LOCUS       NM_001005784            3335 bp    mRNA    linear   ROD 30-APR-2024
DEFINITION  Mus musculus PATJ, crumbs cell polarity complex component (Patj),
            transcript variant 2, mRNA.
ACCESSION   NM_001005784
VERSION     NM_001005784.1
KEYWORDS    RefSeq.
SOURCE      Mus musculus (house mouse)
  ORGANISM  Mus musculus
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
            Muroidea; Muridae; Murinae; Mus; Mus.
REFERENCE   1  (bases 1 to 3335)
  AUTHORS   Adams,D.J., Barlas,B., McIntyre,R.E., Salguero,I., van der
            Weyden,L., Barros,A., Vicente,J.R., Karimpour,N., Haider,A.,
            Ranzani,M., Turner,G., Thompson,N.A., Harle,V., Olvera-Leon,R.,
            Robles-Espinoza,C.D., Speak,A.O., Geisler,N., Weninger,W.J.,
            Geyer,S.H., Hewinson,J., Karp,N.A., Fu,B., Yang,F., Kozik,Z.,
            Choudhary,J., Yu,L., van Ruiten,M.S., Rowland,B.D., Lelliott,C.J.,
            Del Castillo Velasco-Herrera,M., Verstraten,R., Bruckner,L.,
            Henssen,A.G., Rooimans,M.A., de Lange,J., Mohun,T.J., Arends,M.J.,
            Kentistou,K.A., Coelho,P.A., Zhao,Y., Zecchini,H., Perry,J.R.B.,
            Jackson,S.P. and Balmus,G.
  CONSRTM   Sanger Mouse Genetics Project
  TITLE     Genetic determinants of micronucleus formation in vivo
  JOURNAL   Nature 627 (8002), 130-136 (2024)
   PUBMED   38355793
REFERENCE   2  (bases 1 to 3335)
  AUTHORS   Baliova,M., Jahodova,I. and Jursky,F.
  TITLE     A Significant Difference in Core PDZ Interactivity of SARS-CoV,
            SARS-CoV2 and MERS-CoV Protein E Peptide PDZ Motifs In Vitro
  JOURNAL   Protein J 42 (4), 253-262 (2023)
   PUBMED   36932261
REFERENCE   3  (bases 1 to 3335)
  AUTHORS   Yu,M., Jiang,X., Cai,W., Yang,X., An,W., Zhang,M., Xu,Y., Zhang,B.
            and Tang,S.
  TITLE     PATJ and MPDZ are required for trophectoderm lineage specification
            in early mouse embryos
  JOURNAL   Reproduction 166 (2), 175-185 (2023)
   PUBMED   37318097
  REMARK    GeneRIF: PATJ and MPDZ are required for trophectoderm lineage
            specification in early mouse embryos.
            Publication Status: Online-Only
REFERENCE   4  (bases 1 to 3335)
  AUTHORS   Jiang,X., An,W., Yang,X., Lin,J., Ma,S., Wang,D. and Tang,S.
  TITLE     Asymmetric distribution of CRUMBS polarity complex proteins from
            compacted 8-cell to blastocyst stage during mouse preimplantation
            development
  JOURNAL   Gene Expr Patterns 27, 93-98 (2018)
   PUBMED   29155075
REFERENCE   5  (bases 1 to 3335)
  AUTHORS   Ramkumar,N., Omelchenko,T., Silva-Gagliardi,N.F., McGlade,C.J.,
            Wijnholds,J. and Anderson,K.V.
  TITLE     Crumbs2 promotes cell ingression during the
            epithelial-to-mesenchymal transition at gastrulation
  JOURNAL   Nat Cell Biol 18 (12), 1281-1291 (2016)
   PUBMED   27870829
REFERENCE   6  (bases 1 to 3335)
  AUTHORS   Stryke,D., Kawamoto,M., Huang,C.C., Johns,S.J., King,L.A.,
            Harper,C.A., Meng,E.C., Lee,R.E., Yee,A., L'Italien,L.,
            Chuang,P.T., Young,S.G., Skarnes,W.C., Babbitt,P.C. and Ferrin,T.E.
  TITLE     BayGenomics: a resource of insertional mutations in mouse embryonic
            stem cells
  JOURNAL   Nucleic Acids Res 31 (1), 278-281 (2003)
   PUBMED   12520002
REFERENCE   7  (bases 1 to 3335)
  AUTHORS   Poliak,S., Matlis,S., Ullmer,C., Scherer,S.S. and Peles,E.
  TITLE     Distinct claudins and associated PDZ proteins form different
            autotypic tight junctions in myelinating Schwann cells
  JOURNAL   J Cell Biol 159 (2), 361-372 (2002)
   PUBMED   12403818
REFERENCE   8  (bases 1 to 3335)
  AUTHORS   Anzai,N., Deval,E., Schaefer,L., Friend,V., Lazdunski,M. and
            Lingueglia,E.
  TITLE     The multivalent PDZ domain-containing protein CIPP is a partner of
            acid-sensing ion channel 3 in sensory neurons
  JOURNAL   J Biol Chem 277 (19), 16655-16661 (2002)
   PUBMED   11872753
REFERENCE   9  (bases 1 to 3335)
  AUTHORS   Piao,Y., Ko,N.T., Lim,M.K. and Ko,M.S.
  TITLE     Construction of long-transcript enriched cDNA libraries from
            submicrogram amounts of total RNAs by a universal PCR amplification
            method
  JOURNAL   Genome Res 11 (9), 1553-1558 (2001)
   PUBMED   11544199
REFERENCE   10 (bases 1 to 3335)
  AUTHORS   Kurschner,C., Mermelstein,P.G., Holden,W.T. and Surmeier,D.J.
  TITLE     CIPP, a novel multivalent PDZ domain protein, selectively interacts
            with Kir4.0 family members, NMDA receptor subunits, neurexins, and
            neuroligins
  JOURNAL   Mol Cell Neurosci 11 (3), 161-172 (1998)
   PUBMED   9647694
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from CK340630.1, AK050545.1,
            AK077268.1, CD547724.1 and AL671229.11.
            
            Summary: This gene encodes a multivalent PDZ domain protein, which
            is expressed exclusively in brain and kidney. This protein
            selectively interacts with inward rectifier K+ (Kir) family
            members, N-methyl-D-aspartate receptor subunits, neurexins and
            neuroligins, as well as cell surface molecules enriched in synaptic
            membranes. Thus, this protein may serve as a scaffold that brings
            structurally diverse but functionally connected proteins into close
            proximity at the synapse. Multiple alternatively spliced transcript
            variants encoding different isoforms have been found for this gene.
            [provided by RefSeq, Jul 2008].
            
            Transcript Variant: This variant (2) lacks multiple 3' exons but
            has an alternate 3' segment, as compared to variant 1. The encoded
            isoform (2) has a much shorter and distinct C-terminus, as compared
            to isoform 1.
            
            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##
            RNAseq introns :: single sample supports all introns SAMN00849375,
                              SAMN00849378 [ECO:0000348]
            ##Evidence-Data-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-29                CK340630.1         1-29
            30-1822             AK050545.1         2-1794
            1823-2350           AK077268.1         105-632
            2351-2360           CD547724.1         223-232
            2361-2983           AK077268.1         643-1265
            2984-3335           AL671229.11        113146-113497
FEATURES             Location/Qualifiers
     source          1..3335
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="4"
                     /map="4 45.6 cM"
     gene            1..3335
                     /gene="Patj"
                     /gene_synonym="Cipp; Inadl"
                     /note="PATJ, crumbs cell polarity complex component"
                     /db_xref="GeneID:12695"
                     /db_xref="MGI:MGI:1277960"
     exon            1..99
                     /gene="Patj"
                     /gene_synonym="Cipp; Inadl"
                     /inference="alignment:Splign:2.1.0"
     exon            100..155
                     /gene="Patj"
                     /gene_synonym="Cipp; Inadl"
                     /inference="alignment:Splign:2.1.0"
     CDS             134..3061
                     /gene="Patj"
                     /gene_synonym="Cipp; Inadl"
                     /note="isoform 2 is encoded by transcript variant 2;
                     channel-interacting PDZ domain protein; PALS1-associated
                     tight junction protein; inactivation no after-potential
                     D-like protein; inaD-like protein; novel ankyrin-repeat
                     protein; protein associated to tight junctions;
                     channel-interacting PDZ domain-containing protein"
                     /codon_start=1
                     /product="inaD-like protein isoform 2"
                     /protein_id="NP_001005784.1"
                     /db_xref="GeneID:12695"
                     /db_xref="MGI:MGI:1277960"
                     /translation="MPENPAAEKMQVLQVLDRLRGKLQEKGDTTQNEKLSAFYETLKS
                     PLFNQILTLQQSIKQLKGQLSHIPSDCSANFDFSRKGLLVFTDGSITNGNAQRPCSNV
                     TASELLPWTQKSASEDFNSVIQQMAQGRHVEYIDIERPSTGGLGFSVVALRSQSLGLI
                     DIFVKEVHPGSVADRDHRLKENDQILAINDTPLDQNISHQQAIALLQQATGSLRLVVA
                     REVGHTQGRASTSSADTTLPETVCWGHTEEVELINDGSGLGFGIVGGKSSGVVVRTIV
                     PGGLADRDGRLQTGDHILKIGGTNVQGMTSEQVAQVLRNCGNSVRMLVARDPVGEIAV
                     TPPTPVSLPVALPAVATRTLDSDRSPFETYSVELVKKDGQSLGIRIVGYVGTAHPGEA
                     SGIYVKSIIPGSAAYHNGQIQVNDKIVAVDGVNIQGFANQDVVEVLRNAGQVVHLTLV
                     RRKTSLSASPFEHSSSRETVAEPPKVPERAGSPKPEANLSVEAEEIGERLDNLKNNTV
                     QALEKPDVYPEKVPGSPENELKSRWENLLGPDYEVMVATLDAQIADDEELQKYSKLLP
                     IHTLRLGMEVDSFDGHHYISSVAPGGPVDTLNLLQPEDELLEVNGMQLYGKSRREAVS
                     FLKEVPPPFTLVCCRRLFDDEASVDEPRTMEPALLEAEVDHSVDVNIEDDDDGELALW
                     SPEVKTVELVKDCKGLGFSILDYQDPLDPTRSVIVIRSLVADGVAERSGELLPGDRLV
                     SVNEFSLDNATLAEAVEVLKAVPPGVVHLGICKPLVEDEKEERFSLHSNNNGDSSEPA
                     DAVHEIHSSLILEAPQGFRDEPYLEELVDEPFLDLGKSLQFQQKDVDSSSEAWEMHEF
                     LSPPLDGRGEEREMLVDEEYELYQDHLRAMESNPPPPHIREAAPASPVLELQAGTQWL
                     HANLSGGERLECHDAESMMSAYPQEMQQYSYSTADMVRLCDTATTCSPLCPHTPRSCY
                     FHS"
     exon            156..322
                     /gene="Patj"
                     /gene_synonym="Cipp; Inadl"
                     /inference="alignment:Splign:2.1.0"
     exon            323..517
                     /gene="Patj"
                     /gene_synonym="Cipp; Inadl"
                     /inference="alignment:Splign:2.1.0"
     exon            518..657
                     /gene="Patj"
                     /gene_synonym="Cipp; Inadl"
                     /inference="alignment:Splign:2.1.0"
     exon            658..853
                     /gene="Patj"
                     /gene_synonym="Cipp; Inadl"
                     /inference="alignment:Splign:2.1.0"
     exon            854..982
                     /gene="Patj"
                     /gene_synonym="Cipp; Inadl"
                     /inference="alignment:Splign:2.1.0"
     exon            983..1201
                     /gene="Patj"
                     /gene_synonym="Cipp; Inadl"
                     /inference="alignment:Splign:2.1.0"
     exon            1202..1301
                     /gene="Patj"
                     /gene_synonym="Cipp; Inadl"
                     /inference="alignment:Splign:2.1.0"
     exon            1302..1393
                     /gene="Patj"
                     /gene_synonym="Cipp; Inadl"
                     /inference="alignment:Splign:2.1.0"
     exon            1394..1535
                     /gene="Patj"
                     /gene_synonym="Cipp; Inadl"
                     /inference="alignment:Splign:2.1.0"
     exon            1536..1676
                     /gene="Patj"
                     /gene_synonym="Cipp; Inadl"
                     /inference="alignment:Splign:2.1.0"
     exon            1677..1765
                     /gene="Patj"
                     /gene_synonym="Cipp; Inadl"
                     /inference="alignment:Splign:2.1.0"
     exon            1766..1822
                     /gene="Patj"
                     /gene_synonym="Cipp; Inadl"
                     /inference="alignment:Splign:2.1.0"
     exon            1823..1957
                     /gene="Patj"
                     /gene_synonym="Cipp; Inadl"
                     /inference="alignment:Splign:2.1.0"
     exon            1958..2119
                     /gene="Patj"
                     /gene_synonym="Cipp; Inadl"
                     /inference="alignment:Splign:2.1.0"
     exon            2120..2251
                     /gene="Patj"
                     /gene_synonym="Cipp; Inadl"
                     /inference="alignment:Splign:2.1.0"
     exon            2252..2461
                     /gene="Patj"
                     /gene_synonym="Cipp; Inadl"
                     /inference="alignment:Splign:2.1.0"
     exon            2462..2575
                     /gene="Patj"
                     /gene_synonym="Cipp; Inadl"
                     /inference="alignment:Splign:2.1.0"
     exon            2576..3335
                     /gene="Patj"
                     /gene_synonym="Cipp; Inadl"
                     /inference="alignment:Splign:2.1.0"
     regulatory      3311..3316
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Patj"
                     /gene_synonym="Cipp; Inadl"
                     /note="hexamer: AATAAA"
     polyA_site      3335
                     /gene="Patj"
                     /gene_synonym="Cipp; Inadl"
                     /note="major polyA site"
ORIGIN      
        1 acttccgtcc aggtgagggc agcagctgta cttccgccag gtgaggaggc cgtccgtgcc
       61 cgcagccccg gggctcccac cccgccgtcg cccgatcaga ctttttggaa gtgattgaaa
      121 agaatatccc aaaatgcctg aaaaccctgc tgcagagaag atgcaggtcc tgcaggtcct
      181 ggatcgcctt cgagggaagc tgcaggagaa gggagacacg acgcagaacg agaagctgtc
      241 tgcgttctac gagacgctga agagccctct cttcaaccag atccttacac tgcagcagtc
      301 catcaagcag ctgaagggac agcttagcca catcccctca gattgctcag ccaactttga
      361 cttttctcgc aagggcttgc tagtgttcac ggatggttcc attacaaacg ggaatgccca
      421 aaggccttgt agtaatgtga ctgcatctga actgttgccc tggactcaaa agtcagcaag
      481 tgaagacttt aactcagtca ttcagcagat ggctcagggc cggcacgttg agtatataga
      541 tattgaacgt ccttcaactg gaggccttgg attcagtgtg gtggctctga gaagccaaag
      601 cctgggatta attgatatct ttgtgaagga agtccatccc gggagtgtag cagacaggga
      661 tcacagattg aaggaaaatg accagatttt ggccattaat gacaccccat tggatcagaa
      721 tatttcccat cagcaggcga ttgcattact acaacaagcc actggatctc tgcggctggt
      781 tgtggccagg gaagtgggcc acacacaggg ccgagcatcc accagctcag ctgatacaac
      841 tctgccagaa acggtgtgtt ggggccacac ggaagaggtt gagctcatta acgatggctc
      901 tggattaggt tttgggatag ttggagggaa atccagcggc gtggtcgtga ggactattgt
      961 tcctggagga ctggcagacc gagatggaag actgcagaca ggggatcaca tcttgaagat
     1021 tggtggtaca aatgttcaag ggatgaccag tgaacaagtt gctcaagtgc taaggaactg
     1081 tgggaattca gtgaggatgc tggtggccag agaccctgtt ggtgaaattg cagtaacacc
     1141 tcctacccct gtatccttac ctgttgccct acctgctgta gccacaagga cccttgattc
     1201 tgacaggtct ccttttgaaa cttacagtgt tgaacttgtt aagaaagatg ggcagagtct
     1261 tgggattaga attgttggct atgttggaac agctcatcca ggggaagctt ccgggattta
     1321 tgtgaaaagt ataattccag gcagcgctgc ataccacaat ggccaaattc aagtgaatga
     1381 taaaatcgtg gctgtggatg gtgtgaatat tcaaggtttt gctaatcagg atgttgtcga
     1441 agtattgcgg aatgctgggc aggtggtaca cctgaccctt gttcgaagga aaacatcttt
     1501 atctgcttct ccgtttgagc actcttcaag cagagaaact gttgcagaac cacctaaagt
     1561 accagaacga gcaggatccc cgaaaccaga agctaatttg agtgtggaag cagaggaaat
     1621 tggagaaaga ctggataatc taaaaaacaa cactgtacaa gccttagaaa aaccagatgt
     1681 atatccagag aaagttccag gctctccaga aaatgagctg aaatccagat gggaaaacct
     1741 actgggccca gattatgaag taatggtagc cactttggat gctcagattg cagacgatga
     1801 ggagctacag aaatactcga agctgctgcc tatccacacg ctcaggcttg ggatggaagt
     1861 cgactccttc gatgggcacc actatatctc ctcagttgct cctgggggtc ctgtggatac
     1921 cctgaacctc cttcagccag aggatgaact tcttgaggtc aacggcatgc agctttatgg
     1981 gaagtctcgc cgagaagcag tctccttcct taaagaagtg cccccaccat ttaccttggt
     2041 ctgctgccgc cggctgtttg atgatgaggc ctcagttgat gagccaagaa ccatggagcc
     2101 tgctcttctt gaggccgagg ttgaccacag tgtagatgtc aacattgaag atgatgatga
     2161 tggagaatta gccctgtggt ctcctgaagt caagactgtg gagctggtga aagactgcaa
     2221 aggcttagga ttcagtattt tggattatca ggaccccctg gatcccacgc ggtcagtgat
     2281 tgtgattcgc tccttggtgg cagatggtgt agcggaaaga agtggagaac ttttacctgg
     2341 agatcgccta gtctccgtca atgagttctc cttggacaat gccactcttg ctgaggctgt
     2401 ggaagtgttg aaggctgtac ccccaggtgt ggtgcatctt ggcatctgta agcctttggt
     2461 ggaagatgag aaggaagagc gttttagttt acattcaaac aacaatggtg acagcagcga
     2521 gcctgcagac gctgttcatg agatccactc atctttaatc cttgaggcac cccagggatt
     2581 tagagatgag ccatatcttg aagaactcgt ggatgaacct tttctagatt tgggaaagtc
     2641 tttgcagttc caacaaaaag acgtggacag cagctcggaa gcttgggaaa tgcatgagtt
     2701 cctgagtcct ccgctggacg gcaggggtga ggagagagag atgcttgtcg atgaggagta
     2761 tgaactttat caagatcacc tccgggccat ggagtcaaac ccaccaccac cacacattcg
     2821 ggaggccgct cctgcatctc ccgtgctgga actccaggct ggtacacagt ggctgcatgc
     2881 taacctctca ggaggcgaaa ggctggagtg tcacgatgca gagtccatga tgagtgccta
     2941 tccccaggag atgcagcagt atagctacag cactgcagac atggtacggc tttgcgacac
     3001 agccaccacc tgctccccgc tctgccccca cacccctcgc tcatgttact tccattcata
     3061 aggcagaact gaatgggctt ctcacagtta gcatggccga caggatgcac tgccaggagc
     3121 tgagctgtgt ccttgaggtc actccttttt gtgtctcacc gcttctctgg aatcatgagc
     3181 tagtgggttt tcgctggttt tttgttttgt tttatttttc tgttgttgtt attggtagtg
     3241 gtggtggtgg gttttttggt tttgttttgt ttgtcgtgtg tgtaacattt ttctcctcac
     3301 ttcttagttc aataaagagt ccttttaatc cttaa
//
