LOCUS       NM_018908               5384 bp    mRNA    linear   PRI 06-JUN-2024
DEFINITION  Homo sapiens protocadherin alpha 5 (PCDHA5), transcript variant 1,
            mRNA.
ACCESSION   NM_018908
VERSION     NM_018908.3
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 5384)
  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   2  (bases 1 to 5384)
  AUTHORS   Wu,C., Ma,M.H., Brown,K.R., Geisler,M., Li,L., Tzeng,E., Jia,C.Y.,
            Jurisica,I. and Li,S.S.
  TITLE     Systematic identification of SH3 domain-mediated human
            protein-protein interactions by peptide array target screening
  JOURNAL   Proteomics 7 (11), 1775-1785 (2007)
   PUBMED   17474147
REFERENCE   3  (bases 1 to 5384)
  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 5384)
  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 5384)
  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 5384)
  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 5384)
  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 5384)
  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, AF152313.1 and
            AC010223.6.
            
            On Nov 23, 2018 this sequence version replaced NM_018908.2.
            
            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 :: SRR1803611.59560.1,
                                           SRR1660805.38503.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA2142586, SAMEA2145743
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000529859.2/ ENSP00000436557.1
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-163               AC005609.1         70323-70485         c
            164-5381            AF152313.1         1-5218
            5382-5384           AC010223.6         50266-50268         c
FEATURES             Location/Qualifiers
     source          1..5384
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="5"
                     /map="5q31.3"
     gene            1..5384
                     /gene="PCDHA5"
                     /gene_synonym="CNR6; CNRN6; CNRS6; CRNR6; PCDH-ALPHA5"
                     /note="protocadherin alpha 5"
                     /db_xref="GeneID:56143"
                     /db_xref="HGNC:HGNC:8671"
                     /db_xref="MIM:606311"
     exon            1..2515
                     /gene="PCDHA5"
                     /gene_synonym="CNR6; CNRN6; CNRS6; CRNR6; PCDH-ALPHA5"
                     /inference="alignment:Splign:2.1.0"
     CDS             164..2974
                     /gene="PCDHA5"
                     /gene_synonym="CNR6; CNRN6; CNRS6; CRNR6; PCDH-ALPHA5"
                     /note="isoform 1 precursor is encoded by transcript
                     variant 1; ortholog of mouse CNR6; KIAA0345-like 9;
                     PCDH-alpha-5"
                     /codon_start=1
                     /product="protocadherin alpha-5 isoform 1 precursor"
                     /protein_id="NP_061731.1"
                     /db_xref="CCDS:CCDS54917.1"
                     /db_xref="GeneID:56143"
                     /db_xref="HGNC:HGNC:8671"
                     /db_xref="MIM:606311"
                     /translation="MVYSRRGSLGSRLLLLWLLLAYWKAGSGQLHYSIPEEAKHGTFV
                     GRIAQDLGLELAELVPRLFRVASKGRGDLLEVNLQNGILFVNSRIDREELCRRRAECS
                     IHLEVIVDRPLQVFHVEVAVKDINDNPPRFSRQEQRLFILESRMPDSRFPLEGASDLD
                     IGANAQLRYRLNPNEYFDLDVKTNEEETNFLELVLRKSLDREETQEHRLLVIATDGGK
                     PELTGTVQLLINVLDANDNAPEFDKSIYNVRLLENAPSGTLVIKLNASDADEGINKEI
                     VYFFSNLVLDDVKSKFIINSNTGEIKVNGELDYEDYNSYEINIDAMDKSTFPLSGHCK
                     VVVKLLDVNDNTPEMAITTLFLPVKEDAPLSTVIALISVSDRDSGANGQVTCSLMPHV
                     PFKLVSTFKNYYSLVLDSALDRESVSVYELVVTARDGGSPSLWATASVSVEVADVNDN
                     APAFAQPQYTVFVKENNPPGCHIFTVSARDADAQENALVSYSLVERRVGERPLSSYVS
                     VHAESGKVYALQPLDHEEVELLQFQVSARDAGVPPLGSNVTLQVFVLDENDNAPALLV
                     PRVGGTGGAVSELVPRSVGAGHVVAKVRAVDPDSGYNAWLSYELQPAPGSARIPFRVG
                     LYTGEISTTRSLDETEAPRHRLLVLVKDHGEPPLTATATVLVSLVESGQAPKASSRAS
                     AGAVGPEAALVDVNVYLIIAICAVSSLLVLTLLLYTALRCSAQPTEAVCTRGKPTLLC
                     SSAVGSWSYSQQRRQRVCSGEAPPKTDLMAFSPSLPQGPTSTDNPRQPNPDWRYSASL
                     RAGMHSSVHLEEAGILRAGPGGPDQQWPTVSSATPEPEAGEVSPPVGAGVNSNSWTFK
                     YGPGNPKQSGPGELPDKFIIPGSPAIISIRQEPTNSQIDKSDFITFGKKEETKKKKKK
                     KKGNKTQEKKEKGNSTTDNSDQ"
     exon            2516..2574
                     /gene="PCDHA5"
                     /gene_synonym="CNR6; CNRN6; CNRS6; CRNR6; PCDH-ALPHA5"
                     /inference="alignment:Splign:2.1.0"
     exon            2575..2663
                     /gene="PCDHA5"
                     /gene_synonym="CNR6; CNRN6; CNRS6; CRNR6; PCDH-ALPHA5"
                     /inference="alignment:Splign:2.1.0"
     exon            2664..5384
                     /gene="PCDHA5"
                     /gene_synonym="CNR6; CNRN6; CNRS6; CRNR6; PCDH-ALPHA5"
                     /inference="alignment:Splign:2.1.0"
     regulatory      4595..4600
                     /regulatory_class="polyA_signal_sequence"
                     /gene="PCDHA5"
                     /gene_synonym="CNR6; CNRN6; CNRS6; CRNR6; PCDH-ALPHA5"
                     /note="hexamer: AGTAAA"
     polyA_site      4618
                     /gene="PCDHA5"
                     /gene_synonym="CNR6; CNRN6; CNRS6; CRNR6; PCDH-ALPHA5"
     regulatory      5364..5369
                     /regulatory_class="polyA_signal_sequence"
                     /gene="PCDHA5"
                     /gene_synonym="CNR6; CNRN6; CNRS6; CRNR6; PCDH-ALPHA5"
                     /note="hexamer: AATGAA"
     polyA_site      5384
                     /gene="PCDHA5"
                     /gene_synonym="CNR6; CNRN6; CNRS6; CRNR6; PCDH-ALPHA5"
                     /note="major polyA site"
ORIGIN      
        1 agattttcct tagacagaaa ggaaaagaac cttccatttt tggctgtgcc aagaagctca
       61 gaaaggcgat aatataaaaa atatatagtt aattgggaat tgaatttaca aaatacattg
      121 tgtggtgatg caatagaaag ctcataattg gaacgagatt gagatggtat attcccggag
      181 aggaagtctg ggatcccggc tcctgctgct ctggcttctc cttgcctact ggaaggcagg
      241 gagcggccag ctccactact cgatcccgga ggaagccaaa cacggaacct tcgttggccg
      301 catcgcgcag gacctagggc tggagctggc ggagctggtg ccgcgcctgt tccgggtggc
      361 gtccaagggc cgcggggacc ttctggaggt aaatctgcag aatggcattt tgtttgtgaa
      421 ttctcggatc gaccgggagg agctgtgccg gcggagggcg gagtgcagca tccacctgga
      481 ggtgatcgtg gacaggccgc tgcaggtttt ccatgtggag gtggcagtga aggacatcaa
      541 tgacaatccg cccaggttct ccagacaaga acaaagatta ttcattttag agtcaagaat
      601 gccagattcg cggtttccgc tagagggcgc gtcggatttg gatattggag caaatgcaca
      661 attgagatac aggttaaatc caaacgaata ttttgactta gatgttaaaa caaatgaaga
      721 agaaacgaac tttttagagc tggttttgag gaaatcctta gatagagaag aaacacaaga
      781 acaccgttta ttagtgattg caactgatgg aggaaaaccc gaactaacag gtacagttca
      841 gttgttgatc aatgtattgg atgctaatga taacgcccca gaatttgata aatccattta
      901 taatgtcaga ttgttggaaa atgcaccaag tgggacatta gttattaaac tgaacgcctc
      961 agatgcagat gagggcatca ataaggaaat agtgtatttc tttagtaatc ttgttcttga
     1021 cgatgtaaag tccaaattta taattaattc taatactggt gaaataaaag ttaacgggga
     1081 actggattat gaagactata actcatatga aattaatatt gatgccatgg ataaaagtac
     1141 attcccatta tcaggacact gtaaagtagt agtgaaactc ctggatgtga atgataatac
     1201 cccagagatg gccataacca cccttttcct gcctgtcaaa gaggacgctc cactcagcac
     1261 ggtcattgct ctgatcagcg tgtctgaccg tgactcaggt gccaacgggc aggtgacctg
     1321 ctccctaatg ccccacgttc ccttcaagct ggtgtccacc ttcaagaatt actactcgtt
     1381 ggtgctggac agcgccctgg accgcgagag cgtgtcggtc tatgagctgg tggtgaccgc
     1441 gcgggacggg ggctcgcctt cgctgtgggc caccgccagc gtgtctgtgg aagtggccga
     1501 cgtgaacgac aacgctccgg cgttcgcgca gccccagtat accgtgttcg tgaaggagaa
     1561 caacccgcca ggctgccaca tcttcacggt gtctgcacgg gacgcggacg cgcaggagaa
     1621 cgccctggtg tcctactcgc tggtggagcg gcgggtgggc gagcgcccgc tgtcgagtta
     1681 cgtttcggtg cacgcggaga gcggcaaggt gtacgcgctg cagccgctgg accacgagga
     1741 agtggagctg ctgcagttcc aggtgagcgc gcgcgacgcg ggcgtgccgc ctctgggcag
     1801 caacgtgacg ctgcaggtgt tcgtgctgga cgagaacgac aacgcgccgg cgctgctggt
     1861 gcctcgagtg ggtggcaccg gcggcgcagt gagcgagctg gtgccgaggt cagtgggtgc
     1921 gggccacgtg gtggcgaagg tgcgcgcagt ggaccctgat tcgggctaca acgcttggct
     1981 ttcgtatgag ctgcagccag cgcctggcag tgcgcgcatc ccgttccgcg tggggctgta
     2041 cacaggcgag atcagcacaa cacgctctct ggatgagacc gaagcaccgc gccaccgcct
     2101 tctggtgctg gtgaaggacc atggagagcc cccgctgaca gccacagcca cagtgctggt
     2161 gtcgctggtg gaaagtggcc aggcgccgaa ggcctcatcg cgggcgtcgg cgggcgctgt
     2221 gggtcccgag gctgccctgg tggatgtcaa cgtgtacctg atcatcgcca tctgtgcggt
     2281 gtccagcctg ctggtgctca cgctgctgct gtacaccgcg ctgcggtgct cggcgcagcc
     2341 caccgaggcc gtgtgcacac ggggcaagcc cactctgttg tgctccagcg cggtggggag
     2401 ctggtcgtac tcgcagcaga ggagacagag ggtgtgctct ggggaagctc cacccaaaac
     2461 agacctcatg gccttcagtc caagccttcc tcagggtccc acctctacag acaacccacg
     2521 acagcccaac cctgactggc gttactctgc ctccctgaga gcaggcatgc acagctctgt
     2581 gcacctagag gaggctggca ttctacgggc tggtccagga gggcctgatc agcagtggcc
     2641 aacagtatcc agtgcaacac cagaaccaga ggcaggagaa gtgtcccctc cagtcggtgc
     2701 gggtgtcaac agcaacagct ggacctttaa atacggacca ggcaacccca aacaatccgg
     2761 tcccggtgag ttgcccgaca aattcattat cccaggatct cctgcaatca tctccatccg
     2821 gcaggagcct actaacagcc aaattgacaa aagtgacttc ataaccttcg gcaaaaagga
     2881 ggagaccaag aaaaagaaga aaaagaagaa gggtaacaag acccaggaga aaaaagagaa
     2941 agggaacagc acgactgaca acagtgacca gtgaggtcct caaatggaaa caagccactt
     3001 agccagtttt tgtaataatg gcaaatctct cccatgtagc aattccctgc tcctttttcc
     3061 tatctacatg agccctctta gagacctcag aaatctgcag aaagttccct gtgtctgtct
     3121 agaacgcatt taacaggttt tgtcgtaaaa gctttactaa gtctggtgtt aactctttct
     3181 ctccactctg gcttgttttc agaacctaaa aagcagaccc aagtttcctt tctcctccgc
     3241 cgcaaaggag aggcttccca gccccgccag tgagaggttg gactctctgc cctgtgctcc
     3301 ggggatcctg tcttgatgac acttgcaggg caggctgaaa agttttgaga ttgagcagct
     3361 tgggagtttg tggccactgg gtatgtgtgg ctaccgcggg tatgcgagtg ccagatattg
     3421 gctgagacga gccagcttag actaattggt acaaggaagg caagaaaaca aagacaaata
     3481 aacagcggaa gttatcagta tggaggggaa gtgtaaactt aaagggacca gactttctaa
     3541 atcttacaac tcaagaggtg gcagccaccc tctaggagac aaaactaccc ccactgacaa
     3601 ggctttagga gaccctaaag tctgttggct gtgacgtcat tatacctaaa atctgcatca
     3661 tacctgcaag ccaacagttc agtgttttaa cagagaacca ccctgggaaa cagaagcaga
     3721 tctgatgtgt ttcctataca tgtcctgtgc tcactttatt aaaaattctt ttgcacacaa
     3781 tgtttatgaa aaggccagat ccttttccaa tacttatgca aaagcaaaag aaaaccccga
     3841 cacctcacct ttcgctgttt gttgtttcat agatttattt aaaaaaagag aaagtctata
     3901 gctataaatc tttaaagaga aatatgaata caattcccct aaactctcct caaaagagaa
     3961 ttcagtctac agccatttaa atgatcattg ctgctacaga agtgctttaa gagaattgcc
     4021 tgaaacatct gtattatatc ggccacctgc caatcacagc tttactcttt caggtcactc
     4081 tggggctgcc tcttgcatgt attactaaat aaaatgatct ctctttctct ctctctctct
     4141 cttttctaag aaacaattat gtgcactttg atacacaacc ttctctaacc aactatatat
     4201 caagacccaa aaattgaaga aaaatattgt tttctcatac agtgagcaga tttttcaatc
     4261 tactaattct gtgacttgtc ttggtgtgct agcctacacc ttctctttgg tttagttttc
     4321 cttttctata acactctgaa ttgctaatct tactaacacc tatgatgtta cctgaaatca
     4381 atctcccata tgtatgctgt atgctatgct aagactcctg aaatatactt actctgtgct
     4441 tgtgtatgtg aatgttaatg caactattac ctagagtgaa ctttaagctt tattgttgaa
     4501 tgtaattcca ttatatttcc ttttgtacac ctgtgaaaaa gtggagtagt gtttttttaa
     4561 ccattgttaa tcagcttttg tgtatgaaag acacagtaaa atttctttct taaatcaaga
     4621 tactggtgat tcaaggaatt ttatttatgg tccagccaag agccatctcg tgccaagact
     4681 tctgctggca agggaatgga taaagctgtt ttgttctagt aacaattttg gaatgaatac
     4741 tgacaatatt ccatgagggt gtgcaagcac aaattttacc aatctgacct ctttgaagtt
     4801 gcagaatgct ttgaaattct aatggtatct gaaatatcag ctcatagaaa gtaacaaaat
     4861 ttgctgtcac cttaaataag acattttaat tttgttataa tgtacaattt agaagtttga
     4921 ttaattatat tatctattta ggcattaata taaaagaggt aggagtctgt tatttaaaaa
     4981 aagcattaaa tttaaaaaaa aactgtcttg tctactttta gcttcattct cccatatttt
     5041 gaagggtgtg taacttcagc tctgcaggat tgcatggggt aaaacttgtt accaacacat
     5101 gtgaaccatt gctacattgt aggttgtgat cattttgccc cactgaagcc catgtatctg
     5161 accttacgtg ccttttgaac taggagaatc gggctaattt attaatgatg ataattataa
     5221 tgtatctgta cagcactttt tacatttgcg aagtgctttc caatccatgt tagttactag
     5281 ttattacagc tgtaaggata aaacacgtca tgtggattca ttttgaattg gtgctattgg
     5341 tatttcctct gttattgcta ataaatgaaa atggtggtat gaaa
//
