LOCUS       NM_018899               5725 bp    mRNA    linear   PRI 04-APR-2024
DEFINITION  Homo sapiens protocadherin alpha subfamily C, 2 (PCDHAC2),
            transcript variant 1, mRNA.
ACCESSION   NM_018899
VERSION     NM_018899.6
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 5725)
  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 5725)
  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 5725)
  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 5725)
  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 5725)
  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 5725)
  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 5725)
  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 and AF152304.1.
            
            On Nov 22, 2018 this sequence version replaced NM_018899.5.
            
            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).
            
            Sequence Note: This RefSeq record was created from transcript and
            genomic sequence data to make the sequence consistent with the
            reference genome assembly. The genomic coordinates used for the
            transcript record were based on transcript alignments.
            
            ##Evidence-Data-START##
            Transcript exon combination :: SRR1803615.98947.1,
                                           SRR1803612.160009.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1965299, SAMEA1966682
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000289269.7/ ENSP00000289269.5
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-993               AC010223.6         95145-96137         c
            994-5722            AF152304.1         703-5431
            5723-5725           AC010223.6         50266-50268         c
FEATURES             Location/Qualifiers
     source          1..5725
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="5"
                     /map="5q31.3"
     gene            1..5725
                     /gene="PCDHAC2"
                     /gene_synonym="PCDH-ALPHA-C2"
                     /note="protocadherin alpha subfamily C, 2"
                     /db_xref="GeneID:56134"
                     /db_xref="HGNC:HGNC:8677"
                     /db_xref="MIM:606321"
     exon            1..2856
                     /gene="PCDHAC2"
                     /gene_synonym="PCDH-ALPHA-C2"
                     /inference="alignment:Splign:2.1.0"
     CDS             292..3315
                     /gene="PCDHAC2"
                     /gene_synonym="PCDH-ALPHA-C2"
                     /note="isoform 1 precursor is encoded by transcript
                     variant 1; protocadherin alpha-C2"
                     /codon_start=1
                     /product="protocadherin alpha-C2 isoform 1 precursor"
                     /protein_id="NP_061722.1"
                     /db_xref="CCDS:CCDS4242.1"
                     /db_xref="GeneID:56134"
                     /db_xref="HGNC:HGNC:8677"
                     /db_xref="MIM:606321"
                     /translation="MEQAGTRPAATEHPRLRRPMPWLLLLPLLLLLLLLLPGPAASQL
                     RYSVPEEQAPGALVGNVARALGLELRRLGPGCLRINHLGAPSPRYLELDLTSGALFVN
                     ERIDREALCEQRPRCLLSLEVLAHNPVAVSAVEVEILDINDNSPRFPRPNYQLQVSES
                     VAPGARFHIESAQDPDVGANSVQTYELSPSEHFELDLKPLQENSKVLELVLRKGLDRE
                     QAALHHLVLTAVDGGIPARSGTAQISVRVLDTNDNSPAFDQSTYRVQLREDSPPGTLV
                     VKLNASDPDEGSNGELRYSLSSYTSDRERQLFSIDASTGEVRVIGGLDYEEASSYQIY
                     VQATDRGPVPMAGHCKVLVDIVDVNDNAPEVVLTDLYSPVPENATPNTIVAVLSVNDQ
                     DSGPNRKVSLGLEATLPFRLNGFGNSYTLVVSGPLDRERVAVYNITVTATDGGIPQLT
                     SLRTLKVEISDINDNPPSFLEDSYSIYIQENNLPGVLLCTVQATDPDEKENAEVTYSL
                     LEREIQGLPVTSYVSINSASGSLYAVNSFDYEKFREFFVTVEAQDKGSPPLSSTVTAN
                     VYVVDMNDHAPHILYPTSTNSSAAFEMVPRTAPAGYLVTKVIAMDSDSGQNAWLFYHL
                     AQTSDLDLFKVELHTGEIRTTRKMGDESGSTFNLTVVVRDNGEPSLSASVAITVAVVD
                     RVSKILPDTQRHVKSPRTYSEITLYLIIALSTVSFIFLLTIIILSIIKCYRYTAYGTA
                     CCGGFCGVRERSPAELYKQANNNIDARIPHGLKVQPHFIEVRGNGSLTKTYCYKACLT
                     AGSGSDTFMFYNTGAQTGPGPSGAQAAVTDSRNLTGQSGQNAGNLIILKNEAVSQNEP
                     RQPNPDWRYSASLRAGMHSSVHLEEAGILRAGPGGPDQQWPTVSSATPEPEAGEVSPP
                     VGAGVNSNSWTFKYGPGNPKQSGPGELPDKFIIPGSPAIISIRQEPTNSQIDKSDFIT
                     FGKKEETKKKKKKKKGNKTQEKKEKGNSTTDNSDQ"
     exon            2857..2915
                     /gene="PCDHAC2"
                     /gene_synonym="PCDH-ALPHA-C2"
                     /inference="alignment:Splign:2.1.0"
     exon            2916..3004
                     /gene="PCDHAC2"
                     /gene_synonym="PCDH-ALPHA-C2"
                     /inference="alignment:Splign:2.1.0"
     exon            3005..5725
                     /gene="PCDHAC2"
                     /gene_synonym="PCDH-ALPHA-C2"
                     /inference="alignment:Splign:2.1.0"
     regulatory      4936..4941
                     /regulatory_class="polyA_signal_sequence"
                     /gene="PCDHAC2"
                     /gene_synonym="PCDH-ALPHA-C2"
                     /note="hexamer: AGTAAA"
     polyA_site      4959
                     /gene="PCDHAC2"
                     /gene_synonym="PCDH-ALPHA-C2"
     regulatory      5705..5710
                     /regulatory_class="polyA_signal_sequence"
                     /gene="PCDHAC2"
                     /gene_synonym="PCDH-ALPHA-C2"
                     /note="hexamer: AATGAA"
     polyA_site      5725
                     /gene="PCDHAC2"
                     /gene_synonym="PCDH-ALPHA-C2"
                     /note="major polyA site"
ORIGIN      
        1 cttttccctc cccctggagc tgtagcggca gcagcagcag gaagccgagc cgggttgagc
       61 gactcggagg cgagcggagg agctggaata tggggagtca gcgaggacgg tggggccagg
      121 agcccttggg agggcctacg gagggagcgg ccccaggcgc tttctagagc gtgagcggtg
      181 ggggagcagg cgcagggtgg cacgagcgga ggcggggccc gggcgtgggg cacggctggg
      241 gaagctgccg cctccggccc tgcccggctg cctccgccgc ggccagtggc tatggagcag
      301 gcgggcacca gacctgcggc gacagagcat ccacggctcc ggcggcccat gccctggctg
      361 ctgctactgc ctctcctgct gctgttgctg ctgctgctac ctggccctgc ggcctcccag
      421 ctgcgatact ctgtgccaga ggagcaggca cccggcgcgc tcgtgggcaa cgtggctcgc
      481 gcgctggggc ttgagctgcg gcgcttgggg ccgggttgct tgcgcatcaa ccatctgggt
      541 gcgcccagtc cgcgctacct ggagctggac ctgacgagtg gagcgctctt cgtcaacgag
      601 cgcattgatc gggaggcgct gtgtgagcag cggcctcgct gcctgctcag cttggaagtg
      661 ctggcgcaca accccgtggc ggtgagcgcc gttgaggtgg aaatattgga catcaacgac
      721 aactcaccgc gtttcccgcg gcccaactac cagcttcagg taagcgaatc ggtggcgcct
      781 ggagcgcgct ttcacataga gagtgcgcag gaccccgacg tgggcgccaa ctcagtacag
      841 acctacgagc tcagccccag cgagcacttc gagctggacc ttaagcccct gcaggagaac
      901 agtaaagtgc ttgagctggt gctgcgtaag ggcctagacc gggagcaggc agccttgcac
      961 cacctggttc tcacagccgt ggatgggggc atcccagccc gctcgggtac ggcacagatc
     1021 tctgtgcgtg tcctggacac taacgacaac tctcctgcct ttgaccagtc cacttatcgc
     1081 gtccagctac gggaggactc acccccaggc acattggtgg tgaagctgaa tgcctcagac
     1141 ccggatgagg gctccaatgg tgagctcagg tactccttga gcagctacac gtcggaccgg
     1201 gagaggcagc tcttcagcat agatgccagt accggggaag tgcgagtaat tggggggctg
     1261 gattatgagg aagcctcctc ctaccagatc tatgtgcagg cgactgaccg gggtccagtg
     1321 cccatggcag gtcactgcaa ggtgctggtg gacatcgtgg acgtgaatga caatgcccca
     1381 gaggtggtgc tcacggacct gtatagccca gtgcctgaga atgctacacc caacaccatt
     1441 gtggccgttc tcagtgtcaa tgaccaagac tcaggcccca accggaaagt gagcctgggt
     1501 ctggaggcca cactgccttt ccgactgaat ggctttggaa actcctatac actggtggtg
     1561 agcggcccac tggaccgaga gcgggtggct gtctacaaca tcacggtgac agccacagat
     1621 gggggaatac cgcagctcac atccctgcgt acactgaagg ttgagatctc tgacatcaat
     1681 gacaatccac caagcttcct ggaggactcc tattccatct acatacagga gaacaatttg
     1741 ccaggtgtgt tgctctgtac tgtgcaagcc acagacccag atgaaaagga gaatgcagag
     1801 gtgacctact cccttctgga gagggagatt caagggctgc cagtcacctc ctatgtctcc
     1861 attaacagtg ccagtggcag cctttatgct gtcaactcct ttgactatga gaagtttcgg
     1921 gagttctttg tgactgtgga ggctcaggac aaggggagcc caccactgag cagcactgtg
     1981 actgccaacg tatatgtggt ggacatgaat gaccatgccc ctcacattct gtaccctacc
     2041 tcaaccaact cgtcagcagc cttcgagatg gtgcctcgaa ctgcccctgc tggctacctg
     2101 gtcaccaaag tcatagctat ggactcagac tctgggcaaa atgcttggct tttttaccat
     2161 ctagcccaga cttctgacct ggacctcttt aaggtagagc tgcacacagg agaaattagg
     2221 actaccagga agatgggaga tgagagtggt agcactttca acctgaccgt ggtggtccga
     2281 gataatggag agccatcact atcagcctct gtggccatta cagtagctgt ggtggatagg
     2341 gtttccaaaa tcctccctga cactcagagg catgttaaga gccctcggac atactctgaa
     2401 attacccttt atctaataat agcattaagc acagtgtctt ttatatttct tttgacaatc
     2461 atcattttga gcatcatcaa gtgctaccgc tacactgcgt atggcactgc atgctgtgga
     2521 ggcttctgtg gagtaaggga aaggtcccct gcagaactgt acaaacaagc caacaacaat
     2581 attgatgcca ggataccgca tggcctcaaa gtgcagcctc acttcattga agttcgaggg
     2641 aatggctccc tcaccaagac ctactgctac aaggcctgtc tgacagcagg ctcagggagt
     2701 gacactttca tgttttacaa tacaggggcc cagacaggac cagggccttc gggagcccaa
     2761 gcagcagtga ctgacagcag gaatctcaca ggccaaagtg gtcagaatgc tgggaacctg
     2821 attattctca aaaatgaggc tgtttctcaa aatgagccac gacagcccaa ccctgactgg
     2881 cgttactctg cctccctgag agcaggcatg cacagctctg tgcacctaga ggaggctggc
     2941 attctacggg ctggtccagg agggcctgat cagcagtggc caacagtatc cagtgcaaca
     3001 ccagaaccag aggcaggaga agtgtcccct ccagtcggtg cgggtgtcaa cagcaacagc
     3061 tggaccttta aatacggacc aggcaacccc aaacaatccg gtcccggtga gttgcccgac
     3121 aaattcatta tcccaggatc tcctgcaatc atctccatcc ggcaggagcc tactaacagc
     3181 caaattgaca aaagtgactt cataaccttc ggcaaaaagg aggagaccaa gaaaaagaag
     3241 aaaaagaaga agggtaacaa gacccaggag aaaaaagaga aagggaacag cacgactgac
     3301 aacagtgacc agtgaggtcc tcaaatggaa acaagccact tagccagttt ttgtaataat
     3361 ggcaaatctc tcccatgtag caattccctg ctcctttttc ctatctacat gagccctctt
     3421 agagacctca gaaatctgca gaaagttccc tgtgtctgtc tagaacgcat ttaacaggtt
     3481 ttgtcgtaaa agctttacta agtctggtgt taactctttc tctccactct ggcttgtttt
     3541 cagaacctaa aaagcagacc caagtttcct ttctcctccg ccgcaaagga gaggcttccc
     3601 agccccgcca gtgagaggtt ggactctctg ccctgtgctc cggggatcct gtcttgatga
     3661 cacttgcagg gcaggctgaa aagttttgag attgagcagc ttgggagttt gtggccactg
     3721 ggtatgtgtg gctaccgcgg gtatgcgagt gccagatatt ggctgagacg agccagctta
     3781 gactaattgg tacaaggaag gcaagaaaac aaagacaaat aaacagcgga agttatcagt
     3841 atggagggga agtgtaaact taaagggacc agactttcta aatcttacaa ctcaagaggt
     3901 ggcagccacc ctctaggaga caaaactacc cccactgaca aggctttagg agaccctaaa
     3961 gtctgttggc tgtgacgtca ttatacctaa aatctgcatc atacctgcaa gccaacagtt
     4021 cagtgtttta acagagaacc accctgggaa acagaagcag atctgatgtg tttcctatac
     4081 atgtcctgtg ctcactttat taaaaattct tttgcacaca atgtttatga aaaggccaga
     4141 tccttttcca atacttatgc aaaagcaaaa gaaaaccccg acacctcacc tttcgctgtt
     4201 tgttgtttca tagatttatt taaaaaaaga gaaagtctat agctataaat ctttaaagag
     4261 aaatatgaat acaattcccc taaactctcc tcaaaagaga attcagtcta cagccattta
     4321 aatgatcatt gctgctacag aagtgcttta agagaattgc ctgaaacatc tgtattatat
     4381 cggccacctg ccaatcacag ctttactctt tcaggtcact ctggggctgc ctcttgcatg
     4441 tattactaaa taaaatgatc tctctttctc tctctctctc tcttttctaa gaaacaatta
     4501 tgtgcacttt gatacacaac cttctctaac caactatata tcaagaccca aaaattgaag
     4561 aaaaatattg ttttctcata cagtgagcag atttttcaat ctactaattc tgtgacttgt
     4621 cttggtgtgc tagcctacac cttctctttg gtttagtttt ccttttctat aacactctga
     4681 attgctaatc ttactaacac ctatgatgtt acctgaaatc aatctcccat atgtatgctg
     4741 tatgctatgc taagactcct gaaatatact tactctgtgc ttgtgtatgt gaatgttaat
     4801 gcaactatta cctagagtga actttaagct ttattgttga atgtaattcc attatatttc
     4861 cttttgtaca cctgtgaaaa agtggagtag tgttttttta accattgtta atcagctttt
     4921 gtgtatgaaa gacacagtaa aatttctttc ttaaatcaag atactggtga ttcaaggaat
     4981 tttatttatg gtccagccaa gagccatctc gtgccaagac ttctgctggc aagggaatgg
     5041 ataaagctgt tttgttctag taacaatttt ggaatgaata ctgacaatat tccatgaggg
     5101 tgtgcaagca caaattttac caatctgacc tctttgaagt tgcagaatgc tttgaaattc
     5161 taatggtatc tgaaatatca gctcatagaa agtaacaaaa tttgctgtca ccttaaataa
     5221 gacattttaa ttttgttata atgtacaatt tagaagtttg attaattata ttatctattt
     5281 aggcattaat ataaaagagg taggagtctg ttatttaaaa aaagcattaa atttaaaaaa
     5341 aaactgtctt gtctactttt agcttcattc tcccatattt tgaagggtgt gtaacttcag
     5401 ctctgcagga ttgcatgggg taaaacttgt taccaacaca tgtgaaccat tgctacattg
     5461 taggttgtga tcattttgcc ccactgaagc ccatgtatct gaccttacgt gccttttgaa
     5521 ctaggagaat cgggctaatt tattaatgat gataattata atgtatctgt acagcacttt
     5581 ttacatttgc gaagtgcttt ccaatccatg ttagttacta gttattacag ctgtaaggat
     5641 aaaacacgtc atgtggattc attttgaatt ggtgctattg gtatttcctc tgttattgct
     5701 aataaatgaa aatggtggta tgaaa
//
