LOCUS       XM_039097353           10143 bp    mRNA    linear   ROD 11-JUN-2023
DEFINITION  PREDICTED: Rattus norvegicus protocadherin 1 (Pcdh1), transcript
            variant X1, mRNA.
ACCESSION   XM_039097353
VERSION     XM_039097353.1
DBLINK      BioProject: PRJNA677964
KEYWORDS    RefSeq.
SOURCE      Rattus norvegicus (Norway rat)
  ORGANISM  Rattus norvegicus
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
            Muroidea; Muridae; Murinae; Rattus.
COMMENT     MODEL REFSEQ:  This record is predicted by automated computational
            analysis. This record is derived from a genomic sequence
            (NC_051353.1) annotated using gene prediction method: Gnomon,
            supported by mRNA and EST evidence.
            Also see:
                Documentation of NCBI's Annotation Process
            
            [WARNING] On Feb 22, 2024 this sequence was replaced by
            XM_039097353.2.
            
            ##Genome-Annotation-Data-START##
            Annotation Provider         :: NCBI RefSeq
            Annotation Status           :: Updated annotation
            Annotation Name             :: GCF_015227675.2-RS_2023_06
            Annotation Pipeline         :: NCBI eukaryotic genome annotation
                                           pipeline
            Annotation Software Version :: 10.1
            Annotation Method           :: Best-placed RefSeq; Gnomon;
                                           cmsearch; tRNAscan-SE
            Features Annotated          :: Gene; mRNA; CDS; ncRNA
            Annotation Date             :: 06/06/2023
            ##Genome-Annotation-Data-END##
FEATURES             Location/Qualifiers
     source          1..10143
                     /organism="Rattus norvegicus"
                     /mol_type="mRNA"
                     /strain="BN/NHsdMcwi"
                     /db_xref="taxon:10116"
                     /chromosome="18"
                     /sex="male"
                     /tissue_type="kidney"
                     /geo_loc_name="USA: Wisconsin, Milwaukee, Medical College
                     of Wisconsin"
                     /collection_date="2019-03-08"
                     /collected_by="Rebecca Schilling"
     gene            1..10143
                     /gene="Pcdh1"
                     /note="protocadherin 1; Derived by automated computational
                     analysis using gene prediction method: Gnomon. Supporting
                     evidence includes similarity to: 1 mRNA, 12 ESTs, 1 long
                     SRA read, 2 Proteins, and 100% coverage of the annotated
                     genomic feature by RNAseq alignments, including 80 samples
                     with support for all annotated introns"
                     /db_xref="GeneID:307481"
                     /db_xref="RGD:1308490"
     CDS             1362..5057
                     /gene="Pcdh1"
                     /codon_start=1
                     /product="protocadherin-1 isoform X1"
                     /protein_id="XP_038953281.1"
                     /db_xref="GeneID:307481"
                     /db_xref="RGD:1308490"
                     /translation="MRRRKTVLLILEPARMGPLRPSPGPGGQRLLLPPLLLALLLLLA
                     PSASHTTQVVYKVPEEQPPNTLIGSLAADYGLPDVGHLYKLEVGAPYLRVDGKTGDIF
                     TTETSIDREGLRECQNQISGSPCILEFEVSITDLVQNGSPRLLEGQIEVQDINDNTPN
                     FASPVITLAIPENTNIGSLFPIPLATDRDAGPNGVASYELQAGPEAQELFGLQVAEDQ
                     EEKQPQLIVMGNLDRERWDSYDLTIKVQDGGSPPRASSALLRVTVLDTNDNAPKFERP
                     TYEAELSENSPIGHSVIQVKANDSDQGANAEIDYTFHQAPEVVRRLLRLDRNTGLITV
                     QGPVDREDLSTLRFSVLAKDRGANPKSARAQVVVTVKDMNDNAPTIEIRGIGLVTHQD
                     GMANISEDVAEETAVALVQVSDRDEGENAAVTCVVAGDVPFQLRQASETGSDSKKKYF
                     LQTTTPLDYEKVKDYTIEIVAVDSGNPPLSSTNSLRVQVVDVNDNAPVFTQSITEVAF
                     PENNKPGEVVAEVTASDADSGSNAELVYSLEPEPAAQGLFTISPENGEVRVKTSLDRE
                     QRDSYELKVVAADRGSPSLQGTATVLVNVLDCNDNDPKFMLSGYNFSVMENMPALSPV
                     GMVTVIDGDKGENARVQLSVEQDNGDFVIQNGTGTILSSLSFDREQQSTYTFQLKAVD
                     GGVPPRSAYVGVTINVLDENDNAPFITAPSNTSHRLLTPQTRLGETVSQVTAEDIDSG
                     INAELTYSIAGGNPYGLFQIGSHSGAITLEKEIERRHHGLHRLVVKVSDRGKPPRYGT
                     ALVHLYVNETLANRTLLETLLVHSLDTPLDIDIAGDPEYERSKQRGNILFGVVAGVVA
                     VALLIALAVLVRYCRQREAKSGYQAGKKETKDLYAPKPSGKAAKGSKSKGKKSKSPKP
                     VKPVEDEDDTGLQKSLKFNLMSDAPGDSPRIHLPLNYPPGSPDLGRHYRSNSPLPSIQ
                     LQPQSPSASKKHQVVQDLPPANTFVGTGDTTSTGSEQYSDYSYRTNPPKYPSKQLPHR
                     RVTFSATSQAQELQDPSQHSYYDSGLEESETPSSKSSSGPRLGPLALPEDHYERTTPD
                     GSIGEMEHPENDLRPLPDVAMTGTCTRECSEFGHSDTCWMPGQSSPSRRTKSSALKLS
                     TFVPYQDRGGQEPAGAGSPSPPEDRNTKTAPVRLLPSYSAFSHSSHDSCKDSATLEEI
                     PLTQTSDFPPTATPASAQTSAKREIYL"
ORIGIN      
        1 agtggggggt tgcggccggg gctccctagc ctccaaggtc cactgcaaga agcggagaga
       61 agggaggggg tgccgagttg gaccccggcc ccggcgtccg cactcgggcg cgctccaagc
      121 cgcggggatg agagactcct ggagcgcgcg gaatggagaa ggtttcgggg aagcgcaagg
      181 ccctcagctc agccgggggc tgccggagga ctagggaagc taggaacatt atccacgaca
      241 cacacttgtt gggcgatttg ctcagctcac tcaggcgctt ccagctcgtc gcggacacct
      301 ggaagagcca catcacagac acatacacac atacattgat ccgtacatat gtgagcacag
      361 acatacctcc cgcacaccag cgcccactgg ggcacagtca ccagctcaga atctgcttca
      421 gcgcctgcac gatcagcagc ggggacacac aacccgtggc catagatagc tacagcacaa
      481 tcgggtatga tattgagcaa tgccggacac acaaacacaa cctcgtgcct tcctgtacga
      541 atataactgc ctcggttcgc cagatgaacg ctgaacctag ttccctacac ataccgctga
      601 aggaacacac cctaacacaa atgggtgccc actccttggc caggatatag gtatacagca
      661 caggtcttgc ttgcccctct actgcaccca cacatacaca acccagtgtc tcataacacg
      721 cttagatagc acactcctta gcagagaggt acctacagca gcgcctcaca agcagaattc
      781 actgcttcaa gcatcttaac actggttgtc acacacacct tacaccaaca gtgtcacatt
      841 acactctgca gcgcgcgcgc acacgcacac acacacacat atacacacgc gcgcgcacac
      901 acacacacac accacaccac actccactct ccctggccag attccctcgg gagaagcctc
      961 caggctctcc tagagagcac ccagagccct gtcacctcaa tcgggacttt gttattgtaa
     1021 atatcggcac aaccggagcc cccgggccgg ccagaccggc ttctcggcga cacctccccc
     1081 ccacttccac tccggggcct gaccagctgg gtattccggg aacaagctga acctgacagg
     1141 ccgcgccggg ccgccaccct ggagctgtgt ggccctagat ccctttgcac aatactagag
     1201 gtgtttgaaa cctttttcgg gccgtttagc tgctttctcc gagctacctg ggtccctagc
     1261 acacctaggt cccgcacacc tgcgtgcccc tctactgggg cccggtcgca ggccagttcg
     1321 gtgtaccgac aaagcctcgg ggccagaatg gagaccgcag catgcgcaga agaaaaactg
     1381 ttctcctgat tctggagcct gccaggatgg ggcctctgag gcccagccca gggcctgggg
     1441 ggcagcggtt gctgctgccc cccttactgc tggcactgct gctcctattg gctccatctg
     1501 ccagccatac cacccaggta gtatacaagg tgccagagga acagccgccc aacacactca
     1561 ttgggagcct tgccgctgac tacggtttgc cagacgtggg tcatctgtac aaactagagg
     1621 taggtgctcc atatcttcga gtggatggca agactggaga cattttcacc acagagacct
     1681 ccattgatcg agaggggctt cgtgaatgcc agaaccagat ctccgggagt ccctgtatcc
     1741 tggagtttga ggtgtcaatc acggaccttg tgcagaacgg cagcccccga ctgctagagg
     1801 gccagataga ggtgcaagac atcaatgaca acacgccgaa ctttgcctca ccagtcatca
     1861 ccctggctat cccggagaac accaacatcg gctcactctt ccccatccca ctggccacag
     1921 accgtgacgc tggccccaat ggcgtagcat cctatgagct gcaggctggg cctgaggccc
     1981 aggagctatt tggactgcag gtggctgagg accaggagga gaagcagcca cagctcattg
     2041 tcatgggcaa cctggaccgc gaacggtggg actcctacga cctcaccatc aaggtacagg
     2101 atggtggcag tcctccacgt gccagcagcg ccctgcttcg tgtcactgtg cttgatacaa
     2161 atgacaacgc tcccaagttt gaacggccaa cctacgaagc cgagctgtct gagaacagtc
     2221 ccattggcca ctcggtcatc caggtgaaag ctaatgactc ggaccaaggt gccaatgcgg
     2281 agattgacta cacgttccac caggcacccg aggttgtcag gcgtcttttg cgactagaca
     2341 gaaacactgg acttatcacc gtccagggcc ctgtggatcg tgaggatcta agcactctgc
     2401 gtttctcagt gctcgccaag gaccgaggtg ccaaccccaa gagtgcccgt gcccaggtag
     2461 ttgtgactgt gaaagacatg aatgacaatg ccccgaccat tgagatccga ggcatagggc
     2521 tggtgactca tcaagatggg atggctaaca tatcagagga tgtggcagag gagaccgcgg
     2581 tggccttggt acaggtgtct gatcgagatg agggagagaa tgcagctgtc acctgtgtag
     2641 tagcaggtga tgtgcccttc cagctacgcc aggccagcga gacaggcagc gacagcaaga
     2701 aaaagtattt cctgcagacc accacccctc tcgactatga gaaagtcaaa gactacacca
     2761 ttgagatcgt ggcggtggac tccggcaacc ctccgctctc tagcaccaac tccctcaggg
     2821 tgcaggtggt agacgtcaat gacaatgccc ccgtcttcac ccagagcatc actgaagttg
     2881 ccttcccaga aaacaacaag cctggtgaag tggtagccga ggtcacggcc agcgacgccg
     2941 actctggctc taacgcagag ctggtgtatt ctctggaacc tgagccagct gcccaggggc
     3001 tgttcactat ctcacccgag aacggagagg tcagggtaaa gacatcgctg gatcgggaac
     3061 agagagacag ctatgagctg aaggtggtgg cagccgacag gggcagtccc agccttcagg
     3121 gcacagccac ggtccttgtc aacgtgcttg actgtaatga caatgacccc aaatttatgc
     3181 tgagtggcta caacttctca gtgatggaga acatgccagc gctgagtcca gtgggtatgg
     3241 tgactgtcat cgacggagac aagggggaga atgcccgggt gcagctctca gtcgagcagg
     3301 acaatggtga ctttgttatc cagaatggca caggcaccat cttatccagt ttgagctttg
     3361 atcgggaaca acagagtacc tacaccttcc aactgaaggc cgtggatggt ggtgtcccac
     3421 ctcgttcggc gtacgtcggt gtcaccatca atgtgttgga tgagaatgac aatgcgccct
     3481 ttatcaccgc cccctccaac acgtctcacc ggctgctgac cccgcagaca cgtctcggcg
     3541 agacagtcag ccaggtgaca gcggaggaca ttgactctgg tatcaatgcc gagctgacct
     3601 atagcatcgc tggcggcaac ccttacggac tcttccagat tggatcacat tcaggtgcca
     3661 tcacgctgga gaaggagatt gaacggcgcc accacgggtt acaccgcctt gtggtgaagg
     3721 tcagcgaccg tggcaagccc cctcgctatg gtacagcctt ggtccacctt tacgtcaacg
     3781 agaccttagc caaccgcacg ctgctagaga ccctccttgt ccatagcctg gacacgcccc
     3841 tggatattga cattgccggg gatccagaat atgagcgttc caagcaacgt ggcaacattc
     3901 tctttggtgt tgtagccggc gtggtggccg tcgccttact catcgccctg gcagtactcg
     3961 tgcgctactg ccggcagcgg gaggccaaga gtggctacca ggcgggtaag aaggagacta
     4021 aggacctata cgcccccaag cctagcggca aagctgctaa gggaagcaag agcaagggga
     4081 agaaaagcaa gtcgccgaaa cctgtgaagc ccgtggagga tgaggatgac actgggctac
     4141 aaaagtctct caagttcaac cttatgagtg atgcccccgg ggacagtccc cgaatccacc
     4201 tacccctcaa ctacccgccc ggcagccccg acttaggccg ccattaccgc tccaattccc
     4261 cactgccttc catccagctg caaccccagt caccctcggc ctccaagaag caccaggtgg
     4321 tgcaggacct gccgcccgca aacacatttg tgggcactgg ggacaccacg tccacgggct
     4381 ccgagcagta ctccgactac agctatcgca ccaacccccc caaatacccc agcaagcagt
     4441 tacctcaccg ccgtgtcacc ttctcggcca ccagtcaggc ccaggagctg caggatccat
     4501 cacagcacag ttattatgac agtggcctgg aagagtctga aacgccatct agcaagtcat
     4561 cctcaggccc ccgacttggt cccctggccc tcccggagga ccactatgag cgcaccaccc
     4621 ctgacggcag cataggtgaa atggaacacc ctgagaacga cctccgccct ttgcccgacg
     4681 tcgccatgac gggcacatgt acccgggagt gcagcgagtt tggtcactct gacacatgct
     4741 ggatgcctgg ccagtcgtct cccagccgcc ggaccaagag cagcgccctc aaactctcca
     4801 ccttcgtgcc ttaccaggac cgaggagggc aggagcctgc gggcgccgga agccccagcc
     4861 ccccggaaga ccggaacacc aaaacggccc ccgtgcgcct cctgccctcc tacagtgcct
     4921 tctcccacag tagccatgac tcctgcaagg actcggccac cttggaggaa attcccttga
     4981 cccagacctc ggacttccca cccacagcca caccggcatc tgcccagaca tccgccaagc
     5041 gtgagatcta cctgtgagcc cccttctggc cggcggccac ccctccccca gtcgccggcc
     5101 agctcccaac tgggtctatt ccagggcccc actccttccc tccagcgtgg actctgtggc
     5161 cagggcccga tctgtgggag tactggcttc aagaccacgt tggcccttgc ccccatgcag
     5221 ggtccaagtc ctttccccca ttcctacccc ttagccccga ggagcccctt cttcccccca
     5281 ctatggggct ccacccagtg gatgcccttg agggctcctc tgcaatgact gggctccctt
     5341 ccatctactt ctggggagca cccccttgct ttgggcagac ggtggagtca agagtgggca
     5401 gcacacttta aatcattgtt tcctgtatgg ctgaccaggg cagtgtagcc ttgcagctgg
     5461 gtaaacctgg ggacttactc cccgggaatg ctcaaaggaa actttccacc accggggctc
     5521 tctgaagggc tgttgttacc aaaggtgggg gtggggattt gggtgagagt gctgtgaagg
     5581 cctcttccag tactgctcct gggctggccc acctgcctgt cataggctca tgcctgatcc
     5641 cacctgggca cccccttccc tgctggtctt gcggtgtctg tatataagga ccttggaatg
     5701 atgtccccca cttctgcctg atttgcaact tttcttgttg atgttgtgtt gtcttggggg
     5761 ggcccctctg ggggggcctg ccctgtgccc ctcctccctg ccccagtgcc cccccaggcc
     5821 tctattgttc catgttgtaa atacccctgg ggctgtggaa ggatggggtg caggccaagg
     5881 aaacaaaggg tgggtggggg tggggacggg ggtaacattc gcctatcagc agagctgggc
     5941 ttttatttaa tttttttttt taaaaataca aatctctatt tttttggaac tgttgcgctg
     6001 tgccctgggg gggggatccc cgctcagact ggcctcccac acccagatga gcatcacaag
     6061 aggggccctg aggctgtggg gggtgcagct ggacagggat gggatgactg tgcctctggc
     6121 ctggttgggt gagttgggag caggaaagtt tgctcaggag gtggctggct gctgcctcct
     6181 atatggggga ccttgcctcc cccctgccct ccaaccccca gcccctgcca tgactgaccc
     6241 gtcagcctgt aaaaccacca ttgccttgat ctcagggggt gggaagggct gcctcagggc
     6301 accctgggct ccaggcccct tcttccagtt gggcttccct tttaccaggg tcaggggtcc
     6361 cagggggagg gggtggggag gttagggggc agagaagccc agtcagccat gatgaggtgg
     6421 gggtgtttct tcacctcggg gggccaaggt gtgaggggta tcctgcagag ccccccgtct
     6481 cccactgtgg ccatctcata gcctctcttc cttccagaag cccccactgc cttggcccct
     6541 acctctccag ctctccaagg gcctaggctg ggaggctgga gactcaggta tggttcccac
     6601 ttgacttagt ctaagcttgg ggacggtggc ccattgtgga aggggtggac aggctgctgg
     6661 gttgtctggt gcctttggga gctgtgctgc tggagtcttg actcctgtaa ccccagagac
     6721 cctactccca tccccagaaa agccagggac tgtagaatca ccctattatc tgcctcctcc
     6781 tttcccccca cttgtgtttg gggtaacagt gctggaatgc actgttaggg tggtggccct
     6841 ggcatctaca gcccttctat ggagggcagt ggggtagggt ggctaaggtg acaacagcca
     6901 ggtctagggg ttggccaaag gctcccatcc ctgggggagg cccagaaagt gggccagggg
     6961 cttgttaaag acacaatccc tttcccctgc acaaatgggg caggtgcaat agtggcagag
     7021 ctggtagcat tgaggtgccc ggctagtggg gcagtggcct gggggggctg tcctgggtcc
     7081 taaaggttag gatcaggaca aaaagattgt atgaggcccg tctgctcagt ggggagggga
     7141 atccagccaa gaggcgtccc tggggtcagt aggactccca ctggaagccc ctggtagctt
     7201 gggtaccctg acctggcctt ggagactcct gagcactgag cgggagggca gaggaacatt
     7261 ttgcacaatg gagaagccag aaggaagggg gtagcctaga tggctgggag ggctcagaag
     7321 cacagagcag aagtccttcc acaggcaagg cagggccctg accccctggt tggggtaagg
     7381 gtactgagtc tgtcaccacc tgggcactca agaggtgaaa ccaaaggtgg gcagggggtg
     7441 ggtgacagca ctagagacta gctttgttgg tcctaggtct gtgagatccc tccccaatgc
     7501 cttgtgtcgc gtacagtttt atgtaccaat aggcgacatt tggccagagg agacccccct
     7561 caaacccagc ctgacccagt cagtgtcttc ctagagggga ccaagttggt ccccatctct
     7621 ctacttcaga gcatgtctgt tagtagggga agggtatgtg gggacacatt tcctagggtc
     7681 cccgaagaag catctctcac atcaggaggg gagctgtttc taggcatcct gaacctgggg
     7741 gctccctact ccttatatct ccccttggga gtctctgggg acatggtttc ccaccggggg
     7801 ccacgggaac atgtctccct tccctaccca ggctctctgg ggagcctgtt tgcctcccag
     7861 ggttcctggg agtacctaag acaagtcagt cttgggccgg ctctctttcc aggcaagagc
     7921 tgtctctgaa gctccctgga agagaagtct ctgacctcca tctctcagat gggagtgtct
     7981 gccctgcagc actaggaatg aggccgagca tctctgaatt gtcttttctc ctaggggctc
     8041 taggatacca ctctctccag agcgcggccc cctggagcca tttcttccct gggtgggggc
     8101 tgtctccggt gttgggaggg cttgtgttga ccaagagaaa gtctcttagg ggagtatctc
     8161 cttgtgagac ttctctggga gggggggggg cgtctcgccg aaggggattc cagggcgggt
     8221 atgtctgccc atggggaggg gagactgtgt ctcctcgggt tatctgagtg gggagggggg
     8281 ccgtgtctct ctcgtgtgtc gggtgggagg gttggggagg gggggtttgg gcgcgtcagt
     8341 tgcccacttc ggggtcgtgt ttctctgggt tcgtgccact tcccaccgcc tcgctcctcc
     8401 cgggaagggc cccgccccca caccatcccc acccccggcg ctgcgagcac aatcccgttg
     8461 atttgtaatg atttctgtct tttctgtctt tctctttctc tgacctccct cccctcgccg
     8521 cgagcatgcg caggcaccgc ccctaccccc tccggttcgg ttcgtttccg gtttgtttgc
     8581 tgagctgtca atgaaagacc cgtgtaatta ttcccgagct ttacaataaa agtgtgaaaa
     8641 ccggacccca ctccgcttct tccagtccct cgggtgaata gccgtgggag aatagagcta
     8701 ttcttgggta gatgccttga gctaggggga cgagtgagag agacccacac tgggatcaat
     8761 gacgccctca ggggttgtag gcgggggggg gggggggaat tcaagcgagt aaaacacctg
     8821 gttcgtgcac ctcaaagtga catctatctg ctctctgtgc accccatccg ccctgagctc
     8881 aggtgtaggt cagggacgga gggcctctct gggaggacgg tgctctatta ccttcttcag
     8941 tggggaaacc ctacagggat ttgagggtgg gagctggggc ccttgtgtcg ttccctggtg
     9001 tatcacttcc cgctcctttg gcaatgagta gggattgcgg aactggatgg gggggtgagg
     9061 ggcgggaagc atctgtgtgt ctggcgcttc ctcccacgct caagaacgag ggttggaagt
     9121 tgattttggg gaaggggaca gacaaggtct ctgtcctggg ctccgactgc gttctcctcc
     9181 cctttccgta atactggagc ggcctggcct cctctgtcca gctcccagct aaactggctg
     9241 gagagaggtc gaggaactga tacaggatcg gcctgttccc agccccgcct tcgcggacgc
     9301 gcctcctcgc ctatcccggc tcgtttccgc tccgcctacg cgctccctgc ggggcctgcg
     9361 ctttcagggc ctcggactct gggtccaccc agccaccggg attagttgag cacagggact
     9421 aatcctggat gagccacggt gtaaacccgg attgactagg ggacggggac gctggcgggg
     9481 gccgggggtt gggggagggc cttggtctct ggttcccctt catccattcc tacaggcaca
     9541 gcatgatggg gtctagagtc tcactccaag tctctggtac ttttgaaatg acctgtagct
     9601 agctgtatgt tgaaaggtga gaatggatgg gggaagtaag agaggatgtc atgaagacac
     9661 agctggatca tgcactccga aatgtggcac attggtagga gtgggaatgg agatgaggga
     9721 ggcaaagttc ttggcagcct tgagtccaca ggattaggtc agctccctgg ccgagtctgc
     9781 aagccagtca acccccctgt accccagcta cagactcata agccctcccc tctaccagtg
     9841 gccgtggtta tggttcctcc acgatgagga ggcagtgtgg aaggtagtta agaccaaggg
     9901 gggagcatgc caaggaaagg tcaaggaagt tgaagaagat ggggtgtggc cagctgggta
     9961 cccgaatcct gaccctggtt cacttactaa ttctacaaac atttcctgag cctctccctc
    10021 ttaccagtca agaactagat actgggacac cggggctggg gatttagctc agtggtagag
    10081 cgcttaccta gaaagcgcaa agccctgggt tcggccccca gctcaaaaaa aaaaaaaaca
    10141 aaa
//
