LOCUS       NM_022843               5105 bp    mRNA    linear   PRI 12-JUN-2024
DEFINITION  Homo sapiens protocadherin 20 (PCDH20), mRNA.
ACCESSION   NM_022843
VERSION     NM_022843.4
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 5105)
  AUTHORS   Huang,S., Xie,Z., Han,J., Wang,H., Yang,G., Li,M., Zhou,G.,
            Wang,Y., Li,L., Li,L., Zeng,Z., Yu,J., Chen,M. and Zhang,S.
  TITLE     Protocadherin 20 maintains intestinal barrier function to protect
            against Crohn's disease by targeting ATF6
  JOURNAL   Genome Biol 24 (1), 159 (2023)
   PUBMED   37407995
  REMARK    GeneRIF: Protocadherin 20 maintains intestinal barrier function to
            protect against Crohn's disease by targeting ATF6.
            Publication Status: Online-Only
REFERENCE   2  (bases 1 to 5105)
  AUTHORS   Jun,L., Chen,W., Han,L., Yanmin,L., Qinglei,Z. and Pengfei,Z.
  TITLE     Protocadherin 20 promotes ferroptosis by suppressing the expression
            of Sirtuin 1 and promoting the acetylation of nuclear factor
            erythroid 2-related factor 2 in hepatocellular carcinoma
  JOURNAL   Int J Biochem Cell Biol 156, 106363 (2023)
   PUBMED   36641129
  REMARK    GeneRIF: Protocadherin 20 promotes ferroptosis by suppressing the
            expression of Sirtuin 1 and promoting the acetylation of nuclear
            factor erythroid 2-related factor 2 in hepatocellular carcinoma.
REFERENCE   3  (bases 1 to 5105)
  AUTHORS   Gong,Z. and Hu,G.
  TITLE     PCDH20 acts as a tumour-suppressor gene through the
            Wnt/beta-catenin signalling pathway in hypopharyngeal squamous cell
            carcinoma
  JOURNAL   Cancer Biomark 26 (2), 209-217 (2019)
   PUBMED   31450490
  REMARK    GeneRIF: Low PCDH20 expression is associated with hypopharyngeal
            squamous cell carcinoma through the Wnt/beta-catenin signalling
            pathway.
REFERENCE   4  (bases 1 to 5105)
  AUTHORS   Wu,Y., Zheng,S., Yao,J., Li,M., Yang,G., Zhang,N., Zhang,S. and
            Zhong,B.
  TITLE     Decreased expression of protocadherin 20 is associated with poor
            prognosis in hepatocellular carcinoma
  JOURNAL   Oncotarget 8 (2), 3018-3028 (2017)
   PUBMED   27935871
  REMARK    GeneRIF: low expression of PCDH20 was found to be associated with
            poor OS in HCC patients; hence, this protein represents a promising
            potential prognostic biomarker
REFERENCE   5  (bases 1 to 5105)
  AUTHORS   Vuckovic,D., Dawson,S., Scheffer,D.I., Rantanen,T., Morgan,A., Di
            Stazio,M., Vozzi,D., Nutile,T., Concas,M.P., Biino,G., Nolan,L.,
            Bahl,A., Loukola,A., Viljanen,A., Davis,A., Ciullo,M., Corey,D.P.,
            Pirastu,M., Gasparini,P. and Girotto,G.
  TITLE     Genome-wide association analysis on normal hearing function
            identifies PCDH20 and SLC28A3 as candidates for hearing function
            and loss
  JOURNAL   Hum Mol Genet 24 (19), 5655-5664 (2015)
   PUBMED   26188009
  REMARK    GeneRIF: Genome-wide association analysis on normal hearing
            function identifies PCDH20 and SLC28A3 as good candidates for
            modulatory genes in the auditory system. [meta-analysis]
REFERENCE   6  (bases 1 to 5105)
  AUTHORS   Suzuki,S.T.
  TITLE     Recent progress in protocadherin research
  JOURNAL   Exp Cell Res 261 (1), 13-18 (2000)
   PUBMED   11082270
  REMARK    Review article
REFERENCE   7  (bases 1 to 5105)
  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   8  (bases 1 to 5105)
  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   9  (bases 1 to 5105)
  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   10 (bases 1 to 5105)
  AUTHORS   Cross,S.H., Charlton,J.A., Nan,X. and Bird,A.P.
  TITLE     Purification of CpG islands using a methylated DNA binding column
  JOURNAL   Nat Genet 6 (3), 236-244 (1994)
   PUBMED   8012384
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            AL592490.8 and AL162575.15.
            
            On Jul 20, 2021 this sequence version replaced NM_022843.3.
            
            Summary: This gene belongs to the protocadherin gene family, a
            subfamily of the cadherin superfamily. This gene encodes a protein
            which contains 6 extracellular cadherin domains, a transmembrane
            domain and a cytoplasmic tail differing from those of the classical
            cadherins. Although its specific function is undetermined, the
            cadherin-related neuronal receptor is thought to play a role in the
            establishment and function of specific cell-cell connections in the
            brain. [provided by RefSeq, Jul 2008].
            
            Sequence Note: The RefSeq transcript and protein were derived from
            genomic sequence to make the sequence consistent with the reference
            genome assembly. The genomic coordinates used for the transcript
            record were based on alignments.
            
            Publication Note:  This RefSeq record includes a subset of the
            publications that are available for this gene. Please see the Gene
            record to access additional publications.
            
            ##Evidence-Data-START##
            Transcript exon combination :: AF169693.1, BC027907.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA2158188, SAMN03267763
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000409204.5/ ENSP00000387250.3
            RefSeq Select criteria :: based on manual assertion, conservation,
                                      expression, longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-823               AL592490.8         6749-7571           c
            824-4511            AL592490.8         2001-5688           c
            4512-5105           AL162575.15        162638-163231       c
FEATURES             Location/Qualifiers
     source          1..5105
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="13"
                     /map="13q21.2"
     gene            1..5105
                     /gene="PCDH20"
                     /gene_synonym="PCDH13"
                     /note="protocadherin 20"
                     /db_xref="GeneID:64881"
                     /db_xref="HGNC:HGNC:14257"
                     /db_xref="MIM:614449"
     exon            1..823
                     /gene="PCDH20"
                     /gene_synonym="PCDH13"
                     /inference="alignment:Splign:2.1.0"
     CDS             692..3547
                     /gene="PCDH20"
                     /gene_synonym="PCDH13"
                     /note="protocadherin 13"
                     /codon_start=1
                     /product="protocadherin-20 precursor"
                     /protein_id="NP_073754.2"
                     /db_xref="CCDS:CCDS9442.2"
                     /db_xref="GeneID:64881"
                     /db_xref="HGNC:HGNC:14257"
                     /db_xref="MIM:614449"
                     /translation="MRGRGNARSSQALGVSWCPATWHPRLDMGRLHRPRSSTSYRNLP
                     HLFLFFLFVGPFSCLGSYSRATELLYSLNEGLPAGVLIGSLAEDLRLLPRSAGRPDPQ
                     SQLPERTGAEWNPPLSFSLASRGLSGQYVTLDNRSGELHTSAQEIDREALCVEGGGGT
                     AWSGSVSISSSPSDSCLLLLDVLVLPQEYFRFVKVKIAIRDINDNAPQFPVSQISVWV
                     PENAPVNTRLAIEHPAVDPDVGINGVQTYRLLDYHGMFTLDVEENENGERTPYLIVMG
                     ALDRETQDQYVSIIIAEDGGSPPLLGSATLTIGISDINDNCPLFTDSQINVTVYGNAT
                     VGTPIAAVQAVDKDLGTNAQITYSYSQKVPQASKDLFHLDENTGVIKLFSKIGGSVLE
                     SHKLTILANGPGCIPAVITALVSIIKVIFRPPEIVPRYIANEIDGVVYLKELEPVNTP
                     IAFFTIRDPEGKYKVNCYLDGEGPFRLSPYKPYNNEYLLETTKPMDYELQQFYEVAVV
                     AWNSEGFHVKRVIKVQLLDDNDNAPIFLQPLIELTIEENNSPNAFLTKLYATDADSEE
                     RGQVSYFLGPDAPSYFSLDSVTGILTVSTQLDREEKEKYRYTVRAVDCGKPPRESVAT
                     VALTVLDKNDNSPRFINKDFSFFVPENFPGYGEIGVISVTDADAGRNGWVALSVVNQS
                     DIFVIDTGKGMLRAKVSLDREQQSSYTLWVEAVDGGEPALSSTAKITILLLDINDNPP
                     LVLFPQSNMSYLLVLPSTLPGSPVTEVYAVDKDTGMNAVIAYSIIGRRGPRPESFRID
                     PKTGNITLEEALLQTDYGLHRLLVKVSDHGYPEPLHSTVMVNLFVNDTVSNESYIESL
                     LRKEPEINIEEKEPQISIEPTHRKVESVSCMPTLVALSVISLGSITLVTGMGIYICLR
                     KGEKHPREDENLEVQIPLKGKIDLHMRERKPMDISNI"
     exon            824..5105
                     /gene="PCDH20"
                     /gene_synonym="PCDH13"
                     /inference="alignment:Splign:2.1.0"
     regulatory      4910..4915
                     /regulatory_class="polyA_signal_sequence"
                     /gene="PCDH20"
                     /gene_synonym="PCDH13"
                     /note="hexamer: ATTAAA"
     polyA_site      4932
                     /gene="PCDH20"
                     /gene_synonym="PCDH13"
                     /note="major polyA site"
     regulatory      5064..5069
                     /regulatory_class="polyA_signal_sequence"
                     /gene="PCDH20"
                     /gene_synonym="PCDH13"
                     /note="hexamer: AATGAA"
     regulatory      5081..5086
                     /regulatory_class="polyA_signal_sequence"
                     /gene="PCDH20"
                     /gene_synonym="PCDH13"
                     /note="hexamer: ATTAAA"
     polyA_site      5086
                     /gene="PCDH20"
                     /gene_synonym="PCDH13"
     polyA_site      5105
                     /gene="PCDH20"
                     /gene_synonym="PCDH13"
ORIGIN      
        1 aaacacccag agacatttga gcctccaact aggaaactag cagaagctct accactgccc
       61 acagcaaaga ttcaaaattg gggtatgtcg aaaccttcac tgaattcata tatttacttt
      121 tccggttcac cctacgttac acagaagttg agattccttc cctccgctga gaaaagtgca
      181 ttttctttct ctgtgccaac actgctggat ccgaggctcc aggaggaact gttggcaaag
      241 caggcgtttt gggaccgcgc ctgtgattgc tctgtggcgc cgacttcctc tctctgttac
      301 atccatatac aaatgcaagc ttatttattt attttaattc tccctctctt gctagcaacc
      361 tgtggacttg gcatctgact ggtgcggcaa ggaaggaggc tggtaggtaa gcgctactgt
      421 gcccaacccc gagctgcctc ttcgcagtct tcaggagcaa gtcccccatt ccagctcctc
      481 tggcagagta tggagttacc tgcgtccggg gcaggaaacc atgaatgtgc ccttctgccc
      541 tcttgccttt ctgccactct ttgagttccc gtccttaatt gaagagccag tgactattgg
      601 ctgaagttcc cccagcgatt tgcatgaacc gagagggagt gtcttctgcc gccctccctt
      661 caagagcgct ctgactgcag cctcccaggg aatgcgcggc cgagggaatg cgcgcagctc
      721 acaggccctg ggagtgagct ggtgcccggc gacctggcac ccgcgcctgg atatggggcg
      781 tctacatcgt cccaggagca gcaccagcta caggaacctg ccgcatctgt ttctgttttt
      841 cctcttcgtg ggacccttca gctgcctcgg gagttacagc cgggccaccg agcttctgta
      901 cagcctaaac gagggactac ccgcgggggt gctcatcggc agcctggccg aggacctgcg
      961 gctgctgccc aggtctgcag ggaggccgga cccgcagtcg cagctgccag agcgcaccgg
     1021 tgctgagtgg aacccccctc tctccttcag cctggcctcc cggggactga gtggccagta
     1081 cgtgacccta gacaaccgct ctggggagct gcacacttca gctcaggaga tcgacaggga
     1141 ggccctgtgt gttgaagggg gtggagggac tgcgtggagc ggcagcgttt ccatctcctc
     1201 ctctccttct gactcttgtc ttttgctgct ggatgtgctt gtcctgcctc aggaatactt
     1261 caggtttgtg aaggtgaaga tcgccatcag agacatcaat gacaacgccc cgcagttccc
     1321 tgtttcccag atctcggtgt gggtcccgga aaatgcacct gtaaacaccc gactggccat
     1381 agagcatcct gctgtggacc cagatgtagg cattaatggg gtacagacct atcgcttact
     1441 ggactaccat ggtatgttca ccctggacgt ggaggagaat gagaatgggg agcgcacccc
     1501 ctacctaatt gtcatgggtg ctttggacag ggaaacccag gaccagtatg tgagcatcat
     1561 catagctgag gatggtgggt ctccaccact tttgggcagt gccactctca ccattggcat
     1621 cagtgacatt aatgacaatt gccctctctt cacagactca caaatcaatg tcactgtgta
     1681 tgggaatgct acagtgggca ccccaattgc agctgtccag gctgtggata aagacttggg
     1741 gaccaatgct caaattactt attcttacag tcagaaagtt ccacaagcat ctaaggattt
     1801 atttcacctg gatgaaaaca ctggagtcat taaacttttc agtaagattg gaggaagtgt
     1861 tctggagtcc cacaagctca ccatccttgc taatggacca ggctgcatcc ctgctgtaat
     1921 cactgctctt gtgtccatta ttaaagttat tttcagaccc cctgaaattg tccctcgtta
     1981 catagcaaac gagatagatg gtgtggttta tctgaaagaa ctggaacccg ttaacactcc
     2041 cattgcgttt ttcaccataa gagatccaga aggtaaatac aaggttaact gctacctgga
     2101 tggtgaaggg ccgtttaggt tatcacctta caaaccatac aataatgaat atttactaga
     2161 gaccacaaaa cctatggact atgagctaca gcagttctat gaagtagctg tggtggcttg
     2221 gaactctgag ggatttcatg tcaaaagggt cattaaagtg caacttttag atgacaatga
     2281 taatgctcca attttccttc aacccttaat agaactaacc atcgaagaga acaactcacc
     2341 caatgccttt ttgactaagc tgtatgctac agatgccgac agcgaggaga gaggccaagt
     2401 ttcatatttt ctgggacctg atgctccatc atatttttcc ttagacagtg tcacaggaat
     2461 tctgacagtt tctactcagc tggaccgaga agagaaagaa aagtacagat acactgtcag
     2521 agctgttgac tgtgggaagc cacccagaga atcagtagcc actgtggccc tcacagtgtt
     2581 ggataaaaat gacaacagtc ctcggtttat caacaaggac ttcagctttt ttgtgcctga
     2641 aaactttcca ggctatggtg agattggagt aattagtgta acagatgctg acgctggacg
     2701 aaatggatgg gtcgccctct ctgtggtgaa ccagagtgat atttttgtca tagatacagg
     2761 aaagggtatg ctgagggcta aagtctcttt ggacagagag cagcaaagct cctatacttt
     2821 gtgggttgaa gctgttgatg ggggtgagcc tgccctctcc tctacagcaa aaatcacaat
     2881 tctccttcta gatatcaatg acaaccctcc tcttgttttg tttcctcagt ctaatatgtc
     2941 ttatctgtta gtactgcctt ctactctgcc aggctccccg gttacagaag tctatgctgt
     3001 cgacaaagac acaggcatga atgctgtcat agcttacagc atcataggga gaagaggtcc
     3061 taggcctgag tccttcagga ttgaccctaa aactggcaac attactttgg aagaggcatt
     3121 gctgcagaca gattatgggc tccatcgctt actggtgaaa gtgagtgatc atggttatcc
     3181 cgagcctctc cactccacag tcatggtgaa cctatttgtc aatgacactg tcagtaatga
     3241 gagttacatt gagagtcttt taagaaaaga accagagatt aatatagagg agaaagaacc
     3301 acaaatctca atagaaccga ctcataggaa ggtagaatct gtgtcttgta tgcccacctt
     3361 agtagctctg tctgtaataa gcttgggttc catcacactg gtcacaggga tgggcatata
     3421 catctgttta aggaaagggg aaaagcatcc cagggaagat gaaaatttgg aagtacagat
     3481 tccactgaaa ggaaaaattg acttgcatat gcgagagaga aagccaatgg atatttctaa
     3541 tatttgatat ttcatggtgg aataacacag agaaatgttt taactgactt tggatcttca
     3601 tcacctaaaa aagagtgtgt tgatggcagt tccaatgaag gacaactaat ttataacttg
     3661 ttctatattg taaatagctg tttacaggtt tttaaattta aattcagagg ttataaaatg
     3721 tgtacagcat ttttaagtga aaattagtac taacagctat aggacttgta tttaaaaaaa
     3781 aaaaaaaagc ttggacatgg tttgcagctt tcatacacca agcagatgat tgataaaacc
     3841 tgggagtaag gtaagaaaaa tggaacaaat ttttatctaa aaattcctgt caccacaaga
     3901 gggcatcagc tgctcctttg caggaaactg gggtattgta cttggcagtt gtacatgaaa
     3961 ttaatgaaag agtatatttt aaatatattg tttttaacat taaacaaata tgaaattaaa
     4021 gtaaattaaa tttcacccta tttaaacata tgataaaaaa agaaatgcac ttgtaaacag
     4081 aatgtttatt acctcataag tgcatatata gtgtgaaaga gaaggcatta aaaagaagtg
     4141 caattccttt ttagcaagga taaaatcatt gccttgtgtt acagattcag cctgctgaag
     4201 agtattccac tttctgtgta ctcgaattgc tttctgtttg ctttaccact gcacttgtta
     4261 ttattacaag ggaaatagat ttatacatac atatatatat tcttcattac aggaaatgta
     4321 actagatatt gtgcccaaga aaaacagcca gaagcaaaga aatgcttcaa tctttagttg
     4381 cttcataggc attcatgaca ttttagtgct ttcacaactt gttggtcgta ctttatactt
     4441 gggttatata ttagactttt ataggcttga aatcatccat cacataagaa aatagaaatc
     4501 atattaaaag tgaattcttc tagaggcttg tgtacactac tggttgtttt agttgggcct
     4561 tttatatgaa agttatactg tacttatctt tttgttgttg tttaggtttg ttgactacca
     4621 tttctggctt cctttctttg gttttggatt aaatccaaca gtttatttgt aagccctgca
     4681 gcagatttct ttgataattt agcttttact gaatctcttg caatgaagaa agctatttca
     4741 tcagtgattt atcactttca attcattgtg tgagctggaa atattatttt atatgagagc
     4801 tatagcaaaa taatctgtat aaacaaggaa tgtgttagct taaactggat cattttactt
     4861 tttggcatca tgcatctgta ctgtaccaaa agtgtttata tgtctgcaaa ttaaaggtat
     4921 atattttcat aatttctttc tcacttttag cattttatat ttgaacatgg gcttgttatt
     4981 tcactgaagt gcctgtcatt tgtttgtttt tagggttaaa tgtgggtaac ctgtagtatt
     5041 ctgctatact aaagtttata ttaaatgaat tcattactca attaaacatt gggtaaatta
     5101 ttaaa
//
