LOCUS       NM_018898               5896 bp    mRNA    linear   PRI 09-JUN-2024
DEFINITION  Homo sapiens protocadherin alpha subfamily C, 1 (PCDHAC1),
            transcript variant 1, mRNA.
ACCESSION   NM_018898
VERSION     NM_018898.5
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 5896)
  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   2  (bases 1 to 5896)
  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 5896)
  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 5896)
  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 5896)
  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 5896)
  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   7  (bases 1 to 5896)
  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 AC010223.6.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Dec 30, 2019 this sequence version replaced NM_018898.4.
            
            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).
            
            ##Evidence-Data-START##
            Transcript exon combination :: AF152303.1, SRR11853561.23898.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1968540, SAMEA2142680
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000253807.3/ ENSP00000253807.2
            RefSeq Select criteria :: based on manual assertion, conservation,
                                      expression, longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-3027              AC010223.6         133288-136314       c
            3028-3086           AC010223.6         83606-83664         c
            3087-3175           AC010223.6         80050-80138         c
            3176-5896           AC010223.6         50266-52986         c
FEATURES             Location/Qualifiers
     source          1..5896
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="5"
                     /map="5q31.3"
     gene            1..5896
                     /gene="PCDHAC1"
                     /gene_synonym="PCDH-ALPHA-C1"
                     /note="protocadherin alpha subfamily C, 1"
                     /db_xref="GeneID:56135"
                     /db_xref="HGNC:HGNC:8676"
                     /db_xref="MIM:606320"
     exon            1..3027
                     /gene="PCDHAC1"
                     /gene_synonym="PCDH-ALPHA-C1"
                     /inference="alignment:Splign:2.1.0"
     CDS             595..3486
                     /gene="PCDHAC1"
                     /gene_synonym="PCDH-ALPHA-C1"
                     /note="isoform 1 precursor is encoded by transcript
                     variant 1; protocadherin alpha-C1"
                     /codon_start=1
                     /product="protocadherin alpha-C1 isoform 1 precursor"
                     /protein_id="NP_061721.2"
                     /db_xref="CCDS:CCDS4241.1"
                     /db_xref="GeneID:56135"
                     /db_xref="HGNC:HGNC:8676"
                     /db_xref="MIM:606320"
                     /translation="MVGCGVAVLCLWVSCGAAAGQLEYSVPEETERGVAVGNLSADLR
                     LPAAAMSSRNFRFLSSHRELYFGVDLPSGNLVVREPADREQLCRAKAACVLTYDLVLE
                     DPLELHKIRIHVLDTNDNSPLFPAGDVQLHIPEFLTPGARFTLPNAQDDDEGSNGILS
                     YSLSPSQHFRLDMGSRVDGSEYPELVLEKALDREQRATHLLVLTARDGGLPARSGDAQ
                     VTIIVVDTNDNAPVFERSVYRTKVPETAPNGTVLFRVQALDPDEGSNGEVQYSLSNST
                     QAELRHRFHVHPKSGEVQVAASLGPPETLLEAYIEARDEGVFGLASTAKLLVEVTDVN
                     DHAPELDFLTLSNPVPEDAAPGTVIALFSVKDEDLDSNGRVICGMSSAGPFQLTASFD
                     NYYSLLIDGPLDREQISEYQVLITASDSGSPPLSTRRTITVSVADVNDNTPNFPQPQQ
                     ELFVAENNGPGASLGRVFAQDPDLGKNGLVSYELLDVISEGPSASSLLAVESSSGAIT
                     AKTSFDFEQLRGFHFQVEGRDGGIPPRSATVTINLFVVDRNDNYPVILFPLPRNGSVP
                     VEIVPRSARTGHLVTKVVAEDADSGSNAWLSYHISRASDSSLFRISANIGELRTARLV
                     LPTDAVKQRVVVVVRDHGDPPLSSSVTLGVLLSNSVPQLLPDFEDVWEPGGQLSAQNL
                     YLVIALACISFLFLGCLLFFVCTKLHQSPGCCAQSCCRSTEDLRYGSKMVSNPCMTSA
                     TIDVTTVERLSQTYLYRASLGLGSDNNSLLLRGEYNAADLRNLATGVGLNLPISCIQI
                     RNRKGDHANVNAMPRQPNPDWRYSASLRAGMHSSVHLEEAGILRAGPGGPDQQWPTVS
                     SATPEPEAGEVSPPVGAGVNSNSWTFKYGPGNPKQSGPGELPDKFIIPGSPAIISIRQ
                     EPTNSQIDKSDFITFGKKEETKKKKKKKKGNKTQEKKEKGNSTTDNSDQ"
     exon            3028..3086
                     /gene="PCDHAC1"
                     /gene_synonym="PCDH-ALPHA-C1"
                     /inference="alignment:Splign:2.1.0"
     exon            3087..3175
                     /gene="PCDHAC1"
                     /gene_synonym="PCDH-ALPHA-C1"
                     /inference="alignment:Splign:2.1.0"
     exon            3176..5896
                     /gene="PCDHAC1"
                     /gene_synonym="PCDH-ALPHA-C1"
                     /inference="alignment:Splign:2.1.0"
     regulatory      5107..5112
                     /regulatory_class="polyA_signal_sequence"
                     /gene="PCDHAC1"
                     /gene_synonym="PCDH-ALPHA-C1"
                     /note="hexamer: AGTAAA"
     polyA_site      5130
                     /gene="PCDHAC1"
                     /gene_synonym="PCDH-ALPHA-C1"
     regulatory      5876..5881
                     /regulatory_class="polyA_signal_sequence"
                     /gene="PCDHAC1"
                     /gene_synonym="PCDH-ALPHA-C1"
                     /note="hexamer: AATGAA"
     polyA_site      5896
                     /gene="PCDHAC1"
                     /gene_synonym="PCDH-ALPHA-C1"
                     /note="major polyA site"
ORIGIN      
        1 ctctccgccg gagaggtgcg ccggggtcag agcgccggga cccgacgcgc ggctcccaaa
       61 gggcggcagg aagagcccag ctgggctcag ccacagttat cagcaatctg cgggcagagg
      121 atgtggaggt taagatctgg gcagcctcag ggcgttgtcc tagaaaacac cgtttaagga
      181 gagaagtgtt agtgtctcgg ggcgtctccc aggctccgcc ctgcgcccgc agccagcgtg
      241 gtggtcgaga ccccagcccg ctgctactgg agacagcacc tctcgcgccc gggcgggcgg
      301 cctcgtctct gcacccctag gcggcgctgc gctcctcaac acccggccgg ctccgctttc
      361 ccagacggct gcccagcctc cagcctagca agcccggctc ccagctggcc agccccggca
      421 atgccggcgt tcgggaggcg caacgtcggc ggtcgctgag tatccagccc gcagcagtga
      481 cggccggcag gagcgtgctc ttccccgcgg ctcgtgctct ccaggagtcc ggagcatggt
      541 cctgggtcac cgttggtgta gcgtgttggt ggaacgtgga cgcctagagg gaggatggtg
      601 ggctgtgggg tggcagtttt atgtttgtgg gtttcctgcg gcgctgcagc gggacagctc
      661 gagtactcag tgccggagga gacggagcgg ggcgtagccg taggcaatct ctccgcggac
      721 ttgaggctgc cagcggccgc tatgtcctcg cggaactttc gcttcctttc cagccaccgc
      781 gagctctact tcggggtgga tctacccagc ggcaatttgg tggtcagaga gccggcggac
      841 cgcgaacagc tgtgcagggc caaagctgcc tgcgtcttga cctacgacct ggtgctcgag
      901 gacccgctgg agctgcacaa gattcggatt cacgtcctgg acaccaatga caactcacct
      961 ctctttcctg ccggcgacgt gcagctgcac atccccgagt tcctgacgcc cggagcccgc
     1021 tttactctcc cgaatgccca agatgacgac gagggaagca atgggatact aagctacagc
     1081 ctaagcccca gtcagcactt tcgcctggac atgggatcgc gggttgacgg cagcgaatac
     1141 ccggagttgg tgttggagaa agcactggat cgcgaacagc gcgccaccca cctgctggtg
     1201 cttacagctc gggacggcgg gctacctgcc cgctcaggag acgcacaagt caccatcatt
     1261 gtggtggaca caaatgacaa cgcgcctgta tttgagcgct ccgtataccg caccaaggtt
     1321 ccagagactg cacccaatgg gactgtgtta ttccgagttc aagccttgga tccagatgaa
     1381 gggtccaatg gggaagtcca gtactcccta agcaacagca cgcaagcaga gctgcgacac
     1441 cgctttcacg tgcaccctaa aagtggggag gtgcaagtag ctgcttcact aggtccgcct
     1501 gaaacgctct tggaggcata cattgaggcg agggacgaag gtgtctttgg tttagctagc
     1561 accgctaaac tgctggtgga ggtgactgac gtgaacgatc atgcccccga actggacttc
     1621 ctgactcttt cgaacccagt acctgaggac gctgcccctg gcacagtgat tgctctcttt
     1681 agtgtaaagg atgaagacct cgattctaat ggtagggtca tttgtggcat gtctagtgca
     1741 ggcccttttc agctgacggc ttcctttgac aactactaca gcctgctgat tgatgggccc
     1801 ctggaccggg agcagatcag tgaataccaa gtcctgatca cggcctcaga tagtggctca
     1861 cccccactta gcacccgaag gacaatcact gtgtcagttg ctgatgtgaa tgacaataca
     1921 ccaaactttc ctcaacccca gcaggaactt ttcgttgctg aaaacaatgg ccctggggcc
     1981 tctctaggcc gagtgtttgc ccaggacccc gacctgggga agaatggcct tgtctcttat
     2041 gagctgttgg atgttatctc tgaagggcca tcagcctcta gcttgctggc agtggaatca
     2101 tccagtgggg ccatcactgc caaaacttcc tttgactttg agcagctcag ggggtttcat
     2161 ttccaagtag aaggccggga tggtggcatt cctcccagaa gtgcaacagt gactataaac
     2221 ttgtttgtgg tagataggaa tgacaattat ccggttatct tgtttccctt gcccagaaat
     2281 ggttctgtcc cagtggaaat tgtgccccgc tctgccagga ctggacactt ggtcacaaaa
     2341 gtggtagcag aggatgctga cagtggttct aatgcctggc tttcctacca catctcccgg
     2401 gcgtctgact ctagtctctt tagaatttca gccaatatag gtgagctccg tactgctcgc
     2461 ttagttcttc ccactgatgc agttaagcag agggtggtgg tagtggttcg ggaccatgga
     2521 gacccaccac tttcctcctc tgtcactctg ggtgtgctgt tgagcaactc tgtccctcag
     2581 ttacttccag actttgaaga tgtctgggaa ccaggagggc agctttctgc ccagaacttg
     2641 tatttagtaa ttgccttggc ttgtatttcc tttttatttc tggggtgctt acttttcttc
     2701 gtgtgtacca agttgcacca gagcccaggc tgttgcgctc agagctgctg tcgctctaca
     2761 gaggatctga ggtatggaag taagatggtt tcaaatcctt gcatgacatc agccaccata
     2821 gatgtcacta cagttgagag actttctcag acttatctct atcgggcctc tctgggactt
     2881 ggttctgata ataacagttt gctgttgcgt ggggagtaca atgctgccga cctgcgaaat
     2941 cttgccactg gggtaggact gaatttgcca atatcctgta ttcagattcg gaataggaaa
     3001 ggggatcacg ctaatgtcaa tgccatgcca cgacagccca accctgactg gcgttactct
     3061 gcctccctga gagcaggcat gcacagctct gtgcacctag aggaggctgg cattctacgg
     3121 gctggtccag gagggcctga tcagcagtgg ccaacagtat ccagtgcaac accagaacca
     3181 gaggcaggag aagtgtcccc tccagtcggt gcgggtgtca acagcaacag ctggaccttt
     3241 aaatacggac caggcaaccc caaacaatcc ggtcccggtg agttgcccga caaattcatt
     3301 atcccaggat ctcctgcaat catctccatc cggcaggagc ctactaacag ccaaattgac
     3361 aaaagtgact tcataacctt cggcaaaaag gaggagacca agaaaaagaa gaaaaagaag
     3421 aagggtaaca agacccagga gaaaaaagag aaagggaaca gcacgactga caacagtgac
     3481 cagtgaggtc ctcaaatgga aacaagccac ttagccagtt tttgtaataa tggcaaatct
     3541 ctcccatgta gcaattccct gctccttttt cctatctaca tgagccctct tagagacctc
     3601 agaaatctgc agaaagttcc ctgtgtctgt ctagaacgca tttaacaggt tttgtcgtaa
     3661 aagctttact aagtctggtg ttaactcttt ctctccactc tggcttgttt tcagaaccta
     3721 aaaagcagac ccaagtttcc tttctcctcc gccgcaaagg agaggcttcc cagccccgcc
     3781 agtgagaggt tggactctct gccctgtgct ccggggatcc tgtcttgatg acacttgcag
     3841 ggcaggctga aaagttttga gattgagcag cttgggagtt tgtggccact gggtatgtgt
     3901 ggctaccgcg ggtatgcgag tgccagatat tggctgagac gagccagctt agactaattg
     3961 gtacaaggaa ggcaagaaaa caaagacaaa taaacagcgg aagttatcag tatggagggg
     4021 aagtgtaaac ttaaagggac cagactttct aaatcttaca actcaagagg tggcagccac
     4081 cctctaggag acaaaactac ccccactgac aaggctttag gagaccctaa agtctgttgg
     4141 ctgtgacgtc attataccta aaatctgcat catacctgca agccaacagt tcagtgtttt
     4201 aacagagaac caccctggga aacagaagca gatctgatgt gtttcctata catgtcctgt
     4261 gctcacttta ttaaaaattc ttttgcacac aatgtttatg aaaaggccag atccttttcc
     4321 aatacttatg caaaagcaaa agaaaacccc gacacctcac ctttcgctgt ttgttgtttc
     4381 atagatttat ttaaaaaaag agaaagtcta tagctataaa tctttaaaga gaaatatgaa
     4441 tacaattccc ctaaactctc ctcaaaagag aattcagtct acagccattt aaatgatcat
     4501 tgctgctaca gaagtgcttt aagagaattg cctgaaacat ctgtattata tcggccacct
     4561 gccaatcaca gctttactct ttcaggtcac tctggggctg cctcttgcat gtattactaa
     4621 ataaaatgat ctctctttct ctctctctct ctcttttcta agaaacaatt atgtgcactt
     4681 tgatacacaa ccttctctaa ccaactatat atcaagaccc aaaaattgaa gaaaaatatt
     4741 gttttctcat acagtgagca gatttttcaa tctactaatt ctgtgacttg tcttggtgtg
     4801 ctagcctaca ccttctcttt ggtttagttt tccttttcta taacactctg aattgctaat
     4861 cttactaaca cctatgatgt tacctgaaat caatctccca tatgtatgct gtatgctatg
     4921 ctaagactcc tgaaatatac ttactctgtg cttgtgtatg tgaatgttaa tgcaactatt
     4981 acctagagtg aactttaagc tttattgttg aatgtaattc cattatattt ccttttgtac
     5041 acctgtgaaa aagtggagta gtgttttttt aaccattgtt aatcagcttt tgtgtatgaa
     5101 agacacagta aaatttcttt cttaaatcaa gatactggtg attcaaggaa ttttatttat
     5161 ggtccagcca agagccatct cgtgccaaga cttctgctgg caagggaatg gataaagctg
     5221 ttttgttcta gtaacaattt tggaatgaat actgacaata ttccatgagg gtgtgcaagc
     5281 acaaatttta ccaatctgac ctctttgaag ttgcagaatg ctttgaaatt ctaatggtat
     5341 ctgaaatatc agctcataga aagtaacaaa atttgctgtc accttaaata agacatttta
     5401 attttgttat aatgtacaat ttagaagttt gattaattat attatctatt taggcattaa
     5461 tataaaagag gtaggagtct gttatttaaa aaaagcatta aatttaaaaa aaaactgtct
     5521 tgtctacttt tagcttcatt ctcccatatt ttgaagggtg tgtaacttca gctctgcagg
     5581 attgcatggg gtaaaacttg ttaccaacac atgtgaacca ttgctacatt gtaggttgtg
     5641 atcattttgc cccactgaag cccatgtatc tgaccttacg tgccttttga actaggagaa
     5701 tcgggctaat ttattaatga tgataattat aatgtatctg tacagcactt tttacatttg
     5761 cgaagtgctt tccaatccat gttagttact agttattaca gctgtaagga taaaacacgt
     5821 catgtggatt cattttgaat tggtgctatt ggtatttcct ctgttattgc taataaatga
     5881 aaatggtggt atgaaa
//
