LOCUS       NM_018917               4778 bp    mRNA    linear   PRI 05-APR-2024
DEFINITION  Homo sapiens protocadherin gamma subfamily A, 4 (PCDHGA4),
            transcript variant 1, mRNA.
ACCESSION   NM_018917
VERSION     NM_018917.4
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 4778)
  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   2  (bases 1 to 4778)
  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   3  (bases 1 to 4778)
  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   4  (bases 1 to 4778)
  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   5  (bases 1 to 4778)
  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   6  (bases 1 to 4778)
  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, DA392480.1 and
            AF152324.1.
            
            On Nov 23, 2018 this sequence version replaced NM_018917.3.
            
            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 :: SRR1660805.126195.1,
                                           SRR1803616.113152.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1966682, SAMEA1968189
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000571252.3/ ENSP00000458570.2
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-4                 AC005618.1         66533-66536
            5-180               DA392480.1         9-184
            181-4778            AF152324.1         1-4598
FEATURES             Location/Qualifiers
     source          1..4778
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="5"
                     /map="5q31.3"
     gene            1..4778
                     /gene="PCDHGA4"
                     /gene_synonym="PCDH-GAMMA-A4"
                     /note="protocadherin gamma subfamily A, 4"
                     /db_xref="GeneID:56111"
                     /db_xref="HGNC:HGNC:8702"
                     /db_xref="MIM:606291"
     exon            1..2601
                     /gene="PCDHGA4"
                     /gene_synonym="PCDH-GAMMA-A4"
                     /inference="alignment:Splign:2.1.0"
     CDS             88..2976
                     /gene="PCDHGA4"
                     /gene_synonym="PCDH-GAMMA-A4"
                     /note="isoform 1 precursor is encoded by transcript
                     variant 1; protocadherin gamma-A4"
                     /codon_start=1
                     /product="protocadherin gamma-A4 isoform 1 precursor"
                     /protein_id="NP_061740.2"
                     /db_xref="CCDS:CCDS58979.2"
                     /db_xref="GeneID:56111"
                     /db_xref="HGNC:HGNC:8702"
                     /db_xref="MIM:606291"
                     /translation="MHFILDPEDPGAPQASTEGKPKHRRLRGGVVMAAPPARPDHTRL
                     LQICLLLGVLVEIRAEQILYSVFEEQEEGSVVGNIAKDLGLAPRELAERGVRIVSRGR
                     TQLFALNPRSGTLVTAGRIDREELCDRSPNCVTNLEILLEDTVKILRVEVEIIDVNDN
                     PPSFGTEQREIKVAENENPGARFPLPEAFDPDVGVNSLQGYQLNSNGYFSLDVQSGAD
                     GIKYPELVLERALDREEEAVHHLVLTAFDGGDPVRSGTARILIILVDTNDNAPVFTQP
                     EYHVSVRENVPVGTRLLTVKATDPDEGANGDVTYSFRKVRDKISQLFQLNSLSGDITI
                     LGGLDYEDSGFYDIDVEAHDGPGLRARSKVLVTVLDENDNAPEVTVTSLTSSVQESSS
                     PGTVIALFNVHDSDSGGNGLVTCSIPDNLPFTLEKTYGNYYRLLTHRTLDREEVSEYN
                     ITVTATDQGTPPLSTETHISLQVMDINDNPPTFPHASYSAYIPENNPRGASILSMTAQ
                     DPDSGDNARITYSLAEDTFQGAPLSSYVSINSNTGILYALCSFDYEQFRDLQLLMTAS
                     DSGDPPLSSNVSLSLFVLDQNDNVPEILYPTFPTDGSTGVELAPRSADSGYLVTKVVA
                     VDRDSGQNAWLSYSLLKSSEPGLFAVGLHTGEVRTARALLDRDALKQRLVVVVQDHGQ
                     PPLSATVTLTVAVADSIPDVLADLGSLKPSADPDDSGLTLYLVVAVAAVSCVFLAFVT
                     VLLALKLRRWHKSRLLHAEGSRLAGVPASHFVGVDGVRAFLQTYSHEVSLTADSRKSH
                     LIFSQPSYADTLISRESCEKSEPLLITQDLLETKGDPNLQQAPPNTDWRFSQAQRPGT
                     SGSQNGDDTGTWPNNQFDTEMLQAMILASASEAADGSSTLGGGAGTMGLSARYGPQFT
                     LQHVPDYRQNVYIPGSNATLTNAAGKRDGKAPAGGNGNKKKSGKKEKK"
     exon            2602..2660
                     /gene="PCDHGA4"
                     /gene_synonym="PCDH-GAMMA-A4"
                     /inference="alignment:Splign:2.1.0"
     exon            2661..2749
                     /gene="PCDHGA4"
                     /gene_synonym="PCDH-GAMMA-A4"
                     /inference="alignment:Splign:2.1.0"
     exon            2750..4778
                     /gene="PCDHGA4"
                     /gene_synonym="PCDH-GAMMA-A4"
                     /inference="alignment:Splign:2.1.0"
     regulatory      4757..4762
                     /regulatory_class="polyA_signal_sequence"
                     /gene="PCDHGA4"
                     /gene_synonym="PCDH-GAMMA-A4"
                     /note="hexamer: AATAAA"
     polyA_site      4778
                     /gene="PCDHGA4"
                     /gene_synonym="PCDH-GAMMA-A4"
                     /note="major polyA site"
ORIGIN      
        1 agaatcacaa gatttctgca gcacaaagca ctggctctgg agctttatga aagcttcaag
       61 cggaagccct gagagctctg gctgtgaatg cactttattt tggacccaga agatcctggg
      121 gctcctcagg cctcgacaga gggaaaaccg aagcacaggc gactccgcgg cggggttgta
      181 atggcggcgc ctcctgctcg cccagaccac acccggctgc tccagatctg ccttctcctg
      241 ggggttctgg tggaaatcag ggccgaacag attctctact cggtgtttga ggagcaggaa
      301 gaaggctcag tggtgggcaa catcgccaag gacctggggt tggcgccccg ggagctggcg
      361 gagcgcggag tccgcatcgt ctccagaggt aggacgcagc ttttcgccct gaacccgcgc
      421 agcggcacct tggtcaccgc gggtaggata gacagggagg agctctgcga cagatctcca
      481 aactgtgtga caaacctgga gattcttcta gaagatacag tgaagatttt gcgggtagag
      541 gtggaaataa tcgatgttaa tgataaccca cccagttttg ggacagaaca gagggaaata
      601 aaagttgctg aaaatgaaaa tcctggggca agatttcctc ttcctgaagc ttttgatccg
      661 gatgtaggtg taaactccct gcagggttac cagctcaact caaacggtta cttttccctg
      721 gacgtgcaaa gtggggccga tgggattaag tacccagagc tggtgctgga acgcgctcta
      781 gatcgcgagg aagaggcggt tcaccacctc gttctcacgg ccttcgatgg aggtgacccg
      841 gttcgctctg gcactgccag gattctcata atacttgtgg ataccaacga taatgctccc
      901 gtgttcactc agcccgagta ccacgtaagt gttcgtgaga acgttcctgt aggcactcgg
      961 ctactcaccg taaaagccac tgatccagat gaaggagcca atggagacgt gacgtattct
     1021 ttccggaaag taagagacaa aatatcacag ctatttcagt tgaattctct gagtggggat
     1081 ataacaatat tggggggtct agattatgag gactctggat tctatgacat agatgtagaa
     1141 gcccatgatg ggcctggtct ccgagctaga agcaaggtac tggtgacagt tctggatgaa
     1201 aatgacaacg caccagaagt cacagttaca tctctcacca gctcagtcca ggaatcttct
     1261 tccccgggta cagtaattgc acttttcaac gtgcatgaca gtgactcagg aggaaatggc
     1321 ctagtcacat gttctattcc agataatctg ccattcacac ttgaaaagac ctatggaaat
     1381 tattatcggt tgttgacaca cagaacactg gacagggaag aagtctcaga atataacatc
     1441 actgtaactg ccactgacca gggaactcct ccactgtcta cagaaactca tatttcactg
     1501 caagtgatgg acatcaatga caacccaccc actttccctc atgcttccta ctctgcttac
     1561 attcctgaaa acaaccccag aggagcctcc atcttatcta tgactgctca agaccctgac
     1621 agtggtgaca atgcccgaat cacttactcc ctggccgaag acaccttcca gggtgcacct
     1681 ctgtcctcct atgtctccat caactccaat acagggatcc tatatgctct ttgctccttc
     1741 gactatgagc agtttagaga cctgcagctg ctgatgacag ccagtgacag tggagaccct
     1801 ccactcagca gcaatgtgtc actgagcctc tttgtgctgg accagaacga caatgtccct
     1861 gagatcctgt accccacctt ccctactgat ggctccactg gtgtggagct ggcaccccgc
     1921 tccgcagatt ccggctacct ggtgaccaaa gtggtggcag tggacagaga ctcaggtcag
     1981 aatgcctggc tgtcctacag cctactcaag tccagcgagc cgggactatt tgcagtgggg
     2041 ctgcacacag gcgaggtgcg caccgcacgg gccctgctgg acagagacgc gctcaagcag
     2101 aggcttgtag tggtcgtcca ggaccatggc cagccccctc tctcggccac cgtcacactc
     2161 actgtggctg tggccgacag catcccagat gtcctggctg acttgggcag cctcaagcct
     2221 tcagcagacc cagacgactc gggcctcaca ctctatctcg tggtggcagt ggccgctgtc
     2281 tcctgcgtct tcctggcttt tgtcacggtg ctgctagcac tcaagctgag acgctggcac
     2341 aagtcacgcc tgcttcacgc tgaaggcagc aggttggcag gtgtgcctgc ctcgcacttt
     2401 gtgggcgtgg acggggttcg ggctttcctg cagacctatt cccacgaggt ctccctcacc
     2461 gcggactcgc ggaagagtca cctgatcttc tcccaaccca gctatgcaga cacgctcatc
     2521 agccgggaga gttgtgagaa aagcgagcct cttctgataa ctcaggattt acttgaaaca
     2581 aaaggagacc ctaatcttca gcaagccccg cccaacacgg actggcgttt ctctcaggcc
     2641 cagagacccg gcaccagcgg ctcccaaaat ggcgatgaca ccggcacctg gcccaacaac
     2701 cagtttgaca cagagatgct gcaagccatg atcttggcgt ccgccagtga agctgctgat
     2761 gggagctcca ccctgggagg gggtgccggc accatgggat tgagcgcccg ctacggaccc
     2821 cagttcaccc tgcagcacgt gcccgactac cgccagaatg tctacatccc aggcagcaat
     2881 gccacactga ccaacgcagc tggcaagcgg gatggcaagg ccccagcagg tggcaatggc
     2941 aacaagaaga agtcgggcaa gaaggagaag aagtaacatg gaggccaggc caagagccac
     3001 agggcggcct ctccccaacc agcccagctt ctccttacct gcacccaggc ctcagagttt
     3061 cagggctaac ccccagaata ctggtagggg ccaaggccat gctccccttg ggaaacagaa
     3121 acaagtgccc agtcagcacc taccccttcc cccccagggg gttgaatatg caaaagcagt
     3181 tccgctggga acccccatcc aatcaactgc tgtacccatg ggggtagtgg ggttactgta
     3241 gacaccaaga accatttgcc acaccccgtt tagttacagc tgaactcctc catcttccaa
     3301 atcaatcagg cccatccatc ccatgcctcc ctcctcccca ccccactcca acagttcctc
     3361 tttcccgagt aaggtggttg gggtgttgaa gtaccaagta acctacaagc ctcctagttc
     3421 tgaaaagttg gaagggcatc atgacctctt ggcctctcct ttgattctca atcttccccc
     3481 aaagcatggt ttggtgccag ccccttcacc tccttccaga gcccaagatc aatgctcaag
     3541 ttttggagga catgatcacc atccccatgg tactgatgct tgctggattt agggagggca
     3601 ttttgctacc aagcctcttc ccaacgccct ggggaccagt cttctgtttt gtttttcatt
     3661 gtttgacgtt tccactgcat gccttgactt cccccacctc ctcctcaaac aagagactcc
     3721 actgcatgtt ccaagacagt atggggtggt aagataagga agggaagtgt gtggatgtgg
     3781 atggtggggg catggacaaa gcttgacaca tcaagttatc aaggccttgg aggaggctct
     3841 gtatgtcctc aggggactga caacatcctc cagattccag ccataaacca ataactaggc
     3901 tggacccttc ccactacata atagggctca gcccaggcag ccagctttgg gctgagctaa
     3961 caggaccaat ggattaaact ggcatttcag tccaaggaag ctcgaagcag gtttaggacc
     4021 aggtcccctt gagaggtcag aggggcctct gtgggtgctg ggtactccag aggtgccact
     4081 ggtggaaggg tcagcggagc cccagcagga agggtgggcc agccaggcca ttcttagtcc
     4141 ctgggttggg gaggcaggga gctagggcag ggaccaaatg aacagaaagt ctcagcccag
     4201 gatggggctt cttcaacagg gcccctgccc tcctgaagcc tcagtccttc accttgccag
     4261 gtgccgtttc tcttccgtga aggccactgc ccaggtcccc agtgcgcccc ctagtggcca
     4321 tagcctggtt aaagttcccc agtgcctcct tgtgcataga ccttcttctc ccaccccctt
     4381 ctgcccctgg gtccccggcc atccagcggg gctgccagag aaccccagac ctgcccttac
     4441 agtagtgtag cgccccctcc ctctttcggc tggtgtagaa tagccagtag tgtagtgcgg
     4501 tgtgctttta cgtgatggcg ggtgggcagc gggcggcggg ctccgcgcag ccgtctgtcc
     4561 ttgatctgcc cgcggcggcc cgtgttgtgt tttgtgctgt gtccacgcgc taaggcgacc
     4621 ccctcccccg tactgacttc tcctataagc gcttctcttc gcatagtcac gtagctccca
     4681 ccccaccctc ttcctgtgtc tcacgcaagt tttatactct aatatttata tggctttttt
     4741 tcttcgacaa aaaaataata aaacgtttct tctgaaaa
//
