LOCUS       NM_031411               4622 bp    mRNA    linear   PRI 09-JUN-2024
DEFINITION  Homo sapiens protocadherin alpha 1 (PCDHA1), transcript variant 3,
            mRNA.
ACCESSION   NM_031411
VERSION     NM_031411.3
KEYWORDS    RefSeq.
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 4622)
  AUTHORS   Du,J. and Wu,K.
  TITLE     PCDHA1 High Expression is Associated With Poor Prognosis and
            Correlated With Immune Cell Infiltration in Breast Cancer
  JOURNAL   Clin Breast Cancer 23 (4), 397-407 (2023)
   PUBMED   36858841
  REMARK    GeneRIF: PCDHA1 High Expression is Associated With Poor Prognosis
            and Correlated With Immune Cell Infiltration in Breast Cancer.
REFERENCE   2  (bases 1 to 4622)
  AUTHORS   Guo,Y., Monahan,K., Wu,H., Gertz,J., Varley,K.E., Li,W.,
            Myers,R.M., Maniatis,T. and Wu,Q.
  TITLE     CTCF/cohesin-mediated DNA looping is required for protocadherin
            alpha promoter choice
  JOURNAL   Proc Natl Acad Sci U S A 109 (51), 21081-21086 (2012)
   PUBMED   23204437
  REMARK    GeneRIF: CTCF/cohesin-mediated DNA looping is required for
            protocadherin alpha promoter choice
REFERENCE   3  (bases 1 to 4622)
  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   4  (bases 1 to 4622)
  AUTHORS   Lachman,H.M., Petruolo,O.A., Pedrosa,E., Novak,T., Nolan,K. and
            Stopkova,P.
  TITLE     Analysis of protocadherin alpha gene deletion variant in bipolar
            disorder and schizophrenia
  JOURNAL   Psychiatr Genet 18 (3), 110-115 (2008)
   PUBMED   18496207
  REMARK    GeneRIF: A polymorphic copy number variation in this locus, a
            16.7-kb deletion affecting PCDH-alpha exons 8-10 (alpha 8-alpha 10
            Delta), was analyzed in this study as a potential candidate variant
            in schizophrenia and bipolar disorder.
            GeneRIF: Observational study of gene-disease association. (HuGE
            Navigator)
REFERENCE   5  (bases 1 to 4622)
  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   6  (bases 1 to 4622)
  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 4622)
  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 4622)
  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 4622)
  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 4622)
  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 and AC010223.6.
            
            On Nov 22, 2019 this sequence version replaced NM_031411.2.
            
            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 (3) utilizes an alternative splice
            donor site that truncates exon 1. This shortest isoform (3) lacks
            the transmembrane region and has four complete and one partial
            cadherin domain.
            
            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.
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-1753              AC005609.1         104206-105958       c
            1754-1812           AC010223.6         83606-83664         c
            1813-1901           AC010223.6         80050-80138         c
            1902-4622           AC010223.6         50266-52986         c
FEATURES             Location/Qualifiers
     source          1..4622
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="5"
                     /map="5q31.3"
     gene            1..4622
                     /gene="PCDHA1"
                     /gene_synonym="PCDH-ALPHA1"
                     /note="protocadherin alpha 1"
                     /db_xref="GeneID:56147"
                     /db_xref="HGNC:HGNC:8663"
                     /db_xref="MIM:606307"
     exon            1..1753
                     /gene="PCDHA1"
                     /gene_synonym="PCDH-ALPHA1"
                     /inference="alignment:Splign:2.1.0"
     CDS             152..2212
                     /gene="PCDHA1"
                     /gene_synonym="PCDH-ALPHA1"
                     /note="isoform 3 precursor is encoded by transcript
                     variant 3; KIAA0345-like 13; PCDH-alpha-1"
                     /codon_start=1
                     /product="protocadherin alpha-1 isoform 3 precursor"
                     /protein_id="NP_113599.1"
                     /db_xref="CCDS:CCDS54912.1"
                     /db_xref="GeneID:56147"
                     /db_xref="HGNC:HGNC:8663"
                     /db_xref="MIM:606307"
                     /translation="MVFSRRGGLGARDLLLWLLLLAAWEVGSGQLHYSIPEEAKHGTF
                     VGRVAQDLGLELAELVPRLFRVASKTHRDLLEVNLQNGILFVNSRIDREELCQWSAEC
                     SIHLELIADRPLQVFHVEVKVKDINDNPPVFRGREQIIFIPESRLLNSRFPIEGAADA
                     DIGANALLTYTLSPSDYFSLDVEASDELSKSLWLELRKYLDREETPELHLLLTATDGG
                     KPELQGTVELLITVLDVNDNAPLFDQAVYRVHLLETTANGTLVTTLNASDADEGVNGE
                     VVFSFDSGISRDIQEKFKVDSSSGEIRLIDKLDYEETKSYEIQVKAVDKGSPPMSNHC
                     KVLVKVLDVNDNAPELAVTSLYLPIREDAPLSTVIALITVSDRDSGANGQVTCSLMPH
                     VPFKLVSTFKNYYSLVLDSALDRESLSVYELVVTARDGGSPSLWATARVSVEVADVND
                     NAPAFAQPEYTVFVKENNPPGCHIFTVSARDADAQENALVSYSLVERRVGERALSNYV
                     SVHAESGKVYALQPLDHEELELLQFQPRQPNPDWRYSASLRAGMHSSVHLEEAGILRA
                     GPGGPDQQWPTVSSATPEPEAGEVSPPVGAGVNSNSWTFKYGPGNPKQSGPGELPDKF
                     IIPGSPAIISIRQEPTNSQIDKSDFITFGKKEETKKKKKKKKGNKTQEKKEKGNSTTD
                     NSDQ"
     exon            1754..1812
                     /gene="PCDHA1"
                     /gene_synonym="PCDH-ALPHA1"
                     /inference="alignment:Splign:2.1.0"
     exon            1813..1901
                     /gene="PCDHA1"
                     /gene_synonym="PCDH-ALPHA1"
                     /inference="alignment:Splign:2.1.0"
     exon            1902..4622
                     /gene="PCDHA1"
                     /gene_synonym="PCDH-ALPHA1"
                     /inference="alignment:Splign:2.1.0"
     regulatory      3833..3838
                     /regulatory_class="polyA_signal_sequence"
                     /gene="PCDHA1"
                     /gene_synonym="PCDH-ALPHA1"
                     /note="hexamer: AGTAAA"
     polyA_site      3856
                     /gene="PCDHA1"
                     /gene_synonym="PCDH-ALPHA1"
     regulatory      4602..4607
                     /regulatory_class="polyA_signal_sequence"
                     /gene="PCDHA1"
                     /gene_synonym="PCDH-ALPHA1"
                     /note="hexamer: AATGAA"
     polyA_site      4622
                     /gene="PCDHA1"
                     /gene_synonym="PCDH-ALPHA1"
                     /note="major polyA site"
ORIGIN      
        1 actgatcact aaaagtgaag gaggaagctc cattttgtca ccgcctgaga gaagacagaa
       61 acggtaaaga gataaatgat tggaaatatt agataaaatg gcatgatttt gaagtaagag
      121 gagagcataa gaaaggtgta gtccttttgc aatggtgttt tctaggagag ggggcctggg
      181 agcccgggat ctgcttcttt ggcttctgct cctcgcagcc tgggaggtgg ggagcggcca
      241 gctccactac tcgatcccgg aggaagccaa acacggcacc ttcgttggcc gcgttgctca
      301 ggacctggga ctggagctgg cggagctggt gcctcgcctg ttccgggtgg cgtccaaaac
      361 acacagggac cttctggagg taaatctgca gaatggcatt ttgtttgtga attctcggat
      421 cgatcgcgag gagctgtgcc agtggagcgc ggagtgcagc atccacctgg agttgatcgc
      481 cgacaggccg ctgcaggttt tccatgtgga ggtgaaggtg aaagacatta acgataatcc
      541 acccgtcttc aggggcagag aacaaataat atttattcct gaatctagac tcctgaattc
      601 gcgttttccg atagaaggag ctgctgatgc agacattggt gctaacgctc ttctaacgta
      661 cacgctcagc ccgagtgatt atttctcttt ggatgtagag gcaagtgatg aactgagtaa
      721 atctctttgg cttgaattga gaaaatattt ggatagagaa gaaacaccag aacttcactt
      781 attactgact gccactgatg ggggcaaacc ggagctgcaa ggtacagttg agctgctgat
      841 caccgtcctc gacgttaatg ataacgcccc actgtttgac caggccgtat acagagtcca
      901 cttgttagag actacagcaa atggaacatt agtgaccaca ttaaatgcct ctgatgctga
      961 cgaaggtgta aatggtgaag tcgtcttttc ctttgacagt ggtatttctc gtgacattca
     1021 agaaaaattc aaagttgatt ccagctcagg agaaattagg ttaattgata aactggatta
     1081 tgaagaaaca aaatcctacg aaattcaagt aaaggcagtt gataaaggaa gtcctccgat
     1141 gtcaaatcac tgtaaggttt tggtgaaagt gctggatgta aatgataatg ctccagaact
     1201 ggcggtcact tcattgtatt tgcctatcag agaggacgct ccactcagca ccgtcatcgc
     1261 cctcatcacc gtgtctgacc gtgactcagg tgccaacggg caggtgactt gctccttaat
     1321 gccccacgtc cccttcaagc tggtgtccac cttcaagaat tactactcgt tggtgttgga
     1381 cagcgccctg gatcgcgaga gcctgtcggt ctatgagctg gtggtgaccg cgcgggacgg
     1441 gggctcgcct tcgctgtggg ccacggccag ggtgtccgtg gaggtggccg acgtgaatga
     1501 caacgcgcct gcgttcgcgc agcccgagta cacagtattc gtgaaggaga acaacccgcc
     1561 gggctgccac atcttcacgg tgtctgcgcg ggacgcggac gcgcaggaga acgcgctggt
     1621 gtcctattcg ctggtggaac ggcgggtggg cgagcgcgcg ctgtcgaact acgtgtcagt
     1681 gcacgcggag agcggcaagg tgtacgcact gcagcccctg gaccacgagg agctggagct
     1741 gctgcagttc cagccacgac agcccaaccc tgactggcgt tactctgcct ccctgagagc
     1801 aggcatgcac agctctgtgc acctagagga ggctggcatt ctacgggctg gtccaggagg
     1861 gcctgatcag cagtggccaa cagtatccag tgcaacacca gaaccagagg caggagaagt
     1921 gtcccctcca gtcggtgcgg gtgtcaacag caacagctgg acctttaaat acggaccagg
     1981 caaccccaaa caatccggtc ccggtgagtt gcccgacaaa ttcattatcc caggatctcc
     2041 tgcaatcatc tccatccggc aggagcctac taacagccaa attgacaaaa gtgacttcat
     2101 aaccttcggc aaaaaggagg agaccaagaa aaagaagaaa aagaagaagg gtaacaagac
     2161 ccaggagaaa aaagagaaag ggaacagcac gactgacaac agtgaccagt gaggtcctca
     2221 aatggaaaca agccacttag ccagtttttg taataatggc aaatctctcc catgtagcaa
     2281 ttccctgctc ctttttccta tctacatgag ccctcttaga gacctcagaa atctgcagaa
     2341 agttccctgt gtctgtctag aacgcattta acaggttttg tcgtaaaagc tttactaagt
     2401 ctggtgttaa ctctttctct ccactctggc ttgttttcag aacctaaaaa gcagacccaa
     2461 gtttcctttc tcctccgccg caaaggagag gcttcccagc cccgccagtg agaggttgga
     2521 ctctctgccc tgtgctccgg ggatcctgtc ttgatgacac ttgcagggca ggctgaaaag
     2581 ttttgagatt gagcagcttg ggagtttgtg gccactgggt atgtgtggct accgcgggta
     2641 tgcgagtgcc agatattggc tgagacgagc cagcttagac taattggtac aaggaaggca
     2701 agaaaacaaa gacaaataaa cagcggaagt tatcagtatg gaggggaagt gtaaacttaa
     2761 agggaccaga ctttctaaat cttacaactc aagaggtggc agccaccctc taggagacaa
     2821 aactaccccc actgacaagg ctttaggaga ccctaaagtc tgttggctgt gacgtcatta
     2881 tacctaaaat ctgcatcata cctgcaagcc aacagttcag tgttttaaca gagaaccacc
     2941 ctgggaaaca gaagcagatc tgatgtgttt cctatacatg tcctgtgctc actttattaa
     3001 aaattctttt gcacacaatg tttatgaaaa ggccagatcc ttttccaata cttatgcaaa
     3061 agcaaaagaa aaccccgaca cctcaccttt cgctgtttgt tgtttcatag atttatttaa
     3121 aaaaagagaa agtctatagc tataaatctt taaagagaaa tatgaataca attcccctaa
     3181 actctcctca aaagagaatt cagtctacag ccatttaaat gatcattgct gctacagaag
     3241 tgctttaaga gaattgcctg aaacatctgt attatatcgg ccacctgcca atcacagctt
     3301 tactctttca ggtcactctg gggctgcctc ttgcatgtat tactaaataa aatgatctct
     3361 ctttctctct ctctctctct tttctaagaa acaattatgt gcactttgat acacaacctt
     3421 ctctaaccaa ctatatatca agacccaaaa attgaagaaa aatattgttt tctcatacag
     3481 tgagcagatt tttcaatcta ctaattctgt gacttgtctt ggtgtgctag cctacacctt
     3541 ctctttggtt tagttttcct tttctataac actctgaatt gctaatctta ctaacaccta
     3601 tgatgttacc tgaaatcaat ctcccatatg tatgctgtat gctatgctaa gactcctgaa
     3661 atatacttac tctgtgcttg tgtatgtgaa tgttaatgca actattacct agagtgaact
     3721 ttaagcttta ttgttgaatg taattccatt atatttcctt ttgtacacct gtgaaaaagt
     3781 ggagtagtgt ttttttaacc attgttaatc agcttttgtg tatgaaagac acagtaaaat
     3841 ttctttctta aatcaagata ctggtgattc aaggaatttt atttatggtc cagccaagag
     3901 ccatctcgtg ccaagacttc tgctggcaag ggaatggata aagctgtttt gttctagtaa
     3961 caattttgga atgaatactg acaatattcc atgagggtgt gcaagcacaa attttaccaa
     4021 tctgacctct ttgaagttgc agaatgcttt gaaattctaa tggtatctga aatatcagct
     4081 catagaaagt aacaaaattt gctgtcacct taaataagac attttaattt tgttataatg
     4141 tacaatttag aagtttgatt aattatatta tctatttagg cattaatata aaagaggtag
     4201 gagtctgtta tttaaaaaaa gcattaaatt taaaaaaaaa ctgtcttgtc tacttttagc
     4261 ttcattctcc catattttga agggtgtgta acttcagctc tgcaggattg catggggtaa
     4321 aacttgttac caacacatgt gaaccattgc tacattgtag gttgtgatca ttttgcccca
     4381 ctgaagccca tgtatctgac cttacgtgcc ttttgaacta ggagaatcgg gctaatttat
     4441 taatgatgat aattataatg tatctgtaca gcacttttta catttgcgaa gtgctttcca
     4501 atccatgtta gttactagtt attacagctg taaggataaa acacgtcatg tggattcatt
     4561 ttgaattggt gctattggta tttcctctgt tattgctaat aaatgaaaat ggtggtatga
     4621 aa
//
