LOCUS       NM_018921               4776 bp    mRNA    linear   PRI 22-SEP-2024
DEFINITION  Homo sapiens protocadherin gamma subfamily A, 9 (PCDHGA9),
            transcript variant 1, mRNA.
ACCESSION   NM_018921
VERSION     NM_018921.3
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 4776)
  AUTHORS   Zhou,Z., Lai,Y., Cao,S., Zhuo,Q. and Tang,H.
  TITLE     Long non-coding RNA HHIP-AS1 inhibits lung cancer
            epithelial-mesenchymal transition and stemness by regulating
            PCDHGA9
  JOURNAL   Mol Med Rep 24 (6) (2021)
   PUBMED   34643245
  REMARK    GeneRIF: Long noncoding RNA HHIPAS1 inhibits lung cancer
            epithelialmesenchymal transition and stemness by regulating
            PCDHGA9.
REFERENCE   2  (bases 1 to 4776)
  AUTHORS   Huttlin,E.L., Bruckner,R.J., Navarrete-Perea,J., Cannon,J.R.,
            Baltier,K., Gebreab,F., Gygi,M.P., Thornock,A., Zarraga,G., Tam,S.,
            Szpyt,J., Gassaway,B.M., Panov,A., Parzen,H., Fu,S., Golbazi,A.,
            Maenpaa,E., Stricker,K., Guha Thakurta,S., Zhang,T., Rad,R.,
            Pan,J., Nusinow,D.P., Paulo,J.A., Schweppe,D.K., Vaites,L.P.,
            Harper,J.W. and Gygi,S.P.
  TITLE     Dual proteome-scale networks reveal cell-specific remodeling of the
            human interactome
  JOURNAL   Cell 184 (11), 3022-3040 (2021)
   PUBMED   33961781
REFERENCE   3  (bases 1 to 4776)
  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   4  (bases 1 to 4776)
  AUTHORS   Weng,J., Li,S., Lin,H., Mei,H., Liu,Y., Xiao,C., Zhu,Z., Cai,W.,
            Ding,X., Mi,Y. and Wen,Y.
  TITLE     PCDHGA9 represses epithelial-mesenchymal transition and metastatic
            potential in gastric cancer cells by reducing beta-catenin
            transcriptional activity
  JOURNAL   Cell Death Dis 11 (3), 206 (2020)
   PUBMED   32231199
  REMARK    GeneRIF: PCDHGA9 represses epithelial-mesenchymal transition and
            metastatic potential in gastric cancer cells by reducing
            beta-catenin transcriptional activity.
            Publication Status: Online-Only
REFERENCE   5  (bases 1 to 4776)
  AUTHORS   Baltz,A.G., Munschauer,M., Schwanhausser,B., Vasile,A.,
            Murakawa,Y., Schueler,M., Youngs,N., Penfold-Brown,D., Drew,K.,
            Milek,M., Wyler,E., Bonneau,R., Selbach,M., Dieterich,C. and
            Landthaler,M.
  TITLE     The mRNA-bound proteome and its global occupancy profile on
            protein-coding transcripts
  JOURNAL   Mol Cell 46 (5), 674-690 (2012)
   PUBMED   22681889
REFERENCE   6  (bases 1 to 4776)
  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   7  (bases 1 to 4776)
  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   8  (bases 1 to 4776)
  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   9  (bases 1 to 4776)
  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   10 (bases 1 to 4776)
  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 AC005618.1 and AF152329.1.
            
            On Sep 17, 2020 this sequence version replaced NM_018921.2.
            
            Summary: This gene is a member of the protocadherin gamma gene
            cluster, one of three related clusters tandemly linked on
            chromosome five. These gene clusters have an immunoglobulin-like
            organization, suggesting that a novel mechanism may be involved in
            their regulation and expression. The gamma gene cluster includes 22
            genes divided into 3 subfamilies. Subfamily A contains 12 genes,
            subfamily B contains 7 genes and 2 pseudogenes, and the more
            distantly related subfamily C contains 3 genes. The tandem array of
            22 large, variable region exons are followed by a constant region,
            containing 3 exons shared by all genes in the cluster. Each
            variable region exon encodes the extracellular region, which
            includes 6 cadherin ectodomains and a transmembrane region. The
            constant region exons encode the common cytoplasmic region. These
            neural cadherin-like cell adhesion proteins most likely play a
            critical role in the establishment and function of specific
            cell-cell connections in the brain. Alternative splicing has been
            described for the gamma cluster genes. [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 :: AF152329.1, SRR14038194.4376237.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1968189, SAMEA1968540
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000573521.2/ ENSP00000460274.1
            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
            1-175               AC005618.1         114290-114464
            176-4776            AF152329.1         1-4601
FEATURES             Location/Qualifiers
     source          1..4776
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="5"
                     /map="5q31.3"
     gene            1..4776
                     /gene="PCDHGA9"
                     /gene_synonym="PCDH-GAMMA-A9"
                     /note="protocadherin gamma subfamily A, 9"
                     /db_xref="GeneID:56107"
                     /db_xref="HGNC:HGNC:8707"
                     /db_xref="MIM:606296"
     exon            1..2599
                     /gene="PCDHGA9"
                     /gene_synonym="PCDH-GAMMA-A9"
                     /inference="alignment:Splign:2.1.0"
     CDS             176..2974
                     /gene="PCDHGA9"
                     /gene_synonym="PCDH-GAMMA-A9"
                     /note="isoform 1 precursor is encoded by transcript
                     variant 1; protocadherin gamma-A9"
                     /codon_start=1
                     /product="protocadherin gamma-A9 isoform 1 precursor"
                     /protein_id="NP_061744.1"
                     /db_xref="CCDS:CCDS58981.1"
                     /db_xref="GeneID:56107"
                     /db_xref="HGNC:HGNC:8707"
                     /db_xref="MIM:606296"
                     /translation="MAAPTKCQLRGRLVLLCSLLGMLWEARASQIRYSVPEETEKGYI
                     VGNISKDLALEPRELAERRVRIVSRGRTQLFSLNPRSGTLVTAGRIDREELCAQSPRC
                     LVNFKVLVEDRVKLYGIEIEVTDINDSAPKFQAESLEVKINEIAVPGARYPLPEAIDP
                     DVGVNSLQSYQLSPNHHFSLNVQTGDNGAINPELVLERALDREEATAHHLVLTASDGG
                     EPRRSSTVRIHVTVLDTNDNAPVFAQRIYRVKVLENVPPGTWLLTATASDLDEGINGK
                     VAYKFWKINEKQSLLFQLNENTGEISTAKSLDYEECSFYEMEIQAEDGGGLKGWTKVL
                     ISVEDVNDNRPEVTITSLFSPVREDAPQGTVILLFNAHDRDSGKNGQVVCSIQENLSF
                     TLENSEEDYYRLLTAQILDREKASEYNITVTATDRGTPPLSTEIHITLQVTDINDNPP
                     AFSQASYSVYLPENNARGTSIFSVIAYDPDSNENSRVIYSLAEDTIQGSPLSTYVSIN
                     SDTGVLYALCSFDYEQFRDLQMQVTASDSGSPPLSSNVSLRLFVLDQNDNAPEILYPA
                     LPTDGSTGVELAPRSAEPGYLVTKVVAVDRDSGQNAWLSYRLFKASEPGLFSVGLHTG
                     EVRTARALLDRDALKQSLVVAVQDHGQPPLSATVTLTVAIADSIPDILADLGSLQIPA
                     DLEASDLTLYLVVAVAVVSCVFLTFVITLLALRLRHWHSSHLLRATSDGLAGVPTSHF
                     VGVDGVRAFLQTYSQEFSLTADSRKSHLIFPQPNYADTLISQQSCEKNEPLCVSVDSK
                     FPIEDTPLVPQAPPNTDWRFSQAQRPGTSGSQNGDDTGTWPNNQFDTEMLQAMILASA
                     SEAADGSSTLGGGAGTMGLSARYGPQFTLQHVPDYRQNVYIPGSNATLTNAAGKRDGK
                     APAGGNGNKKKSGKKEKK"
     exon            2600..2658
                     /gene="PCDHGA9"
                     /gene_synonym="PCDH-GAMMA-A9"
                     /inference="alignment:Splign:2.1.0"
     exon            2659..2747
                     /gene="PCDHGA9"
                     /gene_synonym="PCDH-GAMMA-A9"
                     /inference="alignment:Splign:2.1.0"
     exon            2748..4776
                     /gene="PCDHGA9"
                     /gene_synonym="PCDH-GAMMA-A9"
                     /inference="alignment:Splign:2.1.0"
     regulatory      4755..4760
                     /regulatory_class="polyA_signal_sequence"
                     /gene="PCDHGA9"
                     /gene_synonym="PCDH-GAMMA-A9"
                     /note="hexamer: AATAAA"
     polyA_site      4776
                     /gene="PCDHGA9"
                     /gene_synonym="PCDH-GAMMA-A9"
                     /note="major polyA site"
ORIGIN      
        1 agttctgcgg ctacacaaaa cccggcagat accacaaacc tgctcccagg ctgcagcaaa
       61 actcagcctc tttcttctaa ggaaaagatc accatacttt gcagggtgga agaaagaacc
      121 tgatgaagca gcgcgcacag agatcctttt gagaaaattc caaagcgagg cagcaatggc
      181 agctccaacc aaatgccagc tccgcggaag attagtcctg ctatgctcgc tcctggggat
      241 gctatgggag gccagggcca gtcagattcg ctactcagtg cctgaagaga cagaaaaggg
      301 ctatattgtg ggcaacatct ccaaggacct ggctctggag ccccgggagc tggcggagcg
      361 ccgagtccgc atcgtctcta gaggtaggac gcagcttttc tctctgaacc cgcgcagcgg
      421 caccttggtc accgcgggta ggatagaccg ggaggagctc tgtgctcaga gcccgcggtg
      481 tctggtgaac tttaaagtcc tggttgaaga cagagtgaaa ctgtacggaa tagaaataga
      541 agtaactgat attaacgaca gcgccccaaa gttccaggcc gaaagtctgg aagtaaaaat
      601 taacgaaatc gcggttcctg gagcacgtta tccacttcca gaagctattg atccggatgt
      661 tggcgtgaac tccctccaga gctaccagct cagccccaat caccacttct ccctgaacgt
      721 gcagactgga gacaatggag ccataaaccc agagctggtg ctggagcgcg ccctggacag
      781 ggaggaggca actgcccacc acctggtcct cacggcctcg gatggcggcg agccgcgtcg
      841 ctccagcaca gtgcgcatcc atgtgacagt gttggataca aatgataatg ccccggtttt
      901 tgctcaacgg atttaccgag ttaaagtcct tgagaacgtg cccccaggca cctggctgct
      961 tactgcaaca gccagcgacc tggatgaggg aatcaacgga aaagtggcat acaaattctg
     1021 gaaaattaat gaaaaacaat ctctgctatt ccagcttaat gaaaatactg gggaaatatc
     1081 aacagcaaaa agtctagatt atgaagaatg ttcattttat gaaatggaaa tacaagctga
     1141 agatggtggg ggattgaaag ggtggacaaa agtgctcatt tcggtggaag atgtaaatga
     1201 caatagacct gaagtgacca ttacatctct gtttagccca gtgagagaag acgcacctca
     1261 gggaacagta attcttcttt tcaatgctca tgaccgagac tccgggaaga atggtcaagt
     1321 tgtctgttct atccaggaga atctatcttt tacattagaa aattcagaag aagattatta
     1381 cagattgttg acggcccaaa ttcttgaccg agaaaaagcc tcagaatata atatcacggt
     1441 gactgcaaca gacagaggaa ctccgcccct gtccacagaa attcacatca ccctgcaagt
     1501 gactgacatc aatgataatc cacctgcttt ctctcaagcc tcctactcag tctacctccc
     1561 ggaaaacaac gccagaggta cttccatctt ctccgtgatt gcctatgacc ctgatagcaa
     1621 tgagaattct agagttattt actccttggc agaggatacc atccaagggt ctcctctctc
     1681 cacctatgtc tctattaact cagacactgg tgtgctgtat gctctgtgct cctttgacta
     1741 tgagcagttt agagatttgc aaatgcaggt gacggcaagt gacagtggaa gcccaccact
     1801 tagcagcaat gtgtcattga gactgtttgt tttggaccag aatgacaatg ccccagaaat
     1861 cctgtaccct gccctcccca ctgatggttc tactggtgtg gagctggcac cccgctctgc
     1921 agagcctggc tacctggtga ccaaggtggt ggcagtggac agagactcag gccagaatgc
     1981 ttggctctcc taccgcctat tcaaggccag tgagccaggg ctcttctcgg tggggctgca
     2041 cacaggtgaa gtgcgcacag ctcgggccct gctagataga gatgcgctca aacagagcct
     2101 tgtggtggct gtacaggacc atggccagcc ccctctctcg gccactgtca cgctcacagt
     2161 agccatagct gacagcatcc cagacatcct ggctgacctg ggcagtcttc agatccctgc
     2221 agacctggag gcctcagacc ttaccctcta cctcgttgtg gctgtggcag tcgtctcctg
     2281 tgtcttcctc accttcgtta tcacgctgct ggccctcagg ctgaggcact ggcactcctc
     2341 gcatctgctg cgggctacca gtgatgggtt ggctggtgtg cccacctcac actttgtggg
     2401 tgtagatggg gttcgagctt tcctacagac ctattctcag gagttctccc tcaccgctga
     2461 ctcaaggaag agtcacctga tcttccccca gcccaactat gcagacacac tcatcagcca
     2521 gcagagctgt gagaaaaatg agcctttgtg cgtctctgtt gattccaagt ttcctataga
     2581 agacacccct ttggttccgc aagccccgcc caacacggac tggcgtttct ctcaggccca
     2641 gagacccggc accagcggct cccaaaatgg cgatgacacc ggcacctggc ccaacaacca
     2701 gtttgacaca gagatgctgc aagccatgat cttggcgtcc gccagtgaag ctgctgatgg
     2761 gagctccacc ctgggagggg gtgccggcac catgggattg agcgcccgct acggacccca
     2821 gttcaccctg cagcacgtgc ccgactaccg ccagaatgtc tacatcccag gcagcaatgc
     2881 cacactgacc aacgcagctg gcaagcggga tggcaaggcc ccagcaggtg gcaatggcaa
     2941 caagaagaag tcgggcaaga aggagaagaa gtaacatgga ggccaggcca agagccacag
     3001 ggcggcctct ccccaaccag cccagcttct ccttacctgc acccaggcct cagagtttca
     3061 gggctaaccc ccagaatact ggtaggggcc aaggccatgc tccccttggg aaacagaaac
     3121 aagtgcccag tcagcaccta ccccttcccc cccagggggt tgaatatgca aaagcagttc
     3181 cgctgggaac ccccatccaa tcaactgctg tacccatggg ggtagtgggg ttactgtaga
     3241 caccaagaac catttgccac accccgttta gttacagctg aactcctcca tcttccaaat
     3301 caatcaggcc catccatccc atgcctccct cctccccacc ccactccaac agttcctctt
     3361 tcccgagtaa ggtggttggg gtgttgaagt accaagtaac ctacaagcct cctagttctg
     3421 aaaagttgga agggcatcat gacctcttgg cctctccttt gattctcaat cttcccccaa
     3481 agcatggttt ggtgccagcc ccttcacctc cttccagagc ccaagatcaa tgctcaagtt
     3541 ttggaggaca tgatcaccat ccccatggta ctgatgcttg ctggatttag ggagggcatt
     3601 ttgctaccaa gcctcttccc aacgccctgg ggaccagtct tctgttttgt ttttcattgt
     3661 ttgacgtttc cactgcatgc cttgacttcc cccacctcct cctcaaacaa gagactccac
     3721 tgcatgttcc aagacagtat ggggtggtaa gataaggaag ggaagtgtgt ggatgtggat
     3781 ggtgggggca tggacaaagc ttgacacatc aagttatcaa ggccttggag gaggctctgt
     3841 atgtcctcag gggactgaca acatcctcca gattccagcc ataaaccaat aactaggctg
     3901 gacccttccc actacataat agggctcagc ccaggcagcc agctttgggc tgagctaaca
     3961 ggaccaatgg attaaactgg catttcagtc caaggaagct cgaagcaggt ttaggaccag
     4021 gtccccttga gaggtcagag gggcctctgt gggtgctggg tactccagag gtgccactgg
     4081 tggaagggtc agcggagccc cagcaggaag ggtgggccag ccaggccatt cttagtccct
     4141 gggttgggga ggcagggagc tagggcaggg accaaatgaa cagaaagtct cagcccagga
     4201 tggggcttct tcaacagggc ccctgccctc ctgaagcctc agtccttcac cttgccaggt
     4261 gccgtttctc ttccgtgaag gccactgccc aggtccccag tgcgccccct agtggccata
     4321 gcctggttaa agttccccag tgcctccttg tgcatagacc ttcttctccc acccccttct
     4381 gcccctgggt ccccggccat ccagcggggc tgccagagaa ccccagacct gcccttacag
     4441 tagtgtagcg ccccctccct ctttcggctg gtgtagaata gccagtagtg tagtgcggtg
     4501 tgcttttacg tgatggcggg tgggcagcgg gcggcgggct ccgcgcagcc gtctgtcctt
     4561 gatctgcccg cggcggcccg tgttgtgttt tgtgctgtgt ccacgcgcta aggcgacccc
     4621 ctcccccgta ctgacttctc ctataagcgc ttctcttcgc atagtcacgt agctcccacc
     4681 ccaccctctt cctgtgtctc acgcaagttt tatactctaa tatttatatg gctttttttc
     4741 ttcgacaaaa aaataataaa acgtttcttc tgaaaa
//
