LOCUS       NM_018904               5408 bp    mRNA    linear   PRI 05-APR-2024
DEFINITION  Homo sapiens protocadherin alpha 13 (PCDHA13), transcript variant
            1, mRNA.
ACCESSION   NM_018904
VERSION     NM_018904.3
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 5408)
  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 5408)
  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 5408)
  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 5408)
  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 5408)
  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 5408)
  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 5408)
  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, AF152309.1 and
            AC010223.6.
            
            On Nov 22, 2018 this sequence version replaced NM_018904.2.
            
            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 :: AF152309.1, SRR1803617.84377.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1968189, SAMEA1968968
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000289272.3/ ENSP00000289272.2
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-145               AC005609.1         9830-9974           c
            146-5405            AF152309.1         1-5260
            5406-5408           AC010223.6         50266-50268         c
FEATURES             Location/Qualifiers
     source          1..5408
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="5"
                     /map="5q31.3"
     gene            1..5408
                     /gene="PCDHA13"
                     /gene_synonym="CNR5; CNRN5; CNRS5; CRNR5; PCDH-ALPHA13"
                     /note="protocadherin alpha 13"
                     /db_xref="GeneID:56136"
                     /db_xref="HGNC:HGNC:8667"
                     /db_xref="MIM:606319"
     exon            1..2539
                     /gene="PCDHA13"
                     /gene_synonym="CNR5; CNRN5; CNRS5; CRNR5; PCDH-ALPHA13"
                     /inference="alignment:Splign:2.1.0"
     CDS             146..2998
                     /gene="PCDHA13"
                     /gene_synonym="CNR5; CNRN5; CNRS5; CRNR5; PCDH-ALPHA13"
                     /note="isoform 1 precursor is encoded by transcript
                     variant 1; KIAA0345-like 1; ortholog of mouse CNR5;
                     PCDH-alpha-13"
                     /codon_start=1
                     /product="protocadherin alpha-13 isoform 1 precursor"
                     /protein_id="NP_061727.1"
                     /db_xref="CCDS:CCDS4240.1"
                     /db_xref="GeneID:56136"
                     /db_xref="HGNC:HGNC:8667"
                     /db_xref="MIM:606319"
                     /translation="MLSSWQGGPRPRQLLLWLLILAAWETGSGQLHYSVPEEAKHGTF
                     VGRIAQDLGLELAELVPRLFRVASKRHGDLLEVNLQNGILFVNSRIDREELCGRSAEC
                     SIHLEVIVDRPLQVFHVEVKVRDINDNPPIFPESKKRIIIAESRPPETRFPLDGASDA
                     DIGVNSALTYRLDPNDYFTLDAQNSLEQMSSLSLVLRKTLDREEIQEHSLLLTASDGG
                     KPELTGTVQLLITILDVNDNAPEFYQSVYKVTVLENAFNGTLVIKLNATDPDDGTNGD
                     IVYSFRRPVWPAVVYAFTINPNNGEIRTKGKLDFEEKKLYEISVEAVDKGNIPMAGHC
                     TLLVEVLDVNDNAPEVTITSLSLPIREDTQPSAIIALISVSDRDSGSNGQVTCTLTPH
                     VPFKLVSTYKNYYSLVLDSALDRESVSAYELVVTARDGGSPSLWATASVSVGVADVND
                     NAPAFAQPEYTVFVKENNPPGCHIFTVSAQDADAQENALVSYSLVERRVGERALSSYV
                     SVHAESGKVYALQPLDHEELELLQFQVSARDSGVPPLGSNVTLQVFVLDENDNAPALL
                     TPGAGSAGGTVSELMPRSVGAGHVVAKVRAVDADSGYNAWLSYELQLAAVGARIPFRV
                     GLYTGEISTTRPLDEVDAPHHRLLVLVKDHGEPALTATATVLLSLVESGQAPQASSRA
                     SAGAVGPEAALVDVNVYLIIAICAVSSLLVLTLLLYTALRCSAPPTEGACAPGKPTLV
                     CSSAAGSWSYSQQRRPRVCSGEGPHKTDLMAFSPSLPPCLGSAEGTGQREEDSECLKE
                     PRQPNPDWRYSASLRAGMHSSVHLEEAGILRAGPGGPDQQWPTVSSATPEPEAGEVSP
                     PVGAGVNSNSWTFKYGPGNPKQSGPGELPDKFIIPGSPAIISIRQEPTNSQIDKSDFI
                     TFGKKEETKKKKKKKKGNKTQEKKEKGNSTTDNSDQ"
     exon            2540..2598
                     /gene="PCDHA13"
                     /gene_synonym="CNR5; CNRN5; CNRS5; CRNR5; PCDH-ALPHA13"
                     /inference="alignment:Splign:2.1.0"
     exon            2599..2687
                     /gene="PCDHA13"
                     /gene_synonym="CNR5; CNRN5; CNRS5; CRNR5; PCDH-ALPHA13"
                     /inference="alignment:Splign:2.1.0"
     exon            2688..5408
                     /gene="PCDHA13"
                     /gene_synonym="CNR5; CNRN5; CNRS5; CRNR5; PCDH-ALPHA13"
                     /inference="alignment:Splign:2.1.0"
     regulatory      4619..4624
                     /regulatory_class="polyA_signal_sequence"
                     /gene="PCDHA13"
                     /gene_synonym="CNR5; CNRN5; CNRS5; CRNR5; PCDH-ALPHA13"
                     /note="hexamer: AGTAAA"
     polyA_site      4642
                     /gene="PCDHA13"
                     /gene_synonym="CNR5; CNRN5; CNRS5; CRNR5; PCDH-ALPHA13"
     regulatory      5388..5393
                     /regulatory_class="polyA_signal_sequence"
                     /gene="PCDHA13"
                     /gene_synonym="CNR5; CNRN5; CNRS5; CRNR5; PCDH-ALPHA13"
                     /note="hexamer: AATGAA"
     polyA_site      5408
                     /gene="PCDHA13"
                     /gene_synonym="CNR5; CNRN5; CNRS5; CRNR5; PCDH-ALPHA13"
                     /note="major polyA site"
ORIGIN      
        1 cttcctgcag aaaatatagc agaaagcgga atacctcttg cgaatccttc cgcactagga
       61 agccataaaa attgggcctt gagagacagt ttgaggtaag gcgttgtata tattgcagat
      121 agctctgagg tttttggagt gtaccatgct gtcttcctgg caaggaggcc caagaccgcg
      181 gcaactactg ctctggcttc tgatcctcgc agcctgggag acgggtagtg gccagctcca
      241 ctactccgtc cccgaggaag caaaacacgg caccttcgtg ggccgcatcg ctcaggacct
      301 ggggctggag ctggcggagc tggtgccgcg cctgttccgg gtggcgtcca aaagacacgg
      361 ggaccttctg gaggtaaatc tgcagaatgg cattttgttt gtgaattctc ggatcgaccg
      421 cgaggagctg tgtgggcgga gcgcggagtg cagcatccac ctggaggtga tcgtggacag
      481 gcctctgcag gttttccatg tggaggtgaa ggtgagggac attaacgaca acccgcccat
      541 attccctgaa agcaagaaac gaataatcat tgcagaatct agacctccgg aaactcgatt
      601 tccactagat ggcgcatccg atgcagatat tggagtaaac tcggcattga cctaccgact
      661 ggatcccaac gattatttca ctttggacgc acaaaacagt cttgagcaaa tgtcttcatt
      721 atcacttgta ctgaggaaaa cactggacag agaggaaatt caggaacata gtttattact
      781 gacagccagt gatggaggta aacccgagct gactggcaca gttcagctgc tcatcacgat
      841 tctggacgtg aatgacaacg ccccggaatt ttaccaatcc gtttataaag tgacggtgtt
      901 agagaacgcc ttcaatggaa cattagtgat caagctaaat gccacagatc ctgatgatgg
      961 tacaaatgga gatatagttt actcatttag aaggcctgta tggcctgcag tggtatatgc
     1021 atttaccata aatccgaaca atggagaaat taggacaaaa ggcaaactag atttcgaaga
     1081 aaagaaatta tatgaaatat ccgtggaggc agttgacaaa ggaaatattc caatggcggg
     1141 tcattgtacc cttttggtgg aagtactaga tgtaaatgat aacgccccag aggttaccat
     1201 cacttctttg tcactcccca tcagagaaga cactcagcct agcgccatta ttgccctaat
     1261 cagtgtgtcc gatcgtgact ctggctcaaa tggacaggtc acctgcacct tgacgccgca
     1321 tgtccccttc aagctggtgt ccacctacaa gaactactac tcattagtgc tggacagcgc
     1381 cctggaccgc gagagcgtat cagcctatga actggtggtg accgcgcggg acgggggctc
     1441 gccttcgctg tgggccacgg ccagcgtgtc ggtgggggtg gccgacgtga acgacaacgc
     1501 gccggcgttc gcgcagcccg agtacacggt gttcgtgaag gaaaacaatc cgccgggctg
     1561 ccacatcttc acggtgtctg ctcaggacgc ggacgcacag gagaacgcgc tggtctccta
     1621 ctcgctggtg gagcggcggg tgggcgagcg tgcgctgtcg agctacgtgt cggtgcacgc
     1681 ggagagcggc aaggtgtacg cgctgcagcc gttggaccac gaggagctgg agctgttgca
     1741 gttccaggtg agcgcgcgcg actctggcgt gccgcctctg ggcagcaacg tgacgctgca
     1801 ggtgttcgtg ctggacgaga acgacaacgc tccggcgctg ctgacgcccg gggctggcag
     1861 cgcgggaggc acagtgagcg agctgatgcc gcggtcggtg ggtgcaggcc acgtggtggc
     1921 gaaggtgcgc gcggtggacg ccgattcggg ctacaatgcg tggctttcgt atgaattgca
     1981 gctggcggcg gtcggcgcgc gcatcccgtt ccgcgtgggg ctgtacactg gcgagatcag
     2041 cacgacgcgc cctctggacg aggtggacgc gccgcaccac cgccttctgg tgctggtgaa
     2101 ggaccacggt gagcccgcgc tgacggccac ggcaacggtg ctgttgtcgc tggtggagag
     2161 cggccaagcg ccacaggctt cgtcgagggc gtcggcaggc gctgtgggtc cagaagcggc
     2221 gctggtggat gtcaatgttt acttgatcat tgccatctgc gcggtgtcca gcctgttggt
     2281 gctcacgttg ctgctgtata ctgcgctgcg gtgctcggca ccgcccaccg agggcgcgtg
     2341 cgcgccgggc aagcccactc tagtgtgctc cagcgcggca gggagttggt cgtactcgca
     2401 gcagaggcgg ccgagggtgt gctctgggga gggcccgcat aagacggacc tcatggcctt
     2461 cagtcccagc cttcctcctt gtctgggttc tgcagaggga acaggccaga gggaggagga
     2521 ctcagaatgc ttgaaagagc cacgacagcc caaccctgac tggcgttact ctgcctccct
     2581 gagagcaggc atgcacagct ctgtgcacct agaggaggct ggcattctac gggctggtcc
     2641 aggagggcct gatcagcagt ggccaacagt atccagtgca acaccagaac cagaggcagg
     2701 agaagtgtcc cctccagtcg gtgcgggtgt caacagcaac agctggacct ttaaatacgg
     2761 accaggcaac cccaaacaat ccggtcccgg tgagttgccc gacaaattca ttatcccagg
     2821 atctcctgca atcatctcca tccggcagga gcctactaac agccaaattg acaaaagtga
     2881 cttcataacc ttcggcaaaa aggaggagac caagaaaaag aagaaaaaga agaagggtaa
     2941 caagacccag gagaaaaaag agaaagggaa cagcacgact gacaacagtg accagtgagg
     3001 tcctcaaatg gaaacaagcc acttagccag tttttgtaat aatggcaaat ctctcccatg
     3061 tagcaattcc ctgctccttt ttcctatcta catgagccct cttagagacc tcagaaatct
     3121 gcagaaagtt ccctgtgtct gtctagaacg catttaacag gttttgtcgt aaaagcttta
     3181 ctaagtctgg tgttaactct ttctctccac tctggcttgt tttcagaacc taaaaagcag
     3241 acccaagttt cctttctcct ccgccgcaaa ggagaggctt cccagccccg ccagtgagag
     3301 gttggactct ctgccctgtg ctccggggat cctgtcttga tgacacttgc agggcaggct
     3361 gaaaagtttt gagattgagc agcttgggag tttgtggcca ctgggtatgt gtggctaccg
     3421 cgggtatgcg agtgccagat attggctgag acgagccagc ttagactaat tggtacaagg
     3481 aaggcaagaa aacaaagaca aataaacagc ggaagttatc agtatggagg ggaagtgtaa
     3541 acttaaaggg accagacttt ctaaatctta caactcaaga ggtggcagcc accctctagg
     3601 agacaaaact acccccactg acaaggcttt aggagaccct aaagtctgtt ggctgtgacg
     3661 tcattatacc taaaatctgc atcatacctg caagccaaca gttcagtgtt ttaacagaga
     3721 accaccctgg gaaacagaag cagatctgat gtgtttccta tacatgtcct gtgctcactt
     3781 tattaaaaat tcttttgcac acaatgttta tgaaaaggcc agatcctttt ccaatactta
     3841 tgcaaaagca aaagaaaacc ccgacacctc acctttcgct gtttgttgtt tcatagattt
     3901 atttaaaaaa agagaaagtc tatagctata aatctttaaa gagaaatatg aatacaattc
     3961 ccctaaactc tcctcaaaag agaattcagt ctacagccat ttaaatgatc attgctgcta
     4021 cagaagtgct ttaagagaat tgcctgaaac atctgtatta tatcggccac ctgccaatca
     4081 cagctttact ctttcaggtc actctggggc tgcctcttgc atgtattact aaataaaatg
     4141 atctctcttt ctctctctct ctctcttttc taagaaacaa ttatgtgcac tttgatacac
     4201 aaccttctct aaccaactat atatcaagac ccaaaaattg aagaaaaata ttgttttctc
     4261 atacagtgag cagatttttc aatctactaa ttctgtgact tgtcttggtg tgctagccta
     4321 caccttctct ttggtttagt tttccttttc tataacactc tgaattgcta atcttactaa
     4381 cacctatgat gttacctgaa atcaatctcc catatgtatg ctgtatgcta tgctaagact
     4441 cctgaaatat acttactctg tgcttgtgta tgtgaatgtt aatgcaacta ttacctagag
     4501 tgaactttaa gctttattgt tgaatgtaat tccattatat ttccttttgt acacctgtga
     4561 aaaagtggag tagtgttttt ttaaccattg ttaatcagct tttgtgtatg aaagacacag
     4621 taaaatttct ttcttaaatc aagatactgg tgattcaagg aattttattt atggtccagc
     4681 caagagccat ctcgtgccaa gacttctgct ggcaagggaa tggataaagc tgttttgttc
     4741 tagtaacaat tttggaatga atactgacaa tattccatga gggtgtgcaa gcacaaattt
     4801 taccaatctg acctctttga agttgcagaa tgctttgaaa ttctaatggt atctgaaata
     4861 tcagctcata gaaagtaaca aaatttgctg tcaccttaaa taagacattt taattttgtt
     4921 ataatgtaca atttagaagt ttgattaatt atattatcta tttaggcatt aatataaaag
     4981 aggtaggagt ctgttattta aaaaaagcat taaatttaaa aaaaaactgt cttgtctact
     5041 tttagcttca ttctcccata ttttgaaggg tgtgtaactt cagctctgca ggattgcatg
     5101 gggtaaaact tgttaccaac acatgtgaac cattgctaca ttgtaggttg tgatcatttt
     5161 gccccactga agcccatgta tctgacctta cgtgcctttt gaactaggag aatcgggcta
     5221 atttattaat gatgataatt ataatgtatc tgtacagcac tttttacatt tgcgaagtgc
     5281 tttccaatcc atgttagtta ctagttatta cagctgtaag gataaaacac gtcatgtgga
     5341 ttcattttga attggtgcta ttggtatttc ctctgttatt gctaataaat gaaaatggtg
     5401 gtatgaaa
//
