LOCUS       NM_018907               5374 bp    mRNA    linear   PRI 19-SEP-2024
DEFINITION  Homo sapiens protocadherin alpha 4 (PCDHA4), transcript variant 1,
            mRNA.
ACCESSION   NM_018907
VERSION     NM_018907.4
KEYWORDS    RefSeq; MANE Select.
SOURCE      Homo sapiens (human)
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
            Catarrhini; Hominidae; Homo.
REFERENCE   1  (bases 1 to 5374)
  AUTHORS   Luck,K., Kim,D.K., Lambourne,L., Spirohn,K., Begg,B.E., Bian,W.,
            Brignall,R., Cafarelli,T., Campos-Laborie,F.J., Charloteaux,B.,
            Choi,D., Cote,A.G., Daley,M., Deimling,S., Desbuleux,A., Dricot,A.,
            Gebbia,M., Hardy,M.F., Kishore,N., Knapp,J.J., Kovacs,I.A.,
            Lemmens,I., Mee,M.W., Mellor,J.C., Pollis,C., Pons,C.,
            Richardson,A.D., Schlabach,S., Teeking,B., Yadav,A., Babor,M.,
            Balcha,D., Basha,O., Bowman-Colin,C., Chin,S.F., Choi,S.G.,
            Colabella,C., Coppin,G., D'Amata,C., De Ridder,D., De Rouck,S.,
            Duran-Frigola,M., Ennajdaoui,H., Goebels,F., Goehring,L., Gopal,A.,
            Haddad,G., Hatchi,E., Helmy,M., Jacob,Y., Kassa,Y., Landini,S.,
            Li,R., van Lieshout,N., MacWilliams,A., Markey,D., Paulson,J.N.,
            Rangarajan,S., Rasla,J., Rayhan,A., Rolland,T., San-Miguel,A.,
            Shen,Y., Sheykhkarimli,D., Sheynkman,G.M., Simonovsky,E., Tasan,M.,
            Tejeda,A., Tropepe,V., Twizere,J.C., Wang,Y., Weatheritt,R.J.,
            Weile,J., Xia,Y., Yang,X., Yeger-Lotem,E., Zhong,Q., Aloy,P.,
            Bader,G.D., De Las Rivas,J., Gaudet,S., Hao,T., Rak,J.,
            Tavernier,J., Hill,D.E., Vidal,M., Roth,F.P. and Calderwood,M.A.
  TITLE     A reference map of the human binary protein interactome
  JOURNAL   Nature 580 (7803), 402-408 (2020)
   PUBMED   32296183
REFERENCE   2  (bases 1 to 5374)
  AUTHORS   Fox,C.S., Liu,Y., White,C.C., Feitosa,M., Smith,A.V.,
            Heard-Costa,N., Lohman,K., Johnson,A.D., Foster,M.C.,
            Greenawalt,D.M., Griffin,P., Ding,J., Newman,A.B., Tylavsky,F.,
            Miljkovic,I., Kritchevsky,S.B., Launer,L., Garcia,M.,
            Eiriksdottir,G., Carr,J.J., Gudnason,V., Harris,T.B., Cupples,L.A.
            and Borecki,I.B.
  CONSRTM   GIANT Consortium; MAGIC Consortium; GLGC Consortium
  TITLE     Genome-wide association for abdominal subcutaneous and visceral
            adipose reveals a novel locus for visceral fat in women
  JOURNAL   PLoS Genet 8 (5), e1002695 (2012)
   PUBMED   22589738
REFERENCE   3  (bases 1 to 5374)
  AUTHORS   Wu,Q., Zhang,T., Cheng,J.F., Kim,Y., Grimwood,J., Schmutz,J.,
            Dickson,M., Noonan,J.P., Zhang,M.Q., Myers,R.M. and Maniatis,T.
  TITLE     Comparative DNA sequence analysis of mouse and human protocadherin
            gene clusters
  JOURNAL   Genome Res 11 (3), 389-404 (2001)
   PUBMED   11230163
REFERENCE   4  (bases 1 to 5374)
  AUTHORS   Nollet,F., Kools,P. and van Roy,F.
  TITLE     Phylogenetic analysis of the cadherin superfamily allows
            identification of six major subfamilies besides several solitary
            members
  JOURNAL   J Mol Biol 299 (3), 551-572 (2000)
   PUBMED   10835267
  REMARK    Review article
REFERENCE   5  (bases 1 to 5374)
  AUTHORS   Yagi,T. and Takeichi,M.
  TITLE     Cadherin superfamily genes: functions, genomic organization, and
            neurologic diversity
  JOURNAL   Genes Dev 14 (10), 1169-1180 (2000)
   PUBMED   10817752
  REMARK    Review article
REFERENCE   6  (bases 1 to 5374)
  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 5374)
  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 5374)
  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 5374)
  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
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AC005609.1, AB208925.1,
            AF152312.1 and AC010223.6.
            
            On Nov 22, 2018 this sequence version replaced NM_018907.3.
            
            Summary: This gene is a member of the protocadherin alpha gene
            cluster, one of three related gene clusters tandemly linked on
            chromosome five that demonstrate an unusual genomic organization
            similar to that of B-cell and T-cell receptor gene clusters. The
            alpha gene cluster is composed of 15 cadherin superfamily genes
            related to the mouse CNR genes and consists of 13 highly similar
            and 2 more distantly related coding sequences. The tandem array of
            15 N-terminal exons, or variable exons, are followed by downstream
            C-terminal exons, or constant exons, which are shared by all genes
            in the cluster. The large, uninterrupted N-terminal exons each
            encode six cadherin ectodomains while the C-terminal exons encode
            the cytoplasmic domain. These neural cadherin-like cell adhesion
            proteins are integral plasma membrane proteins that most likely
            play a critical role in the establishment and function of specific
            cell-cell connections in the brain. Alternative splicing has been
            observed and additional variants have been suggested but their
            full-length nature has yet to be determined. [provided by RefSeq,
            Jul 2008].
            
            Transcript Variant: This variant (1) includes the constant region
            exons and encodes the longest isoform (1).
            
            ##Evidence-Data-START##
            Transcript exon combination :: SRR1660807.8381.1,
                                           SRR1803613.230692.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA2145743, SAMEA2146982
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000530339.2/ ENSP00000435300.1
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-6                 AC005609.1         85025-85030         c
            7-120               AB208925.1         1-114
            121-5371            AF152312.1         1-5251
            5372-5374           AC010223.6         50266-50268         c
FEATURES             Location/Qualifiers
     source          1..5374
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="5"
                     /map="5q31.3"
     gene            1..5374
                     /gene="PCDHA4"
                     /gene_synonym="CNR1; CNRN1; CRNR1; PCDH-ALPHA4"
                     /note="protocadherin alpha 4"
                     /db_xref="GeneID:56144"
                     /db_xref="HGNC:HGNC:8670"
                     /db_xref="MIM:606310"
     exon            1..2505
                     /gene="PCDHA4"
                     /gene_synonym="CNR1; CNRN1; CRNR1; PCDH-ALPHA4"
                     /inference="alignment:Splign:2.1.0"
     CDS             121..2964
                     /gene="PCDHA4"
                     /gene_synonym="CNR1; CNRN1; CRNR1; PCDH-ALPHA4"
                     /note="isoform 1 precursor is encoded by transcript
                     variant 1; ortholog of mouse CNR1; KIAA0345-like 10;
                     PCDH-alpha-4; ortholog of mouse CNR1, KIAA0345-like 10"
                     /codon_start=1
                     /product="protocadherin alpha-4 isoform 1 precursor"
                     /protein_id="NP_061730.1"
                     /db_xref="CCDS:CCDS54916.1"
                     /db_xref="GeneID:56144"
                     /db_xref="HGNC:HGNC:8670"
                     /db_xref="MIM:606310"
                     /translation="MEFSWGSGQESRRLLLLLLLLAAWEAGNGQLHYSVSEEAKHGTF
                     VGRIAQDLGLELAELVPRLFRVASKGRGGLLEVNLQNGILFVNSRIDREELCRRSAEC
                     SIHLEVIVDRPLQVFHVDVEVRDINDNPPVFPATQKNLSIAESRPLDSRFPLEGASDA
                     DIGENALLTYRLSPNEYFSLEKPPDDELVKGLGLILRKSLDREEAPEIFLVLTATDGG
                     KPELTGTVQLLITVLDANDNAPAFDRTIYKVRLLENVPNGTLVIKLNASDLDEGLNGD
                     IVYSFSNDISPNVKSKFHIDPITGQIIVKGYIDFEESKSYEIIVEGIDKGQLPLSGHC
                     RVIVEVEDNNDNVPDLEFKSLSLPIREDAPLGTVIALISVSDKDMGVNGLVTCSLTSH
                     VPFKLVSTFKNYYSLVLDSALDRESVSAYELVVTARDGGSPSLWATASVSVEVADVND
                     NAPAFAQPEYTVFVKENNPPGCHIFTVSAWDADAQENALVSYSLVERRVGERALSSYV
                     SVHAESGKVYALQPLDHEELELLQFQVTARDAGVPPLGSNVTLQVFVLDENDNAPALL
                     APRAGGTGGAVSELVPWSVGVGHVVAKVRAVDADSGYNAWLSYELQPGTGGARIPFRV
                     GLYTGEISTTRALDETDAPRHRLLVLVKDHGEPALTATATVLVSLVESGQAPKASSRA
                     LVGAVGPDAALVDVNVYLIIAICAVSSLLVLTLLLYTALRCSALPTEGACAPGKPTLV
                     CSSAVGSWSYSQQRRPRVCSGEGPPKTDLMAFSPSLPDSRDREDQLQTTEESFAKPRQ
                     PNPDWRYSASLRAGMHSSVHLEEAGILRAGPGGPDQQWPTVSSATPEPEAGEVSPPVG
                     AGVNSNSWTFKYGPGNPKQSGPGELPDKFIIPGSPAIISIRQEPTNSQIDKSDFITFG
                     KKEETKKKKKKKKGNKTQEKKEKGNSTTDNSDQ"
     exon            2506..2564
                     /gene="PCDHA4"
                     /gene_synonym="CNR1; CNRN1; CRNR1; PCDH-ALPHA4"
                     /inference="alignment:Splign:2.1.0"
     exon            2565..2653
                     /gene="PCDHA4"
                     /gene_synonym="CNR1; CNRN1; CRNR1; PCDH-ALPHA4"
                     /inference="alignment:Splign:2.1.0"
     exon            2654..5374
                     /gene="PCDHA4"
                     /gene_synonym="CNR1; CNRN1; CRNR1; PCDH-ALPHA4"
                     /inference="alignment:Splign:2.1.0"
     regulatory      4585..4590
                     /regulatory_class="polyA_signal_sequence"
                     /gene="PCDHA4"
                     /gene_synonym="CNR1; CNRN1; CRNR1; PCDH-ALPHA4"
                     /note="hexamer: AGTAAA"
     polyA_site      4608
                     /gene="PCDHA4"
                     /gene_synonym="CNR1; CNRN1; CRNR1; PCDH-ALPHA4"
     regulatory      5354..5359
                     /regulatory_class="polyA_signal_sequence"
                     /gene="PCDHA4"
                     /gene_synonym="CNR1; CNRN1; CRNR1; PCDH-ALPHA4"
                     /note="hexamer: AATGAA"
     polyA_site      5374
                     /gene="PCDHA4"
                     /gene_synonym="CNR1; CNRN1; CRNR1; PCDH-ALPHA4"
                     /note="major polyA site"
ORIGIN      
        1 atatacactc tttggagtct gaaatatgga ggatgcagct gcacttgact gaccgattaa
       61 aagatttccc ttgactttga gaaacgatat ttaatcagaa caaaatactg tgcactaaag
      121 atggagtttt cctggggaag cggccaggaa tcccggcgtc tgctgctctt acttcttctc
      181 ctcgcagcct gggaggcagg gaacggtcag ctccactact cggtctccga ggaggccaaa
      241 cacggcacct tcgtgggccg catcgcgcag gacctgggac tggagctggc ggagctggtg
      301 ccgcgcctgt tccgggtggc gtccaagggc cgcggaggcc ttctggaggt aaatctgcag
      361 aatggcattt tgtttgtgaa ttctcggatc gaccgggagg agctgtgccg gcggagcgcg
      421 gagtgcagca tccacctgga ggtgatcgta gacaggccgc tgcaggtttt ccatgtggac
      481 gtggaggtga gggacattaa cgataacccg ccggtgttcc cagcaacaca aaagaacctg
      541 tccatcgcgg aatccaggcc gcttgactct cggtttccac tagagggcgc ctcggatgca
      601 gatatcgggg agaacgccct gctcacttac agactgagcc caaatgaata cttttctctg
      661 gaaaaaccac ctgatgacga gctggtaaaa ggtcttgggc ttatattacg gaaatcttta
      721 gacagagaag aagctccgga gattttttta gtgctcacag ccactgatgg aggcaaaccc
      781 gagttgactg gcaccgttca gttactcatc acagtactgg atgccaatga caatgcccca
      841 gcttttgaca gaaccattta taaggtgaga ttactagaaa atgttcctaa tggaacattg
      901 gtaattaaac ttaacgcctc agatttagac gaaggattga atggggacat tgtttattca
      961 ttctcaaatg atatttcgcc aaatgtgaaa tccaagtttc acatagatcc aattactgga
     1021 caaattattg taaagggata tattgacttt gaagaaagca aatcctatga aattattgta
     1081 gagggcattg ataagggaca gctcccactt tctggccatt gtagagttat tgtggaagta
     1141 gaagacaaca acgataatgt cccagatttg gaattcaagt ctttatcact tccaattaga
     1201 gaggacgctc cactgggtac agtcatcgcc ctgatcagcg tgtccgacaa agacatgggt
     1261 gtcaatgggc tggtcacctg ctccttgacg tcccacgtcc ccttcaagct ggtgtccacc
     1321 ttcaagaatt actactcgtt ggtgctggac agtgccctgg accgcgagag cgtgtcagcc
     1381 tatgagctgg tggtgaccgc gcgagacggg ggctcgcctt cgctgtgggc cacggccagt
     1441 gtttctgtgg aggtggctga tgtgaacgac aacgctccgg cgttcgcgca gcccgagtac
     1501 acagtgttcg tgaaggagaa caacccgccg ggctgccaca tcttcactgt gtctgcgtgg
     1561 gacgcggacg cgcaggagaa cgcgctggtg tcctactcgc tggtagagcg gcgggtaggg
     1621 gagcgcgcgc tgtcgagcta cgtttcggtg catgcggaga gcggcaaggt gtacgcgctg
     1681 cagccgctgg accacgagga gctagagctg ctgcagtttc aggtgaccgc tcgcgatgcc
     1741 ggcgtgccac ctctgggcag caacgtgacg ctgcaggtgt tcgtgctgga cgaaaacgac
     1801 aacgcgccag cactgctagc gcctcgggcg ggtggcactg gtggcgcagt gagcgagctg
     1861 gtgccatggt cggtgggtgt gggccacgtg gtggcaaagg tgcgcgcggt ggatgctgac
     1921 tcgggctaca acgcgtggct ttcgtacgag ctgcagccgg ggactggtgg cgcgcgcatc
     1981 ccgttccgcg tggggctgta cactggcgag atcagcacaa cgcgtgccct ggacgaaacg
     2041 gacgctccgc gccaccgcct actggtactg gtgaaggacc acggcgagcc cgcgctgacg
     2101 gccacggcca ctgtgctggt gtcacttgtg gagagtggac aggcgccaaa ggcctcctca
     2161 cgggcgttgg tgggcgctgt gggtcccgat gctgcgctgg tggatgtcaa cgtatacctg
     2221 atcattgcca tctgcgcggt gtccagcctt ttggtgctca cgctgctgct gtacaccgcg
     2281 ctgcggtgct ctgcgctgcc caccgagggc gcgtgcgctc cgggcaagcc cacgctggtg
     2341 tgctccagtg cggtggggag ctggtcatac tcgcagcaga ggaggccgag ggtgtgctct
     2401 ggtgagggcc cacccaagac cgacctcatg gccttcagcc ccagtttacc tgactctagg
     2461 gacagagaag atcagctgca gacaactgag gaatcctttg caaagccacg acagcccaac
     2521 cctgactggc gttactctgc ctccctgaga gcaggcatgc acagctctgt gcacctagag
     2581 gaggctggca ttctacgggc tggtccagga gggcctgatc agcagtggcc aacagtatcc
     2641 agtgcaacac cagaaccaga ggcaggagaa gtgtcccctc cagtcggtgc gggtgtcaac
     2701 agcaacagct ggacctttaa atacggacca ggcaacccca aacaatccgg tcccggtgag
     2761 ttgcccgaca aattcattat cccaggatct cctgcaatca tctccatccg gcaggagcct
     2821 actaacagcc aaattgacaa aagtgacttc ataaccttcg gcaaaaagga ggagaccaag
     2881 aaaaagaaga aaaagaagaa gggtaacaag acccaggaga aaaaagagaa agggaacagc
     2941 acgactgaca acagtgacca gtgaggtcct caaatggaaa caagccactt agccagtttt
     3001 tgtaataatg gcaaatctct cccatgtagc aattccctgc tcctttttcc tatctacatg
     3061 agccctctta gagacctcag aaatctgcag aaagttccct gtgtctgtct agaacgcatt
     3121 taacaggttt tgtcgtaaaa gctttactaa gtctggtgtt aactctttct ctccactctg
     3181 gcttgttttc agaacctaaa aagcagaccc aagtttcctt tctcctccgc cgcaaaggag
     3241 aggcttccca gccccgccag tgagaggttg gactctctgc cctgtgctcc ggggatcctg
     3301 tcttgatgac acttgcaggg caggctgaaa agttttgaga ttgagcagct tgggagtttg
     3361 tggccactgg gtatgtgtgg ctaccgcggg tatgcgagtg ccagatattg gctgagacga
     3421 gccagcttag actaattggt acaaggaagg caagaaaaca aagacaaata aacagcggaa
     3481 gttatcagta tggaggggaa gtgtaaactt aaagggacca gactttctaa atcttacaac
     3541 tcaagaggtg gcagccaccc tctaggagac aaaactaccc ccactgacaa ggctttagga
     3601 gaccctaaag tctgttggct gtgacgtcat tatacctaaa atctgcatca tacctgcaag
     3661 ccaacagttc agtgttttaa cagagaacca ccctgggaaa cagaagcaga tctgatgtgt
     3721 ttcctataca tgtcctgtgc tcactttatt aaaaattctt ttgcacacaa tgtttatgaa
     3781 aaggccagat ccttttccaa tacttatgca aaagcaaaag aaaaccccga cacctcacct
     3841 ttcgctgttt gttgtttcat agatttattt aaaaaaagag aaagtctata gctataaatc
     3901 tttaaagaga aatatgaata caattcccct aaactctcct caaaagagaa ttcagtctac
     3961 agccatttaa atgatcattg ctgctacaga agtgctttaa gagaattgcc tgaaacatct
     4021 gtattatatc ggccacctgc caatcacagc tttactcttt caggtcactc tggggctgcc
     4081 tcttgcatgt attactaaat aaaatgatct ctctttctct ctctctctct cttttctaag
     4141 aaacaattat gtgcactttg atacacaacc ttctctaacc aactatatat caagacccaa
     4201 aaattgaaga aaaatattgt tttctcatac agtgagcaga tttttcaatc tactaattct
     4261 gtgacttgtc ttggtgtgct agcctacacc ttctctttgg tttagttttc cttttctata
     4321 acactctgaa ttgctaatct tactaacacc tatgatgtta cctgaaatca atctcccata
     4381 tgtatgctgt atgctatgct aagactcctg aaatatactt actctgtgct tgtgtatgtg
     4441 aatgttaatg caactattac ctagagtgaa ctttaagctt tattgttgaa tgtaattcca
     4501 ttatatttcc ttttgtacac ctgtgaaaaa gtggagtagt gtttttttaa ccattgttaa
     4561 tcagcttttg tgtatgaaag acacagtaaa atttctttct taaatcaaga tactggtgat
     4621 tcaaggaatt ttatttatgg tccagccaag agccatctcg tgccaagact tctgctggca
     4681 agggaatgga taaagctgtt ttgttctagt aacaattttg gaatgaatac tgacaatatt
     4741 ccatgagggt gtgcaagcac aaattttacc aatctgacct ctttgaagtt gcagaatgct
     4801 ttgaaattct aatggtatct gaaatatcag ctcatagaaa gtaacaaaat ttgctgtcac
     4861 cttaaataag acattttaat tttgttataa tgtacaattt agaagtttga ttaattatat
     4921 tatctattta ggcattaata taaaagaggt aggagtctgt tatttaaaaa aagcattaaa
     4981 tttaaaaaaa aactgtcttg tctactttta gcttcattct cccatatttt gaagggtgtg
     5041 taacttcagc tctgcaggat tgcatggggt aaaacttgtt accaacacat gtgaaccatt
     5101 gctacattgt aggttgtgat cattttgccc cactgaagcc catgtatctg accttacgtg
     5161 ccttttgaac taggagaatc gggctaattt attaatgatg ataattataa tgtatctgta
     5221 cagcactttt tacatttgcg aagtgctttc caatccatgt tagttactag ttattacagc
     5281 tgtaaggata aaacacgtca tgtggattca ttttgaattg gtgctattgg tatttcctct
     5341 gttattgcta ataaatgaaa atggtggtat gaaa
//
