LOCUS       NM_001314003            2327 bp    mRNA    linear   ROD 29-MAR-2024
DEFINITION  Rattus norvegicus nephrocystin 1 (Nphp1), transcript variant 2,
            mRNA.
ACCESSION   NM_001314003
VERSION     NM_001314003.1
KEYWORDS    RefSeq; RefSeq Select.
SOURCE      Rattus norvegicus (Norway rat)
  ORGANISM  Rattus norvegicus
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
            Muroidea; Muridae; Murinae; Rattus.
REFERENCE   1  (bases 1 to 2327)
  AUTHORS   Dharmat,R., Eblimit,A., Robichaux,M.A., Zhang,Z., Nguyen,T.T.,
            Jung,S.Y., He,F., Jain,A., Li,Y., Qin,J., Overbeek,P., Roepman,R.,
            Mardon,G., Wensel,T.G. and Chen,R.
  TITLE     SPATA7 maintains a novel photoreceptor-specific zone in the distal
            connecting cilium
  JOURNAL   J Cell Biol 217 (8), 2851-2865 (2018)
   PUBMED   29899041
REFERENCE   2  (bases 1 to 2327)
  AUTHORS   Lindstrand,A., Davis,E.E., Carvalho,C.M., Pehlivan,D., Willer,J.R.,
            Tsai,I.C., Ramanathan,S., Zuppan,C., Sabo,A., Muzny,D., Gibbs,R.,
            Liu,P., Lewis,R.A., Banin,E., Lupski,J.R., Clark,R. and Katsanis,N.
  TITLE     Recurrent CNVs and SNVs at the NPHP1 locus contribute pathogenic
            alleles to Bardet-Biedl syndrome
  JOURNAL   Am J Hum Genet 94 (5), 745-754 (2014)
   PUBMED   24746959
REFERENCE   3  (bases 1 to 2327)
  AUTHORS   Cui,C., Chatterjee,B., Lozito,T.P., Zhang,Z., Francis,R.J.,
            Yagi,H., Swanhart,L.M., Sanker,S., Francis,D., Yu,Q., San
            Agustin,J.T., Puligilla,C., Chatterjee,T., Tansey,T., Liu,X.,
            Kelley,M.W., Spiliotis,E.T., Kwiatkowski,A.V., Tuan,R.,
            Pazour,G.J., Hukriede,N.A. and Lo,C.W.
  TITLE     Wdpcp, a PCP protein required for ciliogenesis, regulates
            directional cell migration and cell polarity by direct modulation
            of the actin cytoskeleton
  JOURNAL   PLoS Biol 11 (11), e1001720 (2013)
   PUBMED   24302887
REFERENCE   4  (bases 1 to 2327)
  AUTHORS   Soliman,N.A., Hildebrandt,F., Otto,E.A., Nabhan,M.M., Allen,S.J.,
            Badr,A.M., Sheba,M., Fadda,S., Gawdat,G. and El-Kiky,H.
  TITLE     Clinical characterization and NPHP1 mutations in nephronophthisis
            and associated ciliopathies: a single center experience
  JOURNAL   Saudi J Kidney Dis Transpl 23 (5), 1090-1098 (2012)
   PUBMED   22982934
REFERENCE   5  (bases 1 to 2327)
  AUTHORS   Sang,L., Miller,J.J., Corbit,K.C., Giles,R.H., Brauer,M.J.,
            Otto,E.A., Baye,L.M., Wen,X., Scales,S.J., Kwong,M.,
            Huntzicker,E.G., Sfakianos,M.K., Sandoval,W., Bazan,J.F.,
            Kulkarni,P., Garcia-Gonzalo,F.R., Seol,A.D., O'Toole,J.F., Held,S.,
            Reutter,H.M., Lane,W.S., Rafiq,M.A., Noor,A., Ansar,M., Devi,A.R.,
            Sheffield,V.C., Slusarski,D.C., Vincent,J.B., Doherty,D.A.,
            Hildebrandt,F., Reiter,J.F. and Jackson,P.K.
  TITLE     Mapping the NPHP-JBTS-MKS protein network reveals ciliopathy
            disease genes and pathways
  JOURNAL   Cell 145 (4), 513-528 (2011)
   PUBMED   21565611
REFERENCE   6  (bases 1 to 2327)
  AUTHORS   Otto,E.A., Helou,J., Allen,S.J., O'Toole,J.F., Wise,E.L.,
            Ashraf,S., Attanasio,M., Zhou,W., Wolf,M.T. and Hildebrandt,F.
  TITLE     Mutation analysis in nephronophthisis using a combined approach of
            homozygosity mapping, CEL I endonuclease cleavage, and direct
            sequencing
  JOURNAL   Hum Mutat 29 (3), 418-426 (2008)
   PUBMED   18076122
REFERENCE   7  (bases 1 to 2327)
  AUTHORS   Hoefele,J., Wolf,M.T., O'Toole,J.F., Otto,E.A., Schultheiss,U.,
            Deschenes,G., Attanasio,M., Utsch,B., Antignac,C. and
            Hildebrandt,F.
  TITLE     Evidence of oligogenic inheritance in nephronophthisis
  JOURNAL   J Am Soc Nephrol 18 (10), 2789-2795 (2007)
   PUBMED   17855640
REFERENCE   8  (bases 1 to 2327)
  AUTHORS   Tory,K., Lacoste,T., Burglen,L., Moriniere,V., Boddaert,N.,
            Macher,M.A., Llanas,B., Nivet,H., Bensman,A., Niaudet,P.,
            Antignac,C., Salomon,R. and Saunier,S.
  TITLE     High NPHP1 and NPHP6 mutation rate in patients with Joubert
            syndrome and nephronophthisis: potential epistatic effect of NPHP6
            and AHI1 mutations in patients with NPHP1 mutations
  JOURNAL   J Am Soc Nephrol 18 (5), 1566-1575 (2007)
   PUBMED   17409309
REFERENCE   9  (bases 1 to 2327)
  AUTHORS   Fliegauf,M., Horvath,J., von Schnakenburg,C., Olbrich,H.,
            Muller,D., Thumfart,J., Schermer,B., Pazour,G.J., Neumann,H.P.,
            Zentgraf,H., Benzing,T. and Omran,H.
  TITLE     Nephrocystin specifically localizes to the transition zone of renal
            and respiratory cilia and photoreceptor connecting cilia
  JOURNAL   J Am Soc Nephrol 17 (9), 2424-2433 (2006)
   PUBMED   16885411
REFERENCE   10 (bases 1 to 2327)
  AUTHORS   Caridi,G., Dagnino,M., Trivelli,A., Emma,F., Perfumo,F. and
            Ghiggeri,G.M.
  TITLE     Stop codon at arginine 586 is the prevalent nephronopthisis type 1
            mutation in Italy
  JOURNAL   Nephrol Dial Transplant 21 (8), 2301-2303 (2006)
   PUBMED   16762963
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            JAXUCZ010000003.1.
            
            Transcript Variant: This variant (2) uses an alternate in-frame
            splice site in the central coding region, compared to variant 1,
            resulting in an isoform (b) that is 1 aa shorter than isoform a.
            
            Sequence Note: This RefSeq record was created from genomic sequence
            data to make the sequence consistent with the reference genome
            assembly. The genomic coordinates used for the transcript record
            were based on transcript alignments and orthologous data.
            
            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 :: SRR26643299.15912.1,
                                           SRR26360176.2249700.1 [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMEA5760383,
                                           SAMEA5760389 [ECO:0006172]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on conservation, expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-104               JAXUCZ010000003.1  135469402-135469505 c
            105-178             JAXUCZ010000003.1  135465062-135465135 c
            179-239             JAXUCZ010000003.1  135464083-135464143 c
            240-364             JAXUCZ010000003.1  135462185-135462309 c
            365-569             JAXUCZ010000003.1  135455284-135455488 c
            570-671             JAXUCZ010000003.1  135448575-135448676 c
            672-832             JAXUCZ010000003.1  135446449-135446609 c
            833-875             JAXUCZ010000003.1  135445789-135445831 c
            876-963             JAXUCZ010000003.1  135444759-135444846 c
            964-1058            JAXUCZ010000003.1  135441023-135441117 c
            1059-1187           JAXUCZ010000003.1  135438872-135439000 c
            1188-1262           JAXUCZ010000003.1  135433493-135433567 c
            1263-1373           JAXUCZ010000003.1  135431949-135432059 c
            1374-1456           JAXUCZ010000003.1  135430416-135430498 c
            1457-1533           JAXUCZ010000003.1  135428486-135428562 c
            1534-1633           JAXUCZ010000003.1  135426598-135426697 c
            1634-1746           JAXUCZ010000003.1  135420912-135421024 c
            1747-1820           JAXUCZ010000003.1  135418828-135418901 c
            1821-1865           JAXUCZ010000003.1  135416096-135416140 c
            1866-2327           JAXUCZ010000003.1  135413927-135414388 c
FEATURES             Location/Qualifiers
     source          1..2327
                     /organism="Rattus norvegicus"
                     /mol_type="mRNA"
                     /strain="BN"
                     /db_xref="taxon:10116"
                     /chromosome="3"
                     /map="3q36"
     gene            1..2327
                     /gene="Nphp1"
                     /note="nephrocystin 1"
                     /db_xref="GeneID:296136"
                     /db_xref="RGD:1308136"
     exon            1..104
                     /gene="Nphp1"
                     /inference="alignment:Splign:2.1.0"
     CDS             36..2138
                     /gene="Nphp1"
                     /note="isoform b is encoded by transcript variant 2;
                     nephronophthisis 1 (juvenile)"
                     /codon_start=1
                     /product="nephrocystin-1 isoform b"
                     /protein_id="NP_001300932.1"
                     /db_xref="GeneID:296136"
                     /db_xref="RGD:1308136"
                     /translation="MLARRPRDPLQALRRRGQELKLQVDSLVTESQLTGALEPSKRRD
                     IYQRCIQLKQAVDENKNALQKLNKADEAAPVGNYEQRKEEEHTLLEKLACQLQELAVG
                     ISRKDTLKVEAHSDKEEDDTTEDDEEETEETGGEEEESEGDEEGKQEQASPEHAETVT
                     YIALGDFAAQQAGDLTFKKGDILHIIEKRPDGWWLAKDAEGGEGLIPRTYLEPYNKED
                     KLESSEGSEEGDEEGVGEDGEDGEDGEDGEEDVEVVDETADGAQVKQRTDSHWSAVRK
                     AISEQINTVDVLATMGAIPAGFRPSTLSQLLDEGGRFRASYFLQPELTTSQLAFRDLT
                     WDAKTGTIMSRPSRVSLILTLWSCKMIPLPGTSIQVLSRHIRLCLFDGSKVLSNIHTV
                     RAVWQPKKPKTWTFSPQVTGILPCLLDGDCFIRSNSSTPDLGILFELGISYIRNSTGE
                     RGELSCGWVFLKLFDASGVPIPAKTYELFLNGGTPYEKGVEVDPSVSRRAQGSVFRQM
                     ISVRRQPQLLVKLRSLNRRSRAMLSLLPETLVGSMCSAHLLIFYRQILGDVLLRDRTS
                     LQSADLISHPVLATFPLLLEQPDVMDALRSSWAEKESTLKRSEKRDKELLKAEFLLVY
                     HDCVLPLLHSTLLPPFRWAEEETEAARWKAIADFLKQSRENEGSLKALLSPDGVHKPF
                     DLSEQTYDFLGEIRKNSG"
     exon            105..178
                     /gene="Nphp1"
                     /inference="alignment:Splign:2.1.0"
     exon            179..239
                     /gene="Nphp1"
                     /inference="alignment:Splign:2.1.0"
     exon            240..364
                     /gene="Nphp1"
                     /inference="alignment:Splign:2.1.0"
     exon            365..569
                     /gene="Nphp1"
                     /inference="alignment:Splign:2.1.0"
     exon            570..671
                     /gene="Nphp1"
                     /inference="alignment:Splign:2.1.0"
     exon            672..832
                     /gene="Nphp1"
                     /inference="alignment:Splign:2.1.0"
     exon            833..875
                     /gene="Nphp1"
                     /inference="alignment:Splign:2.1.0"
     exon            876..963
                     /gene="Nphp1"
                     /inference="alignment:Splign:2.1.0"
     exon            964..1058
                     /gene="Nphp1"
                     /inference="alignment:Splign:2.1.0"
     exon            1059..1187
                     /gene="Nphp1"
                     /inference="alignment:Splign:2.1.0"
     exon            1188..1262
                     /gene="Nphp1"
                     /inference="alignment:Splign:2.1.0"
     exon            1263..1373
                     /gene="Nphp1"
                     /inference="alignment:Splign:2.1.0"
     exon            1374..1456
                     /gene="Nphp1"
                     /inference="alignment:Splign:2.1.0"
     exon            1457..1533
                     /gene="Nphp1"
                     /inference="alignment:Splign:2.1.0"
     exon            1534..1633
                     /gene="Nphp1"
                     /inference="alignment:Splign:2.1.0"
     exon            1634..1746
                     /gene="Nphp1"
                     /inference="alignment:Splign:2.1.0"
     exon            1747..1820
                     /gene="Nphp1"
                     /inference="alignment:Splign:2.1.0"
     exon            1821..1865
                     /gene="Nphp1"
                     /inference="alignment:Splign:2.1.0"
     exon            1866..2327
                     /gene="Nphp1"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      
        1 caaccggcgc ggtcccgccg gcggcggcta ggccaatgct cgcccggcgg ccgcgggacc
       61 cgctgcaggc gctgaggcgc cgcgggcagg agctgaagct gcaggttgat agtttggtta
      121 ctgaaagcca actaacaggt gctctggaac caagtaaaag gagagatatt taccaaagat
      181 gtatccagtt aaaacaggca gtagatgaaa ataaaaacgc tcttcaaaaa ttaaacaaag
      241 ctgacgaagc tgcacctgtg gggaactatg agcagaggaa ggaggaggag cacacacttc
      301 tggagaagct agcctgccag ctgcaggagc ttgctgtggg catcagcagg aaagacactc
      361 tcaaagttga ggcacacagt gacaaggaag aagatgacac cactgaggat gatgaagaag
      421 aaactgaaga aactggtgga gaggaagaag agtcagaagg ggacgaggaa ggaaagcagg
      481 agcaagcctc cccagaacat gcagaaactg tcacatacat tgctcttggg gacttcgctg
      541 ctcagcaggc tggcgacctg acctttaaga aaggagacat tctccatata attgagaaaa
      601 ggcctgatgg ttggtggctg gctaaagatg ctgaaggagg tgaaggtctc attcccagga
      661 cctacttgga gccctataat aaagaagaca agctggaatc aagcgaaggc agtgaggagg
      721 gtgacgagga gggtgtcggt gaggacggtg aggatggtga ggacggtgag gatggtgagg
      781 aggacgtgga ggtggtggat gaaactgcag acggagccca agtgaaacag agaactgatt
      841 cccactggag tgcggttaga aaagctatct cagagcagat aaacacagtt gatgtgttag
      901 ccacaatggg agccattcct gcagggttcc ggccttccac actctcccag ctgctggatg
      961 aagggggccg ctttcgagca agctacttct tgcagccgga gctcacgaca tcacagctgg
     1021 ccttcaggga tctaacgtgg gatgccaaga caggcacgat catgtcaaga ccaagtcgtg
     1081 tttcattgat tctgacccta tggagctgta aaatgattcc tctcccagga acaagcatac
     1141 aggtcctcag cagacacatc cgcctctgcc tgtttgacgg cagcaaggtc ctgagtaata
     1201 ttcatacagt ccgtgccgtg tggcagccta aaaagccaaa aacatggacc ttttctcctc
     1261 aggtcactgg catcttgcca tgcttgctcg atggtgactg ttttatcagg tccaattctt
     1321 caactccaga cctcgggata ttatttgaac ttggaatttc ttatattcgc aattcgactg
     1381 gtgagagagg agagttaagc tgtggctggg tgtttcttaa gcttttcgat gccagtggag
     1441 ttcctattcc agcaaaaaca tacgaactct tcctgaatgg cggcactcct tatgaaaaag
     1501 gtgttgaagt agacccttca gtgtccagaa gagcacaggg cagtgttttc cgtcagatga
     1561 taagtgtgcg gaggcaacct caacttctgg tgaaacttcg gtctctgaac aggaggtcaa
     1621 gggccatgct cagtctgctg ccagaaacct tggtggggag tatgtgctcc gctcacttgc
     1681 tgatatttta ccgacaaatt cttggagatg tgctcctgag agacaggaca agcctgcaaa
     1741 gtgctgattt aattagtcac cccgtgctgg ccaccttccc tctgctcctg gagcagcccg
     1801 atgtgatgga tgctctcagg agttcctggg ctgagaaaga aagcacacta aagcgatcgg
     1861 agaagagaga caaagagctc ctaaaggccg agttcctcct ggtctaccat gactgcgtgc
     1921 tccctcttct gcattccaca ttgctgcccc cctttaggtg ggccgaggaa gagacagagg
     1981 ctgctagatg gaaagccatc gctgacttcc tcaagcaaag ccgagagaac gagggttccc
     2041 tgaaggctct tctgtcacca gatggagttc acaaaccatt tgacctttca gagcagacct
     2101 atgacttctt gggtgaaata agaaagaact caggctaatg atggccatgg ctcccgattc
     2161 ccactggacc cagtgagttc cccaggatga cttggctcaa acaacagaac caaaagaaac
     2221 agactggtta gaacttaggt catattcttt tgtgtgcaaa taatattttc aaaaaactat
     2281 ctaataattt gatgcatgta aaacaataaa ataaatttta taaggaa
//
