LOCUS       NM_018900               5414 bp    mRNA    linear   PRI 09-JUN-2024
DEFINITION  Homo sapiens protocadherin alpha 1 (PCDHA1), transcript variant 1,
            mRNA.
ACCESSION   NM_018900
VERSION     NM_018900.4
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 5414)
  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 5414)
  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 5414)
  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 5414)
  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 5414)
  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 5414)
  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 5414)
  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 5414)
  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 5414)
  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 5414)
  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_018900.3.
            
            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).
            
            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 :: AF152305.1, SRR1803613.53870.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA2145743, SAMEA2148093
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000504120.4/ ENSP00000420840.3
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-2545              AC005609.1         103414-105958       c
            2546-2604           AC010223.6         83606-83664         c
            2605-2693           AC010223.6         80050-80138         c
            2694-5414           AC010223.6         50266-52986         c
FEATURES             Location/Qualifiers
     source          1..5414
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="5"
                     /map="5q31.3"
     gene            1..5414
                     /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..2545
                     /gene="PCDHA1"
                     /gene_synonym="PCDH-ALPHA1"
                     /inference="alignment:Splign:2.1.0"
     CDS             152..3004
                     /gene="PCDHA1"
                     /gene_synonym="PCDH-ALPHA1"
                     /note="isoform 1 precursor is encoded by transcript
                     variant 1; KIAA0345-like 13; PCDH-alpha-1"
                     /codon_start=1
                     /product="protocadherin alpha-1 isoform 1 precursor"
                     /protein_id="NP_061723.1"
                     /db_xref="CCDS:CCDS54913.1"
                     /db_xref="GeneID:56147"
                     /db_xref="HGNC:HGNC:8663"
                     /db_xref="MIM:606307"
                     /translation="MVFSRRGGLGARDLLLWLLLLAAWEVGSGQLHYSIPEEAKHGTF
                     VGRVAQDLGLELAELVPRLFRVASKTHRDLLEVNLQNGILFVNSRIDREELCQWSAEC
                     SIHLELIADRPLQVFHVEVKVKDINDNPPVFRGREQIIFIPESRLLNSRFPIEGAADA
                     DIGANALLTYTLSPSDYFSLDVEASDELSKSLWLELRKYLDREETPELHLLLTATDGG
                     KPELQGTVELLITVLDVNDNAPLFDQAVYRVHLLETTANGTLVTTLNASDADEGVNGE
                     VVFSFDSGISRDIQEKFKVDSSSGEIRLIDKLDYEETKSYEIQVKAVDKGSPPMSNHC
                     KVLVKVLDVNDNAPELAVTSLYLPIREDAPLSTVIALITVSDRDSGANGQVTCSLMPH
                     VPFKLVSTFKNYYSLVLDSALDRESLSVYELVVTARDGGSPSLWATARVSVEVADVND
                     NAPAFAQPEYTVFVKENNPPGCHIFTVSARDADAQENALVSYSLVERRVGERALSNYV
                     SVHAESGKVYALQPLDHEELELLQFQVSARDAGVPPLGSNVTLQVFVLDENDNAPALL
                     APRVGGTIGAVSELVPRLVGAGHVVAKVRAVDADSGYNAWLSYELQPAAGGARIPFRV
                     GLYTGEISTTRVLDEADLSRYRLLVLVKDHGEPALTATATVLVSLVESGQAPKASSRA
                     SVGVAGPEAALVDVNVYLIIAICAVSSLLVLTLLLYTALRCSVPPTEGAYVPGKPTLV
                     CSSALGSWSNSQQRRQRVCSSEGPPKTDLMAFSPGLSPSLNTSERNEQPEANLDLSGN
                     PRQPNPDWRYSASLRAGMHSSVHLEEAGILRAGPGGPDQQWPTVSSATPEPEAGEVSP
                     PVGAGVNSNSWTFKYGPGNPKQSGPGELPDKFIIPGSPAIISIRQEPTNSQIDKSDFI
                     TFGKKEETKKKKKKKKGNKTQEKKEKGNSTTDNSDQ"
     exon            2546..2604
                     /gene="PCDHA1"
                     /gene_synonym="PCDH-ALPHA1"
                     /inference="alignment:Splign:2.1.0"
     exon            2605..2693
                     /gene="PCDHA1"
                     /gene_synonym="PCDH-ALPHA1"
                     /inference="alignment:Splign:2.1.0"
     exon            2694..5414
                     /gene="PCDHA1"
                     /gene_synonym="PCDH-ALPHA1"
                     /inference="alignment:Splign:2.1.0"
     regulatory      4625..4630
                     /regulatory_class="polyA_signal_sequence"
                     /gene="PCDHA1"
                     /gene_synonym="PCDH-ALPHA1"
                     /note="hexamer: AGTAAA"
     polyA_site      4648
                     /gene="PCDHA1"
                     /gene_synonym="PCDH-ALPHA1"
     regulatory      5394..5399
                     /regulatory_class="polyA_signal_sequence"
                     /gene="PCDHA1"
                     /gene_synonym="PCDH-ALPHA1"
                     /note="hexamer: AATGAA"
     polyA_site      5414
                     /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 caggtgagcg cgcgggatgc gggcgtgccg cctctgggca gcaacgtgac
     1801 gctgcaggtg ttcgtgctgg acgagaacga caacgcgccg gcgctgctgg cgcctcgagt
     1861 gggtggcact attggtgcag tcagtgagct ggtgccgcga ttggtgggtg cgggtcatgt
     1921 ggtggcgaag gtgcgcgcag tggacgccga ctcgggctac aacgcgtggc tgtcctatga
     1981 actgcagccg gcagcaggcg gcgcgcgcat cccgttccgc gtggggctgt acacgggcga
     2041 gatcagcacg actcgtgtcc tggacgaggc tgacttgtcg cgctaccgcc ttctggtgct
     2101 agtgaaggat cacggtgagc cggcgctgac agccacggcc actgtgcttg tatctctggt
     2161 ggagagcggc caggcgccaa aggcgtcttc gcgggcgtcg gtgggtgtcg cgggcccaga
     2221 ggcggcgctg gtggatgtca acgtgtacct gatcatcgcc atctgcgcgg tgtccagcct
     2281 gctggtgctc acactgctgc tgtacacggc gctgcggtgc tcagtgccgc ccactgaggg
     2341 tgcgtatgtg ccgggcaagc ccactctggt gtgctccagc gcgttgggga gctggtcgaa
     2401 ctcacagcag aggcggcaga gggtgtgctc tagcgagggc ccacccaaga ccgacctcat
     2461 ggccttcagc ccaggcctat ctccaagtct taacacgtca gaaagaaatg aacaaccaga
     2521 agcaaatttg gatctttctg gtaatccacg acagcccaac cctgactggc gttactctgc
     2581 ctccctgaga gcaggcatgc acagctctgt gcacctagag gaggctggca ttctacgggc
     2641 tggtccagga gggcctgatc agcagtggcc aacagtatcc agtgcaacac cagaaccaga
     2701 ggcaggagaa gtgtcccctc cagtcggtgc gggtgtcaac agcaacagct ggacctttaa
     2761 atacggacca ggcaacccca aacaatccgg tcccggtgag ttgcccgaca aattcattat
     2821 cccaggatct cctgcaatca tctccatccg gcaggagcct actaacagcc aaattgacaa
     2881 aagtgacttc ataaccttcg gcaaaaagga ggagaccaag aaaaagaaga aaaagaagaa
     2941 gggtaacaag acccaggaga aaaaagagaa agggaacagc acgactgaca acagtgacca
     3001 gtgaggtcct caaatggaaa caagccactt agccagtttt tgtaataatg gcaaatctct
     3061 cccatgtagc aattccctgc tcctttttcc tatctacatg agccctctta gagacctcag
     3121 aaatctgcag aaagttccct gtgtctgtct agaacgcatt taacaggttt tgtcgtaaaa
     3181 gctttactaa gtctggtgtt aactctttct ctccactctg gcttgttttc agaacctaaa
     3241 aagcagaccc aagtttcctt tctcctccgc cgcaaaggag aggcttccca gccccgccag
     3301 tgagaggttg gactctctgc cctgtgctcc ggggatcctg tcttgatgac acttgcaggg
     3361 caggctgaaa agttttgaga ttgagcagct tgggagtttg tggccactgg gtatgtgtgg
     3421 ctaccgcggg tatgcgagtg ccagatattg gctgagacga gccagcttag actaattggt
     3481 acaaggaagg caagaaaaca aagacaaata aacagcggaa gttatcagta tggaggggaa
     3541 gtgtaaactt aaagggacca gactttctaa atcttacaac tcaagaggtg gcagccaccc
     3601 tctaggagac aaaactaccc ccactgacaa ggctttagga gaccctaaag tctgttggct
     3661 gtgacgtcat tatacctaaa atctgcatca tacctgcaag ccaacagttc agtgttttaa
     3721 cagagaacca ccctgggaaa cagaagcaga tctgatgtgt ttcctataca tgtcctgtgc
     3781 tcactttatt aaaaattctt ttgcacacaa tgtttatgaa aaggccagat ccttttccaa
     3841 tacttatgca aaagcaaaag aaaaccccga cacctcacct ttcgctgttt gttgtttcat
     3901 agatttattt aaaaaaagag aaagtctata gctataaatc tttaaagaga aatatgaata
     3961 caattcccct aaactctcct caaaagagaa ttcagtctac agccatttaa atgatcattg
     4021 ctgctacaga agtgctttaa gagaattgcc tgaaacatct gtattatatc ggccacctgc
     4081 caatcacagc tttactcttt caggtcactc tggggctgcc tcttgcatgt attactaaat
     4141 aaaatgatct ctctttctct ctctctctct cttttctaag aaacaattat gtgcactttg
     4201 atacacaacc ttctctaacc aactatatat caagacccaa aaattgaaga aaaatattgt
     4261 tttctcatac agtgagcaga tttttcaatc tactaattct gtgacttgtc ttggtgtgct
     4321 agcctacacc ttctctttgg tttagttttc cttttctata acactctgaa ttgctaatct
     4381 tactaacacc tatgatgtta cctgaaatca atctcccata tgtatgctgt atgctatgct
     4441 aagactcctg aaatatactt actctgtgct tgtgtatgtg aatgttaatg caactattac
     4501 ctagagtgaa ctttaagctt tattgttgaa tgtaattcca ttatatttcc ttttgtacac
     4561 ctgtgaaaaa gtggagtagt gtttttttaa ccattgttaa tcagcttttg tgtatgaaag
     4621 acacagtaaa atttctttct taaatcaaga tactggtgat tcaaggaatt ttatttatgg
     4681 tccagccaag agccatctcg tgccaagact tctgctggca agggaatgga taaagctgtt
     4741 ttgttctagt aacaattttg gaatgaatac tgacaatatt ccatgagggt gtgcaagcac
     4801 aaattttacc aatctgacct ctttgaagtt gcagaatgct ttgaaattct aatggtatct
     4861 gaaatatcag ctcatagaaa gtaacaaaat ttgctgtcac cttaaataag acattttaat
     4921 tttgttataa tgtacaattt agaagtttga ttaattatat tatctattta ggcattaata
     4981 taaaagaggt aggagtctgt tatttaaaaa aagcattaaa tttaaaaaaa aactgtcttg
     5041 tctactttta gcttcattct cccatatttt gaagggtgtg taacttcagc tctgcaggat
     5101 tgcatggggt aaaacttgtt accaacacat gtgaaccatt gctacattgt aggttgtgat
     5161 cattttgccc cactgaagcc catgtatctg accttacgtg ccttttgaac taggagaatc
     5221 gggctaattt attaatgatg ataattataa tgtatctgta cagcactttt tacatttgcg
     5281 aagtgctttc caatccatgt tagttactag ttattacagc tgtaaggata aaacacgtca
     5341 tgtggattca ttttgaattg gtgctattgg tatttcctct gttattgcta ataaatgaaa
     5401 atggtggtat gaaa
//
