LOCUS       NM_018905               5370 bp    mRNA    linear   PRI 03-MAY-2024
DEFINITION  Homo sapiens protocadherin alpha 2 (PCDHA2), transcript variant 1,
            mRNA.
ACCESSION   NM_018905
VERSION     NM_018905.3
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 5370)
  AUTHORS   Hsu,Y.H., Pintacuda,G., Liu,R., Nacu,E., Kim,A., Tsafou,K.,
            Petrossian,N., Crotty,W., Suh,J.M., Riseman,J., Martin,J.M.,
            Biagini,J.C., Mena,D., Ching,J.K.T., Malolepsza,E., Li,T.,
            Singh,T., Ge,T., Egri,S.B., Tanenbaum,B., Stanclift,C.R.,
            Apffel,A.M., Carr,S.A., Schenone,M., Jaffe,J., Fornelos,N.,
            Huang,H., Eggan,K.C. and Lage,K.
  CONSRTM   Schizophrenia Working Group of the Psychiatric Genomics Consortium;
            Stanley Global Asia Initiatives
  TITLE     Using brain cell-type-specific protein interactomes to interpret
            neurodevelopmental genetic signals in schizophrenia
  JOURNAL   iScience 26 (5), 106701 (2023)
   PUBMED   37207277
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 5370)
  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 5370)
  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 5370)
  AUTHORS   Gevaert,K., Goethals,M., Martens,L., Van Damme,J., Staes,A.,
            Thomas,G.R. and Vandekerckhove,J.
  TITLE     Exploring proteomes and analyzing protein processing by mass
            spectrometric identification of sorted N-terminal peptides
  JOURNAL   Nat Biotechnol 21 (5), 566-569 (2003)
   PUBMED   12665801
  REMARK    GeneRIF: Provides evidence for a 22 aa signal peptide.
REFERENCE   5  (bases 1 to 5370)
  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   6  (bases 1 to 5370)
  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   7  (bases 1 to 5370)
  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   8  (bases 1 to 5370)
  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   9  (bases 1 to 5370)
  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   10 (bases 1 to 5370)
  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, BC003126.1,
            AF152310.1 and AC010223.6.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Nov 23, 2018 this sequence version replaced NM_018905.2.
            
            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 :: SRR1660809.156560.1, AF152310.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA2142670, SAMEA2144333
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000526136.2/ ENSP00000431748.1
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-7                 AC005609.1         97240-97246         c
            8-113               BC003126.1         1-106
            114-5367            AF152310.1         1-5254
            5368-5370           AC010223.6         50266-50268         c
FEATURES             Location/Qualifiers
     source          1..5370
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="5"
                     /map="5q31.3"
     gene            1..5370
                     /gene="PCDHA2"
                     /gene_synonym="PCDH-ALPHA2"
                     /note="protocadherin alpha 2"
                     /db_xref="GeneID:56146"
                     /db_xref="HGNC:HGNC:8668"
                     /db_xref="MIM:606308"
     exon            1..2501
                     /gene="PCDHA2"
                     /gene_synonym="PCDH-ALPHA2"
                     /inference="alignment:Splign:2.1.0"
     CDS             114..2960
                     /gene="PCDHA2"
                     /gene_synonym="PCDH-ALPHA2"
                     /note="isoform 1 precursor is encoded by transcript
                     variant 1; KIAA0345-like 12"
                     /codon_start=1
                     /product="protocadherin alpha-2 isoform 1 precursor"
                     /protein_id="NP_061728.1"
                     /db_xref="CCDS:CCDS54914.1"
                     /db_xref="GeneID:56146"
                     /db_xref="HGNC:HGNC:8668"
                     /db_xref="MIM:606308"
                     /translation="MASSIRRGRGAWTRLLSLLLLAAWEVGSGQLRYSVPEEAKHGTF
                     VGRIAQDLGLELEELVPRLFRVASKRHGDLLEVNLQNGILFVNSRIDREELCGRSAEC
                     SIHVEVIVDRPLQVFHVEVEVKDINDNPPIFPMTVKTIRFPESRLLDSRFPLEGASDA
                     DIGVNALLSYKLSSSEFFFLDIQANDELSESLSLVLGKSLDREETAEVNLLLVATDGG
                     KPELTGTVQILIKVLDVNDNEPTFAQSVYKVKLLENTANGTLVVKLNASDADEGPNSE
                     IVYSLGSDVSSTIQTKFTIDPISGEIRTKGKLDYEEAKSYEIQVTATDKGTPSMSGHC
                     KISLKLVDINDNTPEVSITSLSLPISENASLGTVIALITVSDRDSGTNGHVTCSLTPH
                     VPFKLVSTFKNYYSLVLDSALDRESVSAYELVVTARDGGSPSLWATTSVSIEVADVND
                     NAPAFAQPEYTVFVKENNPPGCHIFTVSAWDADAQENALVSYSLVERRVGERALSSYV
                     SVHAESGKVYALQPLDHEEVELLQFQVSARDAGVPPLGSNVTLQVFVLDENDNAPALL
                     APRAGTAAGAVSELVPWSVGAGHVVAKVRAVDADSGYNAWLSYELQLGTGSARIPFRV
                     GLYTGEISTTRALDEADSPRHRLLVLVKDHGEPALTATATVLVSLVESGQAPKASSRA
                     WVGAAGSEATLVDVNVYLIIAICAVSSLLVLTVLLYTALRCSVPPTEGARAPGKPTLV
                     CSSAVGSWSYSQQRRQRVCSGEDPPKTDLMAFSPSLSQGPDSAEEKQLSESEYVGKPR
                     QPNPDWRYSASLRAGMHSSVHLEEAGILRAGPGGPDQQWPTVSSATPEPEAGEVSPPV
                     GAGVNSNSWTFKYGPGNPKQSGPGELPDKFIIPGSPAIISIRQEPTNSQIDKSDFITF
                     GKKEETKKKKKKKKGNKTQEKKEKGNSTTDNSDQ"
     exon            2502..2560
                     /gene="PCDHA2"
                     /gene_synonym="PCDH-ALPHA2"
                     /inference="alignment:Splign:2.1.0"
     exon            2561..2649
                     /gene="PCDHA2"
                     /gene_synonym="PCDH-ALPHA2"
                     /inference="alignment:Splign:2.1.0"
     exon            2650..5370
                     /gene="PCDHA2"
                     /gene_synonym="PCDH-ALPHA2"
                     /inference="alignment:Splign:2.1.0"
     regulatory      4581..4586
                     /regulatory_class="polyA_signal_sequence"
                     /gene="PCDHA2"
                     /gene_synonym="PCDH-ALPHA2"
                     /note="hexamer: AGTAAA"
     polyA_site      4604
                     /gene="PCDHA2"
                     /gene_synonym="PCDH-ALPHA2"
     regulatory      5350..5355
                     /regulatory_class="polyA_signal_sequence"
                     /gene="PCDHA2"
                     /gene_synonym="PCDH-ALPHA2"
                     /note="hexamer: AATGAA"
     polyA_site      5370
                     /gene="PCDHA2"
                     /gene_synonym="PCDH-ALPHA2"
                     /note="major polyA site"
ORIGIN      
        1 acttcagaga agcggaggaa taagagaagc agcaggactt taacagagac tagaatattt
       61 aaatttttgc aaaacatgct cttctaattt gatcaaaaca ttgaggattg gtaatggcgt
      121 cttctatcag aaggggccga ggggcctgga cacggctgct ctcgcttctg ctcctcgcag
      181 cctgggaggt ggggagcggc cagctccgct actccgtccc cgaggaggcc aaacacggca
      241 ccttcgtggg ccgcatcgcg caggacctgg ggctggagct ggaggagctg gtgccgcgcc
      301 tgttccgggt ggcgtccaaa agacacgggg accttctgga ggtaaatctg cagaatggca
      361 ttttgtttgt gaattctcgg atcgaccggg aggagctgtg cgggcggagc gcggaatgta
      421 gcatccacgt ggaggtgatc gtggacaggc cgctgcaggt tttccatgtg gaagtggagg
      481 tgaaggacat taacgacaac ccgccaatat ttccaatgac agtaaagact atccggtttc
      541 ccgaatcaag gctgcttgat tctcggtttc ctctagaggg agcatctgat gcagatatag
      601 gagtaaatgc tcttctctcc tacaagctca gctccagtga gtttttcttc ctagatatac
      661 aggcaaatga tgaactaagc gaatctttgt ctctcgtgct ggggaaatcg ctggacagag
      721 aggaaactgc tgaggttaat ttgttactgg tggctactga tgggggcaaa cctgagctca
      781 cgggcaccgt tcaaatactt attaaggtat tagatgtaaa tgacaatgaa ccaacttttg
      841 cccaatcagt ttacaaagta aaattgttag agaatacggc aaatgggacc ttagtggtta
      901 agttaaacgc ttctgatgca gatgaaggac cgaacagcga gattgtgtat tcactcggta
      961 gtgatgtgtc ctccactata cagactaagt ttaccataga tcccatctca ggggaaatca
     1021 gaactaaggg aaaattagat tatgaagaag caaagtccta cgagattcag gtcactgcaa
     1081 ctgacaaagg aaccccttca atgtcaggac attgtaaaat ttcattaaaa cttgtggaca
     1141 tcaatgataa cacaccagaa gtctcaataa cgtctctctc acttcccatc tcagagaacg
     1201 cttccctggg cactgtcatt gctctcatca cggtgtcgga tcgcgactct ggtacgaatg
     1261 gacatgtcac ctgctccctg acgccccacg tccctttcaa gctggtgtcc accttcaaga
     1321 attactactc gttggtgctg gacagcgccc tggaccgcga gagcgtgtca gcctatgagc
     1381 tggtggtgac cgcacgggac gggggctcgc cttcactgtg ggccaccacc agcgtgtcca
     1441 tcgaggtggc cgacgtgaac gacaacgcgc cggcgttcgc acagcctgag tacacagtat
     1501 tcgtgaagga gaacaacccg ccgggctgcc acatcttcac ggtgtcagcg tgggatgcgg
     1561 acgcgcagga gaacgcgctg gtgtcctact cgctggtgga gcggcgggtg ggcgagcgcg
     1621 cgttgtcgag ctacgtttcg gtgcacgcgg agagcggcaa ggtgtacgcg ctgcagccgc
     1681 tggaccacga ggaagtggag ctgctgcagt tccaggtgag cgcgcgggat gcgggcgtgc
     1741 cgcctctggg cagcaacgtg acgctgcagg tgttcgtgct ggacgagaac gacaacgcgc
     1801 cggcactgtt ggcgcctagg gctggcaccg ctgctggcgc agtgagtgag ctggtgccgt
     1861 ggtcggtggg tgcagggcac gtggtggcga aggtgcgcgc agtggacgct gactcaggct
     1921 acaacgcgtg gctttcgtac gagcttcagc tgggtactgg cagcgctcgc atcccgttcc
     1981 gcgtggggct atacacgggt gagatcagca cgacacgtgc cctagacgag gctgactccc
     2041 ctcgacaccg cctactcgtg ctggtgaagg accacggcga accagcgttg acagccacgg
     2101 ccaccgtgtt agtgtcgttg gtggaaagtg gccaggcacc caaggcctcg tcgcgggcgt
     2161 gggtgggcgc cgcgggctca gaggctacgc tggtggatgt caacgtgtac ctgatcatcg
     2221 ccatctgcgc ggtatccagc ctgttggtgc tcacggtgct gctgtacact gcgctgcggt
     2281 gctcggtgcc acccaccgag ggtgcgcgcg cgccaggaaa gcccacgctg gtgtgctcca
     2341 gcgccgtggg gagctggtct tactcgcagc agaggcggca gagggtgtgc tctggggagg
     2401 acccccccaa gacggacctc atggccttca gccctagctt atctcaaggt ccagactccg
     2461 cagaagagaa acagctctca gaatcagaat acgtaggaaa gccacgacag cccaaccctg
     2521 actggcgtta ctctgcctcc ctgagagcag gcatgcacag ctctgtgcac ctagaggagg
     2581 ctggcattct acgggctggt ccaggagggc ctgatcagca gtggccaaca gtatccagtg
     2641 caacaccaga accagaggca ggagaagtgt cccctccagt cggtgcgggt gtcaacagca
     2701 acagctggac ctttaaatac ggaccaggca accccaaaca atccggtccc ggtgagttgc
     2761 ccgacaaatt cattatccca ggatctcctg caatcatctc catccggcag gagcctacta
     2821 acagccaaat tgacaaaagt gacttcataa ccttcggcaa aaaggaggag accaagaaaa
     2881 agaagaaaaa gaagaagggt aacaagaccc aggagaaaaa agagaaaggg aacagcacga
     2941 ctgacaacag tgaccagtga ggtcctcaaa tggaaacaag ccacttagcc agtttttgta
     3001 ataatggcaa atctctccca tgtagcaatt ccctgctcct ttttcctatc tacatgagcc
     3061 ctcttagaga cctcagaaat ctgcagaaag ttccctgtgt ctgtctagaa cgcatttaac
     3121 aggttttgtc gtaaaagctt tactaagtct ggtgttaact ctttctctcc actctggctt
     3181 gttttcagaa cctaaaaagc agacccaagt ttcctttctc ctccgccgca aaggagaggc
     3241 ttcccagccc cgccagtgag aggttggact ctctgccctg tgctccgggg atcctgtctt
     3301 gatgacactt gcagggcagg ctgaaaagtt ttgagattga gcagcttggg agtttgtggc
     3361 cactgggtat gtgtggctac cgcgggtatg cgagtgccag atattggctg agacgagcca
     3421 gcttagacta attggtacaa ggaaggcaag aaaacaaaga caaataaaca gcggaagtta
     3481 tcagtatgga ggggaagtgt aaacttaaag ggaccagact ttctaaatct tacaactcaa
     3541 gaggtggcag ccaccctcta ggagacaaaa ctacccccac tgacaaggct ttaggagacc
     3601 ctaaagtctg ttggctgtga cgtcattata cctaaaatct gcatcatacc tgcaagccaa
     3661 cagttcagtg ttttaacaga gaaccaccct gggaaacaga agcagatctg atgtgtttcc
     3721 tatacatgtc ctgtgctcac tttattaaaa attcttttgc acacaatgtt tatgaaaagg
     3781 ccagatcctt ttccaatact tatgcaaaag caaaagaaaa ccccgacacc tcacctttcg
     3841 ctgtttgttg tttcatagat ttatttaaaa aaagagaaag tctatagcta taaatcttta
     3901 aagagaaata tgaatacaat tcccctaaac tctcctcaaa agagaattca gtctacagcc
     3961 atttaaatga tcattgctgc tacagaagtg ctttaagaga attgcctgaa acatctgtat
     4021 tatatcggcc acctgccaat cacagcttta ctctttcagg tcactctggg gctgcctctt
     4081 gcatgtatta ctaaataaaa tgatctctct ttctctctct ctctctcttt tctaagaaac
     4141 aattatgtgc actttgatac acaaccttct ctaaccaact atatatcaag acccaaaaat
     4201 tgaagaaaaa tattgttttc tcatacagtg agcagatttt tcaatctact aattctgtga
     4261 cttgtcttgg tgtgctagcc tacaccttct ctttggttta gttttccttt tctataacac
     4321 tctgaattgc taatcttact aacacctatg atgttacctg aaatcaatct cccatatgta
     4381 tgctgtatgc tatgctaaga ctcctgaaat atacttactc tgtgcttgtg tatgtgaatg
     4441 ttaatgcaac tattacctag agtgaacttt aagctttatt gttgaatgta attccattat
     4501 atttcctttt gtacacctgt gaaaaagtgg agtagtgttt ttttaaccat tgttaatcag
     4561 cttttgtgta tgaaagacac agtaaaattt ctttcttaaa tcaagatact ggtgattcaa
     4621 ggaattttat ttatggtcca gccaagagcc atctcgtgcc aagacttctg ctggcaaggg
     4681 aatggataaa gctgttttgt tctagtaaca attttggaat gaatactgac aatattccat
     4741 gagggtgtgc aagcacaaat tttaccaatc tgacctcttt gaagttgcag aatgctttga
     4801 aattctaatg gtatctgaaa tatcagctca tagaaagtaa caaaatttgc tgtcacctta
     4861 aataagacat tttaattttg ttataatgta caatttagaa gtttgattaa ttatattatc
     4921 tatttaggca ttaatataaa agaggtagga gtctgttatt taaaaaaagc attaaattta
     4981 aaaaaaaact gtcttgtcta cttttagctt cattctccca tattttgaag ggtgtgtaac
     5041 ttcagctctg caggattgca tggggtaaaa cttgttacca acacatgtga accattgcta
     5101 cattgtaggt tgtgatcatt ttgccccact gaagcccatg tatctgacct tacgtgcctt
     5161 ttgaactagg agaatcgggc taatttatta atgatgataa ttataatgta tctgtacagc
     5221 actttttaca tttgcgaagt gctttccaat ccatgttagt tactagttat tacagctgta
     5281 aggataaaac acgtcatgtg gattcatttt gaattggtgc tattggtatt tcctctgtta
     5341 ttgctaataa atgaaaatgg tggtatgaaa
//
