ttgacggtta gttccttgtc tctcccagta tccgaggaca
     1201 gtcaacctgg aagagtcgtc actttaatta gcgtatttga ccgtgattcc ggtgccaatg
     1261 ggcaggtgac ctgctccctg actcctcata tccccttcaa gctggtgtcc acattcaaaa
     1321 attactattc gctcgtgctg gacagtgctc tggaccgaga gaccatcgct aactatgatg
     1381 tgattgtgac cgctcgcgat ggcggttcgc cctccctgtg ggccacggcc agcgtgtccg
     1441 tggaggtggc tgatgtgaac gacaatgctc cactgtttgc gcagcctgaa tacacggtgt
     1501 tcgtgaagga gaacaacccg cctggtgcgc acatctttac agtgtcagcg atggatgctg
     1561 atgcgcagga gaatgcgctg gtgtcctact cgctggtgga acggagggtg ggcgagcgct
     1621 tgctgtcgag ctatgtgtct gtgcacgcgg agagcggcaa ggtgttcgct ctgcagcctc
     1681 tggaccatga ggagctggaa ctgctgcagt tccaggtgag cgcgcgggat gctggtgtgc
     1741 ctgccctggg cagcaatgtg actctgcagg tgtttgtact ggacgagaac gacaatgcac
     1801 ctaccctgct ggggcctttg gctaacgggg ttggtggcac aatgaatgag gtagtatcaa
     1861 gagctttggt gcctggtcag gttgtggcga aagtccgggc cgtagatgag gactctggat
     1921 acaatgcgtg gttgtctttt gagctgcagc cagttgcggg tggagttcgt agtcccttcc
     1981 gtgtaggcct gtacacagga gaaatcagca cgacacgtgc tctggaggag acagatgcct
     2041 tgcggcagtg cttgttagtg ttggtgaaag atcacggaga accttctctg accgccacag
     2101 ccacggtgtt gctttctctg gtagacagcg gccaaacaca gaaggtctca tctaaggtgt
     2161 cagctggagc ctccagagtg gatcagaggc tggtggatgt caacgtgtac ctgatcatcg
     2221 ccatctgcgc ggtgtccagc ctgttggtgc tcacgctact gctgtacaca gcgctgcgct
     2281 gttcggcgac gcccaccgat ggagcctgtg ctccagggaa gcccatgctg gtgtgctcca
     2341 gcgcggtggg gagctggtca tactcgcagc agaggcgaca gagagtgtgc tctggagaag
     2401 gcccacccaa gaccgacctc atggccttca gccccagcct acctcagggt cccagctcta
     2461 cagataaccc ccggcagccc aaccctgact ggcgctactc tgcctcgcta agagcaggca
     2521 tgcacagctc tgtgcacctg gaggaggctg gcattctacg ggctggtcca ggagggcctg
     2581 atcagcagtg gccaacagta tccagtgcaa caccagaacc tgaggcagga gaggtgtccc
     2641 ctccggtggg cgccggtgtc aacagcaaca gctggacctt taaatacgga ccaggcaacc
     2701 ccaaacagtc cggtcccggt gagttgccag acaaattcat tatcccagga tctcctgcaa
     2761 tcatctccat ccggcaggag cctgctaaca accaaattga caaaagcgat tttataacct
     2821 tcggcaaaaa ggaggagacc aagaaaaaga agaaaaagaa gaagggtaac aagacccagg
     2881 agaaaaaaga gaaagggaac agcacgacgg acaacagtga ccagtgaggc caccaaatgg
     2941 aaacaagcca cttagccagt ttttgtaata atggcaaatc tctcccatgt agcaactccc
     3001 cgctcctttc tcctatgaca tgagccctca gaaatctgca gaaagttccc tgtgtctgtc
     3061 ttgatcgcat ttaacaggtt ttgtcttaaa aagctttcct aagtctggtg ttaactctct
     3121 ctctctccac tctggcttgt tttcagaacc taaaaagcag acccaggttt cctttctccc
     3181 ccgccgcaaa ggagaagctt cccagccccg ccagtgagag ttggactctc tgccctgtgc
     3241 ttcaagcatc ctgtcttgat gatatttgca gggcaggctg aaaggtattc aggttgagca
     3301 gttgggtgtt tgtggtcact gggtatgtgt ggctaccaag agtgttggag agcctggtat
     3361 tggctgggat ggtccagatt agactagtta acacaaggag ggctggggct caaaggcaca
     3421 tcaacaccgg gagtctttca tctggagggg gaaaatgtga aacttacaag gaccagactt
     3481 tctcaatctc tcaactagac atatgatggc catcctctaa cagacaaaac catccccacc
     3541 ggcaaagctt taggagcccc tcaagtgtgc tggctataac atcactgtat tcaaaacctg
     3601 cagtatgcac acgagccagc agttcaagcg tttaacaaga gggtcggcca gggcaacaga
     3661 agcagatctg atgtgtttcc tgtacacgtc cttgtgctca cgctattaaa aattcttttg
     3721 cacacaatgt ttatgaaaag gtctcatcct tttccaacaa cacatatgca aaagcaaaag
     3781 aaaaacccaa gacctcactt tatgctgttt gttgtttgat agatttatta aaaagaaaag
     3841 agaaagtcga tagctataaa tctttaaagg aatatgatga atacaatccc cccaaccttc
     3901 cctcaaaaga gaatccagtc tacagccatt tgaaatgatc gttgctgcta cagaagtgct
     3961 ttaagagaat tgcctggaac atctgtatta tcccggccac ctgccaatca cagctttact
     4021 ctttcaggtc actctggggc tgcctcttgc atgtattaat tactaaatag aaggatcttt
     4081 ctctcttttc taagaaaaat gatgtgcact ttgattacac aaccttctct aacccacgat
     4141 atcaagaccc agaaactgaa gaaaaatctt gttttctcat gcatacagtg agcagacttt
     4201 tcattcctct ggttctgtgg ttgtctcggt gtgctagcct acacctccac cttgtttagc
     4261 tttccttttc tagaacactc tgaattgcta accttactaa cacctatgat gttacctgaa
     4321 tcaatctccc atatgtatgc tgtatgctat tataagactc ctgagatata cttactctgt
     4381 gcttgtgtat gtgaatgtta atgcaactat tacctagagt gaactttaag ctttattgtt
     4441 gaatgtaagc ccattatatt tccttttgta cacctgtgga aaagtggaat agtgtttttt
     4501 ttaaaaccat tgttaatcag cttttgtgta tgaaagacac agtaaaattt ctttcttaaa
     4561 tcaagatgct ggtgattcaa ggaattttat ttatggtcag ccaagggctg tctcttgcca
     4621 agaatcctgc tggcaaggga aaatggataa agctggtttt tttttttcct agtaagaatt
     4681 ctggaataaa tactgaagaa agtccctgag ggtatgcaag cacaaaattg taccaatctg
     4741 acctctttga atttgcagac tgctttgaaa tgctatccgg aatatcagct tgtagaaagt
     4801 aataaaattt actgttacca taaataagac attttaagtt tattgtgcac aacttagatg
     4861 tttgattaat tatattatct acttaaaagc atataaaaga ggtaggagtc tgttttaaaa
     4921 ggcataaaaa atctcaaaaa aaaaaaacct gtcttgtcta cttttagctt cattctccca
     4981 tattttgaag ggtgtgtaac ttcagctctg caggattgca tggggtaaaa ctcgttgaca
     5041 gcgcatgtga accattgcta cattgtaggt tgtgatcatt ttgccccact gaagcccatg
     5101 taactgacct tacgtgcctt ttgaactagg agaatcgggc tataatttat taatgatgat
     5161 aatgataatg tatatgtaca gcacttttta accttacaaa gtgctttcca attcgtgtta
     5221 gttattagtt attacagctg taaggataaa acacgtcatg tggattcatt tttaattggt
     5281 gctattggta tttcctctgt tcttgctaat aaatggaaat ggtggtgtga aagc
//
