LOCUS       NM_018903               5401 bp    mRNA    linear   PRI 04-APR-2024
DEFINITION  Homo sapiens protocadherin alpha 12 (PCDHA12), transcript variant
            1, mRNA.
ACCESSION   NM_018903
VERSION     NM_018903.4
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 5401)
  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 5401)
  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 5401)
  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 5401)
  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 5401)
  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 5401)
  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 5401)
  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 5401)
  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 5401)
  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
REFERENCE   10 (bases 1 to 5401)
  AUTHORS   Martineau,J., Barthelemy,C., Jouve,J., Muh,J.P. and Lelord,G.
  TITLE     Monoamines (serotonin and catecholamines) and their derivatives in
            infantile autism: age-related changes and drug effects
  JOURNAL   Dev Med Child Neurol 34 (7), 593-603 (1992)
   PUBMED   1380929
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from DA740785.1, AF152308.1 and
            AC010223.6.
            
            On Nov 23, 2018 this sequence version replaced NM_018903.3.
            
            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).
            
            ##Evidence-Data-START##
            Transcript exon combination :: AF152308.1, SRR1660807.238711.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1968189, SAMEA1968968
                                           [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               :: ENST00000398631.3/
                                                ENSP00000381628.2
            RefSeq Select criteria           :: based on conservation,
                                                expression, longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-165               DA740785.1         7-171
            166-5398            AF152308.1         1-5233
            5399-5401           AC010223.6         50266-50268         c
FEATURES             Location/Qualifiers
     source          1..5401
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="5"
                     /map="5q31.3"
     gene            1..5401
                     /gene="PCDHA12"
                     /gene_synonym="PCDH-ALPHA12"
                     /note="protocadherin alpha 12"
                     /db_xref="GeneID:56137"
                     /db_xref="HGNC:HGNC:8666"
                     /db_xref="MIM:606318"
     exon            1..2532
                     /gene="PCDHA12"
                     /gene_synonym="PCDH-ALPHA12"
                     /inference="alignment:Splign:2.1.0"
     CDS             166..2991
                     /gene="PCDHA12"
                     /gene_synonym="PCDH-ALPHA12"
                     /note="isoform 1 precursor is encoded by transcript
                     variant 1; KIAA0345-like 2; PCDH-alpha-12"
                     /codon_start=1
                     /product="protocadherin alpha-12 isoform 1 precursor"
                     /protein_id="NP_061726.1"
                     /db_xref="CCDS:CCDS47285.1"
                     /db_xref="GeneID:56137"
                     /db_xref="HGNC:HGNC:8666"
                     /db_xref="MIM:606318"
                     /translation="MVIIGPRGPGSQRLLLSLLLLAAWEVGSGQLHYSVYEEAKHGTF
                     VGRIAQDLGLELAELVPRLFRVASKRHGDLLEVNLQNGILFVNSRIDREKLCGRSAEC
                     SIHLEVIVDRPLQVFHVDVEVKDINDNPPVFREREQKVPVSESAPLDSHFPLEGASDA
                     DIGVNSLLTYALSLNENFELKIKTKKDKSILPELVLRKLLDREQTPKLNLLLMVIDGG
                     KPELTGSVQIQITVLDVNDNGPAFDKPSYKVVLSENVQNDTRVIQLNASDPDEGLNGE
                     ISYGIKMILPVSEKCMFSINPDTGEIRIYGELDFEENNAYEIQVNAIDKGIPSMAGHS
                     MVLVEVLDVNDNVPEVMVTSLSLPVQEDAQVGTVIALISVSDRDSGANGQVICSLTPH
                     VPFKLVSTYKNYYSLVLDSALDRESVSAYELVVTARDGGSPSLWATARVSVEVADVND
                     NAPAFAQPEYTVFVKENNPPGCHIFTVSAWDADAQKNALVSYSLVERRVGEHALSSYV
                     SVHAESGKVYALQPLDHEELELLQFQVSARDAGVPPLGSNVTLQVFVLDENDNAPALL
                     ATPAGSAGGAVSELVPRSVGAGHVVAKVRAVDADSGYNAWLSYELQPAAVGAHIPFHV
                     GLYTGEISTTRILDEADAPRHRLLVLVKDHGEPALTSTATVLVSLVENGQAPKTSSRA
                     SVGAVDPEAALVDINVYLIIAICAVSSLLVLTLLLYTALRCSAPPTVSRCAPGKPTLV
                     CSSAVGSWSYSQQRRQRVCSAESPPKTDLMAFSPSLQLSREDCLNPPSEPRQPNPDWR
                     YSASLRAGMHSSVHLEEAGILRAGPGGPDQQWPTVSSATPEPEAGEVSPPVGAGVNSN
                     SWTFKYGPGNPKQSGPGELPDKFIIPGSPAIISIRQEPTNSQIDKSDFITFGKKEETK
                     KKKKKKKGNKTQEKKEKGNSTTDNSDQ"
     exon            2533..2591
                     /gene="PCDHA12"
                     /gene_synonym="PCDH-ALPHA12"
                     /inference="alignment:Splign:2.1.0"
     exon            2592..2680
                     /gene="PCDHA12"
                     /gene_synonym="PCDH-ALPHA12"
                     /inference="alignment:Splign:2.1.0"
     exon            2681..5401
                     /gene="PCDHA12"
                     /gene_synonym="PCDH-ALPHA12"
                     /inference="alignment:Splign:2.1.0"
     regulatory      4612..4617
                     /regulatory_class="polyA_signal_sequence"
                     /gene="PCDHA12"
                     /gene_synonym="PCDH-ALPHA12"
                     /note="hexamer: AGTAAA"
     polyA_site      4635
                     /gene="PCDHA12"
                     /gene_synonym="PCDH-ALPHA12"
     regulatory      5381..5386
                     /regulatory_class="polyA_signal_sequence"
                     /gene="PCDHA12"
                     /gene_synonym="PCDH-ALPHA12"
                     /note="hexamer: AATGAA"
     polyA_site      5401
                     /gene="PCDHA12"
                     /gene_synonym="PCDH-ALPHA12"
                     /note="major polyA site"
ORIGIN      
        1 acattccaat cattcacgga ataggatcga ctccataatg actgtgatgc tggaaaaaat
       61 ttactaaata tgtacttaca gaaaagggtg actgctcata aaatacctca ggcaagcgat
      121 cccttaaaac tgattgtccc aactcagagg ccctcatttt ctgcaatggt gattatcgga
      181 ccaagaggcc cgggatccca gcgtctgctg ctctcgcttc tgctccttgc agcctgggag
      241 gtggggagcg gccagctcca ctactccgtc tacgaggagg ccaaacacgg caccttcgtg
      301 ggccgcatcg ctcaggacct ggggctggag ctggcggagc tggtgccgcg cctgttccgg
      361 gtggcgtcca aaagacacgg ggaccttctg gaggtaaatc tgcagaatgg cattttgttt
      421 gtgaattctc ggatcgaccg cgagaagctg tgcgggcgga gcgcggagtg cagtatccac
      481 ctggaggtga tcgtggacag gccgctgcag gttttccatg tggacgtgga ggtgaaggac
      541 attaacgaca acccgccggt gttcagagaa agggaacaaa aggtacctgt ttctgaatct
      601 gcgcctctgg actctcattt tcctctagag ggcgcttctg atgcggatat cggcgtaaac
      661 tctcttttga cctatgcgtt aagtctaaat gagaattttg agcttaaaat aaaaacaaaa
      721 aaagataaaa gtatattgcc tgaattagtt cttcggaagt tattggacag agagcaaacg
      781 ccaaaactca atttattgct gatggtaatc gatggcggta aaccagaact aacagggtct
      841 gtccagattc aaataaccgt cctggatgtg aatgacaatg gtccggcgtt tgataagccc
      901 agctataaag tagtgttgtc tgaaaatgtc caaaacgaca caagagtgat ccaactaaat
      961 gcttccgatc cagacgaagg acttaatgga gaaatttcct atgggatcaa aatgattttg
     1021 ccagtgagtg agaaatgtat gttttcaata aatccagaca caggtgaaat tagaatttat
     1081 ggtgaactgg attttgaaga gaataatgcc tatgaaattc aggttaacgc cattgataaa
     1141 gggattcctt ccatggcagg tcacagcatg gtcctggtgg aagttctgga cgtgaatgac
     1201 aatgtccctg aagtaatggt tacttcactg tcgctccctg tgcaagagga tgctcaggtg
     1261 ggtaccgtca ttgccctgat tagcgtgtcg gatcgtgact ctggagccaa tggacaggtc
     1321 atctgctcac tgacacctca tgttcccttc aagctggtgt ccacctacaa gaattactac
     1381 tcgttggtgc tggacagcgc cctggaccgc gagagcgtgt cggcctatga gctggtggtg
     1441 actgcgcggg atgggggctc gccttcgctg tgggccacgg ctagagtgtc cgtggaggtg
     1501 gccgacgtga acgacaatgc gcctgcgttc gcgcagcccg agtacacagt gttcgtgaag
     1561 gagaacaacc cgccgggctg ccacatcttc acggtgtcgg catgggacgc ggacgcgcag
     1621 aagaacgcgc tggtgtccta ctcgctggtg gagcggcggg tgggcgagca cgcactgtcg
     1681 agctacgtgt cggtgcacgc ggagagcggc aaggtgtacg cgctgcagcc gctagaccac
     1741 gaggagctgg agctgctgca gttccaggtg agcgcgcgcg acgccggcgt gccgcctctg
     1801 ggcagcaacg tgacgctgca ggtgttcgtg ctggacgaga acgacaacgc gccggcactg
     1861 ctggcgactc cggctggcag cgcaggaggc gcagttagcg agttggtacc gcggtcggtg
     1921 ggtgcgggcc acgtggtggc gaaagtgcgc gcggtggacg ctgactccgg ctataacgct
     1981 tggctgtcct acgagttgca accggcggcg gtcggcgcgc acatcccgtt ccacgtgggg
     2041 ctgtacactg gcgagatcag cacgacacgc atcctggatg aggcggacgc tccgcgccac
     2101 cgcctgctgg tgctggtgaa ggaccacggt gagcccgcgc tgacgtccac ggccacggtg
     2161 ctggtgtcgc tggtggagaa cggccaggcc ccaaagacgt cgtcgcgggc ctcagtgggc
     2221 gctgtggatc ccgaagcggc tctggtggat attaacgtgt acctcatcat cgccatctgt
     2281 gcggtgtcca gcctgctggt gctcacgctg ctgctgtaca ctgcgctgcg ttgctcagcg
     2341 ccgcccaccg tgagccggtg cgcgccgggc aagcccacgc tggtgtgctc cagcgccgtg
     2401 gggagttggt cttactcgca gcagaggagg cagagggtgt gctctgcaga gagcccgccc
     2461 aagacggacc tcatggcctt cagcccaagc cttcagctgt ctcgagaaga ttgtttaaat
     2521 cctcccagtg aaccacgaca gcccaaccct gactggcgtt actctgcctc cctgagagca
     2581 ggcatgcaca gctctgtgca cctagaggag gctggcattc tacgggctgg tccaggaggg
     2641 cctgatcagc agtggccaac agtatccagt gcaacaccag aaccagaggc aggagaagtg
     2701 tcccctccag tcggtgcggg tgtcaacagc aacagctgga cctttaaata cggaccaggc
     2761 aaccccaaac aatccggtcc cggtgagttg cccgacaaat tcattatccc aggatctcct
     2821 gcaatcatct ccatccggca ggagcctact aacagccaaa ttgacaaaag tgacttcata
     2881 accttcggca aaaaggagga gaccaagaaa aagaagaaaa agaagaaggg taacaagacc
     2941 caggagaaaa aagagaaagg gaacagcacg actgacaaca gtgaccagtg aggtcctcaa
     3001 atggaaacaa gccacttagc cagtttttgt aataatggca aatctctccc atgtagcaat
     3061 tccctgctcc tttttcctat ctacatgagc cctcttagag acctcagaaa tctgcagaaa
     3121 gttccctgtg tctgtctaga acgcatttaa caggttttgt cgtaaaagct ttactaagtc
     3181 tggtgttaac tctttctctc cactctggct tgttttcaga acctaaaaag cagacccaag
     3241 tttcctttct cctccgccgc aaaggagagg cttcccagcc ccgccagtga gaggttggac
     3301 tctctgccct gtgctccggg gatcctgtct tgatgacact tgcagggcag gctgaaaagt
     3361 tttgagattg agcagcttgg gagtttgtgg ccactgggta tgtgtggcta ccgcgggtat
     3421 gcgagtgcca gatattggct gagacgagcc agcttagact aattggtaca aggaaggcaa
     3481 gaaaacaaag acaaataaac agcggaagtt atcagtatgg aggggaagtg taaacttaaa
     3541 gggaccagac tttctaaatc ttacaactca agaggtggca gccaccctct aggagacaaa
     3601 actaccccca ctgacaaggc tttaggagac cctaaagtct gttggctgtg acgtcattat
     3661 acctaaaatc tgcatcatac ctgcaagcca acagttcagt gttttaacag agaaccaccc
     3721 tgggaaacag aagcagatct gatgtgtttc ctatacatgt cctgtgctca ctttattaaa
     3781 aattcttttg cacacaatgt ttatgaaaag gccagatcct tttccaatac ttatgcaaaa
     3841 gcaaaagaaa accccgacac ctcacctttc gctgtttgtt gtttcataga tttatttaaa
     3901 aaaagagaaa gtctatagct ataaatcttt aaagagaaat atgaatacaa ttcccctaaa
     3961 ctctcctcaa aagagaattc agtctacagc catttaaatg atcattgctg ctacagaagt
     4021 gctttaagag aattgcctga aacatctgta ttatatcggc cacctgccaa tcacagcttt
     4081 actctttcag gtcactctgg ggctgcctct tgcatgtatt actaaataaa atgatctctc
     4141 tttctctctc tctctctctt ttctaagaaa caattatgtg cactttgata cacaaccttc
     4201 tctaaccaac tatatatcaa gacccaaaaa ttgaagaaaa atattgtttt ctcatacagt
     4261 gagcagattt ttcaatctac taattctgtg acttgtcttg gtgtgctagc ctacaccttc
     4321 tctttggttt agttttcctt ttctataaca ctctgaattg ctaatcttac taacacctat
     4381 gatgttacct gaaatcaatc tcccatatgt atgctgtatg ctatgctaag actcctgaaa
     4441 tatacttact ctgtgcttgt gtatgtgaat gttaatgcaa ctattaccta gagtgaactt
     4501 taagctttat tgttgaatgt aattccatta tatttccttt tgtacacctg tgaaaaagtg
     4561 gagtagtgtt tttttaacca ttgttaatca gcttttgtgt atgaaagaca cagtaaaatt
     4621 tctttcttaa atcaagatac tggtgattca aggaatttta tttatggtcc agccaagagc
     4681 catctcgtgc caagacttct gctggcaagg gaatggataa agctgttttg ttctagtaac
     4741 aattttggaa tgaatactga caatattcca tgagggtgtg caagcacaaa ttttaccaat
     4801 ctgacctctt tgaagttgca gaatgctttg aaattctaat ggtatctgaa atatcagctc
     4861 atagaaagta acaaaatttg ctgtcacctt aaataagaca ttttaatttt gttataatgt
     4921 acaatttaga agtttgatta attatattat ctatttaggc attaatataa aagaggtagg
     4981 agtctgttat ttaaaaaaag cattaaattt aaaaaaaaac tgtcttgtct acttttagct
     5041 tcattctccc atattttgaa gggtgtgtaa cttcagctct gcaggattgc atggggtaaa
     5101 acttgttacc aacacatgtg aaccattgct acattgtagg ttgtgatcat tttgccccac
     5161 tgaagcccat gtatctgacc ttacgtgcct tttgaactag gagaatcggg ctaatttatt
     5221 aatgatgata attataatgt atctgtacag cactttttac atttgcgaag tgctttccaa
     5281 tccatgttag ttactagtta ttacagctgt aaggataaaa cacgtcatgt ggattcattt
     5341 tgaattggtg ctattggtat ttcctctgtt attgctaata aatgaaaatg gtggtatgaa
     5401 a
//
