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    Nphp1 nephrocystin 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 296136, updated on 27-Dec-2024

    Summary

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    Official Symbol
    Nphp1provided by RGD
    Official Full Name
    nephrocystin 1provided by RGD
    Primary source
    RGD:1308136
    See related
    EnsemblRapid:ENSRNOG00000015756 AllianceGenome:RGD:1308136
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to be involved in several processes, including photoreceptor cell outer segment organization; positive regulation of bicellular tight junction assembly; and protein localization involved in establishment of planar polarity. Predicted to be located in several cellular components, including ciliary base; motile cilium; and photoreceptor distal connecting cilium. Predicted to be active in cilium and cytoplasm. Human ortholog(s) of this gene implicated in Bardet-Biedl syndrome; Joubert syndrome 4; Senior-Loken syndrome; nephronophthisis; and nephronophthisis 1. Orthologous to human NPHP1 (nephrocystin 1). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Testes (RPKM 256.3), Muscle (RPKM 123.4) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Nphp1 in Genome Data Viewer
    Location:
    3q36
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 3 NC_086021.1 (135413927..135469505, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 3 NC_051338.1 (114960650..115016234, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 3 NC_005102.4 (120316048..120370089, complement)

    Chromosome 3 - NC_086021.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC102555822 Neighboring gene mal, T-cell differentiation protein-like Neighboring gene WW domain containing adaptor with coiled-coil, pseudogene 2 Neighboring gene mitoregulin Neighboring gene BUB1 mitotic checkpoint serine/threonine kinase

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Stop codon at arginine 586 is the prevalent nephronopthisis type 1 mutation in Italy. Caridi G, et al. Nephrol Dial Transplant, 2006 Aug. PMID 16762963
    2. Clinical characterization and NPHP1 mutations in nephronophthisis and associated ciliopathies: a single center experience. Soliman NA, et al. Saudi J Kidney Dis Transpl, 2012 Sep. PMID 22982934, Free PMC Article
    3. Targeted disruption of Nphp1 causes male infertility due to defects in the later steps of sperm morphogenesis in mice. Jiang ST, et al. Hum Mol Genet, 2008 Nov 1. PMID 18684731
    4. Pseudodominant inheritance of nephronophthisis caused by a homozygous NPHP1 deletion. Hoefele J, et al. Pediatr Nephrol, 2011 Jun. PMID 21258817, Free PMC Article
    5. Nephrocystin specifically localizes to the transition zone of renal and respiratory cilia and photoreceptor connecting cilia. Fliegauf M, et al. J Am Soc Nephrol, 2006 Sep. PMID 16885411

    See all (18) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Process Evidence Code Pubs
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    involved_in cell projection organization ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in photoreceptor cell outer segment organization ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of bicellular tight junction assembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein localization ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein localization involved in establishment of planar polarity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in retina development in camera-type eye ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in spermatid differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in cell-cell junction ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in ciliary base ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in ciliary transition zone ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in cilium IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cilium ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in motile cilium ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in photoreceptor connecting cilium ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in photoreceptor distal connecting cilium ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    nephrocystin-1
    Names
    nephronophthisis 1 (juvenile)

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001314002.1 → NP_001300931.1  nephrocystin-1 isoform a

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
      Source sequence(s)
      JAXUCZ010000003
      UniProtKB/TrEMBL
      B5DEX2, D3ZJ87
      Related
      ENSRNOP00000060013.2, ENSRNOT00000067727.4
      Conserved Domains (1) summary
      cd11770
      Location:161 → 213
      SH3_Nephrocystin; Src Homology 3 domain of Nephrocystin (or Nephrocystin-1)

    2. NM_001314003.1 → NP_001300932.1  nephrocystin-1 isoform b

      Status: VALIDATED

      Description
      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.
      Source sequence(s)
      JAXUCZ010000003
      UniProtKB/TrEMBL
      B5DEX2
      Conserved Domains (1) summary
      cd11770
      Location:161 → 213
      SH3_Nephrocystin; Src Homology 3 domain of Nephrocystin (or Nephrocystin-1)

    3. NM_001314004.1 → NP_001300933.1  nephrocystin-1 isoform c

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) uses two alternate in-frame splice sites in the central coding region, compared to variant 1, resulting in an isoform (c) that is 2 aa shorter than isoform a.
      Source sequence(s)
      JAXUCZ010000003
      UniProtKB/TrEMBL
      B5DEX2
      Related
      ENSRNOP00000104569.1, ENSRNOT00000153600.1
      Conserved Domains (1) summary
      cd11770
      Location:161 → 213
      SH3_Nephrocystin; Src Homology 3 domain of Nephrocystin (or Nephrocystin-1)

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCr8

    Genomic

    1. NC_086021.1 Reference GRCr8

      Range
      135413927..135469505 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001106506.1: Suppressed sequence

      Description
      NM_001106506.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein Strain
    Heading Accession and Version

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