LOCUS       NM_003735               4854 bp    mRNA    linear   PRI 04-APR-2024
DEFINITION  Homo sapiens protocadherin gamma subfamily A, 12 (PCDHGA12),
            transcript variant 1, mRNA.
ACCESSION   NM_003735
VERSION     NM_003735.3
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 4854)
  AUTHORS   Clark,H.F., Gurney,A.L., Abaya,E., Baker,K., Baldwin,D., Brush,J.,
            Chen,J., Chow,B., Chui,C., Crowley,C., Currell,B., Deuel,B.,
            Dowd,P., Eaton,D., Foster,J., Grimaldi,C., Gu,Q., Hass,P.E.,
            Heldens,S., Huang,A., Kim,H.S., Klimowski,L., Jin,Y., Johnson,S.,
            Lee,J., Lewis,L., Liao,D., Mark,M., Robbie,E., Sanchez,C.,
            Schoenfeld,J., Seshagiri,S., Simmons,L., Singh,J., Smith,V.,
            Stinson,J., Vagts,A., Vandlen,R., Watanabe,C., Wieand,D., Woods,K.,
            Xie,M.H., Yansura,D., Yi,S., Yu,G., Yuan,J., Zhang,M., Zhang,Z.,
            Goddard,A., Wood,W.I., Godowski,P. and Gray,A.
  TITLE     The secreted protein discovery initiative (SPDI), a large-scale
            effort to identify novel human secreted and transmembrane proteins:
            a bioinformatics assessment
  JOURNAL   Genome Res 13 (10), 2265-2270 (2003)
   PUBMED   12975309
  REMARK    Erratum:[Genome Res. 2003 Dec;13(12):2759]
REFERENCE   2  (bases 1 to 4854)
  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 4854)
  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 4854)
  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 4854)
  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 4854)
  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
REFERENCE   7  (bases 1 to 4854)
  AUTHORS   Matsuyoshi,N. and Imamura,S.
  TITLE     Multiple cadherins are expressed in human fibroblasts
  JOURNAL   Biochem Biophys Res Commun 235 (2), 355-358 (1997)
   PUBMED   9199196
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AC005618.1, AL589367.1 and
            AF152321.1.
            
            On Nov 22, 2018 this sequence version replaced NM_003735.2.
            
            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 :: AB011160.1, SRR1660803.179509.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1965299, SAMEA1966682
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000252085.4/ ENSP00000252085.3
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-84                AC005618.1         142019-142102
            85-253              AL589367.1         28-196
            254-4854            AF152321.1         1-4601
FEATURES             Location/Qualifiers
     source          1..4854
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="5"
                     /map="5q31.3"
     gene            1..4854
                     /gene="PCDHGA12"
                     /gene_synonym="CDH21; FIB3; PCDH-GAMMA-A12"
                     /note="protocadherin gamma subfamily A, 12"
                     /db_xref="GeneID:26025"
                     /db_xref="HGNC:HGNC:8699"
                     /db_xref="MIM:603059"
     exon            1..2677
                     /gene="PCDHGA12"
                     /gene_synonym="CDH21; FIB3; PCDH-GAMMA-A12"
                     /inference="alignment:Splign:2.1.0"
     CDS             254..3052
                     /gene="PCDHGA12"
                     /gene_synonym="CDH21; FIB3; PCDH-GAMMA-A12"
                     /note="isoform 1 precursor is encoded by transcript
                     variant 1; fibroblast cadherin FIB3; cadherin 21;
                     protocadherin gamma-A12; fibroblast cadherin-3"
                     /codon_start=1
                     /product="protocadherin gamma-A12 isoform 1 precursor"
                     /protein_id="NP_003726.1"
                     /db_xref="CCDS:CCDS4260.1"
                     /db_xref="GeneID:26025"
                     /db_xref="HGNC:HGNC:8699"
                     /db_xref="MIM:603059"
                     /translation="MIPARLHRDYKGLVLLGILLGTLWETGCTQIRYSVPEELEKGSR
                     VGDISRDLGLEPRELAERGVRIIPRGRTQLFALNPRSGSLVTAGRIDREELCMGAIKC
                     QLNLDILMEDKVKIYGVEVEVRDINDNAPYFRESELEIKISENAATEMRFPLPHAWDP
                     DIGKNSLQSYELSPNTHFSLIVQNGADGSKYPELVLKRALDREEKAAHHLVLTASDGG
                     DPVRTGTARIRVMVLDANDNAPAFAQPEYRASVPENLALGTQLLVVNATDPDEGVNAE
                     VRYSFRYVDDKAAQVFKLDCNSGTISTIGELDHEESGFYQMEVQAMDNAGYSARAKVL
                     ITVLDVNDNAPEVVLTSLASSVPENSPRGTLIALLNVNDQDSEENGQVICFIQGNLPF
                     KLEKSYGNYYSLVTDIVLDREQVPSYNITVTATDRGTPPLSTETHISLNVADTNDNPP
                     VFPQASYSAYIPENNPRGVSLVSVTAHDPDCEENAQITYSLAENTIQGASLSSYVSIN
                     SDTGVLYALSSFDYEQFRDLQVKVMARDNGHPPLSSNVSLSLFVLDQNDNAPEILYPA
                     LPTDGSTGVELAPRSAEPGYLVTKVVAVDRDSGQNAWLSYRLLKASEPGLFSVGLHTG
                     EVRTARALLDRDALKQSLVVAVQDHGQPPLSATVTLTVAVADSIPQVLADLGSLESPA
                     NSETSDLTLYLVVAVAAVSCVFLAFVILLLALRLRRWHKSRLLQASGGGLTGAPASHF
                     VGVDGVQAFLQTYSHEVSLTTDSRKSHLIFPQPNYADMLVSQESFEKSEPLLLSGDSV
                     FSKDSHGLIEQAPPNTDWRFSQAQRPGTSGSQNGDDTGTWPNNQFDTEMLQAMILASA
                     SEAADGSSTLGGGAGTMGLSARYGPQFTLQHVPDYRQNVYIPGSNATLTNAAGKRDGK
                     APAGGNGNKKKSGKKEKK"
     exon            2678..2736
                     /gene="PCDHGA12"
                     /gene_synonym="CDH21; FIB3; PCDH-GAMMA-A12"
                     /inference="alignment:Splign:2.1.0"
     exon            2737..2825
                     /gene="PCDHGA12"
                     /gene_synonym="CDH21; FIB3; PCDH-GAMMA-A12"
                     /inference="alignment:Splign:2.1.0"
     exon            2826..4854
                     /gene="PCDHGA12"
                     /gene_synonym="CDH21; FIB3; PCDH-GAMMA-A12"
                     /inference="alignment:Splign:2.1.0"
     regulatory      4833..4838
                     /regulatory_class="polyA_signal_sequence"
                     /gene="PCDHGA12"
                     /gene_synonym="CDH21; FIB3; PCDH-GAMMA-A12"
                     /note="hexamer: AATAAA"
     polyA_site      4854
                     /gene="PCDHGA12"
                     /gene_synonym="CDH21; FIB3; PCDH-GAMMA-A12"
                     /note="major polyA site"
ORIGIN      
        1 aagattgtgc agtaattggt taggactctg agcgccgctg ttcaccaatc ggggagagaa
       61 aagcggagat cctgctcgcc ttgcacgcgc ctgaagcaca aagcagatag ctaggaatga
      121 accatccctg ggagtatgtg gaaacaacgg aggagctctg acttcccaac tgtcccattc
      181 tatgggcgaa ggaactgctc ctgacttcag tggttaaggg cagaattgaa aataattctg
      241 gaggaagata agaatgattc ctgcgcgact gcaccgggac tacaaagggc ttgtcctgct
      301 gggaatcctc ctggggactc tgtgggagac cggatgcacc cagatacgct attcagttcc
      361 ggaagagctg gagaaaggct ctagggtggg cgacatctcc agggacctgg ggctggagcc
      421 ccgggagctc gcggagcgcg gagtccgcat catccccaga ggtaggacgc agcttttcgc
      481 cctgaatccg cgcagcggca gcttggtcac ggcgggcagg atagaccggg aggagctctg
      541 tatgggggcc atcaagtgtc aattaaatct agacattctg atggaggata aagtgaaaat
      601 atatggagta gaagtagaag taagggacat taacgacaat gcgccttact ttcgtgaaag
      661 tgaattagaa ataaaaatta gtgaaaatgc agccactgag atgcggttcc ctctacccca
      721 cgcctgggat ccggatatcg ggaagaactc tctgcagagc tacgagctca gcccgaacac
      781 tcacttctcc ctcatcgtgc aaaatggagc cgacggtagt aagtaccccg aattggtgct
      841 gaaacgcgcc ctggaccgcg aagaaaaggc tgctcaccac ctggtcctta cggcctccga
      901 cgggggcgac ccggtgcgca caggcaccgc gcgcatccgc gtgatggttc tggatgcgaa
      961 cgacaacgca ccagcgtttg ctcagcccga gtaccgcgcg agcgttccgg agaatctggc
     1021 cttgggcacg cagctgcttg tagtcaacgc taccgaccct gacgaaggag tcaatgcgga
     1081 agtgaggtat tccttccggt atgtggacga caaggcggcc caagttttca aactagattg
     1141 taattcaggg acaatatcaa caatagggga gttggaccac gaggagtcag gattctacca
     1201 gatggaagtg caagcaatgg ataatgcagg atattctgcg cgagccaaag tcctgatcac
     1261 tgttctggac gtgaacgaca atgccccaga agtggtcctc acctctctcg ccagctcggt
     1321 tcccgaaaac tctcccagag ggacattaat tgccctttta aatgtaaatg accaagattc
     1381 tgaggaaaac ggacaggtga tctgtttcat ccaaggaaat ctgcccttta aattagaaaa
     1441 atcttacgga aattactata gtttagtcac agacatagtc ttggataggg aacaggttcc
     1501 tagctacaac atcacagtga ccgccactga ccggggaacc ccgcccctat ccacggaaac
     1561 tcatatctcg ctgaacgtgg cagacaccaa cgacaacccg ccggtcttcc ctcaggcctc
     1621 ctattccgct tatatcccag agaacaatcc cagaggagtt tccctcgtct ctgtgaccgc
     1681 ccacgacccc gactgtgaag agaacgccca gatcacttat tccctggctg agaacaccat
     1741 ccaaggggca agcctatcgt cctacgtgtc catcaactcc gacactgggg tactgtatgc
     1801 gctgagctcc ttcgactacg agcagttccg agacttgcaa gtgaaagtga tggcgcggga
     1861 caacgggcac ccgcccctca gcagcaacgt gtcgttgagc ctgttcgtgc tggaccagaa
     1921 cgacaatgcg cccgagatcc tgtaccccgc cctccccacg gacggttcca ctggcgtgga
     1981 gctggctccc cgctccgcag agcccggcta cctggtgacc aaggtggtgg cggtggacag
     2041 agactccggc cagaacgcct ggctgtccta ccgtctgctc aaggccagcg agccgggact
     2101 cttctcggtg ggtctgcaca cgggcgaggt gcgcacggcg cgagccctgc tggacagaga
     2161 cgcgctcaag cagagcctcg tagtggccgt ccaggaccac ggccagcccc ctctctccgc
     2221 cactgtcacg ctcaccgtgg ccgtggccga cagcatcccc caagtcctgg cggacctcgg
     2281 cagcctcgag tctccagcta actctgaaac ctcagacctc actctgtacc tggtggtagc
     2341 ggtggccgcg gtctcctgcg tcttcctggc cttcgtcatc ttgctgctgg cgctcaggct
     2401 gcggcgctgg cacaagtcac gcctgctgca ggcttcagga ggcggcttga caggagcgcc
     2461 ggcgtcgcac tttgtgggcg tggacggggt gcaggctttc ctgcagacct attcccacga
     2521 ggtttccctc accacggact cgcggaagag tcacctgatc ttcccccagc ccaactatgc
     2581 agacatgctc gtcagccagg agagctttga aaaaagcgag ccccttttgc tgtcaggtga
     2641 ttcggtattt tctaaagaca gtcatgggtt aattgagcaa gccccgccca acacggactg
     2701 gcgtttctct caggcccaga gacccggcac cagcggctcc caaaatggcg atgacaccgg
     2761 cacctggccc aacaaccagt ttgacacaga gatgctgcaa gccatgatct tggcgtccgc
     2821 cagtgaagct gctgatggga gctccaccct gggagggggt gccggcacca tgggattgag
     2881 cgcccgctac ggaccccagt tcaccctgca gcacgtgccc gactaccgcc agaatgtcta
     2941 catcccaggc agcaatgcca cactgaccaa cgcagctggc aagcgggatg gcaaggcccc
     3001 agcaggtggc aatggcaaca agaagaagtc gggcaagaag gagaagaagt aacatggagg
     3061 ccaggccaag agccacaggg cggcctctcc ccaaccagcc cagcttctcc ttacctgcac
     3121 ccaggcctca gagtttcagg gctaaccccc agaatactgg taggggccaa ggccatgctc
     3181 cccttgggaa acagaaacaa gtgcccagtc agcacctacc ccttcccccc cagggggttg
     3241 aatatgcaaa agcagttccg ctgggaaccc ccatccaatc aactgctgta cccatggggg
     3301 tagtggggtt actgtagaca ccaagaacca tttgccacac cccgtttagt tacagctgaa
     3361 ctcctccatc ttccaaatca atcaggccca tccatcccat gcctccctcc tccccacccc
     3421 actccaacag ttcctctttc ccgagtaagg tggttggggt gttgaagtac caagtaacct
     3481 acaagcctcc tagttctgaa aagttggaag ggcatcatga cctcttggcc tctcctttga
     3541 ttctcaatct tcccccaaag catggtttgg tgccagcccc ttcacctcct tccagagccc
     3601 aagatcaatg ctcaagtttt ggaggacatg atcaccatcc ccatggtact gatgcttgct
     3661 ggatttaggg agggcatttt gctaccaagc ctcttcccaa cgccctgggg accagtcttc
     3721 tgttttgttt ttcattgttt gacgtttcca ctgcatgcct tgacttcccc cacctcctcc
     3781 tcaaacaaga gactccactg catgttccaa gacagtatgg ggtggtaaga taaggaaggg
     3841 aagtgtgtgg atgtggatgg tgggggcatg gacaaagctt gacacatcaa gttatcaagg
     3901 ccttggagga ggctctgtat gtcctcaggg gactgacaac atcctccaga ttccagccat
     3961 aaaccaataa ctaggctgga cccttcccac tacataatag ggctcagccc aggcagccag
     4021 ctttgggctg agctaacagg accaatggat taaactggca tttcagtcca aggaagctcg
     4081 aagcaggttt aggaccaggt ccccttgaga ggtcagaggg gcctctgtgg gtgctgggta
     4141 ctccagaggt gccactggtg gaagggtcag cggagcccca gcaggaaggg tgggccagcc
     4201 aggccattct tagtccctgg gttggggagg cagggagcta gggcagggac caaatgaaca
     4261 gaaagtctca gcccaggatg gggcttcttc aacagggccc ctgccctcct gaagcctcag
     4321 tccttcacct tgccaggtgc cgtttctctt ccgtgaaggc cactgcccag gtccccagtg
     4381 cgccccctag tggccatagc ctggttaaag ttccccagtg cctccttgtg catagacctt
     4441 cttctcccac ccccttctgc ccctgggtcc ccggccatcc agcggggctg ccagagaacc
     4501 ccagacctgc ccttacagta gtgtagcgcc ccctccctct ttcggctggt gtagaatagc
     4561 cagtagtgta gtgcggtgtg cttttacgtg atggcgggtg ggcagcgggc ggcgggctcc
     4621 gcgcagccgt ctgtccttga tctgcccgcg gcggcccgtg ttgtgttttg tgctgtgtcc
     4681 acgcgctaag gcgaccccct cccccgtact gacttctcct ataagcgctt ctcttcgcat
     4741 agtcacgtag ctcccacccc accctcttcc tgtgtctcac gcaagtttta tactctaata
     4801 tttatatggc tttttttctt cgacaaaaaa ataataaaac gtttcttctg aaaa
//
