LOCUS       NM_018902               5407 bp    mRNA    linear   PRI 09-JUN-2024
DEFINITION  Homo sapiens protocadherin alpha 11 (PCDHA11), transcript variant
            1, mRNA.
ACCESSION   NM_018902
VERSION     NM_018902.5
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 5407)
  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 5407)
  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   3  (bases 1 to 5407)
  AUTHORS   Schmutz,J., Martin,J., Terry,A., Couronne,O., Grimwood,J.,
            Lowry,S., Gordon,L.A., Scott,D., Xie,G., Huang,W., Hellsten,U.,
            Tran-Gyamfi,M., She,X., Prabhakar,S., Aerts,A., Altherr,M.,
            Bajorek,E., Black,S., Branscomb,E., Caoile,C., Challacombe,J.F.,
            Chan,Y.M., Denys,M., Detter,J.C., Escobar,J., Flowers,D.,
            Fotopulos,D., Glavina,T., Gomez,M., Gonzales,E., Goodstein,D.,
            Grigoriev,I., Groza,M., Hammon,N., Hawkins,T., Haydu,L., Israni,S.,
            Jett,J., Kadner,K., Kimball,H., Kobayashi,A., Lopez,F., Lou,Y.,
            Martinez,D., Medina,C., Morgan,J., Nandkeshwar,R., Noonan,J.P.,
            Pitluck,S., Pollard,M., Predki,P., Priest,J., Ramirez,L.,
            Retterer,J., Rodriguez,A., Rogers,S., Salamov,A., Salazar,A.,
            Thayer,N., Tice,H., Tsai,M., Ustaszewska,A., Vo,N., Wheeler,J.,
            Wu,K., Yang,J., Dickson,M., Cheng,J.F., Eichler,E.E., Olsen,A.,
            Pennacchio,L.A., Rokhsar,D.S., Richardson,P., Lucas,S.M.,
            Myers,R.M. and Rubin,E.M.
  TITLE     The DNA sequence and comparative analysis of human chromosome 5
  JOURNAL   Nature 431 (7006), 268-274 (2004)
   PUBMED   15372022
REFERENCE   4  (bases 1 to 5407)
  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 5407)
  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 5407)
  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 5407)
  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 5407)
  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 5407)
  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_018902.4.
            
            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 :: AF152307.1, SRR18074969.1854147.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1968540, SAMEA1968832
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000398640.7/ ENSP00000381636.3
            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
            1-2538              AC005609.1         20604-23141         c
            2539-2597           AC010223.6         83606-83664         c
            2598-2686           AC010223.6         80050-80138         c
            2687-5407           AC010223.6         50266-52986         c
FEATURES             Location/Qualifiers
     source          1..5407
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="5"
                     /map="5q31.3"
     gene            1..5407
                     /gene="PCDHA11"
                     /gene_synonym="CNR7; CNRN7; CNRS7; CRNR7; PCDH-ALPHA11"
                     /note="protocadherin alpha 11"
                     /db_xref="GeneID:56138"
                     /db_xref="HGNC:HGNC:8665"
                     /db_xref="MIM:606317"
     exon            1..2538
                     /gene="PCDHA11"
                     /gene_synonym="CNR7; CNRN7; CNRS7; CRNR7; PCDH-ALPHA11"
                     /inference="alignment:Splign:2.1.0"
     CDS             148..2997
                     /gene="PCDHA11"
                     /gene_synonym="CNR7; CNRN7; CNRS7; CRNR7; PCDH-ALPHA11"
                     /note="isoform 1 precursor is encoded by transcript
                     variant 1; KIAA0345-like 3"
                     /codon_start=1
                     /product="protocadherin alpha-11 isoform 1 precursor"
                     /protein_id="NP_061725.1"
                     /db_xref="CCDS:CCDS47284.1"
                     /db_xref="GeneID:56138"
                     /db_xref="HGNC:HGNC:8665"
                     /db_xref="MIM:606317"
                     /translation="MFGFQRRGLGTPRLQLWLLLLEFWEVGSGQLHYSVSEEAKHGTF
                     VGRIAQDLGLELAELVQRLFRVASKTHGDLLEVNLQNGILFVNSRIDREELCGQSAEC
                     SIHLEVIVDRPLQVFHVNVEVKDINDNPPVFSLREQKLLIAESKQSDSRFPLEGASDA
                     DIEENALLTYRLSKNEYFSLDSPTNGKQIKRLSLILKKSLDREKTPELNLLLTATDGG
                     KPELTGTVRLLVQVLDVNDNDPEFDKSEYKVSLMENAAKETLVLKLNATDRDEGVNGE
                     VTYSLMSIKPNGRHLFTLDQNNGEVRVNGTLDYEENKFYKIEVQATDKGTPPMAGHCT
                     VWVEILDTNDNSPEVAVTSLSLPVREDAQPSTVIALISVSDRDSGVNGQVTCSLTPHV
                     PFKLVSTFKNYYSLVLDSALDRENVWAYELVVTARDGGSPSLWATARVSVEVADVNDN
                     APAFAQPEYTVFVKENNPPGCHIFTVSARDADAQENALVSYSLVERRLGDRALSSYVS
                     VHAESGKVYALQPLDHEELELLQFQVSARDAGVPPLSSNVTLQVFVLDENDNAPALLA
                     TQAGSAGGAVNKLVPRSVGAGHVVAKVRAVDADSGYNAWLSYELQPAAGGSRIPFRVG
                     LYTGEISTTRALDEADSPRHRLLVLVKDHGEPALTATATVLVSLVESGQAPKASSRTL
                     AGAASPEAALVDVNVYLIIAICVVSSLLVLTLLLYTALWWSATPTEGACAPGKPTLVC
                     SRAVGSWSYSQQRRQRVCSEEGPPKTDLMAFSPSLPLGLNKEEEGERQEPGSNHPGQP
                     RQPNPDWRYSASLRAGMHSSVHLEEAGILRAGPGGPDQQWPTVSSATPEPEAGEVSPP
                     VGAGVNSNSWTFKYGPGNPKQSGPGELPDKFIIPGSPAIISIRQEPTNSQIDKSDFIT
                     FGKKEETKKKKKKKKGNKTQEKKEKGNSTTDNSDQ"
     exon            2539..2597
                     /gene="PCDHA11"
                     /gene_synonym="CNR7; CNRN7; CNRS7; CRNR7; PCDH-ALPHA11"
                     /inference="alignment:Splign:2.1.0"
     exon            2598..2686
                     /gene="PCDHA11"
                     /gene_synonym="CNR7; CNRN7; CNRS7; CRNR7; PCDH-ALPHA11"
                     /inference="alignment:Splign:2.1.0"
     exon            2687..5407
                     /gene="PCDHA11"
                     /gene_synonym="CNR7; CNRN7; CNRS7; CRNR7; PCDH-ALPHA11"
                     /inference="alignment:Splign:2.1.0"
     regulatory      4618..4623
                     /regulatory_class="polyA_signal_sequence"
                     /gene="PCDHA11"
                     /gene_synonym="CNR7; CNRN7; CNRS7; CRNR7; PCDH-ALPHA11"
                     /note="hexamer: AGTAAA"
     polyA_site      4641
                     /gene="PCDHA11"
                     /gene_synonym="CNR7; CNRN7; CNRS7; CRNR7; PCDH-ALPHA11"
     regulatory      5387..5392
                     /regulatory_class="polyA_signal_sequence"
                     /gene="PCDHA11"
                     /gene_synonym="CNR7; CNRN7; CNRS7; CRNR7; PCDH-ALPHA11"
                     /note="hexamer: AATGAA"
     polyA_site      5407
                     /gene="PCDHA11"
                     /gene_synonym="CNR7; CNRN7; CNRS7; CRNR7; PCDH-ALPHA11"
                     /note="major polyA site"
ORIGIN      
        1 atacaaagga actccatcat accggatgcc accgtttaag gatcctttga aacttcttaa
       61 gaattcaacg agatttttaa cctgaaactg aagaatctgg tactgtaagt gtaaagaagc
      121 ttattttgga agccaatttc gtatgcgatg tttggttttc agagaagggg attgggcacc
      181 ccacgactac agctctggct tctcctcctc gaattctggg aggtggggag cggccagctc
      241 cactactccg tctcggagga ggccaaacac ggcaccttcg tgggccgcat cgcgcaggac
      301 ctggggctgg agctggcgga gctggtgcag cgcctgttcc gggtggcgtc caaaacacat
      361 ggggaccttc tggaggtaaa tctgcagaat ggcattttgt ttgtgaattc tcggatcgac
      421 cgcgaggagc tgtgcgggca gagcgcggag tgcagcatcc acctggaggt gatcgtggac
      481 aggccgctgc aggttttcca tgtgaacgtg gaggtgaagg acattaacga caacccgccg
      541 gtgttctcgc tcagagaaca aaagctgctg attgcggaat ctaagcaatc ggactcgcgt
      601 tttccactag agggagcttc tgatgctgac attgaagaga atgctctatt gacctacagg
      661 ctaagtaaaa atgagtattt ttctttagat tcaccaacaa atggtaagca gattaaaaga
      721 ctgtcactta ttttaaagaa gtctctggat agagagaaaa ctccggaact taatttgctg
      781 ctaacagcta cagacggggg aaaaccagag cttactggca ccgttcggct gttagtccaa
      841 gtcttggatg tcaacgacaa tgatccagag tttgataaat cagaatataa ggtgagcctt
      901 atggaaaatg ctgctaaaga aactcttgtg ctcaaactaa acgccacaga ccgagacgaa
      961 ggagtcaatg gagaggtaac atactcctta atgtcaatta agcccaatgg aagacactta
     1021 tttacactag atcaaaataa tggagaagtg agggtcaatg gaactttaga ttatgaagaa
     1081 aacaagtttt ataaaattga agtacaggct acagataagg ggactccccc aatggcaggt
     1141 cactgtacag tctgggtgga aatcttggac accaacgata actctcctga agtcgccgtg
     1201 acttccttgt ccctcccagt acgagaggac gctcagccca gcacggtcat tgccctgatc
     1261 agcgtgtctg accgtgactc aggtgtcaac ggacaggtga cctgctcgct gacgccccac
     1321 gttcccttca agctggtgtc caccttcaag aattactact cgttggtgct ggacagcgcc
     1381 ctggaccgcg agaacgtgtg ggcctatgaa ctggtggtga ctgcgcggga tgggggttcg
     1441 ccttctctgt gggccacggc cagggtatcc gtggaggtgg ccgacgtgaa cgacaatgcg
     1501 cctgcgttcg cacagcccga gtacaccgtg ttcgtgaagg agaacaaccc accaggctgc
     1561 cacatcttca cagtgtcggc gcgggacgcg gacgcgcagg agaacgcgct ggtgtcctac
     1621 tcgctggtgg agcggcggtt gggcgaccgc gcgctgtcga gctacgtgtc ggtgcacgcg
     1681 gagagcggca aggtgtacgc gctgcagccg ttggaccacg aggagctgga gctgctacag
     1741 ttccaggtga gcgcgcgcga tgcgggcgtg ccgcctctga gcagcaacgt gacgctgcag
     1801 gtgttcgtgc tggacgagaa cgacaacgcg ccggcactgc tggcgactca ggctggcagc
     1861 gcgggaggcg cagttaacaa gctagtaccg cggtcggtgg gtgcgggcca cgtggtggcg
     1921 aaggtgcgcg cagtggatgc ggactcaggc tacaacgcgt ggctttcata tgaattgcag
     1981 ccggcggcgg gcggctcgcg catcccgttc cgcgtggggc tgtacacggg cgagataagc
     2041 acaacgcgtg ccctggacga ggcagactcg ccgcgccacc gacttctagt actggtgaag
     2101 gatcacggtg agccggcgct gacggccacg gccaccgtgc tggtgtcgtt ggtggagagc
     2161 ggacaggcgc caaaggcctc ttcccggact ttggcgggcg ccgcgagccc agaggctgcg
     2221 ctggtggatg tcaacgtgta cctgatcatc gccatctgcg tggtgtccag cctcctggta
     2281 ctcacgctgc tgctgtatac ggcgctgtgg tggtcggcaa cgcccactga gggcgcgtgc
     2341 gcgccgggga agcccacgct ggtgtgctcc cgcgcggtgg ggagctggtc atactcgcag
     2401 cagaggcggc agagggtgtg ctctgaggag ggcccaccta agacggacct catggccttc
     2461 agccccagtc ttcctctagg tctgaataaa gaggaggaag gggaaagaca ggagccaggg
     2521 tcaaatcacc ccggacagcc acgacagccc aaccctgact ggcgttactc tgcctccctg
     2581 agagcaggca tgcacagctc tgtgcaccta gaggaggctg gcattctacg ggctggtcca
     2641 ggagggcctg atcagcagtg gccaacagta tccagtgcaa caccagaacc agaggcagga
     2701 gaagtgtccc ctccagtcgg tgcgggtgtc aacagcaaca gctggacctt taaatacgga
     2761 ccaggcaacc ccaaacaatc cggtcccggt gagttgcccg acaaattcat tatcccagga
     2821 tctcctgcaa tcatctccat ccggcaggag cctactaaca gccaaattga caaaagtgac
     2881 ttcataacct tcggcaaaaa ggaggagacc aagaaaaaga agaaaaagaa gaagggtaac
     2941 aagacccagg agaaaaaaga gaaagggaac agcacgactg acaacagtga ccagtgaggt
     3001 cctcaaatgg aaacaagcca cttagccagt ttttgtaata atggcaaatc tctcccatgt
     3061 agcaattccc tgctcctttt tcctatctac atgagccctc ttagagacct cagaaatctg
     3121 cagaaagttc cctgtgtctg tctagaacgc atttaacagg ttttgtcgta aaagctttac
     3181 taagtctggt gttaactctt tctctccact ctggcttgtt ttcagaacct aaaaagcaga
     3241 cccaagtttc ctttctcctc cgccgcaaag gagaggcttc ccagccccgc cagtgagagg
     3301 ttggactctc tgccctgtgc tccggggatc ctgtcttgat gacacttgca gggcaggctg
     3361 aaaagttttg agattgagca gcttgggagt ttgtggccac tgggtatgtg tggctaccgc
     3421 gggtatgcga gtgccagata ttggctgaga cgagccagct tagactaatt ggtacaagga
     3481 aggcaagaaa acaaagacaa ataaacagcg gaagttatca gtatggaggg gaagtgtaaa
     3541 cttaaaggga ccagactttc taaatcttac aactcaagag gtggcagcca ccctctagga
     3601 gacaaaacta cccccactga caaggcttta ggagacccta aagtctgttg gctgtgacgt
     3661 cattatacct aaaatctgca tcatacctgc aagccaacag ttcagtgttt taacagagaa
     3721 ccaccctggg aaacagaagc agatctgatg tgtttcctat acatgtcctg tgctcacttt
     3781 attaaaaatt cttttgcaca caatgtttat gaaaaggcca gatccttttc caatacttat
     3841 gcaaaagcaa aagaaaaccc cgacacctca cctttcgctg tttgttgttt catagattta
     3901 tttaaaaaaa gagaaagtct atagctataa atctttaaag agaaatatga atacaattcc
     3961 cctaaactct cctcaaaaga gaattcagtc tacagccatt taaatgatca ttgctgctac
     4021 agaagtgctt taagagaatt gcctgaaaca tctgtattat atcggccacc tgccaatcac
     4081 agctttactc tttcaggtca ctctggggct gcctcttgca tgtattacta aataaaatga
     4141 tctctctttc tctctctctc tctcttttct aagaaacaat tatgtgcact ttgatacaca
     4201 accttctcta accaactata tatcaagacc caaaaattga agaaaaatat tgttttctca
     4261 tacagtgagc agatttttca atctactaat tctgtgactt gtcttggtgt gctagcctac
     4321 accttctctt tggtttagtt ttccttttct ataacactct gaattgctaa tcttactaac
     4381 acctatgatg ttacctgaaa tcaatctccc atatgtatgc tgtatgctat gctaagactc
     4441 ctgaaatata cttactctgt gcttgtgtat gtgaatgtta atgcaactat tacctagagt
     4501 gaactttaag ctttattgtt gaatgtaatt ccattatatt tccttttgta cacctgtgaa
     4561 aaagtggagt agtgtttttt taaccattgt taatcagctt ttgtgtatga aagacacagt
     4621 aaaatttctt tcttaaatca agatactggt gattcaagga attttattta tggtccagcc
     4681 aagagccatc tcgtgccaag acttctgctg gcaagggaat ggataaagct gttttgttct
     4741 agtaacaatt ttggaatgaa tactgacaat attccatgag ggtgtgcaag cacaaatttt
     4801 accaatctga cctctttgaa gttgcagaat gctttgaaat tctaatggta tctgaaatat
     4861 cagctcatag aaagtaacaa aatttgctgt caccttaaat aagacatttt aattttgtta
     4921 taatgtacaa tttagaagtt tgattaatta tattatctat ttaggcatta atataaaaga
     4981 ggtaggagtc tgttatttaa aaaaagcatt aaatttaaaa aaaaactgtc ttgtctactt
     5041 ttagcttcat tctcccatat tttgaagggt gtgtaacttc agctctgcag gattgcatgg
     5101 ggtaaaactt gttaccaaca catgtgaacc attgctacat tgtaggttgt gatcattttg
     5161 ccccactgaa gcccatgtat ctgaccttac gtgccttttg aactaggaga atcgggctaa
     5221 tttattaatg atgataatta taatgtatct gtacagcact ttttacattt gcgaagtgct
     5281 ttccaatcca tgttagttac tagttattac agctgtaagg ataaaacacg tcatgtggat
     5341 tcattttgaa ttggtgctat tggtatttcc tctgttattg ctaataaatg aaaatggtgg
     5401 tatgaaa
//
