LOCUS       NM_053933               5241 bp    mRNA    linear   ROD 04-FEB-2024
DEFINITION  Rattus norvegicus protocadherin alpha 4 (Pcdha4), mRNA.
ACCESSION   NM_053933
VERSION     NM_053933.1
KEYWORDS    RefSeq; RefSeq Select.
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 5241)
  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   2  (bases 1 to 5241)
  AUTHORS   Zou,C., Huang,W., Ying,G. and Wu,Q.
  TITLE     Sequence analysis and expression mapping of the rat clustered
            protocadherin gene repertoires
  JOURNAL   Neuroscience 144 (2), 579-603 (2007)
   PUBMED   17110050
REFERENCE   3  (bases 1 to 5241)
  AUTHORS   Wu,Q.
  TITLE     Comparative genomics and diversifying selection of the clustered
            vertebrate protocadherin genes
  JOURNAL   Genetics 169 (4), 2179-2188 (2005)
   PUBMED   15744052
REFERENCE   4  (bases 1 to 5241)
  AUTHORS   Murata,Y., Hamada,S., Morishita,H., Mutoh,T. and Yagi,T.
  TITLE     Interaction with protocadherin-gamma regulates the cell surface
            expression of protocadherin-alpha
  JOURNAL   J Biol Chem 279 (47), 49508-49516 (2004)
   PUBMED   15347688
REFERENCE   5  (bases 1 to 5241)
  AUTHORS   Yanase,H., Sugino,H. and Yagi,T.
  TITLE     Genomic sequence and organization of the family of CNR/Pcdhalpha
            genes in rat
  JOURNAL   Genomics 83 (4), 717-726 (2004)
   PUBMED   15028293
REFERENCE   6  (bases 1 to 5241)
  AUTHORS   Johnson,K.J., Zecevic,A. and Kwon,E.J.
  TITLE     Protocadherin alpha3 acts at sites distinct from classic cadherins
            in rat testis and sperm
  JOURNAL   Biol Reprod 70 (2), 303-312 (2004)
   PUBMED   14522826
REFERENCE   7  (bases 1 to 5241)
  AUTHORS   Fukumoto,E., Sakai,H., Fukumoto,S., Yagi,T., Takagi,O. and Kato,Y.
  TITLE     Cadherin-related neuronal receptors in incisor development
  JOURNAL   J Dent Res 82 (1), 17-22 (2003)
   PUBMED   12508039
REFERENCE   8  (bases 1 to 5241)
  AUTHORS   Takei,Y., Hamada,S., Senzaki,K., Mutoh,T., Sugino,H. and Yagi,T.
  TITLE     Two novel CNRs from the CNR gene cluster have molecular features
            distinct from those of CNR1 to 8
  JOURNAL   Genomics 72 (3), 321-330 (2001)
   PUBMED   11401448
REFERENCE   9  (bases 1 to 5241)
  AUTHORS   Johnson,K.J., Patel,S.R. and Boekelheide,K.
  TITLE     Multiple cadherin superfamily members with unique expression
            profiles are produced in rat testis
  JOURNAL   Endocrinology 141 (2), 675-683 (2000)
   PUBMED   10650949
REFERENCE   10 (bases 1 to 5241)
  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     PROVISIONAL REFSEQ: This record has not yet been subject to final
            NCBI review. The reference sequence was derived from AB113387.1.
            
            [WARNING] On Mar 20, 2024 this sequence was replaced by
            NM_053933.2.
            
            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 :: AB113387.1, AY573978.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMD00132306, SAMD00155326
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on conservation
            ##RefSeq-Attributes-END##
FEATURES             Location/Qualifiers
     source          1..5241
                     /organism="Rattus norvegicus"
                     /mol_type="mRNA"
                     /strain="LE"
                     /db_xref="taxon:10116"
                     /chromosome="18"
                     /map="18p11"
     gene            1..5241
                     /gene="Pcdha4"
                     /gene_synonym="Cnr1; cnr5; Pcdha1; Pcdha10; Pcdha11;
                     Pcdha12; Pcdha13; Pcdha2; Pcdha3; Pcdha5; Pcdha6; Pcdha7;
                     Pcdha8; Pcdha9; Pcdhac1; Pcdhac2; rCNRv01; rCNRv02;
                     rCNRv03; rCNRv05; rCNRv06; rCNRv07; rCNRv08; rCNRv09;
                     rCNRv10; rCNRv11; rCNRv12; rCNRv13; rCNRvc1; rCNRvc2"
                     /note="protocadherin alpha 4"
                     /db_xref="GeneID:116741"
                     /db_xref="RGD:620337"
     CDS             1..2844
                     /gene="Pcdha4"
                     /gene_synonym="Cnr1; cnr5; Pcdha1; Pcdha10; Pcdha11;
                     Pcdha12; Pcdha13; Pcdha2; Pcdha3; Pcdha5; Pcdha6; Pcdha7;
                     Pcdha8; Pcdha9; Pcdhac1; Pcdhac2; rCNRv01; rCNRv02;
                     rCNRv03; rCNRv05; rCNRv06; rCNRv07; rCNRv08; rCNRv09;
                     rCNRv10; rCNRv11; rCNRv12; rCNRv13; rCNRvc1; rCNRvc2"
                     /note="PCDH-alpha-4; cadherin-related neuronal receptor 4;
                     protocadherin alpha 5; cadherin-related neuronal receptor
                     c2; protocadherin alpha c2; cadherin-related neuronal
                     receptor 5; cadherin-related neuronal receptor 7;
                     protocadherin alpha 7; cadherin-related neuronal receptor
                     9; protocadherin alpha 6; protocadherin alpha 9;
                     cadherin-related neuronal receptor 11; protocadherin alpha
                     3; cadherin-related neuronal receptor 3; protocadherin
                     alpha 11; cadherin-related neuronal receptor 2;
                     protocadherin alpha 2; cadherin-related neuronal receptor
                     8; protocadherin alpha 8; cadherin-related neuronal
                     receptor 12; cadherin-related neuronal receptor 13;
                     protocadherin alpha 12; protocadherin alpha 13;
                     cadherin-related neuronal receptor 6; cadherin-related
                     neuronal receptor 10; protocadherin alpha 10;
                     cadherin-related neuronal receptor c1; protocadherin alpha
                     c1"
                     /codon_start=1
                     /product="protocadherin alpha-4 precursor"
                     /protein_id="NP_446385.1"
                     /db_xref="GeneID:116741"
                     /db_xref="RGD:620337"
                     /translation="MEFSWGSGQESQRLLLSFLFLAIWEPGNSQLHYSIPEEAKHGTF
                     VGRIAQDLGLELAELVPRLFRVASKDRGDLLEVNLQNGILFVNSRIDREELCGRSAEC
                     SIHLEVIVDRPLQVFHVEVEVRDINDNPPTFPTTQKNLFIAESRPLDTWFPLEGASDS
                     DIGINAVLTYRLSPNDYFSLEKPTNSERVKGLGLILRKSLDREETPELFLVLTVTDGG
                     KPELTGSVQLLITVLDANDNSPVFDRSLYTVKLPENVPNGTLVVKVNASDLDEGANGE
                     VMYSFSTDISPNVKNKFHIDPVTGEIAVKGYIDFEECTSYEILIEGIDKGQLPLSGHC
                     KVIVQVEDINDNAPELEFKSLSLPIRENAPVGTVIALISVFDPDTGVNGQVTCSLTPQ
                     VPFKLVSTFKNYYSLVLDSALDRETTADYKVVVIARDGGLPSLWATASVSVEVADVND
                     NAPAFAQPEYTVFVKENNPPGAHIFTVSAVDADSQENALVSYSLVERRVGERLLSSYV
                     SVHAESGKVFALQPLDHEELELLQFQVSARDAGVPALGSNVTLQVFVLDENDNAPTLL
                     EPEAGISGGIVSRLVSRSVGAGHVVAKVRAVDADSGYNAWLSYELQSSEGNSRSLFRV
                     GLYTGEISTTRSLDEADSPRQRLLVLVKDHGDPAMMVTATVLVSLVENGPLPKAPSRV
                     STRVTNAEASLVDVNVYLIIAICAVSSLLVLTLLLYSALRCSTVPSESVCGPPKPVMV
                     CSSAVGSWSYSQQRRQRVCSGEYPPKTDLMAFSPSLSDSRDREDQLQSTEDSSGKPRQ
                     PNPDWRYSASLRAGMHSSVHLEEAGILRAGPGGPDQQWPTVSSATPEPEAGEVSPPVG
                     AGVNSNSWTFKYGPGNPKQPGPGELPDKFIIPGSPAIISIRQESANNQIDKSDFITFG
                     KKEETKKKKKKKKGNKTQEKKEKGNSTTDNSDQ"
     exon            1..2385
                     /gene="Pcdha4"
                     /gene_synonym="Cnr1; cnr5; Pcdha1; Pcdha10; Pcdha11;
                     Pcdha12; Pcdha13; Pcdha2; Pcdha3; Pcdha5; Pcdha6; Pcdha7;
                     Pcdha8; Pcdha9; Pcdhac1; Pcdhac2; rCNRv01; rCNRv02;
                     rCNRv03; rCNRv05; rCNRv06; rCNRv07; rCNRv08; rCNRv09;
                     rCNRv10; rCNRv11; rCNRv12; rCNRv13; rCNRvc1; rCNRvc2"
                     /inference="alignment:Splign:2.1.0"
     exon            2386..2444
                     /gene="Pcdha4"
                     /gene_synonym="Cnr1; cnr5; Pcdha1; Pcdha10; Pcdha11;
                     Pcdha12; Pcdha13; Pcdha2; Pcdha3; Pcdha5; Pcdha6; Pcdha7;
                     Pcdha8; Pcdha9; Pcdhac1; Pcdhac2; rCNRv01; rCNRv02;
                     rCNRv03; rCNRv05; rCNRv06; rCNRv07; rCNRv08; rCNRv09;
                     rCNRv10; rCNRv11; rCNRv12; rCNRv13; rCNRvc1; rCNRvc2"
                     /inference="alignment:Splign:2.1.0"
     exon            2445..2533
                     /gene="Pcdha4"
                     /gene_synonym="Cnr1; cnr5; Pcdha1; Pcdha10; Pcdha11;
                     Pcdha12; Pcdha13; Pcdha2; Pcdha3; Pcdha5; Pcdha6; Pcdha7;
                     Pcdha8; Pcdha9; Pcdhac1; Pcdhac2; rCNRv01; rCNRv02;
                     rCNRv03; rCNRv05; rCNRv06; rCNRv07; rCNRv08; rCNRv09;
                     rCNRv10; rCNRv11; rCNRv12; rCNRv13; rCNRvc1; rCNRvc2"
                     /inference="alignment:Splign:2.1.0"
     exon            2534..5241
                     /gene="Pcdha4"
                     /gene_synonym="Cnr1; cnr5; Pcdha1; Pcdha10; Pcdha11;
                     Pcdha12; Pcdha13; Pcdha2; Pcdha3; Pcdha5; Pcdha6; Pcdha7;
                     Pcdha8; Pcdha9; Pcdhac1; Pcdhac2; rCNRv01; rCNRv02;
                     rCNRv03; rCNRv05; rCNRv06; rCNRv07; rCNRv08; rCNRv09;
                     rCNRv10; rCNRv11; rCNRv12; rCNRv13; rCNRvc1; rCNRvc2"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      
        1 atggaatttt cctggggaag tggccaggaa tcccagcgcc tgcttctctc ttttctgttt
       61 cttgcaatct gggagccagg aaacagccag ctccactact ccatcccaga ggaggccaaa
      121 cacggcacct tcgtgggccg catcgcacag gacctggggc tggagctggc ggagctggtg
      181 cctcgcctgt tcagggtggc gtccaaggac cgcggagacc ttctggaggt aaatctgcag
      241 aatggcattt tgtttgtgaa ttctcggatc gatcgggagg agctgtgcgg gaggagtgcg
      301 gagtgtagca tccacttgga ggtgatcgtg gacaggccgc tgcaggtttt ccacgtggag
      361 gtagaggtga gggacattaa cgacaaccct cccacgttcc caaccacaca aaagaatctg
      421 ttcatcgcag aatcaaggcc acttgacact tggtttccac tagagggcgc ttcagattca
      481 gatatcggaa tcaatgctgt gctgacttac agactaagtc caaatgatta cttttctttg
      541 gaaaaaccaa ccaacagtga acgggtaaaa ggtcttgggc ttatattacg gaaatcttta
      601 gaccgggagg aaactccaga gttattttta gtgctcactg tcacggatgg aggaaagccc
      661 gagctgactg gcagtgttca gttactcatc acagtgctgg atgccaacga taattctcca
      721 gtttttgaca gatctctcta taccgtgaaa ttaccagaaa acgtcccaaa tgggacattg
      781 gtagtcaaag tcaatgcctc agatttagat gaaggcgcca atggggaagt tatgtattca
      841 ttttctacag atatttcacc aaatgtgaaa aacaaattcc acatagaccc ggttaccgga
      901 gagatcgctg taaagggata cattgatttt gaagaatgca catcctatga aattctcata
      961 gagggaattg acaagggaca acttcccctc tctggacact gtaaagttat tgtacaagtt
     1021 gaagacatca atgataacgc cccagagttg gaattcaaat ctctatcact tccaatcaga
     1081 gagaatgctc cggtgggaac tgtcatcgca ctcatcagtg tgtttgatcc ggacacgggt
     1141 gtcaatgggc aggttacttg ctccctgact cctcaggtcc ccttcaagct ggtgtccact
     1201 ttcaagaatt actattcgct tgtgttggac agcgccctgg accgggagac cacagctgac
     1261 tataaggtgg tagtgatagc ccgggatggg ggcttgccct cgctgtgggc cacggccagt
     1321 gtgtccgtgg aggtggctga cgtgaacgac aatgcccctg cgttcgcaca gcctgaatac
     1381 acggtgtttg tgaaggagaa caacccacct ggagcgcaca tcttcacggt atccgcggtg
     1441 gacgcagact cacaggagaa cgcgctggtg tcctactcgc tggtggagcg gcgggtgggc
     1501 gagcgcttgc tgtcaagcta tgtctctgtg cacgcggaga gcggcaaggt gttcgcactg
     1561 cagcctctgg accatgagga gctggagctg ctgcagttcc aggtgagcgc gcgggatgct
     1621 ggtgtgcctg ccctgggcag caatgtgact ctgcaggtgt ttgtgctgga tgagaacgac
     1681 aacgcgccca ccctgctgga acccgaggca ggaatctctg gtggaatcgt gagccggcta
     1741 gtgtccagat cagtaggtgc gggccatgtg gtggccaaag tgcgcgcggt ggatgcggac
     1801 tctggctata atgcatggct ctcttatgag ctgcaatcgt cagaaggcaa ttcccgtagc
     1861 ctattccgtg tgggtctata tacgggcgag attagtacta cgcgcagctt ggatgaagca
     1921 gattcgccgc gtcagcgcct tctggtgctg gtgaaggacc atggcgaccc agcaatgatg
     1981 gttactgcca cagtgttggt gtcgctggta gagaatggcc cgctaccaaa ggctccatcg
     2041 cgagtgtcca caagagtcac aaacgcggag gcgtcactgg tggatgtcaa cgtgtatctg
     2101 atcatcgcca tctgtgcagt atccagcctg ttagtgctca cgctgctgct gtacagtgcc
     2161 ctgcgctgct ccactgtccc cagtgagagc gtgtgcgggc ctccaaaacc agtaatggtg
     2221 tgctccagcg cagtggggag ctggtcatac tctcagcaaa ggaggcaaag ggtgtgctct
     2281 ggagagtacc cacctaagac cgacctcatg gcctttagtc ccagtctatc tgattcaagg
     2341 gacagagagg atcaattgca gtccacagag gattcctctg gaaagccccg acagcccaac
     2401 cctgactggc gctactctgc ctcgctaaga gccggcatgc acagctctgt gcacctggag
     2461 gaggctggca ttctacgggc tggtccagga gggcctgatc aacagtggcc aacagtatcc
     2521 agtgcaacac cagaaccaga ggcaggagag gtgtcccctc cagtgggcgc tggtgtcaac
     2581 agcaacagct ggacctttaa atacggaccc ggcaacccca aacagcccgg tcccggtgag
     2641 ttgccagaca aattcattat cccaggatct cctgcaatca tctccatccg gcaggagtct
     2701 gctaacaacc aaattgacaa aagcgatttt ataaccttcg gcaaaaagga ggagaccaag
     2761 aaaaagaaga aaaagaagaa gggtaacaag acccaggaga aaaaagagaa agggaacagc
     2821 acgacggaca acagtgacca gtgaggccac caaatggaaa caagccactt agccagtttt
     2881 tgtaataatg gcaaatctct cccatgtagc aactcccccg ctcctttctc ctatgacatg
     2941 agccctctta gagacctcag aaatctgccg aaagttccct gtgtctgtct tgatcgcatt
     3001 taacaggttt tgtcttaata gctttcctaa gtctggtgtt aactctctct ctccactctg
     3061 gcttgttttc agaacctaaa aagcagaccc aggtttcctt tctcccccgc cgcaaaggag
     3121 aagcttccca gccccgcccg tgagagttgg actctctgcc ctgtgcttca agcatcctgt
     3181 cttgatattt gcagggcagg ctgaaaggta ttcaggctga gcagctgggt gtttgtggtc
     3241 actgggcatg tgtggctacc gagagtgttc gagagccggg tattggctgg gatggtccag
     3301 attagactag ttgacgtaag aagggctggg aaccagaggc acataaacat ctggagtctt
     3361 tgatctggag ggggaatagt gaaacttaaa aggaccagac tttcttaatc tctcaactgg
     3421 aggtgtggtg gtcatcctct agcagacaaa accatcccta ctgacaaagc tttaggagtc
     3481 cctcacatct gttggcagta atatcactct attcaaaacc tgtgttatgc acacaagcca
     3541 gcagttaagt atttaacaag aggttcagcc agggcaacag aagcagatct gatgtgtttc
     3601 ctgtacatgt ccttgtgctc acgctattaa gaattctttt gcacacaatg tttatgaaaa
     3661 ggatgcatcc ttttccgaca acacatatgc aaaaagcaaa agaaaaaccc aagacctcac
     3721 tttatgctgt ttgttgtttg atagatttat taaaaaagag aaagtctata gctataaatc
     3781 tttaaagaaa tatgacaaat acaattcccc ccaaccttcc ctcaagaaga gaatccagtc
     3841 tacagccatt tgaaatgatc attgctgcta cagaagtgct ttaagagaat tgcctggaac
     3901 atctgtatta taccggccac ctgccaatca cagctttact ctttcaggtc actctggggg
     3961 ctgcctcttg catgtattaa ttactaaata aaaggatctt tctctctttt ctaagaaaaa
     4021 tgatgtgcac tttgattaca caaccttctc taacccacta tattaagacc cagaaactga
     4081 agaaaaaata ttgttttctc atacattcaa tgagcagact tttcattcct ctgattctgt
     4141 ggttgtctcg gtgtgctagc ctacaccttc gccttgttta gttttccttt tctataacac
     4201 tctgaattgc taagcttact aacacctatg atgttacctg aatcaatctc ccatatgtat
     4261 gctgtatgct attataagac tcctgagata tacttactct gtgcttgtgt atgtgaatat
     4321 tactgcaact attacctaga gtgaacttta agctttattg ttgaatgtaa gcccgttata
     4381 tttccttttg tacacctgtg gaaaagtgga atagtgtttt ttttaaacca ttgttaatca
     4441 gcttttgtgt atgaaagaca cagtaaaatt tctttcttaa atcaagatgc tggtgattca
     4501 aggaatttta tttatggtca gccaagggct gtctcttgcc aagactcctg ttggcaagag
     4561 aatggataaa gctgtttttt ttttctagta agaattctgg aataaatact gaagaaagtc
     4621 cctgagggta tgcaagcaca aaattgtacc aatctgacct ctttgaattt gcagattgct
     4681 ttgaaatgct atccggaata tcagctcata gaaagtaata aaatttgctg ttaccataaa
     4741 taagacattt taagtttgtt gtgcacaacg taaacatttg attaattata tcatctattt
     4801 aaaagcatat aaaagaggta ggagtctatt ttaaaaggca taaaatctca aaaaaaaaaa
     4861 cctgtcttgt ctacttttag cttcattctc ccatattttg aagggtgtgt aacttcagct
     4921 ctgcaggatt gcatggggta aaacttgttg acagcacatg tgaaccattg ctacattgta
     4981 ggttgtgatc attttgcccc actgaagccc atgtaactga ccttacgtgc cttttgaact
     5041 aggagaatcg ggctataatt tattaatgat gataacgata atgtatatgt acagcacttt
     5101 ttaaatttat gaagtgcttt ccaattcgtg ttagttatta gttattacag ctgtaaggat
     5161 aaaacacgtc atgtggattc atttttaatt ggtgctattg gtatttcctc tgttcttgct
     5221 aataaatgga aatggtggtg t
//
