LOCUS       NM_018906               5404 bp    mRNA    linear   PRI 04-APR-2024
DEFINITION  Homo sapiens protocadherin alpha 3 (PCDHA3), transcript variant 1,
            mRNA.
ACCESSION   NM_018906
VERSION     NM_018906.3
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 5404)
  AUTHORS   Tao,Y., Fei,L., Chang,L., Yongyu,L., Jianhui,J., Yanan,L. and Yi,R.
  TITLE     Protocadherin alpha 3 inhibits lung squamous cell carcinoma
            metastasis and epithelial-mesenchymal transition
  JOURNAL   Genes Genomics 44 (2), 211-218 (2022)
   PUBMED   34086268
  REMARK    GeneRIF: Protocadherin alpha 3 inhibits lung squamous cell
            carcinoma metastasis and epithelial-mesenchymal transition.
REFERENCE   2  (bases 1 to 5404)
  AUTHORS   Lencz,T., Yu,J., Khan,R.R., Flaherty,E., Carmi,S., Lam,M.,
            Ben-Avraham,D., Barzilai,N., Bressman,S., Darvasi,A., Cho,J.H.,
            Clark,L.N., Gumus,Z.H., Vijai,J., Klein,R.J., Lipkin,S., Offit,K.,
            Ostrer,H., Ozelius,L.J., Peter,I., Malhotra,A.K., Maniatis,T.,
            Atzmon,G. and Pe'er,I.
  TITLE     Novel ultra-rare exonic variants identified in a founder population
            implicate cadherins in schizophrenia
  JOURNAL   Neuron 109 (9), 1465-1478 (2021)
   PUBMED   33756103
  REMARK    GeneRIF: Novel ultra-rare exonic variants identified in a founder
            population implicate cadherins in schizophrenia.
REFERENCE   3  (bases 1 to 5404)
  AUTHORS   Weissbach,A., Siegesmund,K., Bruggemann,N., Schmidt,A., Kasten,M.,
            Pichler,I., Muhle,H., Lohmann,E., Lohnau,T., Schwinger,E.,
            Hagenah,J., Stephani,U., Pramstaller,P.P., Klein,C. and Lohmann,K.
  TITLE     Exome sequencing in a family with restless legs syndrome
  JOURNAL   Mov Disord 27 (13), 1686-1689 (2012)
   PUBMED   23192925
  REMARK    GeneRIF: This study suggested that PCDHA3 as a candidate gene for
            restless legs syndrome.
REFERENCE   4  (bases 1 to 5404)
  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   5  (bases 1 to 5404)
  AUTHORS   Gregorio,S.P., Sallet,P.C., Do,K.A., Lin,E., Gattaz,W.F. and
            Dias-Neto,E.
  TITLE     Polymorphisms in genes involved in neurodevelopment may be
            associated with altered brain morphology in schizophrenia:
            preliminary evidence
  JOURNAL   Psychiatry Res 165 (1-2), 1-9 (2009)
   PUBMED   19054571
  REMARK    GeneRIF: Observational study of gene-disease association. (HuGE
            Navigator)
REFERENCE   6  (bases 1 to 5404)
  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   7  (bases 1 to 5404)
  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   8  (bases 1 to 5404)
  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   9  (bases 1 to 5404)
  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   10 (bases 1 to 5404)
  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, AF152311.1 and
            AC010223.6.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Nov 22, 2018 this sequence version replaced NM_018906.2.
            
            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).
            
            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 :: AF152311.1, SRR1803612.278083.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA2142680, SAMEA2144120
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000522353.3/ ENSP00000429808.2
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-141               AC005609.1         90901-91041         c
            142-5401            AF152311.1         1-5260
            5402-5404           AC010223.6         50266-50268         c
FEATURES             Location/Qualifiers
     source          1..5404
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="5"
                     /map="5q31.3"
     gene            1..5404
                     /gene="PCDHA3"
                     /gene_synonym="PCDH-ALPHA3"
                     /note="protocadherin alpha 3"
                     /db_xref="GeneID:56145"
                     /db_xref="HGNC:HGNC:8669"
                     /db_xref="MIM:606309"
     exon            1..2535
                     /gene="PCDHA3"
                     /gene_synonym="PCDH-ALPHA3"
                     /inference="alignment:Splign:2.1.0"
     CDS             142..2994
                     /gene="PCDHA3"
                     /gene_synonym="PCDH-ALPHA3"
                     /note="isoform 1 precursor is encoded by transcript
                     variant 1; KIAA0345-like 11; PCDH-alpha-3"
                     /codon_start=1
                     /product="protocadherin alpha-3 isoform 1 precursor"
                     /protein_id="NP_061729.1"
                     /db_xref="CCDS:CCDS54915.1"
                     /db_xref="GeneID:56145"
                     /db_xref="HGNC:HGNC:8669"
                     /db_xref="MIM:606309"
                     /translation="MLFSWREDPGAQCLLLSLLLLAASEVGSGQLHYSVSEEAKHGTF
                     VGRIAQDLGLELAELVPRLFRVASKRHGDLLEVNLQNGILFVNSRIDREELCGRSAEC
                     SIHLEVIVDRPLQVFHVEVEVKDINDNAPVFPMAVKNLFISESRQPGSRFSLEGASDA
                     DIGTNSLLTYSLDSTEYFTLDVKRNDEEIKSLGLVLKKNLNREDTPKHYLLITAIDGG
                     KPELTGTTQLKITVLDVNDNAPAFERTIYKVRLLENAPNGTLVVTVNATDLDEGVNKD
                     IAYSFNTDMSADILSKFHLDPVNGQISVKGNIDFEESKSYEIQVEATDKGNPPMSDHC
                     TVLLEIVDINDNVPELVIQSLSLPVLEDSPLSTVIALISVSDRDSGVNGQVTCSLTPH
                     VPFKLVSTFKNYYSLVLDSPLDRESVSAYELVVTARDGGSPSLWATASVSVEVADVND
                     NAPAFSQSEYTVFVKENNPPGCHIFTVSARDADAQENALVSYSLVERRVGERALSSYV
                     SVHAESGKVYALQPLDHEELELLQFQVSARDAGVPPLGSNVTLQVFVLDENDNAPALL
                     MPRVGGIGGAVSELVPRSVGAGHVVAKVRAVDADSGYNAWLSYELQPGTGGARIPFRV
                     GLYTGEISTTRALDEVDAPRHRLLVLVKDHGEPSLTATATVLVSLVESGQAPKASSQA
                     SAGATGPEAALVDVNVYLIVAICAVSSLLVLTLLLYTALRCSAPPTEGDCGPGKPTLV
                     CSSAVGSWSYSQQRQQRVCSGEGLPKTDLMAFSPSLPPCPISRDREEKQDVDVDLSAK
                     PRQPNPDWRYSASLRAGMHSSVHLEEAGILRAGPGGPDQQWPTVSSATPEPEAGEVSP
                     PVGAGVNSNSWTFKYGPGNPKQSGPGELPDKFIIPGSPAIISIRQEPTNSQIDKSDFI
                     TFGKKEETKKKKKKKKGNKTQEKKEKGNSTTDNSDQ"
     exon            2536..2594
                     /gene="PCDHA3"
                     /gene_synonym="PCDH-ALPHA3"
                     /inference="alignment:Splign:2.1.0"
     exon            2595..2683
                     /gene="PCDHA3"
                     /gene_synonym="PCDH-ALPHA3"
                     /inference="alignment:Splign:2.1.0"
     exon            2684..5404
                     /gene="PCDHA3"
                     /gene_synonym="PCDH-ALPHA3"
                     /inference="alignment:Splign:2.1.0"
     regulatory      4615..4620
                     /regulatory_class="polyA_signal_sequence"
                     /gene="PCDHA3"
                     /gene_synonym="PCDH-ALPHA3"
                     /note="hexamer: AGTAAA"
     polyA_site      4638
                     /gene="PCDHA3"
                     /gene_synonym="PCDH-ALPHA3"
     regulatory      5384..5389
                     /regulatory_class="polyA_signal_sequence"
                     /gene="PCDHA3"
                     /gene_synonym="PCDH-ALPHA3"
                     /note="hexamer: AATGAA"
     polyA_site      5404
                     /gene="PCDHA3"
                     /gene_synonym="PCDH-ALPHA3"
                     /note="major polyA site"
ORIGIN      
        1 attacgtatt cagatactgc tttgcttcat cctctctaaa atttaacacc gaggagttta
       61 agaaatgaag ataaggaact cgaattattt ttaaactttg gatcaatgta aaggcaatct
      121 aatatttgga aaatacttgc aatgttgttc tcctggcgag aagatcctgg agcccagtgc
      181 ctgctgcttt ctcttctgct cctcgcagcc tcggaggtgg ggagcggcca gctccactac
      241 tccgtctctg aggaggccaa gcatggcacc ttcgtgggcc gcatcgcgca ggacctgggg
      301 ctggagctgg cggagctggt gccgcgcctg ttccgggtgg cgtccaaaag acacggggac
      361 cttctggagg taaatctgca gaatggcatt ttgtttgtga attctcggat agaccgcgag
      421 gaactgtgcg ggcggagcgc ggagtgcagc atccacctgg aggtgatcgt ggacaggccg
      481 ctgcaggttt tccatgtgga ggtggaagtg aaggacatta atgacaacgc gccagttttt
      541 ccaatggctg taaagaatct gtttatttcc gaatcccgac agcctggctc tcggttttcg
      601 ctagagggcg catcagatgc agatatcgga acaaattcgt tgttgactta cagtcttgat
      661 tccactgaat attttacctt ggacgttaaa agaaatgatg aggaaattaa atcccttgga
      721 ctcgtgttga aaaaaaattt aaatcgagag gacactccta agcattattt actaataaca
      781 gcaattgatg gtgggaaacc agagctcact ggcacgactc aactaaagat cactgtttta
      841 gatgtaaacg acaacgcccc agcgtttgag aggacgatct ataaagtcag attactcgaa
      901 aatgcaccaa atggtaccct agtggtgacc gttaacgcca ccgatttgga tgaaggagta
      961 aataaggata tcgcgtattc tttcaatacg gacatgtcag cagatattct gtcaaaattc
     1021 catttagatc cagtcaatgg acaaatcagt gtaaagggta acatagattt cgaggaaagt
     1081 aagtcatatg aaatccaggt agaagccacg gataaaggaa atcccccaat gtcagatcac
     1141 tgcacagttc tactcgaaat tgtggacatc aatgataatg tacctgagtt agttattcaa
     1201 tcactatctt tacctgtatt agaagactct ccacttagca cagtcatcgc tctgatcagc
     1261 gtgtccgacc gcgactcagg agtcaatgga caggtcacct gctcgctgac gccccacgtc
     1321 cccttcaagc tggtgtccac cttcaagaat tactactcat tggtgctgga cagccctctg
     1381 gaccgcgaga gcgtgtcggc ctatgagctg gtggtgactg ctcgggacgg gggctcgcct
     1441 tcactgtggg ccacggccag cgtgtccgtg gaggtggccg acgtgaacga caatgcgccg
     1501 gcattctcgc agtccgagta cacggtgttc gtgaaggaga acaacccgcc gggctgccac
     1561 atcttcacgg tgtctgcgcg ggacgcggac gcgcaggaga acgccctggt gtcctactcg
     1621 ctggtggaac ggcgggtggg ggagcgcgcg ctgtcgagct acgtgtcggt acacgcggag
     1681 agcggcaagg tgtacgcgct gcagccgctg gaccacgagg agctagagct gctgcagttc
     1741 caggtgagtg cgcgcgatgc gggcgtgccg cctctgggca gcaacgtgac gctgcaggtg
     1801 ttcgtgctgg acgagaacga caacgcgccg gcactgctga tgcctcgggt gggtggcatc
     1861 ggtggcgcag tgagcgagct ggtgccgcgg tcagtgggtg cgggccacgt ggtagcgaag
     1921 gtgcgcgcag tggatgcaga ctcaggctac aacgcgtggc tttcgtatga gctgcagcct
     1981 gggaccggcg gtgcgcgcat cccgtttcgc gtggggctgt acacgggaga gatcagcacg
     2041 acccgtgccc tggacgaggt ggacgccccg cgccatcgcc tactggtgct ggtgaaggac
     2101 cacggtgaac cctcattgac cgccacggcc actgtgctgg tgtcgctggt ggagagtggc
     2161 caggcaccca aggcctcgtc ccaggcgtcc gctggcgcca cgggcccgga agctgcactg
     2221 gtggatgtca acgtgtactt gatcgtcgcc atctgcgcgg tgtccagtct gttggtgctc
     2281 acactgctgc tatatactgc tctgcggtgc tccgcgccgc caaccgaagg cgactgtggg
     2341 ccgggcaagc ccacgctggt gtgctccagc gcggtgggga gctggtcata ctcgcagcag
     2401 aggcagcaga gggtgtgctc tggagagggg ttgcccaaga ccgacctcat ggcttttagc
     2461 cctagccttc ctccttgtcc aattagccgg gatagagagg agaaacagga tgtggacgtt
     2521 gatctctcag ccaaaccacg acagcccaac cctgactggc gttactctgc ctccctgaga
     2581 gcaggcatgc acagctctgt gcacctagag gaggctggca ttctacgggc tggtccagga
     2641 gggcctgatc agcagtggcc aacagtatcc agtgcaacac cagaaccaga ggcaggagaa
     2701 gtgtcccctc cagtcggtgc gggtgtcaac agcaacagct ggacctttaa atacggacca
     2761 ggcaacccca aacaatccgg tcccggtgag ttgcccgaca aattcattat cccaggatct
     2821 cctgcaatca tctccatccg gcaggagcct actaacagcc aaattgacaa aagtgacttc
     2881 ataaccttcg gcaaaaagga ggagaccaag aaaaagaaga aaaagaagaa gggtaacaag
     2941 acccaggaga aaaaagagaa agggaacagc acgactgaca acagtgacca gtgaggtcct
     3001 caaatggaaa caagccactt agccagtttt tgtaataatg gcaaatctct cccatgtagc
     3061 aattccctgc tcctttttcc tatctacatg agccctctta gagacctcag aaatctgcag
     3121 aaagttccct gtgtctgtct agaacgcatt taacaggttt tgtcgtaaaa gctttactaa
     3181 gtctggtgtt aactctttct ctccactctg gcttgttttc agaacctaaa aagcagaccc
     3241 aagtttcctt tctcctccgc cgcaaaggag aggcttccca gccccgccag tgagaggttg
     3301 gactctctgc cctgtgctcc ggggatcctg tcttgatgac acttgcaggg caggctgaaa
     3361 agttttgaga ttgagcagct tgggagtttg tggccactgg gtatgtgtgg ctaccgcggg
     3421 tatgcgagtg ccagatattg gctgagacga gccagcttag actaattggt acaaggaagg
     3481 caagaaaaca aagacaaata aacagcggaa gttatcagta tggaggggaa gtgtaaactt
     3541 aaagggacca gactttctaa atcttacaac tcaagaggtg gcagccaccc tctaggagac
     3601 aaaactaccc ccactgacaa ggctttagga gaccctaaag tctgttggct gtgacgtcat
     3661 tatacctaaa atctgcatca tacctgcaag ccaacagttc agtgttttaa cagagaacca
     3721 ccctgggaaa cagaagcaga tctgatgtgt ttcctataca tgtcctgtgc tcactttatt
     3781 aaaaattctt ttgcacacaa tgtttatgaa aaggccagat ccttttccaa tacttatgca
     3841 aaagcaaaag aaaaccccga cacctcacct ttcgctgttt gttgtttcat agatttattt
     3901 aaaaaaagag aaagtctata gctataaatc tttaaagaga aatatgaata caattcccct
     3961 aaactctcct caaaagagaa ttcagtctac agccatttaa atgatcattg ctgctacaga
     4021 agtgctttaa gagaattgcc tgaaacatct gtattatatc ggccacctgc caatcacagc
     4081 tttactcttt caggtcactc tggggctgcc tcttgcatgt attactaaat aaaatgatct
     4141 ctctttctct ctctctctct cttttctaag aaacaattat gtgcactttg atacacaacc
     4201 ttctctaacc aactatatat caagacccaa aaattgaaga aaaatattgt tttctcatac
     4261 agtgagcaga tttttcaatc tactaattct gtgacttgtc ttggtgtgct agcctacacc
     4321 ttctctttgg tttagttttc cttttctata acactctgaa ttgctaatct tactaacacc
     4381 tatgatgtta cctgaaatca atctcccata tgtatgctgt atgctatgct aagactcctg
     4441 aaatatactt actctgtgct tgtgtatgtg aatgttaatg caactattac ctagagtgaa
     4501 ctttaagctt tattgttgaa tgtaattcca ttatatttcc ttttgtacac ctgtgaaaaa
     4561 gtggagtagt gtttttttaa ccattgttaa tcagcttttg tgtatgaaag acacagtaaa
     4621 atttctttct taaatcaaga tactggtgat tcaaggaatt ttatttatgg tccagccaag
     4681 agccatctcg tgccaagact tctgctggca agggaatgga taaagctgtt ttgttctagt
     4741 aacaattttg gaatgaatac tgacaatatt ccatgagggt gtgcaagcac aaattttacc
     4801 aatctgacct ctttgaagtt gcagaatgct ttgaaattct aatggtatct gaaatatcag
     4861 ctcatagaaa gtaacaaaat ttgctgtcac cttaaataag acattttaat tttgttataa
     4921 tgtacaattt agaagtttga ttaattatat tatctattta ggcattaata taaaagaggt
     4981 aggagtctgt tatttaaaaa aagcattaaa tttaaaaaaa aactgtcttg tctactttta
     5041 gcttcattct cccatatttt gaagggtgtg taacttcagc tctgcaggat tgcatggggt
     5101 aaaacttgtt accaacacat gtgaaccatt gctacattgt aggttgtgat cattttgccc
     5161 cactgaagcc catgtatctg accttacgtg ccttttgaac taggagaatc gggctaattt
     5221 attaatgatg ataattataa tgtatctgta cagcactttt tacatttgcg aagtgctttc
     5281 caatccatgt tagttactag ttattacagc tgtaaggata aaacacgtca tgtggattca
     5341 ttttgaattg gtgctattgg tatttcctct gttattgcta ataaatgaaa atggtggtat
     5401 gaaa
//
