LOCUS       NM_001128178            2522 bp    mRNA    linear   PRI 05-OCT-2024
DEFINITION  Homo sapiens nephrocystin 1 (NPHP1), transcript variant 3, mRNA.
ACCESSION   NM_001128178
VERSION     NM_001128178.3
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 2522)
  AUTHORS   Huang,D., Liu,Y., Li,D., Zhang,J., Yang,Y. and Sun,L.
  TITLE     [C/EBPbeta mediates expressions of downstream inflammatory factors
            of the tumor necrosis factor-alpha signaling pathway in renal
            tubular epithelial cells with NPHP1 knockdown]
  JOURNAL   Nan Fang Yi Ke Da Xue Xue Bao 44 (1), 156-165 (2024)
   PUBMED   38293987
  REMARK    GeneRIF: [C/EBPbeta mediates expressions of downstream inflammatory
            factors of the tumor necrosis factor-alpha signaling pathway in
            renal tubular epithelial cells with NPHP1 knockdown].
REFERENCE   2  (bases 1 to 2522)
  AUTHORS   Tong,H., Zhao,F., Yang,Y., Qiu,X., Zhu,L. and Yu,Z.
  TITLE     Scalp Tumor and Hydroureteronephrosis in Patients with
            Nephronophthisis and Homozygous NPHP1 Deletion
  JOURNAL   Clin Pediatr (Phila) 62 (12), 1508-1512 (2023)
   PUBMED   36942623
  REMARK    GeneRIF: Scalp Tumor and Hydroureteronephrosis in Patients with
            Nephronophthisis and Homozygous NPHP1 Deletion.
REFERENCE   3  (bases 1 to 2522)
  AUTHORS   Liu,Y., Qiu,T., Chen,Z., Ma,X., Wang,T., Zhang,Y., Kong,C., Yu,B.,
            Guo,J. and Zhou,J.
  TITLE     A case report of two Chinese monozygotic twins with NPHP1
            gene-associated nephronophthisis undergoing kidney transplantation
            from a related living-donor
  JOURNAL   Transpl Immunol 78, 101828 (2023)
   PUBMED   36948406
  REMARK    GeneRIF: A case report of two Chinese monozygotic twins with NPHP1
            gene-associated nephronophthisis undergoing kidney transplantation
            from a related living-donor.
REFERENCE   4  (bases 1 to 2522)
  AUTHORS   Li,D., Hu,M., Chen,H., Wu,X., Wei,X., Lin,H., Gao,X., Wang,H.,
            Li,M., Ong,A.C.M., Yue,Z. and Sun,L.
  TITLE     An Nphp1 knockout mouse model targeting exon 2-20 demonstrates
            characteristic phenotypes of human nephronophthisis
  JOURNAL   Hum Mol Genet 31 (2), 232-243 (2021)
   PUBMED   34415307
  REMARK    GeneRIF: An Nphp1 knockout mouse model targeting exon 2-20
            demonstrates characteristic phenotypes of human nephronophthisis.
REFERENCE   5  (bases 1 to 2522)
  AUTHORS   Hildebrandt,F., Otto,E., Rensing,C., Nothwang,H.G., Vollmer,M.,
            Adolphs,J., Hanusch,H. and Brandis,M.
  TITLE     A novel gene encoding an SH3 domain protein is mutated in
            nephronophthisis type 1
  JOURNAL   Nat Genet 17 (2), 149-153 (1997)
   PUBMED   9326933
REFERENCE   6  (bases 1 to 2522)
  AUTHORS   Konrad,M., Saunier,S., Heidet,L., Silbermann,F., Benessy,F.,
            Calado,J., Le Paslier,D., Broyer,M., Gubler,M.C. and Antignac,C.
  TITLE     Large homozygous deletions of the 2q13 region are a major cause of
            juvenile nephronophthisis
  JOURNAL   Hum Mol Genet 5 (3), 367-371 (1996)
   PUBMED   8852662
REFERENCE   7  (bases 1 to 2522)
  AUTHORS   Medhioub,M., Cherif,D., Benessy,F., Silbermann,F., Gubler,M.C., Le
            Paslier,D., Cohen,D., Weissenbach,J., Beckmann,J. and Antignac,C.
  TITLE     Refined mapping of a gene (NPH1) causing familial juvenile
            nephronophthisis and evidence for genetic heterogeneity
  JOURNAL   Genomics 22 (2), 296-301 (1994)
   PUBMED   7806215
REFERENCE   8  (bases 1 to 2522)
  AUTHORS   Stokman,M., Lilien,M. and Knoers,N.
  TITLE     Nephronophthisis-Related Ciliopathies
  JOURNAL   (in) Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE and
            Amemiya A (Eds.);
            GENEREVIEWS(R);
            (1993)
   PUBMED   27336129
REFERENCE   9  (bases 1 to 2522)
  AUTHORS   Gunay-Aygun,M., Gahl,W.A. and Heller,T.
  TITLE     Congenital Hepatic Fibrosis Overview horizontal line RETIRED
            CHAPTER, FOR HISTORICAL REFERENCE ONLY
  JOURNAL   (in) Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE and
            Amemiya A (Eds.);
            GENEREVIEWS(R);
            (1993)
   PUBMED   20301743
REFERENCE   10 (bases 1 to 2522)
  AUTHORS   Parisi,M. and Glass,I.
  TITLE     Joubert Syndrome
  JOURNAL   (in) Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE and
            Amemiya A (Eds.);
            GENEREVIEWS(R);
            (1993)
   PUBMED   20301500
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from DB454094.1, AK225600.1,
            AJ001815.1 and BC062574.1.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Sep 17, 2019 this sequence version replaced NM_001128178.2.
            
            Summary: This gene encodes a protein with src homology domain 3
            (SH3) patterns. This protein interacts with Crk-associated
            substrate, and it appears to function in the control of cell
            division, as well as in cell-cell and cell-matrix adhesion
            signaling, likely as part of a multifunctional complex localized in
            actin- and microtubule-based structures. Mutations in this gene
            cause familial juvenile nephronophthisis type 1, a kidney disorder
            involving both tubules and glomeruli. Defects in this gene are also
            associated with Senior-Loken syndrome type 1, also referred to as
            juvenile nephronophthisis with Leber amaurosis, which is
            characterized by kidney and eye disease, and with Joubert syndrome
            type 4, which is characterized by cerebellar ataxia, oculomotor
            apraxia, psychomotor delay and neonatal breathing abnormalities,
            sometimes including retinal dystrophy and renal disease. Multiple
            transcript variants encoding different isoforms have been found for
            this gene. [provided by RefSeq, Jul 2008].
            
            Transcript Variant: This variant (3) uses an alternate in-frame
            splice donor site in the mid-coding region, compared to variant 1,
            resulting in an isoform (3) that is shorter than 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 :: AK225600.1, SRR14038197.1564347.1
                                           [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMEA1965299,
                                           SAMEA1966682 [ECO:0006172]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000445609.7/ ENSP00000389879.3
            RefSeq Select criteria :: based on manual assertion, conservation,
                                      expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-21                DB454094.1         55-75
            22-269              AK225600.1         1-248
            270-698             AJ001815.1         258-686
            699-864             AK225600.1         678-843
            865-2162            BC062574.1         635-1932
            2163-2522           AJ001815.1         2317-2676
FEATURES             Location/Qualifiers
     source          1..2522
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="2"
                     /map="2q13"
     gene            1..2522
                     /gene="NPHP1"
                     /gene_synonym="JBTS4; NPH1; SLSN1"
                     /note="nephrocystin 1"
                     /db_xref="GeneID:4867"
                     /db_xref="HGNC:HGNC:7905"
                     /db_xref="MIM:607100"
     exon            1..114
                     /gene="NPHP1"
                     /gene_synonym="JBTS4; NPH1; SLSN1"
                     /inference="alignment:Splign:2.1.0"
     CDS             46..2079
                     /gene="NPHP1"
                     /gene_synonym="JBTS4; NPH1; SLSN1"
                     /note="isoform 3 is encoded by transcript variant 3;
                     nephronophthisis 1 (juvenile); juvenile nephronophthisis 1
                     protein"
                     /codon_start=1
                     /product="nephrocystin-1 isoform 3"
                     /protein_id="NP_001121650.1"
                     /db_xref="CCDS:CCDS46386.1"
                     /db_xref="GeneID:4867"
                     /db_xref="HGNC:HGNC:7905"
                     /db_xref="MIM:607100"
                     /translation="MLARRQRDPLQALRRRNQELKQQVDSLLSESQLKEALEPNKRQH
                     IYQRCIQLKQAIDENKNALQKLSKADESAPVANYNQRKEEEHTLLDKLTQQLQGLAVT
                     ISRENITEVGAPTEEEEESESEDSEDSGGEEEDAEEEEEEKEENESHKWSTGEEYIAV
                     GDFTAQQVGDLTFKKGEILLVIEKKPDGWWIAKDAKGNEGLVPRTYLEPYSEEEEGQE
                     SSEEGSEEDVEAVDETADGAEVKQRTDPHWSAVQKAISEQINTVDVLTTMGAIPAGFR
                     PSTLSQLLEEGNQFRANYFLQPELMPSQLAFRDLMWDATEGTIRSRPSRISLILTLWS
                     CKMIPLPGMSIQVLSRHVRLCLFDGNKVLSNIHTVRATWQPKKPKTWTFSPQVTRILP
                     CLLDGDCFIRSNSASPDLGILFELGISYIRNSTGERGELSCGWVFLKLFDASGVPIPA
                     KTYELFLNGGTPYEKGIEVDPSISRRAHGSVFYQIMTMRRQPQLLVKLRSLNRRSRNV
                     LSLLPETLIGNMCSIHLLIFYRQILGDVLLKDRMSLQSTDLISHPMLATFPMLLEQPD
                     VMDALRSSWAGKESTLKRSEKRDKEFLKSTFLLVYHDCVLPLLHSTRLPPFRWAEEET
                     ETARWKVITDFLKQNQENQGALQALLSPDGVHEPFDLSEQTYDFLGEMRKNAV"
     exon            115..188
                     /gene="NPHP1"
                     /gene_synonym="JBTS4; NPH1; SLSN1"
                     /inference="alignment:Splign:2.1.0"
     exon            189..249
                     /gene="NPHP1"
                     /gene_synonym="JBTS4; NPH1; SLSN1"
                     /inference="alignment:Splign:2.1.0"
     exon            250..374
                     /gene="NPHP1"
                     /gene_synonym="JBTS4; NPH1; SLSN1"
                     /inference="alignment:Splign:2.1.0"
     exon            375..567
                     /gene="NPHP1"
                     /gene_synonym="JBTS4; NPH1; SLSN1"
                     /inference="alignment:Splign:2.1.0"
     exon            568..669
                     /gene="NPHP1"
                     /gene_synonym="JBTS4; NPH1; SLSN1"
                     /inference="alignment:Splign:2.1.0"
     exon            670..773
                     /gene="NPHP1"
                     /gene_synonym="JBTS4; NPH1; SLSN1"
                     /inference="alignment:Splign:2.1.0"
     exon            774..816
                     /gene="NPHP1"
                     /gene_synonym="JBTS4; NPH1; SLSN1"
                     /inference="alignment:Splign:2.1.0"
     exon            817..904
                     /gene="NPHP1"
                     /gene_synonym="JBTS4; NPH1; SLSN1"
                     /inference="alignment:Splign:2.1.0"
     exon            905..999
                     /gene="NPHP1"
                     /gene_synonym="JBTS4; NPH1; SLSN1"
                     /inference="alignment:Splign:2.1.0"
     exon            1000..1128
                     /gene="NPHP1"
                     /gene_synonym="JBTS4; NPH1; SLSN1"
                     /inference="alignment:Splign:2.1.0"
     exon            1129..1203
                     /gene="NPHP1"
                     /gene_synonym="JBTS4; NPH1; SLSN1"
                     /inference="alignment:Splign:2.1.0"
     exon            1204..1314
                     /gene="NPHP1"
                     /gene_synonym="JBTS4; NPH1; SLSN1"
                     /inference="alignment:Splign:2.1.0"
     exon            1315..1397
                     /gene="NPHP1"
                     /gene_synonym="JBTS4; NPH1; SLSN1"
                     /inference="alignment:Splign:2.1.0"
     exon            1398..1474
                     /gene="NPHP1"
                     /gene_synonym="JBTS4; NPH1; SLSN1"
                     /inference="alignment:Splign:2.1.0"
     exon            1475..1574
                     /gene="NPHP1"
                     /gene_synonym="JBTS4; NPH1; SLSN1"
                     /inference="alignment:Splign:2.1.0"
     exon            1575..1687
                     /gene="NPHP1"
                     /gene_synonym="JBTS4; NPH1; SLSN1"
                     /inference="alignment:Splign:2.1.0"
     exon            1688..1761
                     /gene="NPHP1"
                     /gene_synonym="JBTS4; NPH1; SLSN1"
                     /inference="alignment:Splign:2.1.0"
     exon            1762..1806
                     /gene="NPHP1"
                     /gene_synonym="JBTS4; NPH1; SLSN1"
                     /inference="alignment:Splign:2.1.0"
     exon            1807..2522
                     /gene="NPHP1"
                     /gene_synonym="JBTS4; NPH1; SLSN1"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2141..2146
                     /regulatory_class="polyA_signal_sequence"
                     /gene="NPHP1"
                     /gene_synonym="JBTS4; NPH1; SLSN1"
                     /note="hexamer: AATAAA"
     polyA_site      2162
                     /gene="NPHP1"
                     /gene_synonym="JBTS4; NPH1; SLSN1"
                     /note="major polyA site"
     regulatory      2264..2269
                     /regulatory_class="polyA_signal_sequence"
                     /gene="NPHP1"
                     /gene_synonym="JBTS4; NPH1; SLSN1"
                     /note="hexamer: AATAAA"
     polyA_site      2282
                     /gene="NPHP1"
                     /gene_synonym="JBTS4; NPH1; SLSN1"
     regulatory      2498..2503
                     /regulatory_class="polyA_signal_sequence"
                     /gene="NPHP1"
                     /gene_synonym="JBTS4; NPH1; SLSN1"
                     /note="hexamer: AATAAA"
     polyA_site      2522
                     /gene="NPHP1"
                     /gene_synonym="JBTS4; NPH1; SLSN1"
ORIGIN      
        1 ggtttccctg gcaactggag caatcagagc accgcagcca gggagatgct ggcgagacga
       61 cagcgagatc ctctccaggc cctgcggcgc cgcaatcagg agctgaagca acaggttgat
      121 agtttgcttt ctgagagcca actgaaagaa gctctagaac ccaataaaag acaacatatt
      181 tatcaaagat gtatccagtt aaagcaggca atagatgaaa ataaaaatgc tcttcaaaaa
      241 ttaagcaaag ctgatgaatc tgcacctgtt gcaaactata atcagagaaa agaagaggag
      301 catactcttt tggacaagct tacccaacaa ctgcagggcc ttgctgtgac aataagcaga
      361 gaaaatataa ctgaagttgg ggcacctact gaagaagagg aagaaagtga aagtgaagat
      421 agtgaagaca gtggtgggga ggaagaagat gcagaggagg aagaggaaga gaaagaggaa
      481 aatgaatctc acaaatggtc aaccggtgaa gaatacatcg ctgttggaga ttttactgct
      541 cagcaagttg gagatcttac atttaagaaa ggggaaattc tccttgtaat tgaaaaaaaa
      601 cctgatggtt ggtggatagc taaggatgcc aaaggaaatg aaggtcttgt tcccagaacc
      661 tacctagagc cttatagtga agaagaagaa ggccaagagt caagtgaaga gggcagtgaa
      721 gaagatgtag aggcggtgga tgaaacagca gatggagcag aagttaagca aagaactgat
      781 ccccactgga gtgctgttca gaaagcgatt tcagagcaga taaacactgt tgatgtgtta
      841 actacgatgg gagctattcc tgcagggttc aggccttcca cgctctcaca gcttctggag
      901 gaagggaatc aatttcgagc aaattacttc ttacaaccag agctcatgcc ttcacaactg
      961 gccttcagag atctgatgtg ggatgctaca gaaggcacta ttaggtcgag accaagtcgt
     1021 atttcattga ttctgacatt atggagctgt aaaatgattc ctcttccagg aatgagcata
     1081 caggttctca gcagacatgt acgcctctgt ctatttgatg gtaataaggt tctgagcaac
     1141 attcatacag tcagagccac atggcaacct aaaaagccca aaacatggac cttttctccc
     1201 caggttactc gcatcttacc atgtttgctt gatggtgatt gctttatcag gtctaattct
     1261 gcatctccag atcttggaat attatttgaa cttggaattt cttatattcg caattcaact
     1321 ggtgaaagag gagagttaag ctgtggctgg gtgtttctta aactttttga tgccagtgga
     1381 gttcctattc cagcaaaaac ttatgagctt ttcttgaatg gtggtactcc ttatgaaaaa
     1441 ggtattgaag tggacccttc aatatccaga agagcacacg gcagtgtttt ctaccagatt
     1501 atgacaatga gaaggcagcc tcaacttcta gtgaaactga gatccttgaa cagaagatca
     1561 agaaatgtac taagtctact gccagaaaca ttaattggaa atatgtgttc tattcacttg
     1621 ttgatatttt atcgacaaat tcttggagat gtgctcctga aagacaggat gagcttgcaa
     1681 agtactgatt taattagcca tcccatgctg gccaccttcc ccatgctctt ggagcagcct
     1741 gatgtgatgg atgctctcag gagttcgtgg gctggaaaag aaagcacatt aaaaagatca
     1801 gagaagagag acaaagagtt cctgaagtcc acgtttctcc tggtttacca tgactgcgtg
     1861 ctcccacttc tccactccac acgcctaccc ccattcaggt gggcagaaga agagactgag
     1921 actgcacggt ggaaagttat cactgacttc cttaagcaaa accaagaaaa ccagggcgcc
     1981 ctccaagctc tgctgtcacc agacggagtt catgaacctt ttgacctttc agagcagacc
     2041 tatgacttct tgggtgaaat gagaaagaat gcagtgtgac agtggcagcc tctagccctc
     2101 agcttcccac ggaatcagat ggatcctcca cgattacgtg aataaaatga tggaaccaaa
     2161 aatcactgtc actttacaac ttaggtttta ctcttttctt tctacagacc atatttttaa
     2221 agaaatgttt atacaataat ttaaatattt tttaaaacca taaaataaat ttttataagg
     2281 aatactgtta tatctaaatt taaacagtat ttattttttc aaaaacagct acttaagtta
     2341 atggtataga tttctataaa agcaagattt tgtcaaaaac taaatttatg attattcaag
     2401 aaagtgaaaa aaacaaccta cagaatggga aaacatattt gcaaatcatc taactgataa
     2461 aggtctagta tccaaaatat ttaaatttat gagtgttaat aaaatttatc ttgttcaatg
     2521 aa
//
