LOCUS       NM_018909               5395 bp    mRNA    linear   PRI 04-APR-2024
DEFINITION  Homo sapiens protocadherin alpha 6 (PCDHA6), transcript variant 1,
            mRNA.
ACCESSION   NM_018909 XM_001124723 XM_001124826
VERSION     NM_018909.4
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 5395)
  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 5395)
  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 5395)
  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 5395)
  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 5395)
  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 5395)
  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 5395)
  AUTHORS   Senzaki,K., Ogawa,M. and Yagi,T.
  TITLE     Proteins of the CNR family are multiple receptors for Reelin
  JOURNAL   Cell 99 (6), 635-647 (1999)
   PUBMED   10612399
REFERENCE   8  (bases 1 to 5395)
  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 DA069850.1, AF152314.1 and
            AC010223.6.
            
            On Nov 22, 2018 this sequence version replaced NM_018909.3.
            
            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).
            
            CCDS Note: A downstream start codon is annotated for this CCDS
            representation because its use is more consistent with the presence
            of an N-terminal signal peptide in the protein, which is known to
            contain extracellular cadherin domains. However, it should be noted
            that an alternative upstream start codon exists, which would result
            in a protein that is 9 aa longer at the N-terminus and is less
            likely to contain a signal peptide. The upstream start codon has a
            weak Kozak signal, so it is possible that leaky scanning by
            ribosomes will allow the use of the downstream start codon. There
            is no experimental evidence indicating which start codon is used in
            vivo.
            
            ##Evidence-Data-START##
            Transcript exon combination :: SRR1803613.212371.1,
                                           SRR1803616.61764.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1968189, SAMEA2146982
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            CDS uses downstream in-frame AUG :: downstream AUG is associated
                                                with N-terminal localization
                                                signal
            MANE Ensembl match               :: ENST00000529310.6/
                                                ENSP00000433378.1
            RefSeq Select criteria           :: based on conservation,
                                                expression, longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-132               DA069850.1         40-171
            133-5392            AF152314.1         1-5260
            5393-5395           AC010223.6         50266-50268         c
FEATURES             Location/Qualifiers
     source          1..5395
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="5"
                     /map="5q31.3"
     gene            1..5395
                     /gene="PCDHA6"
                     /gene_synonym="CNR2; CNRN2; CNRS2; CRNR2; PCDH-ALPHA6"
                     /note="protocadherin alpha 6"
                     /db_xref="GeneID:56142"
                     /db_xref="HGNC:HGNC:8672"
                     /db_xref="MIM:606312"
     exon            1..2526
                     /gene="PCDHA6"
                     /gene_synonym="CNR2; CNRN2; CNRS2; CRNR2; PCDH-ALPHA6"
                     /inference="alignment:Splign:2.1.0"
     CDS             133..2985
                     /gene="PCDHA6"
                     /gene_synonym="CNR2; CNRN2; CNRS2; CRNR2; PCDH-ALPHA6"
                     /note="isoform 1 precursor is encoded by transcript
                     variant 1; KIAA0345-like 8; PCDH-alpha-6"
                     /codon_start=1
                     /product="protocadherin alpha-6 isoform 1 precursor"
                     /protein_id="NP_061732.1"
                     /db_xref="CCDS:CCDS47281.1"
                     /db_xref="GeneID:56142"
                     /db_xref="HGNC:HGNC:8672"
                     /db_xref="MIM:606312"
                     /translation="MVFTPEDRLGKQCLLLPLLLLAAWKVGSGQLHYSVPEEAKHGTF
                     VGRIAQDLGLELAELVPRLFRMASKDREDLLEVNLQNGILFVNSRIDREELCGRSAEC
                     SIHLEVIVDRPLQVFHVDVEVRDINDNPPLFPVEEQRVLIYESRLPDSVFPLEGASDA
                     DVGSNSILTYKLSSSEYFGLDVKINSDDNKQIGLLLKKSLDREEAPAHNLFLTATDGG
                     KPELTGTVQLLVTVLDVNDNAPTFEQSEYEVRIFENADNGTTVIRLNASDRDEGANGA
                     ISYSFNSLVAAMVIDHFSIDRNTGEIVIRGNLDFEQENLYKILIDATDKGHPPMAGHC
                     TVLVRILDKNDNVPEIALTSLSLPVREDAQFGTVIALISVNDLDSGANGQVNCSLTPH
                     VPFKLVSTFKNYYSLVLDSALDRESVSAYELVVTARDGGSPSLWATASLSVEVADMND
                     NAPAFAQPEYTVFVKENNPPGCHIFTVSARDADAQENALVSYSLVERRVGERALSSYI
                     SVHAESGKVYALQPLDHEELELLQFQVSARDAGVPPLGSNVTLQVFVLDENDNAPALL
                     APRVGGTGGAVSELVPRSLGAGQVVAKVRAVDADSGYNAWLSYELQPPASSARFPFRV
                     GLYTGEISTTRVLDEADSPRHRLLVLVKDHGEPALTATATVLVSLVESGQAPKASSRA
                     SVGAAGPEAALVDVNVYLIIAICAVSSLLVLTLLLYTALRCSAPPTEGACTADKPTLV
                     CSSAVGSWSYSQQRRQRVCSGEGPPKMDLMAFSPSLSPCPIMMGKAENQDLNEDHDAK
                     PRQPNPDWRYSASLRAGMHSSVHLEEAGILRAGPGGPDQQWPTVSSATPEPEAGEVSP
                     PVGAGVNSNSWTFKYGPGNPKQSGPGELPDKFIIPGSPAIISIRQEPTNSQIDKSDFI
                     TFGKKEETKKKKKKKKGNKTQEKKEKGNSTTDNSDQ"
     exon            2527..2585
                     /gene="PCDHA6"
                     /gene_synonym="CNR2; CNRN2; CNRS2; CRNR2; PCDH-ALPHA6"
                     /inference="alignment:Splign:2.1.0"
     exon            2586..2674
                     /gene="PCDHA6"
                     /gene_synonym="CNR2; CNRN2; CNRS2; CRNR2; PCDH-ALPHA6"
                     /inference="alignment:Splign:2.1.0"
     exon            2675..5395
                     /gene="PCDHA6"
                     /gene_synonym="CNR2; CNRN2; CNRS2; CRNR2; PCDH-ALPHA6"
                     /inference="alignment:Splign:2.1.0"
     regulatory      4606..4611
                     /regulatory_class="polyA_signal_sequence"
                     /gene="PCDHA6"
                     /gene_synonym="CNR2; CNRN2; CNRS2; CRNR2; PCDH-ALPHA6"
                     /note="hexamer: AGTAAA"
     polyA_site      4629
                     /gene="PCDHA6"
                     /gene_synonym="CNR2; CNRN2; CNRS2; CRNR2; PCDH-ALPHA6"
     regulatory      5375..5380
                     /regulatory_class="polyA_signal_sequence"
                     /gene="PCDHA6"
                     /gene_synonym="CNR2; CNRN2; CNRS2; CRNR2; PCDH-ALPHA6"
                     /note="hexamer: AATGAA"
     polyA_site      5395
                     /gene="PCDHA6"
                     /gene_synonym="CNR2; CNRN2; CNRS2; CRNR2; PCDH-ALPHA6"
                     /note="major polyA site"
ORIGIN      
        1 attactgcat cattccctga ctgttgaatg atggcggacg cagaagaaat ggattaataa
       61 attccggaac atacagtatt ttatctttat gcggaagatc ttctaatgga aataaaacca
      121 gaggtatttg acatggtgtt taccccggag gatagattgg gaaagcaatg tctgctcctc
      181 ccgcttctgc tcctcgcagc ctggaaggtg gggagcggcc agctccacta ctccgtaccc
      241 gaggaggcca aacacggcac cttcgtgggc cggatcgcgc aggacctggg gctggagctg
      301 gcggagctgg tgccgcgcct gttcaggatg gcctccaaag accgcgagga ccttctggag
      361 gtaaatctgc agaatggcat tttgtttgtg aattctcgga tcgaccgcga ggagctgtgc
      421 gggcggagcg cggagtgcag catccacctg gaggtgatcg tggacaggcc gctgcaggtt
      481 ttccatgtgg acgtggaggt gagggacatt aacgacaacc cgcccttgtt cccggtagag
      541 gaacaaagag tgctgattta cgaatctagg ctgccagatt ctgtgtttcc actggagggc
      601 gcgtccgatg cagatgttgg ctcaaattcc atcttaacct ataaactcag ttctagcgaa
      661 tacttcgggc tagatgtgaa aataaacagt gatgacaata aacaaattgg gctcttatta
      721 aagaaatcct tggacagaga ggaagctcct gcacacaact tattcctgac agccacagat
      781 gggggcaaac ctgagctcac aggcactgtt cagctgctgg tcacagtgct ggatgtgaat
      841 gataatgctc ccactttcga acagtctgaa tacgaagtaa gaatattcga aaatgcagac
      901 aacggaacaa cagttatcag actgaatgct tctgatcggg atgaaggagc gaatggggca
      961 atttcatatt cttttaatag ccttgttgca gccatggtta ttgaccactt tagcatagat
     1021 cgaaatacgg gagaaatagt gattcggggt aatttggatt ttgaacaaga aaacttatac
     1081 aaaatcctca ttgacgccac ggacaaaggc catcctccca tggcgggtca ttgcaccgtt
     1141 ttagtgagaa ttttggataa aaatgataac gtccctgaga tagcactgac ttccttatcc
     1201 ttgcctgtac gtgaagacgc tcaatttggt actgtcatcg ccctaattag cgtgaacgac
     1261 ctcgattcag gtgccaacgg gcaggtgaac tgctcgctga cgcctcacgt ccctttcaag
     1321 ctggtgtcca ccttcaagaa ttactactcg ttggtgctgg acagtgccct ggaccgcgag
     1381 agcgtgtcgg cctatgagtt ggtggtaacc gcgcgggacg ggggctcgcc ttcgctgtgg
     1441 gccaccgcca gcttgtctgt ggaggtggcc gacatgaatg acaatgctcc ggcgttcgcg
     1501 cagcccgagt acacagtgtt cgtgaaggag aacaacccgc cgggctgcca catcttcacg
     1561 gtgtctgcgc gagacgcgga cgcgcaggag aacgcgctgg tgtcctactc gctggtggag
     1621 cggcgggtgg gcgagcgcgc gttgtcgagc tacatttcgg tgcacgcgga gagcggcaag
     1681 gtgtacgcgc tgcagccgct ggaccacgag gagctagagc tgctgcagtt tcaggtgagc
     1741 gcgcgcgacg cgggcgtgcc gcctctgggc agcaacgtga cgctgcaggt gttcgtgctg
     1801 gacgagaacg acaacgcgcc ggcgctgctg gcgcctcggg tgggtggtac tggtggtgca
     1861 gtgagcgagc tggtgccgcg gtcactgggt gcaggccaag tggtggcgaa ggtgcgcgca
     1921 gttgacgccg actcaggcta caacgcgtgg ctttcgtatg agctgcagcc cccggcaagc
     1981 agcgctcgct tcccgtttcg cgtggggctg tacacgggcg agatcagcac cactcgtgtc
     2041 ctggacgaag cggactctcc gcgccaccgg ctgctggtgc tggtgaaaga ccacggtgag
     2101 ccggcgctga cagcgacggc cacggttctg gtgtcgctgg tggagagtgg ccaggctcca
     2161 aaggcgtcat cacgggcgtc ggtgggcgcc gcgggcccag aggcggcgct ggtggatgtc
     2221 aacgtgtacc tgatcatcgc catctgcgcg gtatccagcc tgctggtcct cacgctactg
     2281 ctgtacacag cgctgcggtg ctcggcgcca cccaccgagg gcgcgtgcac ggcggacaag
     2341 cccacgctgg tgtgctccag cgcagtgggg agctggtcgt actcgcagca gaggcggcag
     2401 agggtgtgct ccggggaggg cccacccaag atggatctca tggcctttag ccccagcctt
     2461 tcaccttgtc ctattatgat gggtaaggcg gagaatcagg atttaaatga agatcatgat
     2521 gccaaaccac gacagcccaa ccctgactgg cgttactctg cctccctgag agcaggcatg
     2581 cacagctctg tgcacctaga ggaggctggc attctacggg ctggtccagg agggcctgat
     2641 cagcagtggc caacagtatc cagtgcaaca ccagaaccag aggcaggaga agtgtcccct
     2701 ccagtcggtg cgggtgtcaa cagcaacagc tggaccttta aatacggacc aggcaacccc
     2761 aaacaatccg gtcccggtga gttgcccgac aaattcatta tcccaggatc tcctgcaatc
     2821 atctccatcc ggcaggagcc tactaacagc caaattgaca aaagtgactt cataaccttc
     2881 ggcaaaaagg aggagaccaa gaaaaagaag aaaaagaaga agggtaacaa gacccaggag
     2941 aaaaaagaga aagggaacag cacgactgac aacagtgacc agtgaggtcc tcaaatggaa
     3001 acaagccact tagccagttt ttgtaataat ggcaaatctc tcccatgtag caattccctg
     3061 ctcctttttc ctatctacat gagccctctt agagacctca gaaatctgca gaaagttccc
     3121 tgtgtctgtc tagaacgcat ttaacaggtt ttgtcgtaaa agctttacta agtctggtgt
     3181 taactctttc tctccactct ggcttgtttt cagaacctaa aaagcagacc caagtttcct
     3241 ttctcctccg ccgcaaagga gaggcttccc agccccgcca gtgagaggtt ggactctctg
     3301 ccctgtgctc cggggatcct gtcttgatga cacttgcagg gcaggctgaa aagttttgag
     3361 attgagcagc ttgggagttt gtggccactg ggtatgtgtg gctaccgcgg gtatgcgagt
     3421 gccagatatt ggctgagacg agccagctta gactaattgg tacaaggaag gcaagaaaac
     3481 aaagacaaat aaacagcgga agttatcagt atggagggga agtgtaaact taaagggacc
     3541 agactttcta aatcttacaa ctcaagaggt ggcagccacc ctctaggaga caaaactacc
     3601 cccactgaca aggctttagg agaccctaaa gtctgttggc tgtgacgtca ttatacctaa
     3661 aatctgcatc atacctgcaa gccaacagtt cagtgtttta acagagaacc accctgggaa
     3721 acagaagcag atctgatgtg tttcctatac atgtcctgtg ctcactttat taaaaattct
     3781 tttgcacaca atgtttatga aaaggccaga tccttttcca atacttatgc aaaagcaaaa
     3841 gaaaaccccg acacctcacc tttcgctgtt tgttgtttca tagatttatt taaaaaaaga
     3901 gaaagtctat agctataaat ctttaaagag aaatatgaat acaattcccc taaactctcc
     3961 tcaaaagaga attcagtcta cagccattta aatgatcatt gctgctacag aagtgcttta
     4021 agagaattgc ctgaaacatc tgtattatat cggccacctg ccaatcacag ctttactctt
     4081 tcaggtcact ctggggctgc ctcttgcatg tattactaaa taaaatgatc tctctttctc
     4141 tctctctctc tcttttctaa gaaacaatta tgtgcacttt gatacacaac cttctctaac
     4201 caactatata tcaagaccca aaaattgaag aaaaatattg ttttctcata cagtgagcag
     4261 atttttcaat ctactaattc tgtgacttgt cttggtgtgc tagcctacac cttctctttg
     4321 gtttagtttt ccttttctat aacactctga attgctaatc ttactaacac ctatgatgtt
     4381 acctgaaatc aatctcccat atgtatgctg tatgctatgc taagactcct gaaatatact
     4441 tactctgtgc ttgtgtatgt gaatgttaat gcaactatta cctagagtga actttaagct
     4501 ttattgttga atgtaattcc attatatttc cttttgtaca cctgtgaaaa agtggagtag
     4561 tgttttttta accattgtta atcagctttt gtgtatgaaa gacacagtaa aatttctttc
     4621 ttaaatcaag atactggtga ttcaaggaat tttatttatg gtccagccaa gagccatctc
     4681 gtgccaagac ttctgctggc aagggaatgg ataaagctgt tttgttctag taacaatttt
     4741 ggaatgaata ctgacaatat tccatgaggg tgtgcaagca caaattttac caatctgacc
     4801 tctttgaagt tgcagaatgc tttgaaattc taatggtatc tgaaatatca gctcatagaa
     4861 agtaacaaaa tttgctgtca ccttaaataa gacattttaa ttttgttata atgtacaatt
     4921 tagaagtttg attaattata ttatctattt aggcattaat ataaaagagg taggagtctg
     4981 ttatttaaaa aaagcattaa atttaaaaaa aaactgtctt gtctactttt agcttcattc
     5041 tcccatattt tgaagggtgt gtaacttcag ctctgcagga ttgcatgggg taaaacttgt
     5101 taccaacaca tgtgaaccat tgctacattg taggttgtga tcattttgcc ccactgaagc
     5161 ccatgtatct gaccttacgt gccttttgaa ctaggagaat cgggctaatt tattaatgat
     5221 gataattata atgtatctgt acagcacttt ttacatttgc gaagtgcttt ccaatccatg
     5281 ttagttacta gttattacag ctgtaaggat aaaacacgtc atgtggattc attttgaatt
     5341 ggtgctattg gtatttcctc tgttattgct aataaatgaa aatggtggta tgaaa
//
