LOCUS       NM_031857               5377 bp    mRNA    linear   PRI 07-APR-2024
DEFINITION  Homo sapiens protocadherin alpha 9 (PCDHA9), transcript variant 1,
            mRNA.
ACCESSION   NM_031857
VERSION     NM_031857.2
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 5377)
  AUTHORS   Shen,Q., Zhang,H., Su,Y., Wen,Z., Zhu,Z., Chen,G., Peng,L., Du,C.,
            Xie,H., Li,H., Lv,X., Lu,C., Xia,Y. and Tang,W.
  TITLE     Identification of two novel PCDHA9 mutations associated with
            Hirschsprung's disease
  JOURNAL   Gene 658, 96-104 (2018)
   PUBMED   29477871
  REMARK    GeneRIF: PCDHAlpha9 is potentially related to Hirschsprung's
            disease and the clustered protocadherins (Pcdhs) may involve in the
            enteric nervous system (ENS) ontogeny.
REFERENCE   2  (bases 1 to 5377)
  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   3  (bases 1 to 5377)
  AUTHORS   Wu,C., Ma,M.H., Brown,K.R., Geisler,M., Li,L., Tzeng,E., Jia,C.Y.,
            Jurisica,I. and Li,S.S.
  TITLE     Systematic identification of SH3 domain-mediated human
            protein-protein interactions by peptide array target screening
  JOURNAL   Proteomics 7 (11), 1775-1785 (2007)
   PUBMED   17474147
REFERENCE   4  (bases 1 to 5377)
  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   5  (bases 1 to 5377)
  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   6  (bases 1 to 5377)
  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   7  (bases 1 to 5377)
  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   8  (bases 1 to 5377)
  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   9  (bases 1 to 5377)
  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 AC005609.1 and AC010223.6.
            
            On Nov 22, 2019 this sequence version replaced NM_031857.1.
            
            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 :: AF152317.1, AJ007610.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA2145743, SAMEA2148874
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000532602.2/ ENSP00000436042.2
            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
            1-2508              AC005609.1         41209-43716         c
            2509-2567           AC010223.6         83606-83664         c
            2568-2656           AC010223.6         80050-80138         c
            2657-5377           AC010223.6         50266-52986         c
FEATURES             Location/Qualifiers
     source          1..5377
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="5"
                     /map="5q31.3"
     gene            1..5377
                     /gene="PCDHA9"
                     /gene_synonym="PCDH-ALPHA9"
                     /note="protocadherin alpha 9"
                     /db_xref="GeneID:9752"
                     /db_xref="HGNC:HGNC:8675"
                     /db_xref="MIM:606315"
     exon            1..2508
                     /gene="PCDHA9"
                     /gene_synonym="PCDH-ALPHA9"
                     /inference="alignment:Splign:2.1.0"
     CDS             115..2967
                     /gene="PCDHA9"
                     /gene_synonym="PCDH-ALPHA9"
                     /note="isoform 1 precursor is encoded by transcript
                     variant 1; KIAA0345-like 5; PCDH-alpha-9"
                     /codon_start=1
                     /product="protocadherin alpha-9 isoform 1 precursor"
                     /protein_id="NP_114063.1"
                     /db_xref="CCDS:CCDS54920.1"
                     /db_xref="GeneID:9752"
                     /db_xref="HGNC:HGNC:8675"
                     /db_xref="MIM:606315"
                     /translation="MLYSSRGDPEGQPLLLSLLILAMWVVGSGQLHYSVPEEAEHGTF
                     VGRIAQDLGLELAELVPRLFQLDSKGRGDLLEVNLQNGILFVNSRIDREELCGRSAEC
                     SIHLEVIVDRPLQVFHVDVEVKDINDNPPVFPATQKNLFIAESRPLDSRFPLEGASDA
                     DIGENALLTYRLSPNEYFFLDVPTSNQQVKPLGLVLRKLLDREETPELHLLLTATDGG
                     KPELTGTVQLLITVLDNNDNAPVFDRTLYTVKLPENVSIGTLVIHPNASDLDEGLNGD
                     IIYSFSSDVSPDIKSKFHMDPLSGAITVIGHMDFEESRAHKIPVEAVDKGFPPLAGHC
                     TLLVEVVDVNDNAPQLTIKTLSVPVKEDAQLGTVIALISVIDLDADANGQVTCSLTPH
                     VPFKLVSTYKNYYSLVLDRALDRESVSAYELVVTARDGGSPSLWATARVSVEVADVND
                     NAPAFAQSEYTVFVKENNPPGCHIFTVSARDADAQENALVSYSLVERRLGERSLSSYV
                     SVHAESGKVYALQPLDHEELELLQFQVSARDAGVPPLGSNVTLQVFVLDENDNAPALL
                     TPRMRGTDGAVSEMVLRSVGAGVVVGKVRAVDADSGYNAWLSYELQPETASASIPFRV
                     GLYTGEISTTRALDETDAPRQRLLVLVKDHGEPALTATATVLVSLVESGQAPKSSSRA
                     SVGATGPEVTLVDVNVYLIIAICAVSSLLVLTLLLYTVLRCSAMPTEGECAPGKPTLV
                     CSSAVGSWSYSQQRRQRVCSGEGKQKTDLMAFSPGLSPCAGSTERTGEPSASSDSTGK
                     PRQPNPDWRYSASLRAGMHSSVHLEEAGILRAGPGGPDQQWPTVSSATPEPEAGEVSP
                     PVGAGVNSNSWTFKYGPGNPKQSGPGELPDKFIIPGSPAIISIRQEPTNSQIDKSDFI
                     TFGKKEETKKKKKKKKGNKTQEKKEKGNSTTDNSDQ"
     exon            2509..2567
                     /gene="PCDHA9"
                     /gene_synonym="PCDH-ALPHA9"
                     /inference="alignment:Splign:2.1.0"
     exon            2568..2656
                     /gene="PCDHA9"
                     /gene_synonym="PCDH-ALPHA9"
                     /inference="alignment:Splign:2.1.0"
     exon            2657..5377
                     /gene="PCDHA9"
                     /gene_synonym="PCDH-ALPHA9"
                     /inference="alignment:Splign:2.1.0"
     regulatory      4588..4593
                     /regulatory_class="polyA_signal_sequence"
                     /gene="PCDHA9"
                     /gene_synonym="PCDH-ALPHA9"
                     /note="hexamer: AGTAAA"
     polyA_site      4611
                     /gene="PCDHA9"
                     /gene_synonym="PCDH-ALPHA9"
     regulatory      5357..5362
                     /regulatory_class="polyA_signal_sequence"
                     /gene="PCDHA9"
                     /gene_synonym="PCDH-ALPHA9"
                     /note="hexamer: AATGAA"
     polyA_site      5377
                     /gene="PCDHA9"
                     /gene_synonym="PCDH-ALPHA9"
                     /note="major polyA site"
ORIGIN      
        1 actctctctg tgctgaacga tggcgaacac agcagaatgg gactgacgaa atcagatgat
       61 ttcttctaat ttggaggcaa ttttcactaa ttagaagaag actgagtatt tgaaatgtta
      121 tactcaagtc gaggagatcc agagggtcag cctctactgc tctcgcttct gatcctcgca
      181 atgtgggtgg tggggagcgg ccagctccac tactccgtcc cggaggaagc cgaacacggc
      241 accttcgtgg gccgcatcgc gcaggacctg gggctggagc tggcggagct ggtgccgcgc
      301 ctgttccagt tggattccaa aggccgcggg gaccttctgg aggtaaatct gcagaatggc
      361 attttgtttg tgaattctcg gatcgaccgc gaggagctgt gcgggcggag cgcggagtgc
      421 agcatccacc tggaggtgat cgtagacagg ccgctgcagg ttttccatgt ggacgtggag
      481 gtgaaggaca ttaacgacaa ccctccagtg ttcccagcga cacaaaagaa tctgttcatc
      541 gcggaatcca ggccgcttga ctctcggttt ccactagagg gcgcgtccga tgcagatatc
      601 ggggagaacg ccctgctcac ttacagactg agccccaatg agtatttctt cctggacgtg
      661 ccaaccagca accagcaggt aaaacctctt ggacttgtat tacggaaact tttagacaga
      721 gaagaaactc cggagcttca tttattgctc acggccaccg atggaggcaa acccgagctg
      781 actggcaccg ttcaattact catcacggta ctggacaaca atgacaatgc cccagtgttc
      841 gacagaaccc tgtatacggt gaaattacca gaaaacgttt ctatcggaac gctggtgatt
      901 caccccaatg cctcagattt agacgaaggc ttgaatgggg atattattta ctccttctcc
      961 agtgatgttt ctccagatat aaaatccaag ttccacatgg accccttaag tggggcaatc
     1021 acagtgatag gacatatgga ttttgaagaa agtagagcac acaagatccc agtcgaggct
     1081 gtcgataaag gcttcccacc cctggctggt cattgtacac ttcttgtgga agttgtggat
     1141 gtaaatgaca atgctccaca gttgactatc aaaacgctct cggttcctgt aaaagaggac
     1201 gcacaactgg ggacagttat tgccctgatt agtgtgatcg acctagacgc agatgccaac
     1261 gggcaggtta cctgctccct gacgccccac gtccccttca agctggtgtc cacctacaag
     1321 aattactact cgttggtgct ggacagagct ctggaccgcg agagtgtgtc cgcctacgag
     1381 ctggtggtta ccgcgcggga cgggggctcg ccttcactgt gggccacggc cagggtgtct
     1441 gtggaggtgg ccgacgtgaa cgacaacgca ccagcgttcg cgcagtccga gtacacggtg
     1501 ttcgtgaagg agaacaaccc gccgggctgc cacatcttca cggtgtctgc gcgggacgct
     1561 gacgcgcagg agaacgccct ggtgtcctac tcgctggtgg agcggcggtt gggcgagcgc
     1621 tcgctgtcga gctacgtgtc agtgcacgcg gagagcggca aggtgtacgc gctgcagccg
     1681 ttggaccacg aggagctgga gctgctacag ttccaggtga gcgcgcgcga cgcgggcgtg
     1741 ccgcctctgg gcagcaacgt gacgctgcag gtgttcgtgc tggacgagaa cgacaatgcg
     1801 ccggcgctgc tgacacctcg gatgaggggc actgacggcg cagtgagcga gatggtgctg
     1861 cggtcggtgg gcgccggcgt agtggtgggg aaggtgcgcg cagtggacgc cgactcgggc
     1921 tacaacgcgt ggctttcata cgagctgcag ccagaaacgg ccagcgcgag catcccgttc
     1981 cgcgtggggc tgtacacggg cgagatcagc acaacgcgtg ccctggacga aacggacgca
     2041 ccgcgccagc gcctactggt gctggtgaaa gaccacgggg agccagcgct gacggccacg
     2101 gccactgtgc tggtgtcgct ggtggagagc ggccaggcgc caaagtcatc gtcgcgggcg
     2161 tcagtgggtg ccacgggccc cgaggtgacg ctggtggatg tcaacgtgta cctgatcatc
     2221 gccatctgcg cggtgtctag cctgttggtt ctcacgctgc tgctgtacac tgtgctgcgg
     2281 tgctcggcga tgcccaccga gggcgagtgc gcgcctggca agccgacgct ggtgtgttct
     2341 agcgcggtgg ggagttggtc gtactcgcag cagaggaggc agagggtgtg ctctggcgag
     2401 ggtaagcaga agaccgacct catggccttc agcccgggcc tttctccttg tgctggatct
     2461 acagagcgaa cgggagaacc ctctgcttcc tcagattcaa ctgggaagcc acgacagccc
     2521 aaccctgact ggcgttactc tgcctccctg agagcaggca tgcacagctc tgtgcaccta
     2581 gaggaggctg gcattctacg ggctggtcca ggagggcctg atcagcagtg gccaacagta
     2641 tccagtgcaa caccagaacc agaggcagga gaagtgtccc ctccagtcgg tgcgggtgtc
     2701 aacagcaaca gctggacctt taaatacgga ccaggcaacc ccaaacaatc cggtcccggt
     2761 gagttgcccg acaaattcat tatcccagga tctcctgcaa tcatctccat ccggcaggag
     2821 cctactaaca gccaaattga caaaagtgac ttcataacct tcggcaaaaa ggaggagacc
     2881 aagaaaaaga agaaaaagaa gaagggtaac aagacccagg agaaaaaaga gaaagggaac
     2941 agcacgactg acaacagtga ccagtgaggt cctcaaatgg aaacaagcca cttagccagt
     3001 ttttgtaata atggcaaatc tctcccatgt agcaattccc tgctcctttt tcctatctac
     3061 atgagccctc ttagagacct cagaaatctg cagaaagttc cctgtgtctg tctagaacgc
     3121 atttaacagg ttttgtcgta aaagctttac taagtctggt gttaactctt tctctccact
     3181 ctggcttgtt ttcagaacct aaaaagcaga cccaagtttc ctttctcctc cgccgcaaag
     3241 gagaggcttc ccagccccgc cagtgagagg ttggactctc tgccctgtgc tccggggatc
     3301 ctgtcttgat gacacttgca gggcaggctg aaaagttttg agattgagca gcttgggagt
     3361 ttgtggccac tgggtatgtg tggctaccgc gggtatgcga gtgccagata ttggctgaga
     3421 cgagccagct tagactaatt ggtacaagga aggcaagaaa acaaagacaa ataaacagcg
     3481 gaagttatca gtatggaggg gaagtgtaaa cttaaaggga ccagactttc taaatcttac
     3541 aactcaagag gtggcagcca ccctctagga gacaaaacta cccccactga caaggcttta
     3601 ggagacccta aagtctgttg gctgtgacgt cattatacct aaaatctgca tcatacctgc
     3661 aagccaacag ttcagtgttt taacagagaa ccaccctggg aaacagaagc agatctgatg
     3721 tgtttcctat acatgtcctg tgctcacttt attaaaaatt cttttgcaca caatgtttat
     3781 gaaaaggcca gatccttttc caatacttat gcaaaagcaa aagaaaaccc cgacacctca
     3841 cctttcgctg tttgttgttt catagattta tttaaaaaaa gagaaagtct atagctataa
     3901 atctttaaag agaaatatga atacaattcc cctaaactct cctcaaaaga gaattcagtc
     3961 tacagccatt taaatgatca ttgctgctac agaagtgctt taagagaatt gcctgaaaca
     4021 tctgtattat atcggccacc tgccaatcac agctttactc tttcaggtca ctctggggct
     4081 gcctcttgca tgtattacta aataaaatga tctctctttc tctctctctc tctcttttct
     4141 aagaaacaat tatgtgcact ttgatacaca accttctcta accaactata tatcaagacc
     4201 caaaaattga agaaaaatat tgttttctca tacagtgagc agatttttca atctactaat
     4261 tctgtgactt gtcttggtgt gctagcctac accttctctt tggtttagtt ttccttttct
     4321 ataacactct gaattgctaa tcttactaac acctatgatg ttacctgaaa tcaatctccc
     4381 atatgtatgc tgtatgctat gctaagactc ctgaaatata cttactctgt gcttgtgtat
     4441 gtgaatgtta atgcaactat tacctagagt gaactttaag ctttattgtt gaatgtaatt
     4501 ccattatatt tccttttgta cacctgtgaa aaagtggagt agtgtttttt taaccattgt
     4561 taatcagctt ttgtgtatga aagacacagt aaaatttctt tcttaaatca agatactggt
     4621 gattcaagga attttattta tggtccagcc aagagccatc tcgtgccaag acttctgctg
     4681 gcaagggaat ggataaagct gttttgttct agtaacaatt ttggaatgaa tactgacaat
     4741 attccatgag ggtgtgcaag cacaaatttt accaatctga cctctttgaa gttgcagaat
     4801 gctttgaaat tctaatggta tctgaaatat cagctcatag aaagtaacaa aatttgctgt
     4861 caccttaaat aagacatttt aattttgtta taatgtacaa tttagaagtt tgattaatta
     4921 tattatctat ttaggcatta atataaaaga ggtaggagtc tgttatttaa aaaaagcatt
     4981 aaatttaaaa aaaaactgtc ttgtctactt ttagcttcat tctcccatat tttgaagggt
     5041 gtgtaacttc agctctgcag gattgcatgg ggtaaaactt gttaccaaca catgtgaacc
     5101 attgctacat tgtaggttgt gatcattttg ccccactgaa gcccatgtat ctgaccttac
     5161 gtgccttttg aactaggaga atcgggctaa tttattaatg atgataatta taatgtatct
     5221 gtacagcact ttttacattt gcgaagtgct ttccaatcca tgttagttac tagttattac
     5281 agctgtaagg ataaaacacg tcatgtggat tcattttgaa ttggtgctat tggtatttcc
     5341 tctgttattg ctaataaatg aaaatggtgg tatgaaa
//
