LOCUS       NM_007704               3855 bp    mRNA    linear   ROD 30-APR-2024
DEFINITION  Mus musculus PATJ, crumbs cell polarity complex component (Patj),
            transcript variant 3, mRNA.
ACCESSION   NM_007704
VERSION     NM_007704.2
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 3855)
  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 3855)
  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 3855)
  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 3855)
  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 3855)
  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 3855)
  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 3855)
  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 3855)
  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 3855)
  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 3855)
  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 BY105808.1, BU851730.1,
            BC037607.1, AV287690.2 and AL670941.11.
            
            On Nov 15, 2004 this sequence version replaced NM_007704.1.
            
            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 (3) lacks multiple 5' exons but
            has an alternate 5' exon, as compared to variant 1. The encoded
            isoform (3) has a much shorter and distinct N-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##
            Transcript exon combination :: AF060539.1, SRR1660815.108532.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN01164131, SAMN01164134
                                           [ECO:0000348]
            ##Evidence-Data-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-214               BY105808.1         31-244
            215-252             BU851730.1         215-252
            253-339             BY105808.1         283-369
            340-2053            BC037607.1         12-1725
            2054-2607           AV287690.2         115-668
            2608-3855           AL670941.11        45671-46918
FEATURES             Location/Qualifiers
     source          1..3855
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="4"
                     /map="4 45.6 cM"
     gene            1..3855
                     /gene="Patj"
                     /gene_synonym="Cipp; Inadl"
                     /note="PATJ, crumbs cell polarity complex component"
                     /db_xref="GeneID:12695"
                     /db_xref="MGI:MGI:1277960"
     exon            1..371
                     /gene="Patj"
                     /gene_synonym="Cipp; Inadl"
                     /inference="alignment:Splign:2.1.0"
     CDS             350..2188
                     /gene="Patj"
                     /gene_synonym="Cipp; Inadl"
                     /note="isoform 3 is encoded by transcript variant 3;
                     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 3"
                     /protein_id="NP_031730.1"
                     /db_xref="CCDS:CCDS18376.1"
                     /db_xref="GeneID:12695"
                     /db_xref="MGI:MGI:1277960"
                     /translation="MVHGGFPEKIRQRYADLPGELHIIELEKDKNGLGLSLAGNKDRS
                     RMSIFVVGINPEGPAAADGRMRIGDELLEINNQILYGRSHQNASAIIKTAPTRVKLVF
                     IRNEDAVSQMAVAPFPELSHSPSPVEDLGGTELVSSEEESSVDAKHLPEPESSKPEDL
                     SQVVDDNMVAEQQKESESPDSAACQIKQQTYSTQVSSSSQDSPSSPAPLCQSAHADVT
                     GSGNFQAPLPVDPAPLSVDPATCPIVPGQEMIIEISKGRSGLGLSIVGGKDTPLDAIV
                     IHEVYEEGAAARDGRLWAGDQILEVNGVDLRSSSHEEAITALRQTPQKVRLVVYRDEA
                     QYRDEENLEVFLVDLQKKTGRGLGLSIVGKRSGSGVFISDIVKGGAADLDGRLIRGDQ
                     ILSVNGEDMRHASQETVATILKCVQGLVQLEIGRLRAGSWAASRKTSQNSQGDQHSAH
                     SSCRPSFAPVITSLQNLVGTKRSSDPPQKCTEEEPRTVEIIRELSDALGISIAGGKGS
                     PLGDIPIFIAMIQANGVAARTQKLKVGDRIVSINGQPLDGLSHTDAVNLLKNAFGRII
                     LQVVADTNISAIATQLEIMSAGSQLGSPTADRHPEDTEEQMQRTAD"
     exon            372..568
                     /gene="Patj"
                     /gene_synonym="Cipp; Inadl"
                     /inference="alignment:Splign:2.1.0"
     exon            569..660
                     /gene="Patj"
                     /gene_synonym="Cipp; Inadl"
                     /inference="alignment:Splign:2.1.0"
     exon            661..733
                     /gene="Patj"
                     /gene_synonym="Cipp; Inadl"
                     /inference="alignment:Splign:2.1.0"
     exon            734..820
                     /gene="Patj"
                     /gene_synonym="Cipp; Inadl"
                     /inference="alignment:Splign:2.1.0"
     exon            821..892
                     /gene="Patj"
                     /gene_synonym="Cipp; Inadl"
                     /inference="alignment:Splign:2.1.0"
     exon            893..1010
                     /gene="Patj"
                     /gene_synonym="Cipp; Inadl"
                     /inference="alignment:Splign:2.1.0"
     exon            1011..1165
                     /gene="Patj"
                     /gene_synonym="Cipp; Inadl"
                     /inference="alignment:Splign:2.1.0"
     exon            1166..1249
                     /gene="Patj"
                     /gene_synonym="Cipp; Inadl"
                     /inference="alignment:Splign:2.1.0"
     exon            1250..1443
                     /gene="Patj"
                     /gene_synonym="Cipp; Inadl"
                     /inference="alignment:Splign:2.1.0"
     exon            1444..1591
                     /gene="Patj"
                     /gene_synonym="Cipp; Inadl"
                     /inference="alignment:Splign:2.1.0"
     exon            1592..1678
                     /gene="Patj"
                     /gene_synonym="Cipp; Inadl"
                     /inference="alignment:Splign:2.1.0"
     exon            1679..1787
                     /gene="Patj"
                     /gene_synonym="Cipp; Inadl"
                     /inference="alignment:Splign:2.1.0"
     exon            1788..1825
                     /gene="Patj"
                     /gene_synonym="Cipp; Inadl"
                     /inference="alignment:Splign:2.1.0"
     exon            1826..1948
                     /gene="Patj"
                     /gene_synonym="Cipp; Inadl"
                     /inference="alignment:Splign:2.1.0"
     exon            1949..2053
                     /gene="Patj"
                     /gene_synonym="Cipp; Inadl"
                     /inference="alignment:Splign:2.1.0"
     exon            2054..2160
                     /gene="Patj"
                     /gene_synonym="Cipp; Inadl"
                     /inference="alignment:Splign:2.1.0"
     exon            2161..3855
                     /gene="Patj"
                     /gene_synonym="Cipp; Inadl"
                     /inference="alignment:Splign:2.1.0"
     regulatory      3837..3842
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Patj"
                     /gene_synonym="Cipp; Inadl"
                     /note="hexamer: AATACA"
     polyA_site      3855
                     /gene="Patj"
                     /gene_synonym="Cipp; Inadl"
                     /note="major polyA site"
ORIGIN      
        1 tgcagtccct aagtatgcag ggtgaccgag cgtcagggcc agcagcagcc tgcagcatcc
       61 aaggatctga ctggagaacc agggattttt gccggcagac cttgcaggca gctctcacct
      121 actggcagat gtgactctta gcttgaggga gagattgaaa tgagcttcag tgattgtttc
      181 ccatggtagg aacagaatgg caggttgccc tttaaaagaa taaaatcgga gggaaaaaga
      241 atagaggccc aaggtcgtgg gaagagagga cagagttgga gagagtggag ctgcttccag
      301 catcttcctg tcaggaatgc agcaaccctg aagagagcag tcctgcagca tggtccacgg
      361 gggcttccca gaaaagatca ggcaaagata tgcagacctg ccgggagaac tacacattat
      421 cgaactggaa aaggacaaga atggactggg gctcagtctc gctggcaata aggacaggtc
      481 acggatgagc atcttcgtgg tggggattaa tccggaggga cctgctgctg cagacggacg
      541 gatgcggatt ggagacgagc tgctagagat aaacaatcag attctttatg gaagaagtca
      601 tcagaacgca tctgccatta ttaagactgc cccaaccagg gtcaaactgg ttttcattag
      661 aaacgaagat gcagtcagtc agatggccgt cgctcccttc ccggagctat cacattctcc
      721 atcgcctgtt gaggatctgg gtggcactga acttgtcagt agtgaagagg agagcagtgt
      781 ggatgctaaa cacctgcctg aaccagaaag ctccaaaccg gaagacctgt cccaggtggt
      841 tgatgacaac atggtggcag agcagcagaa ggaatcggag tcacctgaca gtgctgcctg
      901 ccagataaaa cagcagacat attcaacaca agtctcctcc agctcgcaag atagcccatc
      961 gtcaccggct ccattgtgtc agtcagcaca tgcagacgtc acaggctctg gtaacttcca
     1021 ggctcctctc ccagtggacc ctgctccact ctcggtggac cctgcaacat gtcccatcgt
     1081 ccctggccag gaaatgatca tagaaatatc caagggacgc tccgggctcg ggctcagcat
     1141 tgttggagga aaagacacac ctttggatgc tatagttatc catgaagtct atgaagaagg
     1201 tgcagctgcc agagatggaa gattatgggc tggagaccag atattagagg ttaatggggt
     1261 tgatctgcgg agctccagcc atgaagaagc catcacagcc ctgaggcaga ccccccagaa
     1321 ggtgcggctg gtggtataca gagatgaagc acagtacaga gacgaggaga acttggaggt
     1381 gttccttgtg gacctgcaga agaagactgg ccgaggacta ggcctgagca ttgttgggaa
     1441 acggagtgga agtggagtgt ttatttctga cattgtgaaa ggcggggccg cagacctcga
     1501 tgggaggtta attcgaggag accagatctt gtctgtgaat ggagaggaca tgagacacgc
     1561 ctcacaggag acagtggcca ccatcctgaa gtgtgtccag ggccttgtcc agctggagat
     1621 tgggagactc cgcgccggtt cctgggccgc ctctcggaag acctcgcaga acagccaggg
     1681 ggatcagcac agtgcgcaca gcagctgtcg gccttccttt gccccagtca tcaccagcct
     1741 acaaaacctg gttggcacaa aaagatcttc agatcctcca cagaaatgca cagaggagga
     1801 accaaggact gtagagataa tcagagagct cagcgatgcc cttgggatca gtatcgctgg
     1861 aggaaaaggg agtcctttag gagatatccc catatttatt gccatgattc aggccaacgg
     1921 agtggccgca cggacccaga agcttaaggt tggagatcgg attgtgagca ttaatggaca
     1981 acctctggat ggactgtctc acacagatgc cgttaatcta ctgaagaatg ccttcgggcg
     2041 cattatcctg caggttgtgg cagataccaa cataagtgcc atagcgaccc agctggaaat
     2101 catgtctgca ggctcccagc ttggctctcc gactgctgac cgacatccgg aagacacaga
     2161 ggagcagatg cagaggacgg ctgattaaag tgaagtgacc agatcttagc tgaaatggcg
     2221 agaccctgga aggcattacc atgagcaagc tgcctccatt ctaaagcagc agagagggac
     2281 tgtggccttg actgtgctgc cgtgagctgc gggtcctgat catgacacac tttttcacga
     2341 gactgctgca gaattctgcg gcttctggtt gggatgaaca gttgcctcgg ctaaagccca
     2401 gcatcatcac tggctctgac tctgtttgca gaaacagagc tgctgtctct gcttcctgct
     2461 catatccctc atccccacag aggcttagct gcaagctcct gtggtctcat ctaatgagta
     2521 gaaacaaagg tttagcttgt catcttaact cgtgatttac ttatgctaat ttgcctcttc
     2581 aaataaacca gaaaacatta gcagtgtaat taacttcctc gcaatgaact attcatactc
     2641 tgccgctggg aattactgcg ttctgttctg tgtgactcag tcaagtagac ctcgcatccc
     2701 tgcctctaga ttgatctgct gttagtcctt ggtgattcgg aggagtccat ttacagactt
     2761 tgtaatctac ttggagtcct aacaggcgtt gattctgagt ttgacaagcg cacactgctc
     2821 agcaagtatg ccttggtctc cacaggaaca agtaaccctc gagtttgagt tccacccatg
     2881 ctagctcaca ttactgggac gctaactggg agtggtgggc atctcagcag atcggaatca
     2941 cccgttccct acccccctag actgcaggtg aggaggtgga aaccctagac cacactgtag
     3001 actgtagaga tgagcaagtt cgatcggcct cagccttatc agaagcaagt tacaagtttg
     3061 gttagccttt ctctcacctt cgtaccaacc tgcacagtgg ctcagcctgc agcggctgtg
     3121 tgcagctcgg gaacttaaag caaatgacct gggaatcaga cacagaagtg cttagcttga
     3181 gtttcccagc ctctacctcc tattggctga agttctgtag ctaagaaagc agctgtggct
     3241 gagagcatca agagtcctca gagcatgcaa tgggctggga agggagatgg atggtcatca
     3301 ccaagcaccg tagagtcgtc tgttgaaagc aaaggaaact accacgaagg gtcagcaata
     3361 gacatagctt agcattctag gactataact cgatgcagca gaatgttcag taattaccca
     3421 gaatttaatg ggccctaatt taaaatgtta tttaattagt gaggatttta actgatattc
     3481 cttttgagta gatgcaatcc caaagtgcat taactcttgt ggctattcta aagtgcagaa
     3541 tgcctcaatt ttatgttgat ggtgtattcc aatgactggt attaagcttt ttgagattct
     3601 gtagggtttt tagaatttat aatgtatcca aaatacatgg ttttggtagg ctctcatctc
     3661 ccagttcatg agaagccacc aacctcagtg tcctctgtga atggtaccca aaagaaggtc
     3721 tcaagcagca aaaaccaaat gaagcccaaa tgaaagtgca ccttagaaga caaagataac
     3781 agcattaatg ctctccaagt gcgatcttgc ttacttttga tggaatggcg gcgttaaata
     3841 cacattttga aatga
//
