LOCUS       NM_018926               4777 bp    mRNA    linear   PRI 12-JUN-2024
DEFINITION  Homo sapiens protocadherin gamma subfamily B, 6 (PCDHGB6),
            transcript variant 1, mRNA.
ACCESSION   NM_018926
VERSION     NM_018926.3
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 4777)
  AUTHORS   Powrozek,T., Krawczyk,P., Kuznar-Kaminska,B., Batura-Gabryel,H. and
            Milanowski,J.
  TITLE     Analysis of RTEL1 and PCDHGB6 promoter methylation in
            circulating-free DNA of lung cancer patients using liquid biopsy: A
            pilot study
  JOURNAL   Exp Lung Res 42 (6), 307-313 (2016)
   PUBMED   27485611
  REMARK    GeneRIF: promoter methylation found in 41.4% of lung cancer
            patients and in 1.3% of healthy individuals
REFERENCE   2  (bases 1 to 4777)
  AUTHORS   Sandoval,J., Mendez-Gonzalez,J., Nadal,E., Chen,G., Carmona,F.J.,
            Sayols,S., Moran,S., Heyn,H., Vizoso,M., Gomez,A.,
            Sanchez-Cespedes,M., Assenov,Y., Muller,F., Bock,C., Taron,M.,
            Mora,J., Muscarella,L.A., Liloglou,T., Davies,M., Pollan,M.,
            Pajares,M.J., Torre,W., Montuenga,L.M., Brambilla,E., Field,J.K.,
            Roz,L., Lo Iacono,M., Scagliotti,G.V., Rosell,R., Beer,D.G. and
            Esteller,M.
  TITLE     A prognostic DNA methylation signature for stage I non-small-cell
            lung cancer
  JOURNAL   J Clin Oncol 31 (32), 4140-4147 (2013)
   PUBMED   24081945
  REMARK    GeneRIF: hypermethylation of HIST1H4F, PCDHGB6, NPBWR1, ALX1, and
            HOXA9 was significantly associated with shorter survival in stage 1
            Non-small-cell lung cancer
REFERENCE   3  (bases 1 to 4777)
  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   4  (bases 1 to 4777)
  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   5  (bases 1 to 4777)
  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   6  (bases 1 to 4777)
  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   7  (bases 1 to 4777)
  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 AC005618.1 and AC008781.7.
            
            On Feb 26, 2021 this sequence version replaced NM_018926.2.
            
            Summary: This gene is a member of the protocadherin gamma gene
            cluster, one of three related clusters tandemly linked on
            chromosome five. These gene clusters have an immunoglobulin-like
            organization, suggesting that a novel mechanism may be involved in
            their regulation and expression. The gamma gene cluster includes 22
            genes divided into 3 subfamilies. Subfamily A contains 12 genes,
            subfamily B contains 7 genes and 2 pseudogenes, and the more
            distantly related subfamily C contains 3 genes. The tandem array of
            22 large, variable region exons are followed by a constant region,
            containing 3 exons shared by all genes in the cluster. Each
            variable region exon encodes the extracellular region, which
            includes 6 cadherin ectodomains and a transmembrane region. The
            constant region exons encode the common cytoplasmic region. These
            neural cadherin-like cell adhesion proteins most likely play a
            critical role in the establishment and function of specific
            cell-cell connections in the brain. Alternative splicing has been
            described for the gamma cluster genes. [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 :: AF152335.1, SRR14038191.3218108.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1965299, SAMEA1968189
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000520790.2/ ENSP00000428603.1
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-2600              AC005618.1         119533-122132
            2601-2659           AC008781.7         156232-156290       c
            2660-2748           AC008781.7         145616-145704       c
            2749-4777           AC008781.7         138122-140150       c
FEATURES             Location/Qualifiers
     source          1..4777
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="5"
                     /map="5q31.3"
     gene            1..4777
                     /gene="PCDHGB6"
                     /gene_synonym="PCDH-GAMMA-B6"
                     /note="protocadherin gamma subfamily B, 6"
                     /db_xref="GeneID:56100"
                     /db_xref="HGNC:HGNC:8713"
                     /db_xref="MIM:606303"
     exon            1..2600
                     /gene="PCDHGB6"
                     /gene_synonym="PCDH-GAMMA-B6"
                     /inference="alignment:Splign:2.1.0"
     CDS             183..2975
                     /gene="PCDHGB6"
                     /gene_synonym="PCDH-GAMMA-B6"
                     /note="isoform 1 precursor is encoded by transcript
                     variant 1; protocadherin gamma-B6"
                     /codon_start=1
                     /product="protocadherin gamma-B6 isoform 1 precursor"
                     /protein_id="NP_061749.1"
                     /db_xref="CCDS:CCDS54929.1"
                     /db_xref="GeneID:56100"
                     /db_xref="HGNC:HGNC:8713"
                     /db_xref="MIM:606303"
                     /translation="MGGSCAQRRRAGPRQVLFPLLLPLFYPTLSEPIRYSIPEELAKG
                     SVVGNLAKDLGLSVLDVSARKLRVSAEKLHFSVDAESGDLLVKNRIDREQICKERRRC
                     ELQLEAVVENPLNIFHVIVVIEDVNDHAPQFDKKEIHLEIFESASAGTRLSLDPATDP
                     DININSIKDYKINSNPYFSLMVRVNSDGGKYPELSLEKLLDREEQRSHSLILTALDGG
                     DPPRSATAHIEISVKDTNDNPPVFSRDEYRISLSENLPPGSPVLQVTATDQDEGVNAE
                     INYYFRSTAQSTKHMFSLDEKTGMIKNNQSFDFEDVERYTMEVEAKDGGGLSTQCKVI
                     IEILDENDNSPEIIITSLSDQILENSPPGMVVALFKTRDLDFGGNGEVRCNIETDIPF
                     KIYSSSNNYYKLVTDGALDREQTPEYNVTIVATDRGKPPLSSSRSITLYVADINDNAP
                     VFDQTSYVVHVAENNPPGASIAQVSASDPDLGLNGHISYSIVASDLEPLAVSSYVSVS
                     AQSGVVFAQRAFDHEQLRAFALTLQARDHGSPTLSANVSLRVLVGDRNDNAPRVLYPA
                     LGPDGSAFFDMVPRSAEPGYLVTKVVAVDADSGHNAWLSYHVLQASEPGLFSLGLRTG
                     EVRTARALGDRDAARQRLLVAVRDGGQPPLSATATLHLVFADNLQEILPDLSDRPVLS
                     DPQAELQFYLVVALALISVLFLLAVILAIALRLRRSLSPATWDCFHPGLCVKSGPVVP
                     PNYSEGTLPYSYNLCIAHTGTKEFNFLKCSVPLHSNEDMVCSVSPGALIPPHGGEDLT
                     SHPETLTSQAPPNTDWRFSQAQRPGTSGSQNGDDTGTWPNNQFDTEMLQAMILASASE
                     AADGSSTLGGGAGTMGLSARYGPQFTLQHVPDYRQNVYIPGSNATLTNAAGKRDGKAP
                     AGGNGNKKKSGKKEKK"
     exon            2601..2659
                     /gene="PCDHGB6"
                     /gene_synonym="PCDH-GAMMA-B6"
                     /inference="alignment:Splign:2.1.0"
     exon            2660..2748
                     /gene="PCDHGB6"
                     /gene_synonym="PCDH-GAMMA-B6"
                     /inference="alignment:Splign:2.1.0"
     exon            2749..4777
                     /gene="PCDHGB6"
                     /gene_synonym="PCDH-GAMMA-B6"
                     /inference="alignment:Splign:2.1.0"
     regulatory      4756..4761
                     /regulatory_class="polyA_signal_sequence"
                     /gene="PCDHGB6"
                     /gene_synonym="PCDH-GAMMA-B6"
                     /note="hexamer: AATAAA"
     polyA_site      4777
                     /gene="PCDHGB6"
                     /gene_synonym="PCDH-GAMMA-B6"
                     /note="major polyA site"
ORIGIN      
        1 agaaagaaga aaaccagctc ccacacagag cctcccggct gcgcagacct ttcccagcac
       61 agcggattgc cagctccgag acccgggact cctcctgtcc tgggccgaat gctcttttag
      121 cgcggtagag tgcactttct ccaactggaa aagcggggac ccagcgagaa cccgagcgaa
      181 cgatgggagg gagctgcgcg cagaggcgcc gggccggccc gcggcaggtg ctatttcctt
      241 tgctgctgcc tttgttctac cccaccctga gtgagccgat ccgctactcg attccggagg
      301 agctggccaa gggctcggtg gtggggaacc tcgctaagga tctagggctc agtgtcctgg
      361 atgtgtcggc tcgcaagctg cgagtgagcg cggagaagct gcacttcagc gtagacgcgg
      421 agagcgggga cttacttgtg aagaaccgaa tagaccgtga gcaaatatgc aaagagagaa
      481 gaagatgtga gttgcaattg gaagctgtgg tggaaaatcc tttaaatatt tttcatgtca
      541 ttgtggtgat tgaggatgtt aatgaccacg cccctcaatt tgataaaaag gaaatacatt
      601 tagaaatttt cgaatctgca tccgctggta cacgactatc gcttgaccct gccacggatc
      661 ctgatataaa cataaactca attaaagatt ataagataaa ctctaatcct tatttttcat
      721 taatggttag agttaattcc gatggtggca aatacccaga gttatctctg gagaaactcc
      781 tagaccggga agaacagaga tctcatagct tgatattgac tgccttggac ggaggggacc
      841 caccaagaag tgccaccgct cacatagaaa tttctgtcaa ggataccaat gataaccccc
      901 cggttttcag cagagacgaa tatagaatta gtcttagtga aaatctgccc cctgggtccc
      961 ctgtgttgca agtgacagcc actgaccagg atgagggggt caatgctgag ataaactact
     1021 acttccgaag cactgcccag agcacaaaac atatgttctc attggatgag aaaacaggta
     1081 tgattaagaa taaccagtca tttgattttg aagatgtaga aaggtacacc atggaagtgg
     1141 aagcgaagga cggaggtggt ctctctaccc agtgtaaagt aatcatagaa atccttgatg
     1201 aaaacgacaa cagcccagaa ataatcatca cttctctctc tgatcagatt ttggagaatt
     1261 cacctccagg aatggttgtt gccctcttca aaacacggga tctggatttc ggaggaaatg
     1321 gagaagtcag gtgtaatata gaaacagaca ttccattcaa gatttattct tcttccaata
     1381 actactacaa actggtgaca gatggagccc tggaccgaga gcagacacca gaatacaatg
     1441 tcaccatcgt agccactgac aggggcaagc cgcctctttc ttccagtaga agcatcacct
     1501 tgtatgtcgc tgacatcaac gacaacgccc cagttttcga ccagacgtcc tacgtggtcc
     1561 acgtggccga gaacaacccg ccaggagcct ccattgcgca agtgagcgcc tctgacccgg
     1621 atttggggct caatggccac atctcctact ctatagtggc gagtgaccta gagcccctgg
     1681 cggtgtcgtc atacgtgtca gtgagcgcgc agagcggggt ggtgttcgcg cagcgcgcct
     1741 ttgatcacga gcagctgcgc gccttcgcgc tcacgctgca ggcccgcgac cacggctcgc
     1801 ccacgctcag cgccaacgtg agcctgcgcg tgttggtggg agaccgcaat gacaacgcac
     1861 cgcgggtgct gtacccagct ctgggtcctg acggctccgc gttcttcgat atggtacctc
     1921 gctctgcaga gcccggctac ctagtgacta aggtggtagc ggtggacgcc gactcgggac
     1981 acaacgcctg gctgtcctac cacgtgctgc aggccagtga gcccggactc ttcagcctgg
     2041 ggctgcgcac tggggaggtg cgcacggctc gagccttagg cgacagggac gcagcccgcc
     2101 agcgcctgct ggtcgctgtg cgtgacggtg gacagccgcc actctctgcc accgccacgc
     2161 ttcatctggt cttcgcagac aacttgcaag agatactgcc agacctcagc gaccgccctg
     2221 tactctctga cccccaggct gaactgcagt tttacctggt ggtggccttg gccttaatct
     2281 cagtgctctt cctcctcgcc gtgattctgg ccattgcctt gcgcctgcga cgctctctca
     2341 gccctgctac ttgggactgc ttccatcctg gtctctgtgt caagtctgga cctgtagttc
     2401 cccccaacta cagtgagggg actttgcctt attcttataa tctgtgcatt gcacatacgg
     2461 gtacaaaaga gtttaatttc ctaaaatgca gtgtgcccct acattccaat gaagacatgg
     2521 tttgcagtgt ttctcctgga gccttaattc cacctcatgg tggggaggat ttgacttcac
     2581 atcctgagac tctgacttcg caagccccgc ccaacacgga ctggcgtttc tctcaggccc
     2641 agagacccgg caccagcggc tcccaaaatg gcgatgacac cggcacctgg cccaacaacc
     2701 agtttgacac agagatgctg caagccatga tcttggcgtc cgccagtgaa gctgctgatg
     2761 ggagctccac cctgggaggg ggtgccggca ccatgggatt gagcgcccgc tacggacccc
     2821 agttcaccct gcagcacgtg cccgactacc gccagaatgt ctacatccca ggcagcaatg
     2881 ccacactgac caacgcagct ggcaagcggg atggcaaggc cccagcaggt ggcaatggca
     2941 acaagaagaa gtcgggcaag aaggagaaga agtaacatgg aggccaggcc aagagccaca
     3001 gggcggcctc tccccaacca gcccagcttc tccttacctg cacccaggcc tcagagtttc
     3061 agggctaacc cccagaatac tggtaggggc caaggccatg ctccccttgg gaaacagaaa
     3121 caagtgccca gtcagcacct accccttccc ccccaggggg ttgaatatgc aaaagcagtt
     3181 ccgctgggaa cccccatcca atcaactgct gtacccatgg gggtagtggg gttactgtag
     3241 acaccaagaa ccatttgcca caccccgttt agttacagct gaactcctcc atcttccaaa
     3301 tcaatcaggc ccatccatcc catgcctccc tcctccccac cccactccaa cagttcctct
     3361 ttcccgagta aggtggttgg ggtgttgaag taccaagtaa cctacaagcc tcctagttct
     3421 gaaaagttgg aagggcatca tgacctcttg gcctctcctt tgattctcaa tcttccccca
     3481 aagcatggtt tggtgccagc cccttcacct ccttccagag cccaagatca atgctcaagt
     3541 tttggaggac atgatcacca tccccatggt actgatgctt gctggattta gggagggcat
     3601 tttgctacca agcctcttcc caacgccctg gggaccagtc ttctgttttg tttttcattg
     3661 tttgacgttt ccactgcatg ccttgacttc ccccacctcc tcctcaaaca agagactcca
     3721 ctgcatgttc caagacagta tggggtggta agataaggaa gggaagtgtg tggatgtgga
     3781 tggtgggggc atggacaaag cttgacacat caagttatca aggccttgga ggaggctctg
     3841 tatgtcctca ggggactgac aacatcctcc agattccagc cataaaccaa taactaggct
     3901 ggacccttcc cactacataa tagggctcag cccaggcagc cagctttggg ctgagctaac
     3961 aggaccaatg gattaaactg gcatttcagt ccaaggaagc tcgaagcagg tttaggacca
     4021 ggtccccttg agaggtcaga ggggcctctg tgggtgctgg gtactccaga ggtgccactg
     4081 gtggaagggt cagcggagcc ccagcaggaa gggtgggcca gccaggccat tcttagtccc
     4141 tgggttgggg aggcagggag ctagggcagg gaccaaatga acagaaagtc tcagcccagg
     4201 atggggcttc ttcaacaggg cccctgccct cctgaagcct cagtccttca ccttgccagg
     4261 tgccgtttct cttccgtgaa ggccactgcc caggtcccca gtgcgccccc tagtggccat
     4321 agcctggtta aagttcccca gtgcctcctt gtgcatagac cttcttctcc cacccccttc
     4381 tgcccctggg tccccggcca tccagcgggg ctgccagaga accccagacc tgcccttaca
     4441 gtagtgtagc gccccctccc tctttcggct ggtgtagaat agccagtagt gtagtgcggt
     4501 gtgcttttac gtgatggcgg gtgggcagcg ggcggcgggc tccgcgcagc cgtctgtcct
     4561 tgatctgccc gcggcggccc gtgttgtgtt ttgtgctgtg tccacgcgct aaggcgaccc
     4621 cctcccccgt actgacttct cctataagcg cttctcttcg catagtcacg tagctcccac
     4681 cccaccctct tcctgtgtct cacgcaagtt ttatactcta atatttatat ggcttttttt
     4741 cttcgacaaa aaaataataa aacgtttctt ctgaaaa
//
