LOCUS       NM_018937               3355 bp    mRNA    linear   PRI 04-MAR-2025
DEFINITION  Homo sapiens protocadherin beta 3 (PCDHB3), mRNA.
ACCESSION   NM_018937
VERSION     NM_018937.5
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 3355)
  AUTHORS   Luck,K., Kim,D.K., Lambourne,L., Spirohn,K., Begg,B.E., Bian,W.,
            Brignall,R., Cafarelli,T., Campos-Laborie,F.J., Charloteaux,B.,
            Choi,D., Cote,A.G., Daley,M., Deimling,S., Desbuleux,A., Dricot,A.,
            Gebbia,M., Hardy,M.F., Kishore,N., Knapp,J.J., Kovacs,I.A.,
            Lemmens,I., Mee,M.W., Mellor,J.C., Pollis,C., Pons,C.,
            Richardson,A.D., Schlabach,S., Teeking,B., Yadav,A., Babor,M.,
            Balcha,D., Basha,O., Bowman-Colin,C., Chin,S.F., Choi,S.G.,
            Colabella,C., Coppin,G., D'Amata,C., De Ridder,D., De Rouck,S.,
            Duran-Frigola,M., Ennajdaoui,H., Goebels,F., Goehring,L., Gopal,A.,
            Haddad,G., Hatchi,E., Helmy,M., Jacob,Y., Kassa,Y., Landini,S.,
            Li,R., van Lieshout,N., MacWilliams,A., Markey,D., Paulson,J.N.,
            Rangarajan,S., Rasla,J., Rayhan,A., Rolland,T., San-Miguel,A.,
            Shen,Y., Sheykhkarimli,D., Sheynkman,G.M., Simonovsky,E., Tasan,M.,
            Tejeda,A., Tropepe,V., Twizere,J.C., Wang,Y., Weatheritt,R.J.,
            Weile,J., Xia,Y., Yang,X., Yeger-Lotem,E., Zhong,Q., Aloy,P.,
            Bader,G.D., De Las Rivas,J., Gaudet,S., Hao,T., Rak,J.,
            Tavernier,J., Hill,D.E., Vidal,M., Roth,F.P. and Calderwood,M.A.
  TITLE     A reference map of the human binary protein interactome
  JOURNAL   Nature 580 (7803), 402-408 (2020)
   PUBMED   32296183
REFERENCE   2  (bases 1 to 3355)
  AUTHORS   Ye,W., Ling,S., Liu,R.Y., Pan,Z.Z., Wang,G., Gao,S., Wu,J., Cao,L.,
            Dong,L., Li,Y., Zhou,Y., Du,W., Meng,X., Chen,J., Guan,X., He,Y.,
            Pan,C., Zheng,X.S., Lu,X., Chen,S. and Huang,W.
  TITLE     Exome sequencing reveals the genetic landscape and frequent
            inactivation of PCDHB3 in Chinese rectal cancers
  JOURNAL   J Pathol 245 (2), 222-234 (2018)
   PUBMED   29537081
  REMARK    GeneRIF: PCDHB3 may function as a novel tumor suppressor in
            colorectal via inhibition of the NF-kappaB pathway, and its
            expression and localization may serve as prognostic markers for
            advanced CRc.
REFERENCE   3  (bases 1 to 3355)
  AUTHORS   Frank,M. and Kemler,R.
  TITLE     Protocadherins
  JOURNAL   Curr Opin Cell Biol 14 (5), 557-562 (2002)
   PUBMED   12231349
  REMARK    Review article
REFERENCE   4  (bases 1 to 3355)
  AUTHORS   Vanhalst,K., Kools,P., Vanden Eynde,E. and van Roy,F.
  TITLE     The human and murine protocadherin-beta one-exon gene families show
            high evolutionary conservation, despite the difference in gene
            number
  JOURNAL   FEBS Lett 495 (1-2), 120-125 (2001)
   PUBMED   11322959
REFERENCE   5  (bases 1 to 3355)
  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 3355)
  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 3355)
  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 3355)
  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 3355)
  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 AC244517.2.
            
            On May 21, 2020 this sequence version replaced NM_018937.4.
            
            Summary: This gene is a member of the protocadherin beta gene
            cluster, one of three related gene clusters tandemly linked on
            chromosome five. The gene clusters demonstrate an unusual genomic
            organization similar to that of B-cell and T-cell receptor gene
            clusters. The beta cluster contains 16 genes and 3 pseudogenes,
            each encoding 6 extracellular cadherin domains and a cytoplasmic
            tail that deviates from others in the cadherin superfamily. The
            extracellular domains interact in a homophilic manner to specify
            differential cell-cell connections. Unlike the alpha and gamma
            clusters, the transcripts from these genes are made up of only one
            large exon, not sharing common 3' exons as expected. These neural
            cadherin-like cell adhesion proteins are integral plasma membrane
            proteins. Their specific functions are unknown but they most likely
            play a critical role in the establishment and function of specific
            cell-cell neural connections. [provided by RefSeq, Jul 2008].
            
            ##Evidence-Data-START##
            Transcript is intronless :: AK313451.1, AF217755.1 [ECO:0000345]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000231130.3/ ENSP00000231130.2
            RefSeq Select criteria :: based on single protein-coding transcript
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-3355              AC244517.2         26324-29678
FEATURES             Location/Qualifiers
     source          1..3355
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="5"
                     /map="5q31.3"
     gene            1..3355
                     /gene="PCDHB3"
                     /gene_synonym="PCDH-BETA3"
                     /note="protocadherin beta 3"
                     /db_xref="GeneID:56132"
                     /db_xref="HGNC:HGNC:8688"
                     /db_xref="MIM:606329"
     exon            1..3355
                     /gene="PCDHB3"
                     /gene_synonym="PCDH-BETA3"
                     /inference="alignment:Splign:2.1.0"
     CDS             178..2568
                     /gene="PCDHB3"
                     /gene_synonym="PCDH-BETA3"
                     /codon_start=1
                     /product="protocadherin beta-3 precursor"
                     /protein_id="NP_061760.2"
                     /db_xref="CCDS:CCDS4245.1"
                     /db_xref="GeneID:56132"
                     /db_xref="HGNC:HGNC:8688"
                     /db_xref="MIM:606329"
                     /translation="MEAGGERFLRQRQVLLLFVFLGGSLAGSESRRYSVAEEKEKGFL
                     IANLAKDLGLRVEELAARGAQVVSKGNKQHFQLSHQTGDLLLNEKLDREELCGPTEPC
                     ILHFQILLQNPLQFVTNELRIIDVNDHSPVFFENEMHLKILESTLPGTVIPLGNAEDL
                     DVGRNSLQNYTITPNSHFHVLTRSRRDGRKYPELVLDKALDPEEQPELSLTLTALDGG
                     SPPRSGTAQINIQVLDINDNAPEFAQPLYEVAVLENTPVNSVIVTVSASDLDTGSFGT
                     ISYAFFHASEEIRKTFQLNPITGDMQLVKYLNFEAINSYEVDIEAKDGGGLSGKSTVI
                     VQVVDVNDNPPELTLSSVNSPIPENSGETVLAVFSVSDLDSGDNGRVMCSIENNLPFF
                     LKPSVENFYTLVSEGALDRETRSEYNITITITDLGTPRLKTKYNITVLVSDVNDNAPA
                     FTQISYTLFVRENNSPALHIGSVSATDRDSGTNAQVTYSLLPPQDPHLPLSSLVSINA
                     DNGHLFALRSLDYEALQAFEFRVGATDRGSPALSSEALVRVLVLDANDNSPFVLYPLQ
                     NGSAPCTELVPRAAEPGYLVTKVVAVDGDSGQNAWLSYQLLKATEPGLFGVWAHNGEV
                     RTARLLSERDAAKHRLVVLVKDNGEPPRSATATLHVLLVDGFSQPYLPLPEAAPAQAQ
                     ADLLTVYLVVALASVSSLFLFSVLLFVAVRLCRRSRAASVGRCSVPEGPFPGQMVDVS
                     GTGTLSQSYQYEVCLTGGSGTNEFKFLKPIIPNFVAQGAERVSEANPSFRKSFEFS"
     regulatory      3332..3337
                     /regulatory_class="polyA_signal_sequence"
                     /gene="PCDHB3"
                     /gene_synonym="PCDH-BETA3"
                     /note="hexamer: ATTAAA"
     polyA_site      3355
                     /gene="PCDHB3"
                     /gene_synonym="PCDH-BETA3"
                     /note="major polyA site"
ORIGIN      
        1 agtgtggtaa accagcggtt gagagcccag gcagattttt gagccagcaa gtctgagcct
       61 ctggaaaggc ttattcacta ggccgtctac aaaggttgtg gggcaaaaga ctgtttccca
      121 gctctgtctg aggttcagct tggcgacatt ccctggaaga gcgtgacgga aagtgcaatg
      181 gaggcgggag gagagcgatt tcttagacaa aggcaagtct tgcttctctt tgtttttctg
      241 ggagggtctc tggctgggtc cgagtcaaga cgctattctg tggctgagga aaaagagaag
      301 ggctttttaa tagccaacct agcaaaggat ctgggactaa gggtagagga actggccgcg
      361 aggggggccc aagttgtgtc caaagggaac aaacagcatt ttcagctcag tcatcagaca
      421 ggtgatttgc tcctgaatga gaaattggac cgggaggagc tatgcggccc cacagaacca
      481 tgcatactac attttcagat attactgcaa aaccctttgc aattcgttac aaacgagctc
      541 cgtatcatag atgtaaatga ccattctccg gtattctttg aaaatgaaat gcatctgaaa
      601 atcctagaaa gcactctgcc aggaacagta attcctttgg gaaatgctga ggacttggat
      661 gtgggaagaa acagcctcca aaactacact atcactccga attcccactt ccacgtactc
      721 actcgcagtc gtagggacgg aaggaagtac ccggaactag tactggataa agcgctcgat
      781 ccggaggagc agccggaact cagcttaacg ctcaccgcgc tggacggcgg ctctccccct
      841 cggtctggga cagcccagat aaacatccag gtcttagata taaacgacaa tgcaccagaa
      901 tttgcacagc cgctctatga ggttgcagtt ctagagaata cccccgttaa ctctgtcatt
      961 gtcactgtct cggcttctga cttagataca ggaagttttg ggacaatatc atatgcattt
     1021 tttcatgctt ctgaagaaat tcgcaaaact tttcagctaa atccaattac tggtgatatg
     1081 caactggtca aatatttgaa ttttgaagcg attaatagtt atgaagtcga catcgaggcc
     1141 aaggatggcg gaggcctatc cggaaagtct acagtcatag tccaggtggt tgatgtcaac
     1201 gacaacccac cggaactgac cttgtcttca gtaaacagcc ctattcctga gaactcggga
     1261 gagactgtac tggctgtttt cagtgtttct gatctagact ctggagacaa cggaagagtg
     1321 atgtgttcca ttgagaacaa tctccccttc ttcctgaaac catctgtaga gaatttttac
     1381 accctagtgt cagaaggcgc gctggacaga gagaccagat ccgagtacaa cattaccatc
     1441 actatcactg acctggggac acccaggctg aaaaccaagt acaacataac cgtgctggtc
     1501 tccgacgtca atgacaacgc ccccgccttc acccaaatct cctacaccct gttcgtccgc
     1561 gagaacaaca gccccgccct gcacatcggc agtgtcagcg ccacagacag agactcaggc
     1621 accaacgccc aggtaaccta ctcgctgctg ccgccccagg acccgcacct gcccctctct
     1681 tccctggtct ccatcaacgc ggacaacggc cacctgtttg ccctcaggtc gctggactac
     1741 gaggccctgc aggcgttcga gttccgcgtg ggcgccacag accgtggctc cccggctttg
     1801 agcagcgagg cgctggtgcg cgtgctggtg ctggacgcca acgacaactc gcccttcgtg
     1861 ctgtacccgc tgcagaacgg ctccgcgccc tgcaccgagc tggtgccccg ggcggctgag
     1921 ccgggctacc tggtgaccaa ggtggtggcg gtggacggcg actcgggcca gaacgcctgg
     1981 ctgtcgtacc agctgctcaa ggccacggag cccgggctgt tcggcgtgtg ggcgcacaat
     2041 ggcgaagtgc gcaccgccag gctgctgagc gagcgcgacg cggccaagca caggctggtg
     2101 gtgctggtca aggacaatgg cgagcctccg cgctcggcca ccgccacgct gcatgtgctc
     2161 ctggtggacg gcttctccca gccctacctg cctctcccgg aggcggcacc ggcccaggcc
     2221 caggccgact tgctcaccgt ctacctggtg gtggcattgg cctcggtgtc ttcgctcttc
     2281 ctcttttcgg tgctcctgtt cgtggcggtg cggctgtgca ggaggagcag ggcggcctcg
     2341 gtgggtcgct gctcggtgcc cgagggcccc tttccagggc agatggtgga cgtgagcggc
     2401 accgggaccc tgtcccagag ctaccagtac gaggtgtgtc tgactggagg ctccgggaca
     2461 aatgagttca agttcctgaa gccaattatc cccaacttcg ttgctcaggg tgcagagagg
     2521 gttagcgagg caaatcccag tttcaggaag agctttgaat tcagttaagt gttaataagg
     2581 atctactgag cctcgtctta gttaatctgt ggaaagtcct tttttactgc tttgtccatt
     2641 ggagaggtct tttttggtct ggttcaaggc aagtagcaag aatagagcaa aatatcaaat
     2701 ccagggatgg cttaggtttc attaacagta ctggaaagta gttgtgtggc tctgaatgtt
     2761 ttgtatttca atcgagaatc cttagtcgat agaacatttt gtttatatat tgattctact
     2821 ttttctgtag ttaatccttg catattctcc tttcatcctg gcttgccaac gcagtcttaa
     2881 ttccgccttt tttttttcta atggggagca aaaagaaatt cactgtcttt taatagtgat
     2941 ttcaaatagc ttattaaaat aactccattc aaattttaca ttataaagca atgtagagag
     3001 agttccaaac caccaatttt ataatttccc ttgttgaata tattcatata atgtgttcta
     3061 taatatgccc aaagcagctt tgtctatagt taacaaagtt ttaaggatag acaagaatgt
     3121 gttttcttta ataaatagta atatatcatc tttttaggga tatagtactc aaatgaaagt
     3181 aatttagttc attttctgtg ttgacatttg caattaatat ttcaatattt tatgtgctta
     3241 tattggccaa aatatggaca caaatataga ctaatatggg taattaccct ttggtttatc
     3301 taaagtgtgt tcatgatgac tgaggaaaaa aattaaacct atgccattta aaaaa
//
