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    Nphp4 nephrocystin 4 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 313749, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Nphp4provided by RGD
    Official Full Name
    nephrocystin 4provided by RGD
    Primary source
    RGD:1560172
    See related
    EnsemblRapid:ENSRNOG00000011967 AllianceGenome:RGD:1560172
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    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 negative regulation of canonical Wnt signaling pathway; positive regulation of bicellular tight junction assembly; and protein localization to ciliary transition zone. Predicted to act upstream of or within several processes, including flagellated sperm motility; photoreceptor cell maintenance; and photoreceptor cell outer segment organization. Located in ciliary basal body. Human ortholog(s) of this gene implicated in Joubert syndrome 4; Senior-Loken syndrome; congenital heart disease; nephronophthisis; and nephronophthisis 4. Orthologous to human NPHP4 (nephrocystin 4). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Brain (RPKM 11.4), Adrenal (RPKM 8.7) and 8 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Nphp4 in Genome Data Viewer
    Location:
    5q36
    Exon count:
    32
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 5 NC_086023.1 (168270522..168356393)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 5 NC_051340.1 (162986157..163073708)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 5 NC_005104.4 (169647581..169744662)

    Chromosome 5 - NC_086023.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC120103139 Neighboring gene chromodomain helicase DNA binding protein 5 Neighboring gene potassium voltage-gated channel subfamily A regulatory beta subunit 2 Neighboring gene small ribosomal subunit protein eS27-like Neighboring gene uncharacterized LOC134479049 Neighboring gene uncharacterized LOC102549399

    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. Clinical and histological presentation of 3 siblings with mutations in the NPHP4 gene. Hoefele J, et al. Am J Kidney Dis, 2004 Feb. PMID 14750102
    2. Mutational analysis of the NPHP4 gene in 250 patients with nephronophthisis. Hoefele J, et al. Hum Mutat, 2005 Apr. PMID 15776426
    3. NPHP4 is necessary for normal photoreceptor ribbon synapse maintenance and outer segment formation, and for sperm development. Won J, et al. Hum Mol Genet, 2011 Feb 1. PMID 21078623, Free PMC Article
    4. A gene mutated in nephronophthisis and retinitis pigmentosa encodes a novel protein, nephroretinin, conserved in evolution. Otto E, et al. Am J Hum Genet, 2002 Nov. PMID 12205563, Free PMC Article
    5. Mutation analysis in nephronophthisis using a combined approach of homozygosity mapping, CEL I endonuclease cleavage, and direct sequencing. Otto EA, et al. Hum Mutat, 2008 Mar. PMID 18076122

    See all (17) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC125230

    Gene Ontology Provided by RGD

    Process Evidence Code Pubs
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    acts_upstream_of_or_within flagellated sperm motility ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of canonical Wnt signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of canonical Wnt signaling pathway ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within photoreceptor cell maintenance ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within 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 to ciliary transition zone IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within retina development in camera-type eye 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 centriole ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in centrosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in ciliary basal body IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in ciliary basal body IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in ciliary base IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in ciliary base ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in ciliary transition zone IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in ciliary transition zone ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in intracellular membrane-bounded organelle ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in non-motile cilium IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nuclear body IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nuclear body ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm 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
    		  
    located_in ribbon synapse ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    nephrocystin-4
    Names
    nephronophthisis 4 (juvenile) homolog

    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_001037650.2 → NP_001032739.2  nephrocystin-4

      See identical proteins and their annotated locations for NP_001032739.2

      Status: PROVISIONAL

      Source sequence(s)
      CH473968
      UniProtKB/TrEMBL
      A6IUI8, G3V9Y6
      Related
      ENSRNOP00000063188.2, ENSRNOT00000066623.3
      Conserved Domains (1) summary
      cd22239
      Location:55 → 1420
      NPHP4; Nephrocystin-4

    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_086023.1 Reference GRCr8

      Range
      168270522..168356393
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006239465.5 → XP_006239527.1  nephrocystin-4 isoform X1

      See identical proteins and their annotated locations for XP_006239527.1

      Conserved Domains (1) summary
      cd22239
      Location:55 → 1445
      NPHP4; Nephrocystin-4

    2. XM_039110105.2 → XP_038966033.1  nephrocystin-4 isoform X2

      UniProtKB/TrEMBL
      A6IUI8, G3V9Y6
      Conserved Domains (1) summary
      cd22239
      Location:55 → 1420
      NPHP4; Nephrocystin-4

    3. XM_017593435.3 → XP_017448924.1  nephrocystin-4 isoform X1

      Conserved Domains (1) summary
      cd22239
      Location:55 → 1445
      NPHP4; Nephrocystin-4

    4. XM_039110104.2 → XP_038966032.1  nephrocystin-4 isoform X1

      Conserved Domains (1) summary
      cd22239
      Location:55 → 1445
      NPHP4; Nephrocystin-4
    Nucleotide Protein Strain
    Heading Accession and Version

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